repo stringlengths 7 54 | path stringlengths 4 223 | func_name stringlengths 1 134 | original_string stringlengths 75 104k | language stringclasses 1 value | code stringlengths 75 104k | code_tokens listlengths 20 28.4k | docstring stringlengths 1 46.3k | docstring_tokens listlengths 1 1.66k | sha stringlengths 40 40 | url stringlengths 87 315 | partition stringclasses 1 value | summary stringlengths 4 350 | obf_code stringlengths 7.85k 764k |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
dustin/twitty-twister | twittytwister/twitter.py | Twitter.retweet | def retweet(self, id, delegate):
"""Retweet a post
Returns the retweet status info back to the given delegate
"""
parser = txml.Statuses(delegate)
return self.__postPage('/statuses/retweet/%s.xml' % (id), parser) | python | def retweet(self, id, delegate):
"""Retweet a post
Returns the retweet status info back to the given delegate
"""
parser = txml.Statuses(delegate)
return self.__postPage('/statuses/retweet/%s.xml' % (id), parser) | [
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Returns the retweet status info back to the given delegate | [
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] | 8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3 | https://github.com/dustin/twitty-twister/blob/8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3/twittytwister/twitter.py#L324-L330 | train | Retweet a post
| GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(48) + chr(0b101001 + 0o106) + '\061' + '\061' + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(1005 - 952), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1000110 + 0o51) + chr(0b101 + 0o54) + chr(0b110100) + chr(1915 - 1861), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\062' + '\x34' + '\066', 20539 - 20531), nzTpIcepk0o8(chr(0b110000) + chr(3148 - 3037) + chr(51) + chr(0b101110 + 0o7) + chr(50), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(50) + '\x37' + chr(0b110100), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110010) + chr(53) + '\067', 0b1000), nzTpIcepk0o8(chr(1120 - 1072) + '\x6f' + '\061' + chr(0b10010 + 0o43) + '\x36', 0o10), nzTpIcepk0o8(chr(526 - 478) + '\x6f' + '\063' + chr(1270 - 1218), 23481 - 23473), nzTpIcepk0o8(chr(48) + '\x6f' + '\063' + chr(0b110011) + chr(1024 - 975), 0o10), nzTpIcepk0o8('\060' + chr(111) + '\063' + chr(0b110011) + chr(792 - 743), 8), nzTpIcepk0o8(chr(0b100111 + 0o11) + chr(5313 - 5202) + chr(0b110010) + chr(0b1111 + 0o41) + chr(1253 - 1203), 49313 - 49305), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\062' + chr(2007 - 1955) + chr(1894 - 1844), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(50) + chr(48) + chr(52), 0b1000), nzTpIcepk0o8(chr(2145 - 2097) + chr(111) + '\067', 49117 - 49109), nzTpIcepk0o8('\060' + chr(0b101011 + 0o104) + chr(0b101011 + 0o7) + chr(0b110010) + '\x35', 48395 - 48387), nzTpIcepk0o8('\x30' + chr(111) + chr(0b100110 + 0o15) + chr(0b110000) + '\x37', 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b101011 + 0o11) + chr(0b110000), 27244 - 27236), nzTpIcepk0o8(chr(0b110000) + chr(9081 - 8970) + chr(0b110010) + chr(1068 - 1014) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(1348 - 1300) + chr(0b1100101 + 0o12) + chr(0b100000 + 0o23) + '\062' + chr(0b110101), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(0b10010 + 0o41) + chr(1189 - 1135) + chr(0b100001 + 0o23), 0o10), nzTpIcepk0o8(chr(1366 - 1318) + chr(0b1101111) + '\063' + chr(54) + chr(50), 0b1000), nzTpIcepk0o8('\060' + chr(0b110010 + 0o75) + chr(0b110010) + '\067' + '\x35', 63251 - 63243), nzTpIcepk0o8('\060' + chr(9362 - 9251) + chr(806 - 753) + chr(55), ord("\x08")), nzTpIcepk0o8(chr(1292 - 1244) + '\x6f' + chr(0b110110) + chr(1555 - 1500), 0o10), nzTpIcepk0o8(chr(2173 - 2125) + '\x6f' + chr(0b110011) + '\067' + chr(50), ord("\x08")), nzTpIcepk0o8(chr(551 - 503) + chr(0b1010011 + 0o34) + '\062' + chr(0b1001 + 0o50) + '\065', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(50) + '\066', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\063' + chr(0b100111 + 0o14) + '\062', 14444 - 14436), nzTpIcepk0o8(chr(1437 - 1389) + chr(111) + chr(0b100 + 0o57) + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x33' + chr(0b110101) + chr(54), 43340 - 43332), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(50) + '\x37', 18242 - 18234), nzTpIcepk0o8('\060' + chr(5445 - 5334) + chr(51) + '\x33' + '\063', 7856 - 7848), nzTpIcepk0o8('\x30' + '\157' + chr(0b10111 + 0o33) + chr(53) + chr(0b110010), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(0b110011) + chr(54) + chr(0b100101 + 0o22), 10966 - 10958), nzTpIcepk0o8(chr(0b11000 + 0o30) + chr(111) + chr(0b100110 + 0o14) + chr(0b110 + 0o55) + chr(0b11111 + 0o23), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(2224 - 2175) + '\066' + chr(2678 - 2624), 35560 - 35552), nzTpIcepk0o8(chr(258 - 210) + '\157' + chr(0b1111 + 0o43) + chr(0b100111 + 0o20) + chr(0b110000), 0b1000), nzTpIcepk0o8(chr(1307 - 1259) + chr(9798 - 9687) + chr(51) + chr(55) + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(0b10100 + 0o34) + chr(0b1101101 + 0o2) + chr(1314 - 1263) + chr(0b110000) + chr(2617 - 2562), 8)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(222 - 174) + chr(7104 - 6993) + '\x35' + chr(967 - 919), ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'e'), chr(3447 - 3347) + '\x65' + '\x63' + chr(0b110 + 0o151) + chr(0b1000001 + 0o43) + '\145')(chr(117) + chr(11818 - 11702) + '\x66' + '\055' + chr(0b101100 + 0o14)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def _vbvHjE0xmc5(hXMPsSrOQzbh, maLnLg8O5zPT, sl13tsTzFIJl):
ELQLGvoVr2Z_ = emo0J8LHBNVF.Statuses(sl13tsTzFIJl)
return roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x14Z\x16\xc9\x99\xc8\xff\x0f{\xbc'), chr(0b11011 + 0o111) + chr(1354 - 1253) + '\143' + chr(2033 - 1922) + chr(7826 - 7726) + '\145')(chr(4118 - 4001) + '\164' + chr(8549 - 8447) + '\055' + '\070'))(roI3spqORKae(ES5oEprVxulp(b'dv\x12\xc7\x9e\xc9\xdc\x0bo\xf6\xab\xe7\xd6\xf3b\xf0\xb3\x0f\x91\xa6\xda\x8a\xd0C'), chr(100) + chr(0b100111 + 0o76) + chr(0b1100011) + '\x6f' + chr(5427 - 5327) + chr(0b1100101))('\x75' + chr(8451 - 8335) + '\146' + chr(1025 - 980) + chr(1840 - 1784)) % maLnLg8O5zPT, ELQLGvoVr2Z_) |
dustin/twitty-twister | twittytwister/twitter.py | Twitter.friends | def friends(self, delegate, params={}, extra_args=None):
"""Get updates from friends.
Calls the delgate once for each status object received."""
return self.__get('/statuses/friends_timeline.xml', delegate, params,
txml.Statuses, extra_args=extra_args) | python | def friends(self, delegate, params={}, extra_args=None):
"""Get updates from friends.
Calls the delgate once for each status object received."""
return self.__get('/statuses/friends_timeline.xml', delegate, params,
txml.Statuses, extra_args=extra_args) | [
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Calls the delgate once for each status object received. | [
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] | 8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3 | https://github.com/dustin/twitty-twister/blob/8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3/twittytwister/twitter.py#L332-L337 | train | Get updates from friends.
Calls the delgate once for each status object received. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(48) + chr(0b110100 + 0o73) + chr(0b110010) + chr(54), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(2219 - 2169) + '\x35' + '\x37', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110 + 0o55) + '\067' + '\x37', 0o10), nzTpIcepk0o8(chr(0b10011 + 0o35) + chr(111) + chr(1353 - 1304) + chr(0b110101) + chr(1485 - 1436), 0b1000), nzTpIcepk0o8(chr(0b10010 + 0o36) + chr(0b1001001 + 0o46) + chr(584 - 533) + '\x31' + '\x31', 0o10), nzTpIcepk0o8(chr(527 - 479) + '\x6f' + '\061' + '\063' + chr(50), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\063' + chr(55) + chr(0b110010), 18690 - 18682), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x33' + chr(52) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(2535 - 2424) + chr(215 - 166) + chr(258 - 208) + '\x33', 50131 - 50123), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(49) + chr(0b110100) + '\066', 0b1000), nzTpIcepk0o8(chr(0b10111 + 0o31) + chr(0b1101111) + chr(0b100101 + 0o14) + chr(48) + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(0b100 + 0o54) + '\157' + '\062' + '\x37' + chr(0b100111 + 0o11), ord("\x08")), nzTpIcepk0o8(chr(0b11100 + 0o24) + chr(1789 - 1678) + chr(0b10110 + 0o36) + chr(50), 15285 - 15277), nzTpIcepk0o8(chr(0b100100 + 0o14) + '\157' + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1011010 + 0o25) + chr(50) + chr(1699 - 1650) + '\x34', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b101000 + 0o107) + chr(0b1101 + 0o44) + chr(48) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\063' + '\060' + '\061', 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(254 - 203) + chr(0b10010 + 0o41) + chr(0b100100 + 0o22), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(1215 - 1166) + chr(51) + '\x31', 0b1000), nzTpIcepk0o8(chr(0b11011 + 0o25) + '\157' + '\x33' + chr(50) + chr(99 - 50), ord("\x08")), nzTpIcepk0o8(chr(0b110000 + 0o0) + '\157' + '\x31' + chr(0b110110) + chr(0b110001 + 0o5), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + '\x32' + chr(49) + chr(52), 8), nzTpIcepk0o8('\060' + chr(9621 - 9510) + chr(0b110010) + '\x30' + chr(0b10011 + 0o41), ord("\x08")), nzTpIcepk0o8(chr(2241 - 2193) + '\x6f' + chr(0b100101 + 0o16) + chr(529 - 476) + '\x37', 32134 - 32126), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110011) + chr(51) + chr(2450 - 2397), 59960 - 59952), nzTpIcepk0o8(chr(48) + '\x6f' + chr(669 - 619) + chr(50) + chr(0b11010 + 0o27), 33841 - 33833), nzTpIcepk0o8('\060' + '\157' + chr(0b110010) + chr(154 - 101), 24554 - 24546), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x31' + '\064' + '\x31', 0b1000), nzTpIcepk0o8(chr(48) + chr(9322 - 9211) + chr(0b1010 + 0o47) + chr(1929 - 1879), 0o10), nzTpIcepk0o8('\060' + chr(1188 - 1077) + chr(51) + '\064' + '\062', 60284 - 60276), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(1657 - 1608) + '\062' + chr(0b10101 + 0o33), ord("\x08")), nzTpIcepk0o8(chr(2111 - 2063) + '\x6f' + chr(0b1001 + 0o50) + '\x33' + chr(52), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\062' + chr(0b110011) + chr(2167 - 2115), 0o10), nzTpIcepk0o8('\060' + chr(9033 - 8922) + chr(0b110111) + '\x30', 0b1000), nzTpIcepk0o8(chr(0b1001 + 0o47) + chr(9373 - 9262) + chr(0b110001) + chr(0b11001 + 0o36), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(2848 - 2737) + '\061' + '\x30' + chr(48), 8), nzTpIcepk0o8(chr(0b1110 + 0o42) + '\x6f' + chr(50) + chr(1559 - 1507) + chr(1860 - 1806), 0o10), nzTpIcepk0o8('\060' + chr(5316 - 5205) + chr(0b110010) + chr(0b110100) + chr(0b110001), 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(51) + '\065' + '\x31', 0b1000), nzTpIcepk0o8(chr(0b100110 + 0o12) + '\157' + chr(50) + chr(0b1000 + 0o52) + chr(0b110101), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + chr(0b1011000 + 0o27) + chr(53) + chr(1451 - 1403), ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'8'), chr(0b1100100) + chr(0b1100101) + chr(0b1100011) + '\157' + chr(0b1111 + 0o125) + chr(0b1100101))(chr(0b1100010 + 0o23) + chr(0b1110100) + chr(102) + chr(0b101101) + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def DJu9mD8iVnMR(hXMPsSrOQzbh, sl13tsTzFIJl, GVgFAYMz7Sw8={}, vsHxRdBONQp3=None):
return roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'I\xf0\x98\x0c\xbd'), '\144' + chr(0b1010001 + 0o24) + chr(99) + chr(0b1101111) + chr(0b1100 + 0o130) + chr(0b1000101 + 0o40))(chr(117) + '\164' + chr(102) + chr(182 - 137) + chr(1981 - 1925)))(roI3spqORKae(ES5oEprVxulp(b"9\xdc\x8b\x08\xbd/\x89\x86 I&\xcaK`\xe2'\xb2\x81-\xb8\x1b\xe9\xe8\x86\xb3\xf4;\x19g\x8e"), chr(0b110100 + 0o60) + chr(0b1010000 + 0o25) + chr(0b1100011) + '\x6f' + chr(100) + '\x65')('\165' + chr(116) + chr(0b1100110) + chr(1656 - 1611) + chr(1714 - 1658)), sl13tsTzFIJl, GVgFAYMz7Sw8, roI3spqORKae(emo0J8LHBNVF, roI3spqORKae(ES5oEprVxulp(b'E\xdb\x9e\x1d\xbc)\x9f\x90'), '\x64' + '\x65' + '\x63' + '\157' + chr(100) + chr(0b1100101))('\165' + chr(0b111001 + 0o73) + '\x66' + chr(0b101101) + '\070')), extra_args=vsHxRdBONQp3) |
dustin/twitty-twister | twittytwister/twitter.py | Twitter.home_timeline | def home_timeline(self, delegate, params={}, extra_args=None):
"""Get updates from friends.
Calls the delgate once for each status object received."""
return self.__get('/statuses/home_timeline.xml', delegate, params,
txml.Statuses, extra_args=extra_args) | python | def home_timeline(self, delegate, params={}, extra_args=None):
"""Get updates from friends.
Calls the delgate once for each status object received."""
return self.__get('/statuses/home_timeline.xml', delegate, params,
txml.Statuses, extra_args=extra_args) | [
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Calls the delgate once for each status object received. | [
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] | 8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3 | https://github.com/dustin/twitty-twister/blob/8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3/twittytwister/twitter.py#L339-L344 | train | Get updates from friends.
MimeType Calls the delgate once for each status object received. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8('\x30' + chr(0b1101111) + '\062' + chr(936 - 886) + '\067', 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(736 - 683) + '\062', 0o10), nzTpIcepk0o8(chr(1247 - 1199) + '\157' + chr(0b11111 + 0o24) + chr(0b100101 + 0o13), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b100000 + 0o117) + chr(50) + '\062' + '\x32', 25776 - 25768), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110100) + '\064', 0b1000), nzTpIcepk0o8(chr(48) + chr(6051 - 5940) + chr(0b110001) + chr(52) + '\x37', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1011001 + 0o26) + chr(50) + chr(2840 - 2786) + '\065', 0o10), nzTpIcepk0o8(chr(0b11000 + 0o30) + '\x6f' + chr(0b110011) + chr(0b10111 + 0o31) + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(0b100 + 0o54) + '\157' + chr(0b10100 + 0o35) + chr(50) + chr(0b111 + 0o52), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1011101 + 0o22) + chr(49) + chr(0b111 + 0o56) + '\x37', 0b1000), nzTpIcepk0o8(chr(0b11111 + 0o21) + chr(111) + '\061' + '\x36' + chr(0b110000), 36142 - 36134), nzTpIcepk0o8(chr(2269 - 2221) + '\x6f' + '\x32' + chr(54) + chr(0b110100), ord("\x08")), nzTpIcepk0o8('\x30' + chr(8776 - 8665) + chr(50) + chr(53) + '\x37', 5074 - 5066), nzTpIcepk0o8(chr(297 - 249) + chr(111) + chr(53) + '\x30', 0o10), nzTpIcepk0o8('\x30' + chr(111) + '\061' + chr(0b1 + 0o61) + '\064', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1011110 + 0o21) + '\x31' + chr(0b10000 + 0o41) + chr(0b110111), 35002 - 34994), nzTpIcepk0o8('\060' + chr(0b1000011 + 0o54) + chr(2216 - 2167) + '\x36', 0o10), nzTpIcepk0o8(chr(0b110 + 0o52) + '\157' + chr(817 - 766) + chr(49) + '\064', 55522 - 55514), nzTpIcepk0o8(chr(854 - 806) + '\x6f' + '\x33' + chr(0b101 + 0o56) + '\065', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b1111 + 0o42) + chr(0b110110) + '\x37', 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110010) + chr(50) + '\065', 27019 - 27011), nzTpIcepk0o8(chr(1434 - 1386) + chr(111) + '\x33' + '\x33' + chr(52), ord("\x08")), nzTpIcepk0o8(chr(979 - 931) + chr(0b1101111) + chr(333 - 284) + chr(55) + chr(1830 - 1781), ord("\x08")), nzTpIcepk0o8('\060' + chr(1831 - 1720) + chr(0b110010) + chr(0b110100) + chr(2067 - 2017), ord("\x08")), nzTpIcepk0o8(chr(0b10010 + 0o36) + '\x6f' + '\067' + chr(49), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(0b110001) + chr(0b110111) + '\066', 47643 - 47635), nzTpIcepk0o8('\x30' + '\157' + chr(51) + chr(0b10 + 0o60) + chr(0b110100 + 0o1), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x31' + chr(50) + chr(1321 - 1270), 0o10), nzTpIcepk0o8(chr(2072 - 2024) + chr(0b1101111) + chr(0b100011 + 0o17) + chr(0b100001 + 0o20) + chr(48), 0o10), nzTpIcepk0o8(chr(447 - 399) + chr(0b1101111) + '\x33' + '\062' + chr(939 - 891), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(0b110011) + chr(51) + '\063', 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110011) + chr(2088 - 2034) + '\063', 0b1000), nzTpIcepk0o8('\060' + chr(8450 - 8339) + '\x31' + chr(0b10110 + 0o36) + chr(0b110001 + 0o3), 43414 - 43406), nzTpIcepk0o8('\x30' + '\157' + chr(1581 - 1530) + '\x33' + '\067', 53320 - 53312), nzTpIcepk0o8('\060' + chr(12040 - 11929) + chr(0b110011) + chr(124 - 69) + '\067', ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + '\x31' + chr(52), 0o10), nzTpIcepk0o8(chr(2254 - 2206) + chr(0b1001010 + 0o45) + chr(0b111 + 0o53) + '\060' + '\x32', 0b1000), nzTpIcepk0o8(chr(140 - 92) + chr(0b100100 + 0o113) + chr(0b110000 + 0o1) + '\064' + chr(52), 8), nzTpIcepk0o8(chr(0b100101 + 0o13) + chr(3587 - 3476) + '\062' + '\x35' + chr(2314 - 2263), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(0b110001) + chr(1364 - 1309) + chr(0b11 + 0o62), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + chr(111) + '\x35' + chr(0b110000), 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xb9'), '\x64' + chr(0b1100101) + '\x63' + chr(111) + chr(100) + chr(1996 - 1895))(chr(0b100001 + 0o124) + '\164' + '\146' + chr(605 - 560) + chr(0b100111 + 0o21)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def sPbiZZcb19ld(hXMPsSrOQzbh, sl13tsTzFIJl, GVgFAYMz7Sw8={}, vsHxRdBONQp3=None):
return roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xc8u\x7f\xf7P'), chr(100) + chr(0b1100101) + chr(8414 - 8315) + chr(0b1101111) + '\x64' + chr(0b100 + 0o141))(chr(0b1110101) + chr(10044 - 9928) + '\x66' + chr(0b1011 + 0o42) + chr(0b101010 + 0o16)))(roI3spqORKae(ES5oEprVxulp(b'\xb8Yl\xf3P\x12\xc6\xa1"@\x18\xdb\xc2M\x0b;g\xa1\xb8\x1b\xfc\xb2\x1c\x8cA\x13\xb9'), chr(672 - 572) + chr(0b1100101) + '\x63' + chr(111) + '\144' + chr(0b1100101))(chr(0b1010110 + 0o37) + chr(0b11010 + 0o132) + chr(9478 - 9376) + chr(45) + chr(0b110000 + 0o10)), sl13tsTzFIJl, GVgFAYMz7Sw8, roI3spqORKae(emo0J8LHBNVF, roI3spqORKae(ES5oEprVxulp(b'\xc4^y\xe6Q\x14\xd0\xb7'), chr(8952 - 8852) + chr(0b111 + 0o136) + '\x63' + '\157' + chr(100) + '\x65')(chr(0b1110101) + '\x74' + '\x66' + '\055' + chr(0b110100 + 0o4))), extra_args=vsHxRdBONQp3) |
dustin/twitty-twister | twittytwister/twitter.py | Twitter.user_timeline | def user_timeline(self, delegate, user=None, params={}, extra_args=None):
"""Get the most recent updates for a user.
If no user is specified, the statuses for the authenticating user are
returned.
See search for example of how results are returned."""
if user:
params['id'] = user
return self.__get('/statuses/user_timeline.xml', delegate, params,
txml.Statuses, extra_args=extra_args) | python | def user_timeline(self, delegate, user=None, params={}, extra_args=None):
"""Get the most recent updates for a user.
If no user is specified, the statuses for the authenticating user are
returned.
See search for example of how results are returned."""
if user:
params['id'] = user
return self.__get('/statuses/user_timeline.xml', delegate, params,
txml.Statuses, extra_args=extra_args) | [
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If no user is specified, the statuses for the authenticating user are
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See search for example of how results are returned. | [
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] | 8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3 | https://github.com/dustin/twitty-twister/blob/8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3/twittytwister/twitter.py#L350-L360 | train | Get the most recent updates for a user. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8('\x30' + chr(111) + '\x32' + '\063' + chr(0b101001 + 0o10), 0b1000), nzTpIcepk0o8(chr(1204 - 1156) + '\157' + chr(0b0 + 0o63) + '\060' + chr(49), 0o10), nzTpIcepk0o8(chr(0b10101 + 0o33) + chr(10719 - 10608) + '\065' + chr(714 - 663), 1459 - 1451), nzTpIcepk0o8('\x30' + chr(0b1011001 + 0o26) + chr(51) + '\x32' + '\x30', 47588 - 47580), nzTpIcepk0o8(chr(0b1000 + 0o50) + '\x6f' + chr(0b110010) + '\067' + chr(55), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + '\062' + '\x32', 0o10), nzTpIcepk0o8('\060' + chr(0b11111 + 0o120) + chr(0b110011) + '\x34' + chr(562 - 510), 0o10), nzTpIcepk0o8(chr(0b111 + 0o51) + chr(0b1101111) + chr(0b110011) + chr(0b110001 + 0o2) + chr(0b101110 + 0o3), 0o10), nzTpIcepk0o8('\x30' + chr(8078 - 7967) + chr(0b110011) + '\062' + chr(2070 - 2019), 0b1000), nzTpIcepk0o8(chr(0b11000 + 0o30) + chr(111) + chr(51) + chr(0b110000) + chr(0b110110), ord("\x08")), nzTpIcepk0o8(chr(0b101110 + 0o2) + '\x6f' + '\062' + '\065' + chr(2330 - 2279), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x37' + '\063', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\061' + chr(0b10 + 0o63) + chr(0b10 + 0o64), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110010) + '\061' + chr(0b11011 + 0o25), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(539 - 484) + chr(48), 0b1000), nzTpIcepk0o8('\060' + '\x6f' + '\063' + chr(53) + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b100110 + 0o111) + chr(57 - 7) + '\067' + '\x34', 0o10), nzTpIcepk0o8(chr(766 - 718) + chr(0b100001 + 0o116) + chr(0b100 + 0o57) + chr(0b101011 + 0o11) + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b1111 + 0o42) + chr(940 - 892) + chr(0b110110), 60808 - 60800), nzTpIcepk0o8(chr(1886 - 1838) + '\x6f' + chr(0b110001) + chr(0b110010) + '\x36', ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(0b100 + 0o57) + '\x31' + chr(195 - 142), 62528 - 62520), nzTpIcepk0o8(chr(647 - 599) + chr(6866 - 6755) + '\067' + '\x35', 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(1322 - 1273) + '\062' + '\x35', 16842 - 16834), nzTpIcepk0o8(chr(0b110000) + chr(8718 - 8607) + '\x33' + '\061' + chr(0b1011 + 0o53), 15620 - 15612), nzTpIcepk0o8(chr(798 - 750) + chr(0b10010 + 0o135) + chr(921 - 869) + '\x32', 4662 - 4654), nzTpIcepk0o8(chr(0b100011 + 0o15) + chr(5971 - 5860) + chr(1964 - 1914) + '\065' + chr(52), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b100111 + 0o12) + '\064' + chr(742 - 692), 22330 - 22322), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\061' + chr(50) + chr(106 - 56), 0o10), nzTpIcepk0o8(chr(0b10011 + 0o35) + chr(0b101011 + 0o104) + '\062' + chr(0b110000) + chr(0b100001 + 0o25), 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b11 + 0o56) + chr(0b101100 + 0o12), 0o10), nzTpIcepk0o8(chr(0b101110 + 0o2) + '\157' + chr(0b10100 + 0o37) + '\x37' + '\x37', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1100010 + 0o15) + chr(260 - 209) + chr(50) + '\065', 0o10), nzTpIcepk0o8('\060' + chr(12234 - 12123) + '\062' + chr(1359 - 1307), 61361 - 61353), nzTpIcepk0o8(chr(0b110000) + chr(4151 - 4040) + chr(0b110010) + '\065' + chr(0b10101 + 0o34), 0b1000), nzTpIcepk0o8(chr(0b100101 + 0o13) + chr(0b1101111) + chr(1799 - 1748) + '\061' + chr(604 - 551), 8), nzTpIcepk0o8('\060' + chr(0b1101011 + 0o4) + chr(0b11110 + 0o23) + '\060' + '\x36', 8), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(50) + chr(0b110100) + '\063', 0b1000), nzTpIcepk0o8(chr(48) + '\157' + '\062' + chr(0b110110) + chr(0b110110), 56295 - 56287), nzTpIcepk0o8(chr(1877 - 1829) + '\157' + chr(1783 - 1733) + chr(0b11001 + 0o27) + chr(0b1111 + 0o41), 0o10), nzTpIcepk0o8(chr(0b101010 + 0o6) + chr(0b1101111) + chr(0b110010) + '\062' + chr(0b101 + 0o53), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + chr(10371 - 10260) + chr(53) + chr(48), 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xb7'), '\x64' + chr(10200 - 10099) + '\x63' + chr(0b1101111) + '\x64' + chr(0b1010001 + 0o24))(chr(117) + chr(11236 - 11120) + chr(102) + chr(0b101101) + chr(0b100110 + 0o22)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def x0N4pwKEhhWt(hXMPsSrOQzbh, sl13tsTzFIJl, E63X9RhwfuOn=None, GVgFAYMz7Sw8={}, vsHxRdBONQp3=None):
if E63X9RhwfuOn:
GVgFAYMz7Sw8[roI3spqORKae(ES5oEprVxulp(b'\xf0\xa5'), chr(100) + chr(0b1100101) + chr(5348 - 5249) + chr(0b1000001 + 0o56) + chr(100) + chr(101))(chr(117) + '\x74' + chr(0b1100110) + chr(846 - 801) + chr(56))] = E63X9RhwfuOn
return roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xc6\x9eL\xb5\xcb'), chr(0b1100100) + chr(101) + chr(0b1100011) + '\157' + '\144' + chr(101))('\165' + chr(8606 - 8490) + chr(102) + chr(494 - 449) + '\070'))(roI3spqORKae(ES5oEprVxulp(b'\xb6\xb2_\xb1\xcbg\x97\xbc\xa0\xe9\xdeH\x0b\xfag\x99\xd5\x8d#:\xa4S0\xe0Z\xc1\x0e'), '\x64' + chr(101) + chr(0b1011111 + 0o4) + chr(111) + '\x64' + '\145')(chr(1764 - 1647) + '\x74' + chr(0b1100110) + chr(0b11001 + 0o24) + chr(0b10011 + 0o45)), sl13tsTzFIJl, GVgFAYMz7Sw8, roI3spqORKae(emo0J8LHBNVF, roI3spqORKae(ES5oEprVxulp(b'\xca\xb5J\xa4\xcaa\x81\xaa'), chr(100) + '\145' + chr(0b1001000 + 0o33) + chr(0b1101111) + '\x64' + '\x65')('\x75' + chr(116) + '\x66' + chr(0b1111 + 0o36) + chr(56))), extra_args=vsHxRdBONQp3) |
dustin/twitty-twister | twittytwister/twitter.py | Twitter.public_timeline | def public_timeline(self, delegate, params={}, extra_args=None):
"Get the most recent public timeline."
return self.__get('/statuses/public_timeline.atom', delegate, params,
extra_args=extra_args) | python | def public_timeline(self, delegate, params={}, extra_args=None):
"Get the most recent public timeline."
return self.__get('/statuses/public_timeline.atom', delegate, params,
extra_args=extra_args) | [
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] | 8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3 | https://github.com/dustin/twitty-twister/blob/8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3/twittytwister/twitter.py#L367-L371 | train | Get the most recent public timeline. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x33' + '\x36' + chr(0b11000 + 0o37), 0b1000), nzTpIcepk0o8(chr(0b1110 + 0o42) + chr(4802 - 4691) + chr(0b110011) + chr(0b110111) + '\x34', ord("\x08")), nzTpIcepk0o8(chr(0b1101 + 0o43) + '\x6f' + chr(51) + chr(0b100 + 0o54) + '\065', 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(0b10101 + 0o35) + '\x32' + chr(48), 0b1000), nzTpIcepk0o8(chr(0b100100 + 0o14) + chr(0b1101111) + chr(0b110001) + chr(50) + '\063', 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110 + 0o55) + chr(54) + chr(0b110111), 8), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b11111 + 0o24) + chr(0b110110) + chr(0b110101), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(50) + chr(2253 - 2198) + '\062', 64529 - 64521), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b101100 + 0o5) + '\063' + '\x34', ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + '\x32' + '\x33' + '\x31', 0b1000), nzTpIcepk0o8(chr(176 - 128) + chr(0b1101111) + chr(50) + '\x32' + '\063', 0o10), nzTpIcepk0o8(chr(0b100101 + 0o13) + chr(4375 - 4264) + chr(50) + chr(0b100101 + 0o16), 1122 - 1114), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b100100 + 0o15) + '\x36' + chr(51), 0b1000), nzTpIcepk0o8('\060' + chr(6047 - 5936) + chr(0b10000 + 0o42) + '\063' + chr(0b110110), 53781 - 53773), nzTpIcepk0o8(chr(0b100011 + 0o15) + chr(111) + chr(50) + chr(0b110000) + chr(0b1001 + 0o50), ord("\x08")), nzTpIcepk0o8(chr(0b11011 + 0o25) + chr(0b1001100 + 0o43) + chr(0b110010) + chr(48) + chr(50), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(55) + '\060', ord("\x08")), nzTpIcepk0o8(chr(0b100011 + 0o15) + chr(0b1101111) + '\061' + '\x35' + chr(0b1011 + 0o52), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + '\x37', 56595 - 56587), nzTpIcepk0o8(chr(48) + '\157' + '\x36' + '\067', 0o10), nzTpIcepk0o8(chr(2189 - 2141) + chr(3054 - 2943) + '\x33' + chr(2341 - 2289) + '\x36', 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110010) + chr(0b101011 + 0o7) + chr(1773 - 1720), 21755 - 21747), nzTpIcepk0o8('\x30' + chr(111) + chr(0b1011 + 0o46) + chr(359 - 306) + chr(48), 23052 - 23044), nzTpIcepk0o8(chr(48) + '\x6f' + '\063' + chr(49) + chr(0b0 + 0o62), 0b1000), nzTpIcepk0o8(chr(0b101000 + 0o10) + chr(2510 - 2399) + chr(0b11111 + 0o24) + '\062' + chr(50), 44819 - 44811), nzTpIcepk0o8(chr(2007 - 1959) + '\157' + '\067' + chr(1625 - 1576), 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(67 - 16) + '\x36' + '\x37', 8), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x31' + chr(54) + chr(0b101010 + 0o11), 8), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(401 - 352) + chr(1947 - 1897) + chr(0b10010 + 0o43), 0b1000), nzTpIcepk0o8(chr(48) + chr(2231 - 2120) + '\066' + chr(1747 - 1699), 0o10), nzTpIcepk0o8('\060' + chr(3860 - 3749) + chr(0b110010) + chr(53), 0o10), nzTpIcepk0o8(chr(1121 - 1073) + chr(0b1101111) + chr(50) + chr(251 - 203) + '\x31', 8), nzTpIcepk0o8(chr(2226 - 2178) + '\157' + '\063' + '\064' + chr(0b10100 + 0o43), 15922 - 15914), nzTpIcepk0o8('\060' + chr(111) + '\061' + '\067', 0b1000), nzTpIcepk0o8(chr(48) + chr(11143 - 11032) + '\062' + chr(0b110100) + chr(1558 - 1507), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(1725 - 1676) + chr(0b1110 + 0o42) + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\062' + chr(48) + chr(0b110000), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(1832 - 1783) + '\x36' + chr(0b1101 + 0o45), ord("\x08")), nzTpIcepk0o8(chr(1494 - 1446) + chr(0b1101111) + '\x33' + chr(0b110111) + chr(1921 - 1867), 1970 - 1962), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b11000 + 0o31) + '\060' + '\x33', 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + '\x6f' + chr(394 - 341) + chr(1880 - 1832), ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xd9'), '\144' + chr(0b1100101) + '\x63' + '\157' + '\x64' + '\x65')(chr(12592 - 12475) + chr(0b1110100) + chr(0b1011000 + 0o16) + '\055' + chr(0b1 + 0o67)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def jbBLLmZ3fJqD(hXMPsSrOQzbh, sl13tsTzFIJl, GVgFAYMz7Sw8={}, vsHxRdBONQp3=None):
return roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b"\xa8\xa3\xa2\xf5'"), '\x64' + chr(101) + chr(99) + chr(0b111100 + 0o63) + chr(0b1100100) + chr(0b100010 + 0o103))(chr(117) + chr(0b1110100) + '\x66' + '\x2d' + chr(0b111000)))(roI3spqORKae(ES5oEprVxulp(b"\xd8\x8f\xb1\xf1'\x82\x86\xdf/\xb6\xe3f\x11\xf2\xe8\xe1g\x19nZ\x83\xf9\x01\xa4\xb7\x17\x96\x07:]"), '\x64' + chr(101) + chr(99) + chr(0b1101111) + chr(8688 - 8588) + '\x65')('\x75' + '\x74' + chr(0b111101 + 0o51) + chr(0b101101) + chr(696 - 640)), sl13tsTzFIJl, GVgFAYMz7Sw8, extra_args=vsHxRdBONQp3) |
dustin/twitty-twister | twittytwister/twitter.py | Twitter.direct_messages | def direct_messages(self, delegate, params={}, extra_args=None):
"""Get direct messages for the authenticating user.
Search results are returned one message at a time a DirectMessage
objects"""
return self.__get('/direct_messages.xml', delegate, params,
txml.Direct, extra_args=extra_args) | python | def direct_messages(self, delegate, params={}, extra_args=None):
"""Get direct messages for the authenticating user.
Search results are returned one message at a time a DirectMessage
objects"""
return self.__get('/direct_messages.xml', delegate, params,
txml.Direct, extra_args=extra_args) | [
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Search results are returned one message at a time a DirectMessage
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] | 8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3 | https://github.com/dustin/twitty-twister/blob/8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3/twittytwister/twitter.py#L373-L379 | train | Get the direct messages for the authenticating user. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(48) + chr(543 - 432) + chr(0b100100 + 0o15) + chr(54), 36068 - 36060), nzTpIcepk0o8('\060' + '\x6f' + chr(0b1000 + 0o50), 0o10), nzTpIcepk0o8(chr(0b111 + 0o51) + chr(0b1100110 + 0o11) + '\x33' + chr(51) + chr(0b101000 + 0o13), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1011101 + 0o22) + chr(1412 - 1361) + chr(54) + chr(1007 - 956), 34548 - 34540), nzTpIcepk0o8(chr(48) + chr(111) + chr(1761 - 1712) + chr(55) + chr(51), 0b1000), nzTpIcepk0o8('\060' + chr(0b110101 + 0o72) + chr(844 - 793) + chr(951 - 902) + chr(0b111 + 0o55), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + '\x37' + '\060', 19487 - 19479), nzTpIcepk0o8(chr(0b101101 + 0o3) + chr(111) + '\061' + chr(0b110001) + chr(1213 - 1165), 20386 - 20378), nzTpIcepk0o8(chr(0b110000) + chr(6938 - 6827) + chr(0b110011) + chr(0b1 + 0o61) + chr(55), 0o10), nzTpIcepk0o8(chr(1385 - 1337) + chr(0b10 + 0o155) + chr(49) + chr(54) + '\066', 0o10), nzTpIcepk0o8(chr(85 - 37) + chr(0b1001 + 0o146) + chr(0b1011 + 0o47) + chr(905 - 854) + chr(0b110000), 0o10), nzTpIcepk0o8('\060' + '\x6f' + '\063' + chr(2000 - 1945), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1000110 + 0o51) + chr(2017 - 1968) + '\066' + chr(1168 - 1114), 8), nzTpIcepk0o8('\060' + chr(11100 - 10989) + '\063' + chr(0b101010 + 0o6) + '\x35', 903 - 895), nzTpIcepk0o8(chr(0b10111 + 0o31) + chr(0b1101111) + chr(1004 - 955) + '\060' + chr(54), 0o10), nzTpIcepk0o8(chr(0b0 + 0o60) + '\x6f' + chr(0b110010) + '\x30' + chr(1450 - 1395), ord("\x08")), nzTpIcepk0o8(chr(0b11100 + 0o24) + chr(0b1101111) + '\x31' + '\x37' + chr(0b11001 + 0o27), 17091 - 17083), nzTpIcepk0o8(chr(135 - 87) + chr(0b1101111) + chr(51) + chr(0b100000 + 0o26) + '\x35', 4258 - 4250), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110010) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(50) + chr(476 - 425) + chr(0b110010), 45727 - 45719), nzTpIcepk0o8('\060' + chr(111) + chr(0b10011 + 0o36) + chr(2210 - 2158) + chr(757 - 707), 41447 - 41439), nzTpIcepk0o8(chr(0b101001 + 0o7) + '\x6f' + '\063' + chr(54) + chr(0b110001), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(240 - 190) + '\062', 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110101) + chr(0b110011), 0o10), nzTpIcepk0o8('\x30' + '\157' + '\x33' + chr(0b110111) + '\x31', ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + '\x33' + '\x32' + chr(0b110001), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + '\x31' + '\x33' + chr(0b110110), ord("\x08")), nzTpIcepk0o8('\x30' + chr(2373 - 2262) + '\064' + chr(2315 - 2264), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(0b110001) + '\x36' + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b1000 + 0o52) + chr(48) + chr(844 - 791), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + '\061' + chr(0b110001), 0o10), nzTpIcepk0o8(chr(720 - 672) + '\157' + chr(634 - 583) + '\064' + '\x34', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x31' + '\x32' + '\063', 50016 - 50008), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(51) + '\x36' + chr(55), 2005 - 1997), nzTpIcepk0o8(chr(0b1010 + 0o46) + chr(0b101101 + 0o102) + chr(0b110001) + '\064' + chr(52), 0o10), nzTpIcepk0o8(chr(971 - 923) + chr(0b101010 + 0o105) + chr(50) + chr(54) + '\064', 0o10), nzTpIcepk0o8(chr(48) + chr(0b110110 + 0o71) + '\x37' + '\062', 55271 - 55263), nzTpIcepk0o8(chr(48) + chr(11004 - 10893) + chr(51) + chr(2479 - 2426) + chr(315 - 262), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b11101 + 0o26) + '\x37' + chr(2900 - 2845), 0o10), nzTpIcepk0o8(chr(0b1110 + 0o42) + chr(5428 - 5317) + chr(159 - 109) + chr(0b110010) + chr(54), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + chr(0b10000 + 0o137) + chr(687 - 634) + '\x30', ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b' '), chr(0b101 + 0o137) + chr(0b1100101) + chr(131 - 32) + chr(0b1101111) + '\144' + '\x65')('\165' + '\164' + chr(0b1100110) + chr(0b1010 + 0o43) + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def u6nW0X8ypGTa(hXMPsSrOQzbh, sl13tsTzFIJl, GVgFAYMz7Sw8={}, vsHxRdBONQp3=None):
return roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'Q_\xbc\x96\x0f'), '\x64' + chr(224 - 123) + '\x63' + chr(0b1010011 + 0o34) + chr(100) + chr(101))('\x75' + chr(0b10000 + 0o144) + '\x66' + chr(0b101101) + chr(0b111000)))(roI3spqORKae(ES5oEprVxulp(b'!d\xb2\x81\x1e\xafL\x17\xba\x13\xebl\x17\xa2#\xf4V\x8dy\xf6'), chr(0b1100100) + chr(0b100110 + 0o77) + chr(2423 - 2324) + chr(0b111101 + 0o62) + chr(0b110011 + 0o61) + chr(0b1011011 + 0o12))(chr(0b1100111 + 0o16) + chr(4268 - 4152) + '\x66' + '\x2d' + '\070'), sl13tsTzFIJl, GVgFAYMz7Sw8, roI3spqORKae(emo0J8LHBNVF, roI3spqORKae(ES5oEprVxulp(b'Ji\xa9\x96\x18\xb8'), '\144' + chr(0b11010 + 0o113) + '\143' + '\157' + chr(0b1000011 + 0o41) + chr(0b1100101))(chr(0b10000 + 0o145) + chr(0b1110100) + '\146' + '\x2d' + '\070')), extra_args=vsHxRdBONQp3) |
dustin/twitty-twister | twittytwister/twitter.py | Twitter.send_direct_message | def send_direct_message(self, text, user=None, delegate=None, screen_name=None, user_id=None, params={}):
"""Send a direct message
"""
params = params.copy()
if user is not None:
params['user'] = user
if user_id is not None:
params['user_id'] = user_id
if screen_name is not None:
params['screen_name'] = screen_name
params['text'] = text
parser = txml.Direct(delegate)
return self.__postPage('/direct_messages/new.xml', parser, params) | python | def send_direct_message(self, text, user=None, delegate=None, screen_name=None, user_id=None, params={}):
"""Send a direct message
"""
params = params.copy()
if user is not None:
params['user'] = user
if user_id is not None:
params['user_id'] = user_id
if screen_name is not None:
params['screen_name'] = screen_name
params['text'] = text
parser = txml.Direct(delegate)
return self.__postPage('/direct_messages/new.xml', parser, params) | [
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"message"
] | 8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3 | https://github.com/dustin/twitty-twister/blob/8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3/twittytwister/twitter.py#L381-L393 | train | Send a direct message to the user. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8('\060' + chr(111) + '\x34', 63763 - 63755), nzTpIcepk0o8('\060' + chr(0b1110 + 0o141) + '\x32' + chr(53) + chr(1399 - 1351), 0b1000), nzTpIcepk0o8(chr(48) + chr(7020 - 6909) + chr(0b110001) + chr(2222 - 2167) + chr(0b110110), 21565 - 21557), nzTpIcepk0o8(chr(48) + '\x6f' + chr(51) + '\066' + chr(54), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x32' + chr(0b100000 + 0o20) + chr(0b110000), 40558 - 40550), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(1643 - 1592) + chr(0b1000 + 0o51) + '\062', 47538 - 47530), nzTpIcepk0o8(chr(0b11010 + 0o26) + chr(10854 - 10743) + '\063' + chr(0b110000) + chr(0b1001 + 0o52), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(512 - 401) + '\061' + chr(0b110000) + chr(1760 - 1711), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(634 - 585) + '\x32', 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110010) + '\x34' + chr(0b110101), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1011101 + 0o22) + chr(0b110010) + chr(0b110000) + chr(0b110001), ord("\x08")), nzTpIcepk0o8(chr(1202 - 1154) + chr(111) + chr(51) + chr(0b100110 + 0o16) + chr(0b101101 + 0o3), 0b1000), nzTpIcepk0o8('\060' + chr(2307 - 2196) + '\x31', ord("\x08")), nzTpIcepk0o8(chr(1420 - 1372) + '\157' + chr(532 - 482) + chr(2332 - 2282) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(0b11001 + 0o27) + chr(0b1001 + 0o146) + chr(0b10111 + 0o33) + chr(55) + chr(1163 - 1108), 21740 - 21732), nzTpIcepk0o8('\x30' + '\x6f' + '\061' + '\064' + '\066', 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + '\x33' + chr(0b110111) + chr(1674 - 1626), ord("\x08")), nzTpIcepk0o8(chr(1121 - 1073) + chr(111) + chr(629 - 579) + '\x35' + '\065', 9316 - 9308), nzTpIcepk0o8(chr(48) + chr(111) + '\x31' + chr(51) + chr(0b11111 + 0o24), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(2236 - 2186) + chr(54) + chr(0b100111 + 0o11), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(2416 - 2361) + chr(0b10 + 0o65), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1011101 + 0o22) + '\x32' + chr(606 - 558) + chr(1894 - 1844), 0o10), nzTpIcepk0o8(chr(2018 - 1970) + chr(3013 - 2902) + '\062', ord("\x08")), nzTpIcepk0o8(chr(2275 - 2227) + '\x6f' + '\x33' + chr(0b110000 + 0o2) + '\x31', 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(1093 - 1044) + '\x36' + chr(0b1 + 0o65), 45045 - 45037), nzTpIcepk0o8(chr(515 - 467) + chr(11824 - 11713) + chr(0b100101 + 0o15) + chr(0b110011) + chr(2272 - 2221), ord("\x08")), nzTpIcepk0o8(chr(0b100 + 0o54) + chr(0b1000000 + 0o57) + chr(0b10100 + 0o35) + '\x36' + chr(55), 6743 - 6735), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110001) + chr(0b110111) + chr(0b10111 + 0o33), ord("\x08")), nzTpIcepk0o8(chr(257 - 209) + chr(2993 - 2882) + chr(1892 - 1837) + chr(0b110100), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + '\061' + chr(0b100001 + 0o21) + chr(50), 44135 - 44127), nzTpIcepk0o8('\x30' + '\x6f' + chr(974 - 923) + chr(0b11011 + 0o31) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b100100 + 0o113) + chr(0b11100 + 0o33) + chr(0b110011), ord("\x08")), nzTpIcepk0o8(chr(0b1000 + 0o50) + chr(0b101010 + 0o105) + chr(54) + chr(0b110011), ord("\x08")), nzTpIcepk0o8(chr(553 - 505) + chr(5250 - 5139) + chr(1067 - 1016) + chr(0b110 + 0o53) + chr(0b110110), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + '\x31' + '\060' + chr(50), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b101001 + 0o12) + chr(0b11100 + 0o24) + chr(0b110101), 56910 - 56902), nzTpIcepk0o8(chr(48) + chr(6022 - 5911) + '\063' + chr(2753 - 2700) + '\x37', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\066' + chr(54), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110011) + chr(0b100011 + 0o22) + chr(0b1100 + 0o52), 40813 - 40805), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110011) + chr(48) + chr(48), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + chr(3418 - 3307) + chr(0b10000 + 0o45) + chr(729 - 681), 4150 - 4142)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'*'), chr(336 - 236) + chr(101) + chr(99) + '\157' + chr(5153 - 5053) + chr(101))(chr(13475 - 13358) + chr(0b1110100) + chr(7738 - 7636) + '\x2d' + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def FSMtCRlpFUm3(hXMPsSrOQzbh, cpStk7cY1TJd, E63X9RhwfuOn=None, sl13tsTzFIJl=None, QNJIopUh6qHh=None, ixUxd0qav6Hd=None, GVgFAYMz7Sw8={}):
GVgFAYMz7Sw8 = GVgFAYMz7Sw8.copy()
if E63X9RhwfuOn is not None:
GVgFAYMz7Sw8[roI3spqORKae(ES5oEprVxulp(b'q\xdb\x1b\x84'), '\x64' + '\145' + '\x63' + chr(0b1101111) + '\144' + '\x65')(chr(3974 - 3857) + chr(5591 - 5475) + '\x66' + '\055' + chr(56))] = E63X9RhwfuOn
if ixUxd0qav6Hd is not None:
GVgFAYMz7Sw8[roI3spqORKae(ES5oEprVxulp(b'q\xdb\x1b\x84\xdf\xa3\xa7'), chr(100) + chr(101) + '\143' + chr(0b111100 + 0o63) + chr(100) + chr(101))(chr(10892 - 10775) + chr(116) + chr(102) + chr(45) + '\x38')] = ixUxd0qav6Hd
if QNJIopUh6qHh is not None:
GVgFAYMz7Sw8[roI3spqORKae(ES5oEprVxulp(b'w\xcb\x0c\x93\xe5\xa4\x9c/k\xc8\xe4'), chr(4423 - 4323) + chr(0b1001 + 0o134) + chr(99) + '\157' + chr(0b1010 + 0o132) + '\145')('\x75' + '\164' + '\146' + '\x2d' + chr(56))] = QNJIopUh6qHh
GVgFAYMz7Sw8[roI3spqORKae(ES5oEprVxulp(b'p\xcd\x06\x82'), chr(0b11111 + 0o105) + chr(0b100101 + 0o100) + '\143' + '\x6f' + chr(0b1011001 + 0o13) + '\145')(chr(0b1110101) + chr(116) + '\x66' + '\x2d' + '\070')] = cpStk7cY1TJd
ELQLGvoVr2Z_ = emo0J8LHBNVF.Direct(sl13tsTzFIJl)
return roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'[\xf7\x0e\x99\xf3\xbe\x93 m\xc0'), chr(5894 - 5794) + chr(101) + '\x63' + chr(0b1101111) + '\x64' + chr(5618 - 5517))(chr(10096 - 9979) + '\x74' + '\146' + chr(0b1100 + 0o41) + '\070'))(roI3spqORKae(ES5oEprVxulp(b'+\xcc\x17\x84\xe5\xa9\xb7\x1eg\xc0\xf2\x93`\xf4\xda\x15\xd7\xc3>\xc7\x11\xfao\xbd'), '\x64' + chr(0b1100101) + chr(0b100000 + 0o103) + chr(1068 - 957) + chr(0b1100100) + '\x65')(chr(0b1110101) + chr(116) + '\x66' + '\x2d' + chr(0b11111 + 0o31)), ELQLGvoVr2Z_, GVgFAYMz7Sw8) |
dustin/twitty-twister | twittytwister/twitter.py | Twitter.replies | def replies(self, delegate, params={}, extra_args=None):
"""Get the most recent replies for the authenticating user.
See search for example of how results are returned."""
return self.__get('/statuses/replies.atom', delegate, params,
extra_args=extra_args) | python | def replies(self, delegate, params={}, extra_args=None):
"""Get the most recent replies for the authenticating user.
See search for example of how results are returned."""
return self.__get('/statuses/replies.atom', delegate, params,
extra_args=extra_args) | [
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See search for example of how results are returned. | [
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] | 8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3 | https://github.com/dustin/twitty-twister/blob/8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3/twittytwister/twitter.py#L395-L400 | train | Get the most recent replies for the authenticating user. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b110000) + chr(9632 - 9521) + chr(0b11 + 0o60) + chr(0b100111 + 0o12) + chr(0b101011 + 0o6), 60370 - 60362), nzTpIcepk0o8('\060' + '\157' + '\x31' + chr(0b11011 + 0o32) + chr(48), 45802 - 45794), nzTpIcepk0o8(chr(0b110000) + chr(0b1000001 + 0o56) + '\x31' + '\061' + chr(817 - 767), 0o10), nzTpIcepk0o8(chr(0b101 + 0o53) + chr(0b1100001 + 0o16) + '\x33' + chr(0b101110 + 0o4) + '\x35', ord("\x08")), nzTpIcepk0o8('\060' + '\157' + '\062' + chr(0b101000 + 0o11) + '\x31', ord("\x08")), nzTpIcepk0o8('\x30' + chr(11798 - 11687) + chr(50) + '\065' + '\067', 17098 - 17090), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110001) + '\x33' + '\060', 9938 - 9930), nzTpIcepk0o8('\060' + chr(373 - 262) + chr(50) + chr(2237 - 2183) + chr(55), 0o10), nzTpIcepk0o8(chr(560 - 512) + chr(111) + '\x35' + '\x32', 56138 - 56130), nzTpIcepk0o8(chr(0b110000) + chr(0b1011 + 0o144) + chr(2370 - 2320) + chr(0b10 + 0o61) + chr(2454 - 2399), 0o10), nzTpIcepk0o8(chr(0b101110 + 0o2) + '\x6f' + '\x33' + chr(0b110011) + '\x31', 0b1000), nzTpIcepk0o8(chr(1348 - 1300) + '\x6f' + chr(412 - 358), 14340 - 14332), nzTpIcepk0o8(chr(1887 - 1839) + chr(111) + chr(0b11 + 0o60) + '\x31' + chr(51), 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(0b10000 + 0o43) + chr(0b111 + 0o53) + '\x37', 27824 - 27816), nzTpIcepk0o8(chr(0b10100 + 0o34) + chr(7788 - 7677) + '\x33' + chr(0b11111 + 0o25) + chr(48), 0b1000), nzTpIcepk0o8(chr(0b10111 + 0o31) + chr(0b1001 + 0o146) + '\x31' + '\x30' + '\063', 0o10), nzTpIcepk0o8(chr(457 - 409) + chr(0b10100 + 0o133) + '\062' + chr(1301 - 1248) + chr(52), 53092 - 53084), nzTpIcepk0o8('\060' + chr(111) + chr(1824 - 1775) + chr(49) + chr(0b110010), 8), nzTpIcepk0o8(chr(0b100110 + 0o12) + '\157' + '\061' + '\x31' + '\062', 8), nzTpIcepk0o8(chr(48) + '\x6f' + chr(49) + '\x30' + chr(52), 25089 - 25081), nzTpIcepk0o8('\060' + chr(0b1011111 + 0o20) + chr(0b1111 + 0o44) + '\062', 0o10), nzTpIcepk0o8(chr(0b100000 + 0o20) + chr(111) + chr(0b110010) + '\067' + chr(55), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(1809 - 1760) + chr(2418 - 2366) + chr(1033 - 982), 15164 - 15156), nzTpIcepk0o8(chr(0b110000) + '\157' + '\062' + '\060', 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(0b110011) + chr(0b110100) + chr(0b10011 + 0o41), 0b1000), nzTpIcepk0o8(chr(433 - 385) + '\x6f' + '\x31' + '\062' + chr(50), 41878 - 41870), nzTpIcepk0o8(chr(866 - 818) + '\157' + chr(0b110010) + chr(54) + chr(971 - 920), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b101100 + 0o103) + chr(1996 - 1945) + '\060' + chr(0b110001), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(51) + '\x36' + '\067', 23676 - 23668), nzTpIcepk0o8(chr(0b1111 + 0o41) + chr(0b1101111) + '\062' + '\065' + chr(2254 - 2200), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + '\062' + chr(51) + chr(0b110110), 40235 - 40227), nzTpIcepk0o8(chr(0b110000) + chr(7181 - 7070) + chr(52) + chr(51), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(54) + chr(53), 28409 - 28401), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b11111 + 0o22) + chr(54) + chr(49), 47210 - 47202), nzTpIcepk0o8('\060' + chr(0b1101110 + 0o1) + '\x36', 8), nzTpIcepk0o8(chr(0b10101 + 0o33) + chr(0b1101111) + chr(0b11011 + 0o27) + '\x30' + chr(0b110111), 22550 - 22542), nzTpIcepk0o8(chr(830 - 782) + chr(4675 - 4564) + '\061' + '\060' + chr(1418 - 1365), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1 + 0o156) + chr(0b11001 + 0o31) + chr(0b110110) + chr(52), 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(49) + chr(0b101100 + 0o6) + chr(922 - 868), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(50) + chr(0b110001) + '\065', 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + chr(8570 - 8459) + '\065' + chr(0b110000), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xe7'), chr(0b1100100) + '\x65' + chr(0b11000 + 0o113) + chr(111) + '\x64' + '\145')('\x75' + chr(0b1110100) + '\x66' + '\055' + chr(927 - 871)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def zWVgDY_W74N_(hXMPsSrOQzbh, sl13tsTzFIJl, GVgFAYMz7Sw8={}, vsHxRdBONQp3=None):
return roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x967-\xb0\xfd'), '\144' + chr(0b1100101) + chr(0b1100011) + chr(111) + chr(0b11001 + 0o113) + chr(6774 - 6673))(chr(0b1110101) + chr(2614 - 2498) + chr(2301 - 2199) + chr(45) + chr(2602 - 2546)))(roI3spqORKae(ES5oEprVxulp(b'\xe6\x1b>\xb4\xfd\xda+\xd2Y\xb0\xabc\xbb\xbb\x89&\xdfd+0u\xd2'), chr(0b1100100) + '\x65' + chr(0b10011 + 0o120) + chr(111) + chr(0b110001 + 0o63) + chr(4486 - 4385))(chr(117) + chr(2947 - 2831) + chr(0b111000 + 0o56) + chr(1464 - 1419) + '\070'), sl13tsTzFIJl, GVgFAYMz7Sw8, extra_args=vsHxRdBONQp3) |
dustin/twitty-twister | twittytwister/twitter.py | Twitter.follow_user | def follow_user(self, user, delegate):
"""Follow the given user.
Returns the user info back to the given delegate
"""
parser = txml.Users(delegate)
return self.__postPage('/friendships/create/%s.xml' % (user), parser) | python | def follow_user(self, user, delegate):
"""Follow the given user.
Returns the user info back to the given delegate
"""
parser = txml.Users(delegate)
return self.__postPage('/friendships/create/%s.xml' % (user), parser) | [
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Returns the user info back to the given delegate | [
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] | 8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3 | https://github.com/dustin/twitty-twister/blob/8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3/twittytwister/twitter.py#L414-L420 | train | Follow the given user. Returns the user info back to the given delegate. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\065' + '\x37', 12231 - 12223), nzTpIcepk0o8(chr(0b110000) + chr(0b110 + 0o151) + chr(0b110000 + 0o3) + chr(0b11010 + 0o30) + '\062', 0b1000), nzTpIcepk0o8(chr(48) + '\157' + '\063' + '\063', 54719 - 54711), nzTpIcepk0o8(chr(0b1100 + 0o44) + '\x6f' + '\x33' + chr(1841 - 1786) + chr(2523 - 2471), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b111 + 0o150) + '\x31' + '\x36' + chr(1102 - 1054), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(2419 - 2369) + chr(51), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(2006 - 1957) + chr(50) + chr(0b110011 + 0o4), 57545 - 57537), nzTpIcepk0o8(chr(0b10010 + 0o36) + chr(5314 - 5203) + chr(49) + chr(0b10010 + 0o40) + '\060', 0b1000), nzTpIcepk0o8('\x30' + chr(0b100010 + 0o115) + '\062' + chr(0b10100 + 0o36) + chr(254 - 201), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b11000 + 0o127) + '\x33' + chr(48) + chr(0b110000), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110001) + '\067' + '\063', 0o10), nzTpIcepk0o8('\x30' + '\157' + '\063' + chr(0b100011 + 0o24), 0b1000), nzTpIcepk0o8(chr(413 - 365) + '\157' + chr(0b100011 + 0o20) + chr(52) + chr(1648 - 1593), 24728 - 24720), nzTpIcepk0o8(chr(0b100111 + 0o11) + chr(0b1101111) + chr(0b11000 + 0o33) + chr(0b110101) + chr(55), 45700 - 45692), nzTpIcepk0o8(chr(48) + chr(111) + '\x33' + chr(2835 - 2780), 8), nzTpIcepk0o8('\x30' + chr(8228 - 8117) + '\x33' + chr(172 - 119), 0o10), nzTpIcepk0o8(chr(2092 - 2044) + chr(0b101101 + 0o102) + chr(1727 - 1677) + '\066' + chr(0b10110 + 0o34), 49693 - 49685), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x33' + '\x36', 39682 - 39674), nzTpIcepk0o8(chr(2271 - 2223) + chr(0b1100000 + 0o17) + chr(980 - 929) + chr(0b10111 + 0o34) + chr(54), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110001) + chr(0b111 + 0o54) + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(10370 - 10259) + chr(49) + '\067' + '\062', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b100 + 0o55) + '\x32' + chr(1803 - 1752), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + '\063' + chr(0b0 + 0o60) + chr(0b100111 + 0o16), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110010) + '\x34' + chr(0b100010 + 0o16), 47316 - 47308), nzTpIcepk0o8(chr(0b1111 + 0o41) + chr(11502 - 11391) + '\x32' + chr(48), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x32' + '\060' + chr(52), 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110001) + '\062' + chr(0b110001 + 0o0), 0b1000), nzTpIcepk0o8(chr(0b10010 + 0o36) + chr(7592 - 7481) + '\066' + chr(722 - 672), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x33' + '\x36' + chr(0b1110 + 0o50), 32752 - 32744), nzTpIcepk0o8(chr(48) + '\157' + chr(2415 - 2364) + chr(55) + chr(50), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(1568 - 1519) + chr(2081 - 2027) + chr(0b110001), 26127 - 26119), nzTpIcepk0o8('\060' + '\x6f' + chr(0b10101 + 0o36) + chr(50), 0b1000), nzTpIcepk0o8('\060' + chr(111) + '\x33' + '\x31' + chr(52), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(0b101110 + 0o4) + chr(289 - 234) + chr(0b10101 + 0o40), 33434 - 33426), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(1728 - 1676) + chr(1826 - 1778), 49973 - 49965), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b101100 + 0o6) + chr(53) + '\064', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(3395 - 3284) + chr(49) + chr(48) + chr(48), ord("\x08")), nzTpIcepk0o8('\060' + chr(10157 - 10046) + chr(0b11110 + 0o24) + chr(53), 59578 - 59570), nzTpIcepk0o8(chr(0b110000) + chr(6425 - 6314) + chr(0b110 + 0o54) + '\066' + '\060', 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(0b101111 + 0o3) + chr(0b110001) + chr(0b101001 + 0o15), 60966 - 60958)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(1153 - 1105) + chr(0b1101111) + '\x35' + chr(0b1101 + 0o43), ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x01'), chr(0b1100100) + '\145' + chr(0b111 + 0o134) + chr(0b1010000 + 0o37) + '\x64' + '\145')(chr(0b100110 + 0o117) + chr(0b1110100) + chr(3145 - 3043) + '\x2d' + chr(427 - 371)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def FxmgrJQwIoQh(hXMPsSrOQzbh, E63X9RhwfuOn, sl13tsTzFIJl):
ELQLGvoVr2Z_ = emo0J8LHBNVF.Users(sl13tsTzFIJl)
return roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'p\x8dk\x93\x03g\x071\xf2\xa5'), '\x64' + chr(3612 - 3511) + chr(99) + '\157' + '\x64' + '\x65')('\x75' + chr(0b10000 + 0o144) + chr(2397 - 2295) + '\x2d' + chr(0b111000)))(roI3spqORKae(ES5oEprVxulp(b'\x00\xb4i\x95\x15}3#\xfd\xa9\x0bl\xc8\x8cmx\xd3j\xbbr_ \xeb\xd8}\xe8'), '\144' + '\145' + chr(0b1100011) + '\157' + '\144' + '\145')(chr(0b1110101) + chr(0b1110100) + chr(0b110 + 0o140) + chr(0b101101) + '\x38') % E63X9RhwfuOn, ELQLGvoVr2Z_) |
dustin/twitty-twister | twittytwister/twitter.py | Twitter.unfollow_user | def unfollow_user(self, user, delegate):
"""Unfollow the given user.
Returns the user info back to the given delegate
"""
parser = txml.Users(delegate)
return self.__postPage('/friendships/destroy/%s.xml' % (user), parser) | python | def unfollow_user(self, user, delegate):
"""Unfollow the given user.
Returns the user info back to the given delegate
"""
parser = txml.Users(delegate)
return self.__postPage('/friendships/destroy/%s.xml' % (user), parser) | [
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Returns the user info back to the given delegate | [
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] | 8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3 | https://github.com/dustin/twitty-twister/blob/8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3/twittytwister/twitter.py#L422-L428 | train | Unfollows the given user. Returns the user info back to the given delegate. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(1322 - 1273) + '\065' + chr(0b110101), 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(0b110011) + chr(2066 - 2012) + chr(0b110010), 21199 - 21191), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110011) + chr(54) + chr(2068 - 2018), 8), nzTpIcepk0o8(chr(0b110000) + chr(5570 - 5459) + chr(0b110101) + chr(53), 54410 - 54402), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110001 + 0o5) + '\x35', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b101 + 0o152) + '\x32' + '\062' + '\064', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(4233 - 4122) + '\062' + '\x33' + chr(0b0 + 0o67), ord("\x08")), nzTpIcepk0o8(chr(0b101110 + 0o2) + '\157' + chr(49) + chr(55) + chr(0b1011 + 0o54), 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + '\062' + '\061' + chr(51), 27529 - 27521), nzTpIcepk0o8(chr(0b11011 + 0o25) + chr(0b1101111) + chr(0b110010) + chr(49) + '\x30', 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(51) + chr(0b10001 + 0o40) + chr(912 - 861), 0o10), nzTpIcepk0o8('\060' + '\x6f' + '\061' + chr(53) + chr(0b110110), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1001110 + 0o41) + chr(0b1111 + 0o45) + '\067', 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(50) + chr(0b11000 + 0o34) + '\x37', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b11111 + 0o27) + chr(1995 - 1946), 0o10), nzTpIcepk0o8('\060' + chr(0b1000111 + 0o50) + chr(0b110010) + '\x32' + chr(0b110010 + 0o1), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1001000 + 0o47) + chr(692 - 637) + chr(891 - 837), 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110011) + chr(1476 - 1422) + chr(0b11110 + 0o25), 41286 - 41278), nzTpIcepk0o8(chr(0b110000) + chr(3643 - 3532) + chr(54), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b101110 + 0o5) + '\062' + chr(0b110000), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + '\x31' + '\x33', 59330 - 59322), nzTpIcepk0o8('\060' + '\157' + chr(51) + chr(644 - 593) + '\061', 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110001) + '\064' + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(0b1100 + 0o44) + chr(111) + chr(0b11101 + 0o26) + chr(2049 - 2000) + chr(2070 - 2016), 11186 - 11178), nzTpIcepk0o8(chr(1097 - 1049) + chr(6670 - 6559) + '\061' + chr(0b110001) + '\x33', 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(49) + '\065' + chr(50), 0b1000), nzTpIcepk0o8(chr(0b110000 + 0o0) + chr(0b1101111) + chr(0b110001 + 0o1) + chr(1294 - 1245), 37762 - 37754), nzTpIcepk0o8('\x30' + '\157' + chr(53) + chr(0b11010 + 0o33), 8), nzTpIcepk0o8('\060' + chr(0b1100100 + 0o13) + '\x33' + '\060' + chr(686 - 636), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(1506 - 1451) + chr(0b110001), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(357 - 308) + '\064' + chr(799 - 750), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + '\062' + chr(0b110000) + chr(1010 - 958), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x31' + chr(0b1111 + 0o42) + '\x34', 0o10), nzTpIcepk0o8('\x30' + chr(0b11001 + 0o126) + chr(0b110011) + '\x35' + '\061', 17863 - 17855), nzTpIcepk0o8(chr(0b101010 + 0o6) + chr(6894 - 6783) + '\061' + chr(52), 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(1360 - 1311) + chr(50) + chr(0b110111), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x32' + '\065' + '\060', 56848 - 56840), nzTpIcepk0o8(chr(0b101110 + 0o2) + '\x6f' + chr(2451 - 2400) + '\061' + chr(54), 8), nzTpIcepk0o8(chr(48) + chr(111) + chr(50) + '\x37' + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + '\062' + '\062' + '\064', 8)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(0b1001010 + 0o45) + chr(0b1010 + 0o53) + chr(48), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'C'), chr(0b1100100) + '\145' + chr(99) + chr(111) + chr(8540 - 8440) + chr(101))('\x75' + chr(0b1110100) + '\x66' + chr(45) + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def SrBo3CAACTYc(hXMPsSrOQzbh, E63X9RhwfuOn, sl13tsTzFIJl):
ELQLGvoVr2Z_ = emo0J8LHBNVF.Users(sl13tsTzFIJl)
return roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'2\xad\x82BF\xe0\xcf\x1e\xec\xed'), chr(7425 - 7325) + chr(0b1100101) + chr(0b100101 + 0o76) + chr(6842 - 6731) + chr(100) + '\145')(chr(117) + chr(116) + '\146' + chr(45) + chr(0b10110 + 0o42)))(roI3spqORKae(ES5oEprVxulp(b'B\x94\x80DP\xfa\xfb\x0c\xe3\xe1\xbb\x1d\x08\xc3T\xe0J\x81i\xa9$\xfc\x17\xe03\x07}'), chr(0b1011111 + 0o5) + '\145' + '\143' + chr(10695 - 10584) + chr(0b1100100) + chr(0b1100101))('\165' + chr(0b1110100) + chr(102) + chr(45) + chr(775 - 719)) % E63X9RhwfuOn, ELQLGvoVr2Z_) |
dustin/twitty-twister | twittytwister/twitter.py | Twitter.list_friends | def list_friends(self, delegate, user=None, params={}, extra_args=None, page_delegate=None):
"""Get the list of friends for a user.
Calls the delegate with each user object found."""
if user:
url = '/statuses/friends/' + user + '.xml'
else:
url = '/statuses/friends.xml'
return self.__get_maybe_paging(url, delegate, params, txml.PagedUserList, extra_args, page_delegate) | python | def list_friends(self, delegate, user=None, params={}, extra_args=None, page_delegate=None):
"""Get the list of friends for a user.
Calls the delegate with each user object found."""
if user:
url = '/statuses/friends/' + user + '.xml'
else:
url = '/statuses/friends.xml'
return self.__get_maybe_paging(url, delegate, params, txml.PagedUserList, extra_args, page_delegate) | [
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Calls the delegate with each user object found. | [
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] | 8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3 | https://github.com/dustin/twitty-twister/blob/8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3/twittytwister/twitter.py#L457-L466 | train | Get the list of friends for a user. Calls the delegate with each user object found. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(48) + '\x6f' + '\x32' + chr(49), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\062' + '\060' + chr(2218 - 2168), 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(0b1000 + 0o52) + '\x30', 0b1000), nzTpIcepk0o8('\060' + '\157' + '\x33' + chr(52) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(1028 - 980) + chr(9081 - 8970) + chr(1887 - 1835) + chr(1837 - 1789), 40584 - 40576), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110010) + chr(79 - 29) + chr(52), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + '\x37' + chr(51), 42726 - 42718), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b10110 + 0o35) + '\x37' + '\063', 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + '\063' + chr(0b110100) + chr(0b100100 + 0o17), 8), nzTpIcepk0o8('\060' + chr(0b1000001 + 0o56) + chr(0b110001) + chr(0b100100 + 0o15) + chr(55), 4366 - 4358), nzTpIcepk0o8(chr(0b1000 + 0o50) + chr(9482 - 9371) + chr(0b101111 + 0o4) + chr(0b110000), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(3827 - 3716) + '\067' + chr(49), 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(0b110111) + chr(0b110011), 8), nzTpIcepk0o8(chr(694 - 646) + chr(0b1000100 + 0o53) + chr(0b100110 + 0o14) + chr(0b10100 + 0o42) + chr(850 - 800), 0b1000), nzTpIcepk0o8(chr(0b10011 + 0o35) + chr(111) + chr(0b110011) + chr(0b110000) + chr(49), 0o10), nzTpIcepk0o8('\060' + '\157' + '\065' + chr(52), ord("\x08")), nzTpIcepk0o8(chr(1480 - 1432) + '\157' + chr(0b1100 + 0o45) + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b1101 + 0o44) + '\067' + chr(0b110100 + 0o2), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + '\x31' + '\x30', 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b11111 + 0o22) + chr(49), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(51) + chr(54), 0b1000), nzTpIcepk0o8('\x30' + chr(8910 - 8799) + chr(0b110110) + chr(0b100111 + 0o20), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x37' + '\062', 0b1000), nzTpIcepk0o8(chr(0b1010 + 0o46) + '\157' + chr(0b101001 + 0o12) + '\067' + chr(111 - 57), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b101111 + 0o4) + chr(2572 - 2520) + chr(527 - 475), ord("\x08")), nzTpIcepk0o8(chr(0b1011 + 0o45) + chr(111) + chr(0b110010) + chr(55) + '\062', ord("\x08")), nzTpIcepk0o8(chr(0b11000 + 0o30) + chr(0b1101111) + chr(1982 - 1932) + chr(0b11100 + 0o33) + chr(0b1101 + 0o50), 8942 - 8934), nzTpIcepk0o8(chr(988 - 940) + chr(0b1101001 + 0o6) + '\x37' + '\062', 8), nzTpIcepk0o8(chr(509 - 461) + '\x6f' + chr(0b1111 + 0o50) + chr(2149 - 2094), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(0b1011 + 0o46) + chr(53) + '\x37', 0b1000), nzTpIcepk0o8('\x30' + chr(6632 - 6521) + '\x31' + chr(0b100110 + 0o20) + chr(0b110000), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + '\x33' + chr(52) + '\x34', 8), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110010) + chr(1287 - 1238) + chr(0b110111), 0o10), nzTpIcepk0o8(chr(0b1010 + 0o46) + chr(0b1101111) + '\x31' + chr(0b110101) + '\061', ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + '\x33' + chr(50) + chr(0b110111), 18185 - 18177), nzTpIcepk0o8(chr(0b11100 + 0o24) + chr(0b1011100 + 0o23) + chr(0b110101) + chr(0b10111 + 0o31), 0o10), nzTpIcepk0o8(chr(0b100110 + 0o12) + chr(4873 - 4762) + '\063' + chr(0b100000 + 0o21) + chr(51), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + '\061' + chr(530 - 481), 8), nzTpIcepk0o8(chr(0b1010 + 0o46) + chr(0b1001100 + 0o43) + chr(0b110011) + chr(51) + chr(0b101001 + 0o16), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(51) + chr(0b101 + 0o57) + chr(1375 - 1324), 8)][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + chr(0b1101111) + '\065' + '\x30', 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'?'), chr(9908 - 9808) + chr(0b1100101) + chr(0b1100011) + '\157' + '\144' + chr(0b100001 + 0o104))(chr(117) + chr(116) + chr(5702 - 5600) + chr(0b111 + 0o46) + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def XN9KoL87QL6N(hXMPsSrOQzbh, sl13tsTzFIJl, E63X9RhwfuOn=None, GVgFAYMz7Sw8={}, vsHxRdBONQp3=None, p8fcJgMKXlH3=None):
if E63X9RhwfuOn:
XuBkOpBKZJ5Z = roI3spqORKae(ES5oEprVxulp(b'>\xf1d\x82T\xe1H\x9e\x90`~KR\xd7\xafH~Q'), '\x64' + chr(0b1100101) + chr(0b1100 + 0o127) + chr(7742 - 7631) + chr(0b100001 + 0o103) + chr(0b1100101))(chr(0b1110101) + chr(0b1110100) + '\146' + chr(0b101101 + 0o0) + chr(56)) + E63X9RhwfuOn + roI3spqORKae(ES5oEprVxulp(b'?\xfa}\x8f'), chr(0b1100100) + chr(101) + '\x63' + chr(11082 - 10971) + chr(0b11001 + 0o113) + chr(0b1100101))(chr(117) + chr(9354 - 9238) + chr(0b1100110) + '\055' + chr(0b110011 + 0o5))
else:
XuBkOpBKZJ5Z = roI3spqORKae(ES5oEprVxulp(b'>\xf1d\x82T\xe1H\x9e\x90`~KR\xd7\xafH~Ppdr'), chr(0b1100100) + '\x65' + chr(0b1000100 + 0o37) + chr(6623 - 6512) + '\x64' + chr(101))('\165' + chr(116) + chr(0b100 + 0o142) + chr(45) + '\x38')
return roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'N\xddw\x86T\xcbV\x9a\x9a-}fK\xd3\xa6Ec\x19'), '\x64' + chr(0b111 + 0o136) + '\143' + chr(0b1101111) + '\x64' + '\x65')(chr(117) + '\164' + chr(0b1100110) + chr(957 - 912) + chr(1222 - 1166)))(XuBkOpBKZJ5Z, sl13tsTzFIJl, GVgFAYMz7Sw8, roI3spqORKae(emo0J8LHBNVF, roI3spqORKae(ES5oEprVxulp(b'A\xe3w\x86D\xc1H\x9e\x91\x03qJO'), chr(100) + chr(0b1100101) + chr(99) + '\157' + chr(0b110000 + 0o64) + '\x65')('\165' + chr(116) + chr(0b1100110) + '\x2d' + chr(56))), vsHxRdBONQp3, p8fcJgMKXlH3) |
dustin/twitty-twister | twittytwister/twitter.py | Twitter.show_user | def show_user(self, user):
"""Get the info for a specific user.
Returns a delegate that will receive the user in a callback."""
url = '/users/show/%s.xml' % (user)
d = defer.Deferred()
self.__downloadPage(url, txml.Users(lambda u: d.callback(u))) \
.addErrback(lambda e: d.errback(e))
return d | python | def show_user(self, user):
"""Get the info for a specific user.
Returns a delegate that will receive the user in a callback."""
url = '/users/show/%s.xml' % (user)
d = defer.Deferred()
self.__downloadPage(url, txml.Users(lambda u: d.callback(u))) \
.addErrback(lambda e: d.errback(e))
return d | [
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] | 8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3 | https://github.com/dustin/twitty-twister/blob/8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3/twittytwister/twitter.py#L488-L499 | train | Get the info for a specific user. Returns a delegate that will receive the user in a callback. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(48) + '\x6f' + chr(51) + chr(50) + chr(1800 - 1749), 20528 - 20520), nzTpIcepk0o8(chr(0b110 + 0o52) + chr(0b111010 + 0o65) + chr(523 - 473) + chr(0b110111) + chr(0b110001), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110001) + chr(54) + chr(528 - 477), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(49) + chr(0b111 + 0o51) + '\063', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b10111 + 0o34) + chr(446 - 391) + chr(0b110100 + 0o3), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + chr(1498 - 1445) + '\x37', 0o10), nzTpIcepk0o8(chr(0b11011 + 0o25) + chr(0b1101111) + chr(0b110111) + chr(0b110001), 0o10), nzTpIcepk0o8('\060' + chr(0b111110 + 0o61) + '\063' + '\067' + chr(0b10100 + 0o37), 62687 - 62679), nzTpIcepk0o8(chr(0b10000 + 0o40) + chr(0b1000 + 0o147) + chr(698 - 646) + '\061', 0o10), nzTpIcepk0o8('\060' + chr(2076 - 1965) + chr(0b110 + 0o54) + '\x36', 0b1000), nzTpIcepk0o8(chr(0b1110 + 0o42) + chr(7749 - 7638) + chr(50) + chr(0b110110), 8), nzTpIcepk0o8('\060' + chr(111) + chr(236 - 188), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b11111 + 0o120) + '\061' + chr(54) + chr(426 - 372), 0o10), nzTpIcepk0o8(chr(0b100011 + 0o15) + '\x6f' + chr(642 - 591) + chr(1267 - 1215) + chr(0b110000), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b0 + 0o64), 0b1000), nzTpIcepk0o8(chr(0b1001 + 0o47) + '\x6f' + '\061' + '\x36', 0b1000), nzTpIcepk0o8(chr(0b11101 + 0o23) + chr(0b1101111) + '\x31' + '\065' + chr(54), 0b1000), nzTpIcepk0o8(chr(0b100100 + 0o14) + '\x6f' + chr(0b110110) + chr(0b110011), 54222 - 54214), nzTpIcepk0o8('\060' + chr(0b101110 + 0o101) + chr(0b110101) + chr(2197 - 2149), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + '\x32' + '\x34' + '\x34', 0b1000), nzTpIcepk0o8('\060' + '\x6f' + '\x31' + '\x30' + '\x35', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(1494 - 1443) + chr(0b101011 + 0o5) + chr(0b101001 + 0o15), 0b1000), nzTpIcepk0o8(chr(0b10101 + 0o33) + '\157' + chr(0b10000 + 0o42) + chr(1147 - 1097) + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(2076 - 2028) + '\x6f' + '\x31' + chr(0b110011) + chr(0b110011), 0o10), nzTpIcepk0o8('\060' + chr(4074 - 3963) + chr(0b110010) + chr(0b100000 + 0o26) + '\x36', 0o10), nzTpIcepk0o8(chr(0b10010 + 0o36) + '\x6f' + chr(0b11110 + 0o30) + chr(0b11000 + 0o30), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1010100 + 0o33) + chr(0b10010 + 0o37) + '\060' + '\065', 8), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(51) + chr(0b11010 + 0o35) + '\064', ord("\x08")), nzTpIcepk0o8(chr(1365 - 1317) + '\157' + chr(0b11011 + 0o30) + chr(0b110100) + chr(52), 0o10), nzTpIcepk0o8(chr(48) + chr(0b101000 + 0o107) + chr(2118 - 2067) + chr(52) + '\067', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(849 - 800) + chr(0b110100) + '\063', 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110010) + '\063', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110011) + chr(0b110000) + chr(0b11100 + 0o33), 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(0b1000 + 0o51) + '\063' + chr(0b100100 + 0o22), 29220 - 29212), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110100) + chr(1671 - 1622), 8), nzTpIcepk0o8(chr(48) + '\x6f' + chr(51) + chr(0b110100) + chr(0b110001), 7704 - 7696), nzTpIcepk0o8(chr(0b1000 + 0o50) + chr(0b11101 + 0o122) + chr(49) + chr(0b110100) + chr(1515 - 1463), 0o10), nzTpIcepk0o8(chr(48) + chr(0b11011 + 0o124) + chr(1833 - 1784) + chr(569 - 520) + '\060', 0o10), nzTpIcepk0o8(chr(0b1011 + 0o45) + '\157' + chr(0b10101 + 0o34) + chr(1318 - 1269) + '\064', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1010110 + 0o31) + chr(49) + chr(0b11100 + 0o27) + '\x32', 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(1503 - 1455) + chr(0b1101111) + chr(0b10111 + 0o36) + chr(322 - 274), 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xfd'), chr(100) + chr(0b11 + 0o142) + chr(0b1000110 + 0o35) + '\x6f' + '\x64' + '\x65')('\165' + '\x74' + '\146' + chr(0b101101) + chr(1933 - 1877)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def AeCMab8v39Xi(hXMPsSrOQzbh, E63X9RhwfuOn):
XuBkOpBKZJ5Z = roI3spqORKae(ES5oEprVxulp(b'\xfc\xcc\x00&\x8d\\\x16\x88Iya/S\x93*v\x03_'), chr(100) + chr(0b1000101 + 0o40) + chr(0b1001010 + 0o31) + chr(0b111000 + 0o67) + chr(100) + chr(0b1100101))('\x75' + '\x74' + chr(0b110110 + 0o60) + chr(974 - 929) + chr(137 - 81)) % E63X9RhwfuOn
vPPlOXQgR3SM = hKESOdYBX3yt.Deferred()
roI3spqORKae(hXMPsSrOQzbh.__downloadPage(XuBkOpBKZJ5Z, emo0J8LHBNVF.Users(lambda GRbsaHW8BT5I: vPPlOXQgR3SM.callback(GRbsaHW8BT5I))), roI3spqORKae(ES5oEprVxulp(b'\xb2\xdd\x17\x06\x8d][\x9aB}'), chr(661 - 561) + '\145' + chr(3417 - 3318) + chr(0b1101111) + '\144' + '\x65')(chr(0b1110101) + chr(0b1110100) + chr(0b1000 + 0o136) + '\x2d' + chr(0b111000)))(lambda wgf0sgcu_xPL: roI3spqORKae(vPPlOXQgR3SM, roI3spqORKae(ES5oEprVxulp(b'\x9b\xdaB{\xb9\x1f|\xcbQQYA'), chr(100) + chr(101) + chr(0b1000 + 0o133) + '\157' + chr(100) + '\145')(chr(0b100010 + 0o123) + chr(0b11101 + 0o127) + chr(0b1100110) + '\055' + chr(56)))(wgf0sgcu_xPL))
return vPPlOXQgR3SM |
dustin/twitty-twister | twittytwister/twitter.py | Twitter.search | def search(self, query, delegate, args=None, extra_args=None):
"""Perform a search query.
Results are given one at a time to the delegate. An example delegate
may look like this:
def exampleDelegate(entry):
print entry.title"""
if args is None:
args = {}
args['q'] = query
return self.__doDownloadPage(self.search_url + '?' + self._urlencode(args),
txml.Feed(delegate, extra_args), agent=self.agent) | python | def search(self, query, delegate, args=None, extra_args=None):
"""Perform a search query.
Results are given one at a time to the delegate. An example delegate
may look like this:
def exampleDelegate(entry):
print entry.title"""
if args is None:
args = {}
args['q'] = query
return self.__doDownloadPage(self.search_url + '?' + self._urlencode(args),
txml.Feed(delegate, extra_args), agent=self.agent) | [
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"]",
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"return",
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".",... | Perform a search query.
Results are given one at a time to the delegate. An example delegate
may look like this:
def exampleDelegate(entry):
print entry.title | [
"Perform",
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"."
] | 8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3 | https://github.com/dustin/twitty-twister/blob/8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3/twittytwister/twitter.py#L501-L513 | train | Perform a search query. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8('\x30' + chr(111) + '\061' + '\060' + chr(289 - 238), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(2426 - 2376) + '\x32' + '\x35', 0o10), nzTpIcepk0o8(chr(683 - 635) + chr(0b1000111 + 0o50) + chr(51) + '\x30' + chr(0b110000), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(51) + chr(55) + chr(0b110101), 49645 - 49637), nzTpIcepk0o8(chr(716 - 668) + '\157' + '\x33' + chr(0b10 + 0o56), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x33' + chr(0b110110) + chr(0b100111 + 0o17), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b110011 + 0o74) + chr(0b110011) + chr(48) + chr(0b0 + 0o62), 0o10), nzTpIcepk0o8(chr(48) + chr(0b10000 + 0o137) + chr(0b101000 + 0o11) + chr(55), 0b1000), nzTpIcepk0o8(chr(0b0 + 0o60) + chr(0b1000010 + 0o55) + chr(1870 - 1822), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b101111 + 0o4) + chr(49) + chr(1946 - 1894), 0b1000), nzTpIcepk0o8(chr(510 - 462) + '\157' + chr(50) + chr(0b110000) + chr(55), 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(0b10110 + 0o35) + '\063' + chr(619 - 567), 28239 - 28231), nzTpIcepk0o8(chr(48) + chr(0b1101010 + 0o5) + '\063' + chr(52) + '\x33', 0b1000), nzTpIcepk0o8(chr(1306 - 1258) + chr(0b101111 + 0o100) + chr(0b101001 + 0o11) + chr(560 - 506) + '\062', 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110010) + chr(1483 - 1430) + '\x30', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x31' + '\x31' + '\x32', 0b1000), nzTpIcepk0o8('\060' + chr(7454 - 7343) + chr(0b110011) + chr(1350 - 1295) + chr(0b110100), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(49) + chr(0b110101) + chr(52), 19114 - 19106), nzTpIcepk0o8(chr(0b1110 + 0o42) + chr(0b1101111) + chr(48), 8), nzTpIcepk0o8(chr(48) + '\157' + '\x33' + '\067' + '\065', 8), nzTpIcepk0o8(chr(1364 - 1316) + chr(1639 - 1528) + '\x31' + '\x37' + chr(776 - 725), 0o10), nzTpIcepk0o8(chr(0b101010 + 0o6) + '\157' + chr(0b110010) + '\066' + chr(0b110000), 19340 - 19332), nzTpIcepk0o8(chr(0b110000) + '\157' + '\062' + chr(2371 - 2322) + chr(0b110010), 37595 - 37587), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x31' + chr(201 - 148), 0b1000), nzTpIcepk0o8(chr(0b100010 + 0o16) + chr(0b1101111) + chr(0b1 + 0o62) + chr(0b1110 + 0o51) + chr(1462 - 1413), 33135 - 33127), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110011) + chr(0b110000 + 0o2), ord("\x08")), nzTpIcepk0o8(chr(0b101111 + 0o1) + chr(7489 - 7378) + chr(0b11011 + 0o27) + chr(1085 - 1034) + '\065', 0b1000), nzTpIcepk0o8(chr(0b101100 + 0o4) + '\x6f' + chr(53) + chr(54), 0o10), nzTpIcepk0o8(chr(0b101101 + 0o3) + '\157' + chr(2039 - 1989) + chr(55) + chr(0b110100 + 0o2), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + '\063' + chr(0b110000) + chr(0b110001), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(51) + '\x31' + '\061', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b1100 + 0o45) + '\x32' + chr(1723 - 1673), 19760 - 19752), nzTpIcepk0o8(chr(832 - 784) + '\x6f' + chr(0b110010) + chr(0b1 + 0o62) + chr(0b1001 + 0o51), 0b1000), nzTpIcepk0o8(chr(0b11 + 0o55) + '\157' + '\066' + chr(0b110000), 43881 - 43873), nzTpIcepk0o8('\060' + chr(0b1101111) + '\062' + '\x34' + chr(49), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110100) + chr(0b110111), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(0b110010) + chr(0b110000) + '\062', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b11000 + 0o127) + chr(0b110011) + chr(1734 - 1685) + '\063', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b100111 + 0o110) + chr(51) + chr(0b110011) + chr(0b110100), 8), nzTpIcepk0o8(chr(100 - 52) + chr(5174 - 5063) + chr(0b110001 + 0o2) + chr(185 - 136) + '\x34', 8)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(3588 - 3477) + chr(1550 - 1497) + '\060', 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'm'), '\x64' + '\145' + chr(0b1100011) + '\x6f' + '\144' + chr(0b110101 + 0o60))(chr(11841 - 11724) + '\x74' + chr(0b11010 + 0o114) + chr(45) + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def DaZ8InzQgFJv(hXMPsSrOQzbh, wKKXKFBlqW0G, sl13tsTzFIJl, eemPYp2vtTSr=None, vsHxRdBONQp3=None):
if eemPYp2vtTSr is None:
eemPYp2vtTSr = {}
eemPYp2vtTSr[roI3spqORKae(ES5oEprVxulp(b'2'), chr(0b1100100) + '\145' + chr(0b1100011) + chr(9935 - 9824) + chr(0b1100100) + chr(0b11001 + 0o114))('\x75' + '\x74' + '\146' + chr(45) + chr(56))] = wKKXKFBlqW0G
return roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x1c\xca\xa4\x92\\\x99\xb5al\xa3\xe6\xb8\xb3\xd3\xcf/'), chr(0b100 + 0o140) + '\145' + chr(0b1100011) + chr(111) + '\x64' + '\145')('\165' + chr(116) + chr(9427 - 9325) + chr(45) + chr(0b111000)))(roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'0\xf0\xa1\x8f{\x9e\x9dzr\xa0'), chr(0b10010 + 0o122) + chr(1911 - 1810) + chr(0b1011111 + 0o4) + '\x6f' + '\x64' + chr(0b1100101))(chr(117) + chr(0b111011 + 0o71) + chr(0b100111 + 0o77) + '\055' + chr(0b111000))) + roI3spqORKae(ES5oEprVxulp(b'|'), chr(2058 - 1958) + chr(4700 - 4599) + '\143' + chr(0b1 + 0o156) + chr(100) + chr(8627 - 8526))(chr(0b1110101) + '\x74' + chr(0b11011 + 0o113) + chr(306 - 261) + '\x38') + roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x1c\xe0\xb2\x91}\x98\xa1`d\xa9'), '\x64' + chr(0b1100101) + chr(99) + '\157' + chr(0b1011 + 0o131) + chr(0b1100000 + 0o5))(chr(117) + '\x74' + chr(0b1100010 + 0o4) + '\055' + chr(0b100010 + 0o26)))(eemPYp2vtTSr), roI3spqORKae(emo0J8LHBNVF, roI3spqORKae(ES5oEprVxulp(b'\x05\xf0\xa5\x99'), chr(8396 - 8296) + chr(0b101000 + 0o75) + chr(99) + '\x6f' + chr(5854 - 5754) + chr(0b1100101))(chr(0b1110101) + '\164' + chr(0b100100 + 0o102) + chr(0b101101) + chr(56)))(sl13tsTzFIJl, vsHxRdBONQp3), agent=roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x0b\xc2\xf1\xaa\x7f\x9c\xaaCL\x85\xdd\x92'), chr(2240 - 2140) + '\x65' + chr(99) + chr(111) + chr(100) + chr(0b1100101))(chr(0b1110101) + chr(116) + chr(102) + '\055' + '\x38'))) |
dustin/twitty-twister | twittytwister/twitter.py | TwitterMonitor.startService | def startService(self):
"""
Start the service.
This causes a transition to the C{'idle'} state, and then calls
L{connect} to attempt an initial conection.
"""
service.Service.startService(self)
self._toState('idle')
try:
self.connect()
except NoConsumerError:
pass | python | def startService(self):
"""
Start the service.
This causes a transition to the C{'idle'} state, and then calls
L{connect} to attempt an initial conection.
"""
service.Service.startService(self)
self._toState('idle')
try:
self.connect()
except NoConsumerError:
pass | [
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This causes a transition to the C{'idle'} state, and then calls
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"."
] | 8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3 | https://github.com/dustin/twitty-twister/blob/8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3/twittytwister/twitter.py#L880-L893 | train | Start the service. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x32' + '\x30' + chr(48), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + '\x33' + '\x33' + chr(884 - 836), 8128 - 8120), nzTpIcepk0o8(chr(48) + chr(111) + chr(989 - 938) + chr(0b110110) + chr(0b110110), 15556 - 15548), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b11110 + 0o25) + chr(67 - 19), 0o10), nzTpIcepk0o8(chr(0b101010 + 0o6) + chr(0b1100111 + 0o10) + '\062' + chr(52) + '\x35', 0o10), nzTpIcepk0o8('\060' + chr(0b1100101 + 0o12) + chr(0b110001) + chr(52) + '\061', 0o10), nzTpIcepk0o8('\060' + chr(111) + '\061' + '\060' + chr(0b110101), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(54) + chr(2120 - 2071), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + '\x32' + chr(0b110010) + chr(48), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(49) + chr(50), 10535 - 10527), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110010) + chr(54) + '\x32', 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(0b10100 + 0o35) + chr(54) + '\064', 39976 - 39968), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b100001 + 0o22) + '\060' + chr(0b10110 + 0o33), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110010) + '\x31' + chr(1790 - 1742), 5563 - 5555), nzTpIcepk0o8('\x30' + chr(8182 - 8071) + chr(51) + chr(0b110111) + chr(0b110011), 43184 - 43176), nzTpIcepk0o8(chr(2184 - 2136) + '\x6f' + '\062' + chr(0b1111 + 0o50) + chr(51), 34054 - 34046), nzTpIcepk0o8(chr(0b110000) + chr(8401 - 8290) + chr(2243 - 2192) + '\x33' + '\062', 0o10), nzTpIcepk0o8(chr(1512 - 1464) + '\157' + '\x32' + '\x32', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(49) + chr(1889 - 1839) + chr(0b10101 + 0o42), 36762 - 36754), nzTpIcepk0o8(chr(48) + chr(111) + chr(49) + '\x36' + '\x36', 0o10), nzTpIcepk0o8(chr(504 - 456) + '\x6f' + chr(0b110100) + chr(0b11011 + 0o26), 0b1000), nzTpIcepk0o8(chr(908 - 860) + '\x6f' + chr(0b11110 + 0o25) + chr(0b1001 + 0o55) + chr(1456 - 1405), 34868 - 34860), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(49) + chr(0b110010) + chr(2282 - 2228), 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(1080 - 1031) + chr(55) + chr(282 - 232), 0b1000), nzTpIcepk0o8('\060' + chr(4940 - 4829) + '\x33' + chr(2044 - 1995) + chr(0b11010 + 0o32), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(51) + chr(339 - 287), 29326 - 29318), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(2252 - 2203) + chr(0b110001), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(49) + chr(0b110111 + 0o0) + chr(51), 454 - 446), nzTpIcepk0o8('\060' + chr(7020 - 6909) + chr(0b110001) + chr(2253 - 2203), 8), nzTpIcepk0o8(chr(0b10111 + 0o31) + chr(7510 - 7399) + '\061' + chr(0b10000 + 0o42) + chr(0b110001), 62483 - 62475), nzTpIcepk0o8(chr(1103 - 1055) + chr(0b1001 + 0o146) + chr(0b110001) + '\x34', ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + '\x32' + chr(0b100110 + 0o13) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b10101 + 0o132) + chr(0b110010 + 0o3) + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(51) + chr(50) + chr(0b110011), 648 - 640), nzTpIcepk0o8('\060' + '\157' + chr(0b110001) + chr(0b110111) + '\060', 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + '\062' + '\x30' + chr(54), 0b1000), nzTpIcepk0o8(chr(0b1101 + 0o43) + chr(2435 - 2324) + '\x32' + '\x32' + '\061', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101100 + 0o3) + chr(86 - 37) + chr(0b110010) + '\063', ord("\x08")), nzTpIcepk0o8(chr(1984 - 1936) + chr(111) + chr(2092 - 2041) + chr(49) + chr(0b110011 + 0o2), ord("\x08")), nzTpIcepk0o8(chr(0b10110 + 0o32) + '\157' + chr(0b110001) + '\063' + '\065', 11580 - 11572)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(0b1101101 + 0o2) + chr(0b100111 + 0o16) + chr(0b100 + 0o54), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xae'), '\x64' + chr(0b10111 + 0o116) + chr(0b1100011) + '\x6f' + chr(0b11111 + 0o105) + chr(101))(chr(117) + chr(0b1100101 + 0o17) + '\146' + chr(0b11000 + 0o25) + chr(1938 - 1882)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def n8qTPqznTdgr(hXMPsSrOQzbh):
roI3spqORKae(s3mEJkwJRqJG.Service, roI3spqORKae(ES5oEprVxulp(b'\xf3\xac\x97j\xd12 C\xe6c\xd1\x11'), '\x64' + '\x65' + chr(8203 - 8104) + chr(6180 - 6069) + chr(100) + chr(101))(chr(0b11111 + 0o126) + chr(5860 - 5744) + chr(102) + chr(0b11110 + 0o17) + chr(1095 - 1039)))(hXMPsSrOQzbh)
roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xdf\xac\x99K\xd1\x001T'), '\144' + chr(0b1100101) + chr(6634 - 6535) + chr(111) + chr(1125 - 1025) + chr(101))('\165' + '\x74' + chr(0b110101 + 0o61) + '\x2d' + chr(56)))(roI3spqORKae(ES5oEprVxulp(b'\xe9\xbc\x9a}'), chr(100) + chr(0b1100101) + chr(4406 - 4307) + chr(0b1001101 + 0o42) + '\144' + '\145')('\165' + chr(116) + chr(102) + chr(492 - 447) + chr(381 - 325)))
try:
roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xd2\xec\x9em\xe8\x12#\x7f\xe9R\xe7\x19'), chr(100) + chr(0b1100101) + '\x63' + chr(0b1000010 + 0o55) + '\x64' + chr(101))(chr(0b1110101) + chr(0b1110100) + chr(0b1011010 + 0o14) + '\x2d' + '\070'))()
except SZLedPrfRfG2:
pass |
dustin/twitty-twister | twittytwister/twitter.py | TwitterMonitor.connect | def connect(self, forceReconnect=False):
"""
Check current conditions and initiate connection if possible.
This is called to check preconditions for starting a new connection,
and initating the connection itself.
If the service is not running, this will do nothing.
@param forceReconnect: Drop an existing connection to reconnnect.
@type forceReconnect: C{False}
@raises L{ConnectError}: When a connection (attempt) is already in
progress, unless C{forceReconnect} is set.
@raises L{NoConsumerError}: When there is no consumer for incoming
tweets. No further connection attempts will be made, unless L{connect}
is called again.
"""
if self._state == 'stopped':
raise Error("This service is not running. Not connecting.")
if self._state == 'connected':
if forceReconnect:
self._toState('disconnecting')
return True
else:
raise ConnectError("Already connected.")
elif self._state == 'aborting':
raise ConnectError("Aborting connection in progress.")
elif self._state == 'disconnecting':
raise ConnectError("Disconnect in progress.")
elif self._state == 'connecting':
if forceReconnect:
self._toState('aborting')
return True
else:
raise ConnectError("Connect in progress.")
if self.delegate is None:
if self._state != 'idle':
self._toState('idle')
raise NoConsumerError()
if self._state == 'waiting':
if self._reconnectDelayedCall.called:
self._reconnectDelayedCall = None
pass
else:
self._reconnectDelayedCall.reset(0)
return True
self._toState('connecting')
return True | python | def connect(self, forceReconnect=False):
"""
Check current conditions and initiate connection if possible.
This is called to check preconditions for starting a new connection,
and initating the connection itself.
If the service is not running, this will do nothing.
@param forceReconnect: Drop an existing connection to reconnnect.
@type forceReconnect: C{False}
@raises L{ConnectError}: When a connection (attempt) is already in
progress, unless C{forceReconnect} is set.
@raises L{NoConsumerError}: When there is no consumer for incoming
tweets. No further connection attempts will be made, unless L{connect}
is called again.
"""
if self._state == 'stopped':
raise Error("This service is not running. Not connecting.")
if self._state == 'connected':
if forceReconnect:
self._toState('disconnecting')
return True
else:
raise ConnectError("Already connected.")
elif self._state == 'aborting':
raise ConnectError("Aborting connection in progress.")
elif self._state == 'disconnecting':
raise ConnectError("Disconnect in progress.")
elif self._state == 'connecting':
if forceReconnect:
self._toState('aborting')
return True
else:
raise ConnectError("Connect in progress.")
if self.delegate is None:
if self._state != 'idle':
self._toState('idle')
raise NoConsumerError()
if self._state == 'waiting':
if self._reconnectDelayedCall.called:
self._reconnectDelayedCall = None
pass
else:
self._reconnectDelayedCall.reset(0)
return True
self._toState('connecting')
return True | [
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This is called to check preconditions for starting a new connection,
and initating the connection itself.
If the service is not running, this will do nothing.
@param forceReconnect: Drop an existing connection to reconnnect.
@type forceReconnect: C{False}
@raises L{ConnectError}: When a connection (attempt) is already in
progress, unless C{forceReconnect} is set.
@raises L{NoConsumerError}: When there is no consumer for incoming
tweets. No further connection attempts will be made, unless L{connect}
is called again. | [
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"possible",
"."
] | 8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3 | https://github.com/dustin/twitty-twister/blob/8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3/twittytwister/twitter.py#L906-L958 | train | Connect to the current state of the current Tweets. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(50) + chr(0b110101) + '\067', 465 - 457), nzTpIcepk0o8('\060' + chr(111) + chr(2357 - 2307) + chr(50) + chr(0b10011 + 0o41), 0b1000), nzTpIcepk0o8('\060' + chr(4533 - 4422) + chr(50) + chr(54) + chr(51), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1000110 + 0o51) + chr(2246 - 2195) + '\x37' + '\x35', 29770 - 29762), nzTpIcepk0o8(chr(0b100010 + 0o16) + chr(2607 - 2496) + chr(51) + '\x36' + chr(0b110001), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(0b10100 + 0o36) + chr(0b1110 + 0o44) + chr(1156 - 1106), 0b1000), nzTpIcepk0o8('\060' + chr(0b1001101 + 0o42) + chr(0b1100 + 0o47) + '\x37' + chr(0b110110), 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(50) + '\066' + '\066', 0o10), nzTpIcepk0o8('\x30' + chr(0b1011011 + 0o24) + chr(0b110111) + '\063', 0o10), nzTpIcepk0o8(chr(1179 - 1131) + chr(0b1101111) + '\063' + chr(54) + chr(0b1101 + 0o44), 8), nzTpIcepk0o8(chr(0b110000) + chr(8068 - 7957) + chr(0b10110 + 0o35) + chr(1096 - 1042) + chr(0b11011 + 0o31), ord("\x08")), nzTpIcepk0o8(chr(2288 - 2240) + chr(2057 - 1946) + chr(51) + chr(0b110010) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(0b100000 + 0o20) + chr(0b1101111) + '\x32' + '\x30' + '\x34', 34692 - 34684), nzTpIcepk0o8('\x30' + '\157' + chr(127 - 77) + chr(53) + chr(1927 - 1879), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(1705 - 1654) + '\x30' + '\067', ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(0b10 + 0o60) + chr(53) + chr(0b10 + 0o57), 0b1000), nzTpIcepk0o8('\x30' + chr(3813 - 3702) + '\061' + chr(0b10101 + 0o37) + chr(0b110100), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1001000 + 0o47) + chr(0b110100) + '\066', 53387 - 53379), nzTpIcepk0o8(chr(0b10010 + 0o36) + chr(111) + chr(2039 - 1990) + '\062' + '\x32', 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + '\061' + chr(50) + '\063', 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b101001 + 0o12) + chr(735 - 681) + chr(0b1001 + 0o55), 12874 - 12866), nzTpIcepk0o8('\060' + chr(5516 - 5405) + chr(1565 - 1516) + chr(0b1101 + 0o46) + chr(150 - 102), 0o10), nzTpIcepk0o8(chr(1312 - 1264) + chr(0b1100110 + 0o11) + chr(0b110011) + chr(0b110001) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(0b101101 + 0o3) + chr(0b1101111) + chr(1626 - 1575) + '\061', 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(2311 - 2260) + chr(0b110110) + chr(55), 0b1000), nzTpIcepk0o8('\060' + chr(9042 - 8931) + chr(0b100010 + 0o17) + chr(0b10011 + 0o41) + chr(0b110010), 20819 - 20811), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110001) + chr(0b110101), 25393 - 25385), nzTpIcepk0o8('\060' + '\157' + '\061' + chr(0b110000) + chr(49), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110001) + '\066' + chr(0b110110), 43246 - 43238), nzTpIcepk0o8('\060' + '\157' + chr(0b100100 + 0o17) + chr(0b100100 + 0o15) + '\x30', 0b1000), nzTpIcepk0o8(chr(768 - 720) + '\x6f' + '\x33' + chr(2400 - 2347) + '\x36', ord("\x08")), nzTpIcepk0o8(chr(0b1001 + 0o47) + chr(0b1100110 + 0o11) + chr(0b110011) + chr(0b110001) + chr(51), 8), nzTpIcepk0o8(chr(689 - 641) + '\x6f' + chr(1950 - 1899) + '\x34' + chr(0b110100), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(11850 - 11739) + '\x33' + chr(0b101001 + 0o11) + chr(935 - 881), 0b1000), nzTpIcepk0o8(chr(48) + chr(7873 - 7762) + '\061' + chr(2157 - 2105) + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(698 - 649) + '\x35', 8), nzTpIcepk0o8(chr(0b110000) + chr(6356 - 6245) + chr(1568 - 1517) + chr(0b10001 + 0o46) + '\063', 53772 - 53764), nzTpIcepk0o8(chr(0b10101 + 0o33) + '\157' + chr(657 - 606) + chr(0b10110 + 0o37) + chr(52), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\061' + chr(0b110000) + '\064', 0o10), nzTpIcepk0o8(chr(0b100000 + 0o20) + chr(11740 - 11629) + '\x32' + chr(0b110011) + chr(0b1000 + 0o55), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(0b111101 + 0o62) + chr(53) + '\060', 12369 - 12361)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x81'), '\x64' + chr(4023 - 3922) + chr(0b100111 + 0o74) + chr(10809 - 10698) + '\144' + chr(0b1100101))('\x75' + chr(7845 - 7729) + chr(0b1000 + 0o136) + chr(45) + chr(439 - 383)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def R4huMsfNyXUm(hXMPsSrOQzbh, BTe5gw0Ohl5P=nzTpIcepk0o8(chr(1958 - 1910) + '\x6f' + chr(0b100011 + 0o15), 0b1000)):
if roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xe8\xf6\xc1\xaa\xa3\xd1\x9c\x8e\x03\xa8\xb1\xec'), chr(0b1000 + 0o134) + chr(0b1100101) + chr(99) + chr(111) + chr(100) + '\x65')(chr(117) + chr(0b1000001 + 0o63) + chr(0b101001 + 0o75) + '\x2d' + '\x38')) == roI3spqORKae(ES5oEprVxulp(b'\xdc\xe0\xdc\x8d\x81\xf7\x9a'), '\144' + '\145' + chr(0b1100011) + chr(0b111110 + 0o61) + chr(9000 - 8900) + chr(101))(chr(0b1110101) + chr(12664 - 12548) + chr(0b10000 + 0o126) + '\055' + chr(56)):
raise qzKJvU2YY6AI(roI3spqORKae(ES5oEprVxulp(b"\xfb\xfc\xda\x8e\xd1\xe1\x9b\xc4M\x98\x97\xb1\xa4\xc1\xb4\x89\nI&s\x84-\xa5w\x9e\x0cjoV\x86\x81\xbf\xc4\xb5\x0cc\x95\x89'\xe9\xc6\xfa\xd4\xd3"), chr(9414 - 9314) + chr(101) + chr(0b1001101 + 0o26) + chr(0b1111 + 0o140) + chr(0b111101 + 0o47) + chr(0b1100101))('\165' + chr(0b1100111 + 0o15) + chr(5217 - 5115) + chr(1512 - 1467) + chr(56)))
if roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xe8\xf6\xc1\xaa\xa3\xd1\x9c\x8e\x03\xa8\xb1\xec'), chr(100) + '\x65' + chr(3942 - 3843) + '\x6f' + chr(0b1100100) + chr(6859 - 6758))(chr(132 - 15) + '\164' + chr(102) + chr(0b101101) + '\x38')) == roI3spqORKae(ES5oEprVxulp(b'\xcc\xfb\xdd\x93\x94\xf1\x8a\xd3_'), '\144' + chr(0b1100101) + chr(0b1100011) + chr(0b111010 + 0o65) + '\x64' + chr(0b1100101))(chr(117) + '\x74' + chr(0b1100110) + chr(45) + '\070'):
if BTe5gw0Ohl5P:
roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xf0\xe0\xdc\xae\x85\xf3\x8a\xd3'), chr(9830 - 9730) + chr(0b1100101) + chr(3318 - 3219) + chr(0b101101 + 0o102) + '\144' + chr(101))(chr(117) + chr(0b1010110 + 0o36) + chr(0b1100110) + '\x2d' + chr(1758 - 1702)))(roI3spqORKae(ES5oEprVxulp(b'\xcb\xfd\xc0\x9e\x9e\xfc\x90\xd3X\x85\x9d\xba\xe3'), chr(0b1100100) + '\145' + '\143' + chr(9895 - 9784) + chr(4768 - 4668) + chr(2026 - 1925))(chr(0b1110101) + chr(0b100011 + 0o121) + '\x66' + chr(769 - 724) + chr(0b111000)))
return nzTpIcepk0o8(chr(0b1111 + 0o41) + chr(0b1010101 + 0o32) + chr(0b100001 + 0o20), 0b1000)
else:
raise cIpVpgnwbdbd(roI3spqORKae(ES5oEprVxulp(b'\xee\xf8\xc1\x98\x90\xf6\x87\x96X\x9e\x9a\xba\xe1\xcb\xb3\xcc\x00\x08'), '\x64' + chr(2303 - 2202) + chr(4958 - 4859) + chr(0b1101111) + '\x64' + chr(8156 - 8055))(chr(497 - 380) + chr(0b100010 + 0o122) + chr(0b1001111 + 0o27) + chr(0b101101) + '\x38'))
elif roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xe8\xf6\xc1\xaa\xa3\xd1\x9c\x8e\x03\xa8\xb1\xec'), chr(0b1100100) + '\145' + chr(99) + chr(0b1101111) + chr(0b1100100) + '\x65')(chr(6468 - 6351) + chr(316 - 200) + chr(7425 - 7323) + chr(45) + '\x38')) == roI3spqORKae(ES5oEprVxulp(b'\xce\xf6\xdc\x8f\x85\xfb\x90\xd1'), chr(0b1100100) + chr(5647 - 5546) + chr(99) + '\157' + chr(0b1100100) + '\x65')(chr(12888 - 12771) + chr(10926 - 10810) + chr(0b100011 + 0o103) + chr(0b1100 + 0o41) + '\x38'):
raise cIpVpgnwbdbd(roI3spqORKae(ES5oEprVxulp(b'\xee\xf6\xdc\x8f\x85\xfb\x90\xd1\x1b\x92\x9b\xba\xea\xcd\xa4\xdd\rI<s\x9f6\xebi\x85\rj3\x13\xbb\x9d\xe5'), chr(1267 - 1167) + chr(0b1100101) + chr(6731 - 6632) + chr(0b101001 + 0o106) + chr(0b11001 + 0o113) + '\145')(chr(3040 - 2923) + chr(12835 - 12719) + '\146' + chr(0b101101) + chr(2729 - 2673)))
elif roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xe8\xf6\xc1\xaa\xa3\xd1\x9c\x8e\x03\xa8\xb1\xec'), chr(0b1100100) + chr(5251 - 5150) + chr(4065 - 3966) + '\157' + '\144' + '\145')(chr(13625 - 13508) + '\164' + chr(102) + '\055' + chr(0b10101 + 0o43))) == roI3spqORKae(ES5oEprVxulp(b'\xcb\xfd\xc0\x9e\x9e\xfc\x90\xd3X\x85\x9d\xba\xe3'), chr(4904 - 4804) + chr(0b1011000 + 0o15) + chr(99) + '\x6f' + chr(100) + chr(101))(chr(0b1110101) + chr(116) + chr(102) + chr(45) + chr(678 - 622)):
raise cIpVpgnwbdbd(roI3spqORKae(ES5oEprVxulp(b'\xeb\xfd\xc0\x9e\x9e\xfc\x90\xd3X\x85\xd4\xbd\xea\x88\xb7\xdb\x0bA 6\x85+\xe5'), chr(9395 - 9295) + chr(7179 - 7078) + '\143' + chr(0b110001 + 0o76) + chr(0b1100100) + '\145')('\x75' + chr(116) + '\x66' + chr(1656 - 1611) + chr(0b11001 + 0o37)))
elif roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xe8\xf6\xc1\xaa\xa3\xd1\x9c\x8e\x03\xa8\xb1\xec'), '\144' + chr(101) + '\143' + chr(0b10011 + 0o134) + chr(0b1100100) + chr(0b110110 + 0o57))('\165' + chr(116) + chr(0b1011010 + 0o14) + chr(0b101101) + chr(56))) == roI3spqORKae(ES5oEprVxulp(b'\xcc\xfb\xdd\x93\x94\xf1\x8a\xdfU\x96'), '\144' + '\x65' + '\x63' + chr(0b1010000 + 0o37) + '\x64' + '\145')(chr(8491 - 8374) + chr(0b1110100) + chr(0b1011000 + 0o16) + '\x2d' + chr(0b111000)):
if BTe5gw0Ohl5P:
roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xf0\xe0\xdc\xae\x85\xf3\x8a\xd3'), chr(0b1100100) + chr(0b1100101) + chr(0b11101 + 0o106) + chr(0b1010 + 0o145) + chr(0b1110 + 0o126) + chr(101))('\165' + '\x74' + '\x66' + chr(45) + '\x38'))(roI3spqORKae(ES5oEprVxulp(b'\xce\xf6\xdc\x8f\x85\xfb\x90\xd1'), chr(0b101 + 0o137) + '\x65' + '\x63' + chr(0b1101111) + chr(7071 - 6971) + chr(101))(chr(0b1110101) + chr(0b1110100) + chr(0b111001 + 0o55) + chr(45) + chr(1430 - 1374)))
return nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110001), 8)
else:
raise cIpVpgnwbdbd(roI3spqORKae(ES5oEprVxulp(b'\xec\xfb\xdd\x93\x94\xf1\x8a\x96R\x9f\xd4\xa4\xf6\xc7\xa0\xdb\x01U!}'), chr(0b1100100) + '\145' + chr(0b1100011) + '\x6f' + chr(100) + chr(0b1100101))('\x75' + '\x74' + '\146' + chr(0b101101) + chr(2673 - 2617)))
if roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xcb\xf1\xdf\x98\x96\xf3\x8a\xd3'), '\144' + '\145' + chr(99) + '\x6f' + '\x64' + chr(0b1100101))(chr(117) + '\164' + '\x66' + chr(0b101101) + chr(56))) is None:
if roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xe8\xf6\xc1\xaa\xa3\xd1\x9c\x8e\x03\xa8\xb1\xec'), chr(0b1011101 + 0o7) + '\x65' + chr(8388 - 8289) + chr(6512 - 6401) + chr(0b1100100) + chr(101))('\165' + '\164' + chr(0b1100110) + '\055' + chr(56))) != roI3spqORKae(ES5oEprVxulp(b'\xc6\xf0\xdf\x98'), chr(0b1100100) + chr(101) + chr(99) + '\157' + '\144' + chr(101))(chr(0b1110101) + chr(116) + chr(0b1111 + 0o127) + '\055' + chr(0b110101 + 0o3)):
roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xf0\xe0\xdc\xae\x85\xf3\x8a\xd3'), chr(0b1100100) + chr(101) + chr(99) + chr(0b111111 + 0o60) + '\x64' + chr(0b1100101))(chr(7618 - 7501) + '\x74' + chr(8063 - 7961) + chr(45) + chr(0b110010 + 0o6)))(roI3spqORKae(ES5oEprVxulp(b'\xc6\xf0\xdf\x98'), chr(0b1100100) + chr(3972 - 3871) + chr(0b1100011) + chr(111) + '\x64' + chr(0b1100101))(chr(0b1110101) + '\x74' + chr(0b1000110 + 0o40) + chr(491 - 446) + '\x38'))
raise SZLedPrfRfG2()
if roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xe8\xf6\xc1\xaa\xa3\xd1\x9c\x8e\x03\xa8\xb1\xec'), '\x64' + chr(101) + chr(0b1100011) + chr(0b1101111) + '\x64' + chr(101))(chr(0b1110101) + chr(11317 - 11201) + '\x66' + '\x2d' + chr(1197 - 1141))) == roI3spqORKae(ES5oEprVxulp(b'\xd8\xf5\xda\x89\x98\xfc\x99'), chr(0b11101 + 0o107) + '\x65' + chr(0b100001 + 0o102) + '\x6f' + chr(9687 - 9587) + chr(0b1100101))(chr(0b1110101) + '\x74' + chr(0b1100110) + chr(0b1100 + 0o41) + chr(56)):
if roI3spqORKae(hXMPsSrOQzbh._reconnectDelayedCall, roI3spqORKae(ES5oEprVxulp(b'\xc8\xf1\xc1\xcc\xc4\xc6\x8e\xe1i\xa1\x9d\x99'), chr(8322 - 8222) + '\x65' + '\143' + chr(0b1101 + 0o142) + '\144' + chr(0b1100101))(chr(8035 - 7918) + chr(116) + '\x66' + '\055' + chr(1741 - 1685))):
hXMPsSrOQzbh.lHqFE_YA1rKV = None
pass
else:
roI3spqORKae(hXMPsSrOQzbh._reconnectDelayedCall, roI3spqORKae(ES5oEprVxulp(b'\xf7\xc1\xcb\x9a\xa8\xf7\xbb\xfdd\xa5\xcd\x8b'), chr(0b1000011 + 0o41) + chr(101) + chr(3586 - 3487) + '\x6f' + '\144' + '\x65')(chr(10317 - 10200) + chr(116) + chr(3740 - 3638) + '\055' + '\070'))(nzTpIcepk0o8(chr(2248 - 2200) + chr(111) + chr(0b110000), 8))
return nzTpIcepk0o8(chr(0b111 + 0o51) + chr(0b1101111) + chr(49), 8)
roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xf0\xe0\xdc\xae\x85\xf3\x8a\xd3'), chr(100) + chr(101) + chr(99) + chr(111) + chr(0b1010001 + 0o23) + chr(4350 - 4249))(chr(117) + '\164' + '\x66' + chr(0b101101) + '\070'))(roI3spqORKae(ES5oEprVxulp(b'\xcc\xfb\xdd\x93\x94\xf1\x8a\xdfU\x96'), '\144' + chr(0b11010 + 0o113) + chr(99) + '\x6f' + chr(0b1011100 + 0o10) + chr(252 - 151))(chr(0b110010 + 0o103) + chr(116) + chr(102) + chr(0b101101) + chr(0b100 + 0o64)))
return nzTpIcepk0o8(chr(0b110000) + chr(0b1010110 + 0o31) + chr(0b101011 + 0o6), 8) |
dustin/twitty-twister | twittytwister/twitter.py | TwitterMonitor.makeConnection | def makeConnection(self, protocol):
"""
Called when the connection has been established.
This method is called when an HTTP 200 response has been received,
with the protocol that decodes the individual Twitter stream elements.
That protocol will call the consumer for all Twitter entries received.
The protocol, stored in L{protocol}, has a deferred that fires when
the connection is closed, causing a transition to the
C{'disconnected'} state.
@param protocol: The Twitter stream protocol.
@type protocol: L{TwitterStream}
"""
self._errorState = None
def cb(result):
self.protocol = None
if self._state == 'stopped':
# Don't transition to any other state. We are stopped.
pass
else:
if isinstance(result, failure.Failure):
reason = result
else:
reason = None
self._toState('disconnected', reason)
self.protocol = protocol
d = protocol.deferred
d.addBoth(cb) | python | def makeConnection(self, protocol):
"""
Called when the connection has been established.
This method is called when an HTTP 200 response has been received,
with the protocol that decodes the individual Twitter stream elements.
That protocol will call the consumer for all Twitter entries received.
The protocol, stored in L{protocol}, has a deferred that fires when
the connection is closed, causing a transition to the
C{'disconnected'} state.
@param protocol: The Twitter stream protocol.
@type protocol: L{TwitterStream}
"""
self._errorState = None
def cb(result):
self.protocol = None
if self._state == 'stopped':
# Don't transition to any other state. We are stopped.
pass
else:
if isinstance(result, failure.Failure):
reason = result
else:
reason = None
self._toState('disconnected', reason)
self.protocol = protocol
d = protocol.deferred
d.addBoth(cb) | [
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That protocol will call the consumer for all Twitter entries received.
The protocol, stored in L{protocol}, has a deferred that fires when
the connection is closed, causing a transition to the
C{'disconnected'} state.
@param protocol: The Twitter stream protocol.
@type protocol: L{TwitterStream} | [
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] | 8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3 | https://github.com/dustin/twitty-twister/blob/8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3/twittytwister/twitter.py#L969-L1000 | train | This method is called when a connection is established. It creates a deferred that fires when the connection is closed. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(746 - 698) + '\x6f' + chr(0b1 + 0o65) + chr(54), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110010) + '\x36' + chr(0b110111), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + '\061' + chr(51) + '\067', ord("\x08")), nzTpIcepk0o8(chr(0b0 + 0o60) + chr(111) + chr(0b110001) + chr(55) + chr(0b110001), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b1110 + 0o43) + chr(1591 - 1542) + '\061', 0b1000), nzTpIcepk0o8(chr(0b1111 + 0o41) + chr(111) + chr(0b110001) + '\x33' + chr(0b110011 + 0o1), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\061' + '\066' + '\061', 18199 - 18191), nzTpIcepk0o8('\060' + chr(653 - 542) + '\062' + chr(0b100000 + 0o26) + chr(0b110000), 41714 - 41706), nzTpIcepk0o8(chr(48) + chr(0b1100001 + 0o16) + chr(0b1010 + 0o50) + '\x36' + chr(2805 - 2750), 8), nzTpIcepk0o8(chr(1014 - 966) + chr(0b1011 + 0o144) + chr(0b100001 + 0o23) + chr(55), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(49) + chr(1678 - 1624) + chr(1041 - 989), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110 + 0o60), 38926 - 38918), nzTpIcepk0o8(chr(0b0 + 0o60) + '\x6f' + '\x32' + chr(0b110101) + chr(54), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b100110 + 0o111) + chr(0b1101 + 0o45) + chr(0b101011 + 0o13) + chr(0b110110), 0o10), nzTpIcepk0o8('\x30' + chr(111) + '\061' + chr(0b100101 + 0o13) + chr(54), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + '\x34' + chr(52), 4162 - 4154), nzTpIcepk0o8('\060' + chr(0b10 + 0o155) + '\x32' + chr(0b101011 + 0o10) + chr(1889 - 1837), 13799 - 13791), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x32' + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(649 - 601) + chr(5813 - 5702) + chr(0b110010) + chr(0b110011), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(5604 - 5493) + '\062' + '\061' + chr(0b11011 + 0o31), 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(2060 - 2011) + chr(0b1011 + 0o46) + '\064', 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(805 - 750) + chr(0b110011), 4311 - 4303), nzTpIcepk0o8(chr(48) + chr(11969 - 11858) + chr(0b0 + 0o61) + chr(0b110000) + '\x31', 0b1000), nzTpIcepk0o8(chr(1287 - 1239) + '\x6f' + chr(0b110010) + chr(0b110000 + 0o0) + '\x33', 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110011) + '\x36' + chr(0b100101 + 0o21), ord("\x08")), nzTpIcepk0o8(chr(0b10000 + 0o40) + chr(0b1101111) + chr(0b110011 + 0o1) + '\062', 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(50) + chr(0b110000), 8), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(365 - 316) + '\061' + chr(764 - 714), 58667 - 58659), nzTpIcepk0o8(chr(0b110000) + chr(0b1000010 + 0o55) + chr(0b11000 + 0o33) + chr(1833 - 1779) + '\060', 0b1000), nzTpIcepk0o8(chr(260 - 212) + chr(0b11010 + 0o125) + chr(0b110011) + chr(0b11100 + 0o30) + chr(0b110100), 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(0b101011 + 0o6) + '\x37' + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(10013 - 9902) + chr(51) + chr(1344 - 1296) + chr(55), 33589 - 33581), nzTpIcepk0o8('\060' + '\157' + chr(51) + chr(2431 - 2376) + '\x31', 18057 - 18049), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(422 - 372) + chr(0b110001), 0o10), nzTpIcepk0o8(chr(1694 - 1646) + chr(0b1100001 + 0o16) + chr(51) + chr(2451 - 2399) + '\061', 4399 - 4391), nzTpIcepk0o8(chr(0b100011 + 0o15) + chr(111) + chr(0b10000 + 0o43) + '\x31', 0b1000), nzTpIcepk0o8(chr(0b10111 + 0o31) + chr(5895 - 5784) + chr(312 - 262) + chr(0b1101 + 0o44), 8), nzTpIcepk0o8(chr(48) + chr(0b110110 + 0o71) + chr(239 - 188) + chr(52) + '\x37', ord("\x08")), nzTpIcepk0o8(chr(282 - 234) + chr(0b1100101 + 0o12) + '\x32' + chr(0b10 + 0o63) + '\x34', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x33' + chr(0b11001 + 0o35) + chr(53), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(554 - 506) + '\x6f' + chr(53) + chr(1140 - 1092), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x18'), '\144' + '\x65' + chr(0b1100011) + chr(7638 - 7527) + '\144' + '\145')(chr(0b1110000 + 0o5) + chr(0b111111 + 0o65) + '\x66' + chr(45) + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def dBf64aBhLsBX(hXMPsSrOQzbh, Yk6NhCmIsc7f):
hXMPsSrOQzbh.DHBw8CDUx_1x = None
def RYEhqzIVZREo(POx95m7SPOVy):
hXMPsSrOQzbh.Yk6NhCmIsc7f = None
if roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'q\xd5-.\x1b\x1f\x13\x88\x8f~1>'), chr(0b1001110 + 0o26) + chr(0b1100101) + '\x63' + '\157' + chr(0b1100100) + '\x65')(chr(117) + chr(7212 - 7096) + chr(4671 - 4569) + '\x2d' + chr(0b111000))) == roI3spqORKae(ES5oEprVxulp(b'E\xc30\t99\x15'), chr(100) + '\x65' + chr(8902 - 8803) + chr(12272 - 12161) + chr(100) + chr(0b1000011 + 0o42))(chr(0b1011011 + 0o32) + chr(0b1110100) + '\146' + '\x2d' + '\x38'):
pass
else:
if suIjIS24Zkqw(POx95m7SPOVy, roI3spqORKae(DUbr_vQkcSNT, roI3spqORKae(ES5oEprVxulp(b'p\xd66\x15<.\x14'), chr(100) + chr(0b101110 + 0o67) + '\143' + chr(111) + '\x64' + chr(0b1011001 + 0o14))(chr(0b101111 + 0o106) + chr(6057 - 5941) + chr(0b101010 + 0o74) + '\055' + chr(0b111000)))):
RhxFF63tBU4y = POx95m7SPOVy
else:
RhxFF63tBU4y = None
roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'i\xc30*==\x05\xd5'), '\x64' + chr(0b1100101) + '\x63' + '\157' + '\144' + '\x65')('\x75' + chr(3830 - 3714) + chr(0b1100110) + chr(0b101101) + chr(56)))(roI3spqORKae(ES5oEprVxulp(b'R\xde,\x1a&2\x1f\xd5\xd4S\x11b'), '\x64' + '\x65' + chr(0b1100011) + chr(4710 - 4599) + chr(100) + chr(10053 - 9952))(chr(0b1110101) + '\164' + chr(5775 - 5673) + '\055' + '\x38'), RhxFF63tBU4y)
hXMPsSrOQzbh.Yk6NhCmIsc7f = Yk6NhCmIsc7f
vPPlOXQgR3SM = Yk6NhCmIsc7f.VTs7CTDkBstx
roI3spqORKae(vPPlOXQgR3SM, roI3spqORKae(ES5oEprVxulp(b'W\xd3;;&(\x19'), '\144' + '\x65' + chr(99) + chr(0b1000001 + 0o56) + '\144' + '\145')(chr(0b10011 + 0o142) + chr(4884 - 4768) + chr(4510 - 4408) + chr(1133 - 1088) + chr(399 - 343)))(RYEhqzIVZREo) |
dustin/twitty-twister | twittytwister/twitter.py | TwitterMonitor._reconnect | def _reconnect(self, errorState):
"""
Attempt to reconnect.
If the current back-off delay is 0, L{connect} is called. Otherwise,
it will cause a transition to the C{'waiting'} state, ultimately
causing a call to L{connect} when the delay expires.
"""
def connect():
if self.noisy:
log.msg("Reconnecting now.")
self.connect()
backOff = self.backOffs[errorState]
if self._errorState != errorState or self._delay is None:
self._errorState = errorState
self._delay = backOff['initial']
else:
self._delay = min(backOff['max'], self._delay * backOff['factor'])
if self._delay == 0:
connect()
else:
self._reconnectDelayedCall = self.reactor.callLater(self._delay,
connect)
self._toState('waiting') | python | def _reconnect(self, errorState):
"""
Attempt to reconnect.
If the current back-off delay is 0, L{connect} is called. Otherwise,
it will cause a transition to the C{'waiting'} state, ultimately
causing a call to L{connect} when the delay expires.
"""
def connect():
if self.noisy:
log.msg("Reconnecting now.")
self.connect()
backOff = self.backOffs[errorState]
if self._errorState != errorState or self._delay is None:
self._errorState = errorState
self._delay = backOff['initial']
else:
self._delay = min(backOff['max'], self._delay * backOff['factor'])
if self._delay == 0:
connect()
else:
self._reconnectDelayedCall = self.reactor.callLater(self._delay,
connect)
self._toState('waiting') | [
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If the current back-off delay is 0, L{connect} is called. Otherwise,
it will cause a transition to the C{'waiting'} state, ultimately
causing a call to L{connect} when the delay expires. | [
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] | 8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3 | https://github.com/dustin/twitty-twister/blob/8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3/twittytwister/twitter.py#L1003-L1029 | train | Attempts to reconnect. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(48) + chr(111) + chr(543 - 494) + '\x37' + '\x32', 757 - 749), nzTpIcepk0o8('\x30' + chr(111) + chr(50) + '\x37' + '\x37', 0b1000), nzTpIcepk0o8(chr(0b101011 + 0o5) + chr(111) + chr(50) + chr(0b11110 + 0o27) + '\x31', 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(50) + chr(0b100111 + 0o20) + chr(49), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1011100 + 0o23) + '\063' + chr(0b110110) + chr(0b1010 + 0o51), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110010) + chr(0b100111 + 0o13) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(0b10001 + 0o37) + '\x6f' + chr(55) + '\x31', 56941 - 56933), nzTpIcepk0o8('\060' + chr(0b110011 + 0o74) + '\x33' + chr(0b101111 + 0o5) + '\x35', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b10 + 0o155) + chr(0b1001 + 0o52) + '\x36' + '\066', 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b11011 + 0o27) + chr(229 - 181) + '\x30', 50760 - 50752), nzTpIcepk0o8('\060' + '\157' + chr(0b110011) + '\x32', 0o10), nzTpIcepk0o8('\060' + chr(9675 - 9564) + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(2876 - 2765) + chr(1250 - 1200) + chr(0b110101) + '\x36', 0o10), nzTpIcepk0o8('\x30' + chr(0b1011010 + 0o25) + chr(1414 - 1364) + chr(0b1110 + 0o51) + chr(1589 - 1538), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(917 - 866) + chr(1628 - 1574) + chr(0b100111 + 0o11), 65063 - 65055), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(49) + chr(0b10010 + 0o43) + chr(0b110001), ord("\x08")), nzTpIcepk0o8(chr(0b101111 + 0o1) + chr(1728 - 1617) + '\x31' + '\066' + '\061', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(51) + chr(1832 - 1782) + chr(2225 - 2173), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(0b110001) + chr(110 - 61) + '\066', 38033 - 38025), nzTpIcepk0o8('\060' + chr(1742 - 1631) + chr(51) + chr(55) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b10000 + 0o137) + chr(363 - 311) + chr(284 - 236), 0b1000), nzTpIcepk0o8(chr(0b10100 + 0o34) + chr(0b1101111) + chr(0b110010) + chr(0b110110) + chr(296 - 247), 16866 - 16858), nzTpIcepk0o8(chr(48) + chr(2547 - 2436) + chr(1961 - 1911) + '\x31' + '\x34', 0b1000), nzTpIcepk0o8(chr(0b1110 + 0o42) + '\157' + chr(0b110001) + chr(867 - 818) + chr(2497 - 2446), 34434 - 34426), nzTpIcepk0o8(chr(48) + chr(111) + chr(1779 - 1730) + '\x30' + chr(0b110011), 0o10), nzTpIcepk0o8(chr(0b0 + 0o60) + '\157' + chr(54) + '\x34', 0o10), nzTpIcepk0o8(chr(2236 - 2188) + '\x6f' + chr(0b110010) + '\x37' + chr(49), 8), nzTpIcepk0o8(chr(1085 - 1037) + '\157' + '\x32' + chr(49) + chr(50), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110101) + chr(1525 - 1477), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1000111 + 0o50) + chr(0b110001) + '\x35' + chr(86 - 34), 2850 - 2842), nzTpIcepk0o8('\x30' + '\157' + chr(0b11 + 0o63) + chr(1671 - 1616), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(0b10001 + 0o40) + chr(50) + chr(51), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\061' + '\061' + chr(0b110101), 38359 - 38351), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b10010 + 0o41) + chr(0b10001 + 0o37) + chr(0b101111 + 0o5), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(50) + chr(0b110001), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b100010 + 0o22) + chr(0b1010 + 0o46), 8), nzTpIcepk0o8('\060' + '\157' + chr(0b100011 + 0o17) + '\065' + chr(0b101001 + 0o7), ord("\x08")), nzTpIcepk0o8(chr(0b100111 + 0o11) + chr(7503 - 7392) + chr(0b110010) + chr(0b100000 + 0o20) + chr(50), 0o10), nzTpIcepk0o8(chr(349 - 301) + chr(7335 - 7224) + chr(50) + chr(55) + chr(1762 - 1709), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + '\x31' + chr(0b110100) + chr(2195 - 2141), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + '\157' + '\x35' + chr(48), 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'T'), chr(4226 - 4126) + chr(101) + chr(99) + '\157' + chr(100) + '\145')(chr(0b1110010 + 0o3) + chr(0b1000100 + 0o60) + chr(2755 - 2653) + '\055' + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def XGZrdsNUUy75(hXMPsSrOQzbh, TE3mLnUpwv2m):
def R4huMsfNyXUm():
if roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x14\xd0\xc0\xca\x8a'), chr(2397 - 2297) + '\x65' + '\143' + chr(0b1101111) + chr(0b1100100) + '\x65')(chr(117) + '\x74' + chr(0b1010100 + 0o22) + '\x2d' + chr(1385 - 1329))):
roI3spqORKae(lmiGj7TonZgV, roI3spqORKae(ES5oEprVxulp(b'\t\xd3\xcd\xc3\x91\xdcO\x80\xce\xc7+T'), chr(100) + '\145' + '\143' + chr(0b10110 + 0o131) + '\x64' + '\x65')(chr(0b100001 + 0o124) + chr(0b1001011 + 0o51) + '\x66' + chr(0b10101 + 0o30) + '\x38'))(roI3spqORKae(ES5oEprVxulp(b'(\xda\xca\xd6\x9d\xfa\\\x86\x82\xe9t`\x8e\xd5\x9f\x1e_'), chr(5877 - 5777) + '\x65' + '\143' + chr(111) + '\x64' + chr(0b1100101))('\x75' + '\164' + '\146' + chr(975 - 930) + '\x38'))
roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'(\x8b\xc1\xcc\xbe\xe7_\xab\x8f\xd8Oj'), chr(0b100100 + 0o100) + chr(101) + chr(0b1100011) + '\x6f' + '\144' + '\x65')(chr(117) + '\164' + '\x66' + '\x2d' + chr(56)))()
JzohgM9yG5yn = hXMPsSrOQzbh.backOffs[TE3mLnUpwv2m]
if roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'>\xf7\xeb\xce\xcb\xd7}\xb0\x8e\xdf+\x7f'), '\144' + chr(0b100101 + 0o100) + chr(0b1100011) + chr(0b10010 + 0o135) + chr(0b1001 + 0o133) + '\x65')(chr(117) + chr(0b1001011 + 0o51) + '\x66' + chr(614 - 569) + chr(0b111000))) != TE3mLnUpwv2m or roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'%\xdb\xcc\xd5\x92\xed'), chr(2032 - 1932) + chr(0b1100101) + chr(7396 - 7297) + chr(0b1101010 + 0o5) + chr(100) + '\145')('\165' + '\x74' + chr(0b1010010 + 0o24) + chr(0b100000 + 0o15) + '\x38')) is None:
hXMPsSrOQzbh.DHBw8CDUx_1x = TE3mLnUpwv2m
hXMPsSrOQzbh.mKGIZ4Z_8FTA = JzohgM9yG5yn[roI3spqORKae(ES5oEprVxulp(b'\x13\xd1\xc0\xcd\x9a\xf5U'), '\x64' + chr(0b1100101) + chr(8141 - 8042) + '\x6f' + chr(100) + chr(0b111001 + 0o54))(chr(0b1110101) + '\x74' + chr(2873 - 2771) + chr(0b101101) + chr(0b111000))]
else:
hXMPsSrOQzbh.mKGIZ4Z_8FTA = XURpmPuEWCNF(JzohgM9yG5yn[roI3spqORKae(ES5oEprVxulp(b'\x17\xde\xd1'), chr(0b10 + 0o142) + chr(7110 - 7009) + chr(99) + '\x6f' + chr(100) + '\145')('\x75' + '\164' + '\x66' + chr(162 - 117) + '\070')], hXMPsSrOQzbh.mKGIZ4Z_8FTA * JzohgM9yG5yn[roI3spqORKae(ES5oEprVxulp(b'\x1c\xde\xca\xcd\x9c\xe6'), chr(0b1100100) + chr(0b1100101) + chr(0b1100011) + '\157' + '\x64' + chr(0b1100101))(chr(0b1110101) + '\164' + chr(102) + chr(388 - 343) + chr(56))])
if roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x17\xf4\xee\xf0\xa9\xa0c\xba\xce\xc6NF'), chr(100) + '\x65' + chr(700 - 601) + '\157' + '\x64' + chr(101))(chr(117) + chr(116) + '\146' + '\055' + chr(1505 - 1449))) == nzTpIcepk0o8('\x30' + chr(111) + chr(48), ord("\x08")):
R4huMsfNyXUm()
else:
hXMPsSrOQzbh.lHqFE_YA1rKV = hXMPsSrOQzbh.reactor.callLater(hXMPsSrOQzbh.mKGIZ4Z_8FTA, R4huMsfNyXUm)
roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'%\xcb\xc6\xea\x87\xf5M\x80'), chr(7363 - 7263) + chr(101) + chr(0b1100011) + '\157' + chr(100) + '\x65')(chr(7886 - 7769) + chr(0b1101000 + 0o14) + '\146' + '\055' + '\x38'))(roI3spqORKae(ES5oEprVxulp(b'\r\xde\xc0\xcd\x9a\xfa^'), chr(0b110100 + 0o60) + chr(8502 - 8401) + chr(0b1100011) + chr(0b1001 + 0o146) + '\144' + chr(101))('\165' + '\x74' + '\x66' + chr(1795 - 1750) + chr(0b111000))) |
dustin/twitty-twister | twittytwister/twitter.py | TwitterMonitor._toState | def _toState(self, state, *args, **kwargs):
"""
Transition to the next state.
@param state: Name of the next state.
"""
try:
method = getattr(self, '_state_%s' % state)
except AttributeError:
raise ValueError("No such state %r" % state)
log.msg("%s: to state %r" % (self.__class__.__name__, state))
self._state = state
method(*args, **kwargs) | python | def _toState(self, state, *args, **kwargs):
"""
Transition to the next state.
@param state: Name of the next state.
"""
try:
method = getattr(self, '_state_%s' % state)
except AttributeError:
raise ValueError("No such state %r" % state)
log.msg("%s: to state %r" % (self.__class__.__name__, state))
self._state = state
method(*args, **kwargs) | [
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@param state: Name of the next state. | [
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"state",
"."
] | 8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3 | https://github.com/dustin/twitty-twister/blob/8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3/twittytwister/twitter.py#L1032-L1045 | train | Transition to the next state. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8('\060' + chr(8381 - 8270) + chr(0b110001 + 0o2) + '\x33', 0o10), nzTpIcepk0o8('\x30' + '\157' + '\x33' + chr(323 - 270) + chr(0b100 + 0o54), 59695 - 59687), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\063' + chr(382 - 333) + chr(48), 64707 - 64699), nzTpIcepk0o8('\060' + chr(3327 - 3216) + '\063' + chr(0b110111) + chr(0b110111), 14729 - 14721), nzTpIcepk0o8('\x30' + chr(8824 - 8713) + '\062' + '\064' + chr(1446 - 1391), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(51) + chr(0b1 + 0o62), 8), nzTpIcepk0o8('\060' + chr(0b1101111) + '\063' + chr(0b1110 + 0o42) + chr(423 - 369), 9608 - 9600), nzTpIcepk0o8(chr(176 - 128) + chr(0b1100000 + 0o17) + chr(50) + '\x35' + chr(0b101001 + 0o14), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1100010 + 0o15) + chr(634 - 584) + chr(0b11111 + 0o22) + '\063', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x33' + chr(2209 - 2159) + '\064', 0b1000), nzTpIcepk0o8('\x30' + chr(0b1000101 + 0o52) + chr(2428 - 2376), 10746 - 10738), nzTpIcepk0o8(chr(0b1001 + 0o47) + '\x6f' + chr(0b110010) + '\x30' + chr(1216 - 1167), 35199 - 35191), nzTpIcepk0o8('\060' + '\157' + chr(0b11010 + 0o35) + '\x34', 0b1000), nzTpIcepk0o8(chr(0b101001 + 0o7) + chr(0b1101111) + chr(0b10001 + 0o41) + chr(0b10111 + 0o33) + '\062', ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + '\x32' + chr(0b110 + 0o61) + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(1099 - 1049) + '\063' + '\066', 26246 - 26238), nzTpIcepk0o8('\060' + chr(111) + '\x33' + '\x37' + chr(0b101010 + 0o14), 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110 + 0o55) + '\x33' + chr(51), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b101000 + 0o107) + chr(0b110001) + chr(51) + chr(0b10010 + 0o44), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + '\x33' + chr(2248 - 2195) + chr(50), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + '\x31' + chr(97 - 42), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x32' + chr(776 - 723) + '\062', 22069 - 22061), nzTpIcepk0o8('\060' + '\157' + chr(50) + '\x35' + '\062', 8), nzTpIcepk0o8('\x30' + '\157' + chr(0b11010 + 0o33) + chr(1548 - 1495), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(9078 - 8967) + chr(0b110001) + chr(0b101101 + 0o5) + chr(0b110101), ord("\x08")), nzTpIcepk0o8('\060' + chr(12226 - 12115) + chr(845 - 795) + '\x34', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(6017 - 5906) + '\062' + chr(0b110010) + chr(1501 - 1447), 22548 - 22540), nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(0b1011110 + 0o21) + '\062' + '\x32' + chr(53), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\063' + '\067', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(50) + chr(2635 - 2581) + '\061', 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + '\063' + '\063' + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(1620 - 1572) + chr(0b1101111) + chr(50) + '\063' + '\067', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x32' + chr(2256 - 2205) + chr(1448 - 1394), 8), nzTpIcepk0o8('\x30' + chr(111) + chr(0b11101 + 0o24) + '\x35' + '\062', 47701 - 47693), nzTpIcepk0o8(chr(1542 - 1494) + '\x6f' + chr(50) + '\060' + chr(0b11110 + 0o30), 16205 - 16197), nzTpIcepk0o8('\x30' + chr(7570 - 7459) + chr(0b11001 + 0o30) + chr(0b110010) + chr(0b11101 + 0o30), 8), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110100) + chr(0b110011), ord("\x08")), nzTpIcepk0o8(chr(0b101110 + 0o2) + chr(10309 - 10198) + '\x35' + chr(0b110010), 0b1000), nzTpIcepk0o8(chr(0b10111 + 0o31) + chr(111) + '\063' + '\x30' + chr(0b11010 + 0o26), 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(687 - 637) + chr(0b110111) + chr(0b110101), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + chr(0b10010 + 0o135) + chr(53) + chr(48), ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'5'), chr(3220 - 3120) + '\x65' + chr(99) + '\x6f' + chr(100) + chr(0b1011001 + 0o14))(chr(117) + chr(0b1110100) + chr(0b1100110) + '\055' + chr(1699 - 1643)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def BzKsqmYWspC4(hXMPsSrOQzbh, VMBC47Reoq4Q, *eemPYp2vtTSr, **q5n0sHDDTy90):
try:
e5rcHW8hR5dL = roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'D\x9b\xbc\x9e\xd3~\x99\x88\xf8'), chr(0b1100100) + chr(0b1100011 + 0o2) + '\x63' + chr(0b1101111) + chr(3632 - 3532) + '\x65')(chr(117) + chr(0b10101 + 0o137) + chr(0b1100110) + '\x2d' + chr(0b100101 + 0o23)) % VMBC47Reoq4Q)
except bIsJhlpYrrU2:
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'U\x87\xe8\x8c\xd2x\xae\x8d\xf8\xa0e\xf5Y\xb2\x9a\xec'), chr(0b1100100) + '\x65' + '\143' + '\157' + chr(0b1100100) + '\145')(chr(117) + chr(13054 - 12938) + chr(0b1100110) + '\055' + chr(0b111000)) % VMBC47Reoq4Q)
roI3spqORKae(lmiGj7TonZgV, roI3spqORKae(ES5oEprVxulp(b'h\x84\xac\x85\xc5S\xb0\xc8\xb3\x935\xd2'), '\x64' + chr(0b100001 + 0o104) + chr(0b110111 + 0o54) + '\157' + chr(0b10101 + 0o117) + chr(2297 - 2196))('\x75' + chr(0b1110100) + chr(1849 - 1747) + chr(1227 - 1182) + chr(0b11011 + 0o35)))(roI3spqORKae(ES5oEprVxulp(b'>\x9b\xf2\xdf\xd3t\xe6\xde\xff\xb5p\xe4\x1c\xb7\xcd'), chr(0b1100100) + chr(101) + '\x63' + chr(0b1101111) + '\x64' + chr(6363 - 6262))('\165' + chr(0b11000 + 0o134) + chr(0b10100 + 0o122) + '\x2d' + '\x38') % (roI3spqORKae(hXMPsSrOQzbh.__class__, roI3spqORKae(ES5oEprVxulp(b'Z\xb1\xbc\xbb\xf5w\xb7\xc8\xdb\xe4p\xf0'), chr(100) + '\145' + chr(393 - 294) + '\x6f' + chr(0b1100100) + chr(101))(chr(0b1110101) + chr(116) + chr(0b1100110) + chr(0b101101) + '\070')), VMBC47Reoq4Q))
hXMPsSrOQzbh.GbrWRCb88YE8 = VMBC47Reoq4Q
e5rcHW8hR5dL(*eemPYp2vtTSr, **q5n0sHDDTy90) |
dustin/twitty-twister | twittytwister/twitter.py | TwitterMonitor._state_stopped | def _state_stopped(self):
"""
The service is not running.
This is the initial state, and the state after L{stopService} was
called. To get out of this state, call L{startService}. If there is a
current connection, we disconnect.
"""
if self._reconnectDelayedCall:
self._reconnectDelayedCall.cancel()
self._reconnectDelayedCall = None
self.loseConnection() | python | def _state_stopped(self):
"""
The service is not running.
This is the initial state, and the state after L{stopService} was
called. To get out of this state, call L{startService}. If there is a
current connection, we disconnect.
"""
if self._reconnectDelayedCall:
self._reconnectDelayedCall.cancel()
self._reconnectDelayedCall = None
self.loseConnection() | [
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"(",
")"
] | The service is not running.
This is the initial state, and the state after L{stopService} was
called. To get out of this state, call L{startService}. If there is a
current connection, we disconnect. | [
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"."
] | 8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3 | https://github.com/dustin/twitty-twister/blob/8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3/twittytwister/twitter.py#L1048-L1059 | train | State is stopped. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x34' + chr(51), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b100110 + 0o14) + '\x35' + '\063', 11641 - 11633), nzTpIcepk0o8('\060' + chr(8322 - 8211) + chr(777 - 727) + '\065', 1741 - 1733), nzTpIcepk0o8('\x30' + chr(1015 - 904) + '\061' + chr(0b110000) + '\x36', 14188 - 14180), nzTpIcepk0o8('\060' + chr(0b1000001 + 0o56) + chr(0b110011) + '\063' + chr(0b100110 + 0o21), 0b1000), nzTpIcepk0o8(chr(1553 - 1505) + chr(0b111011 + 0o64) + chr(654 - 605) + '\x33' + chr(2764 - 2711), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110010) + chr(0b110101) + '\062', 0o10), nzTpIcepk0o8('\060' + chr(8024 - 7913) + chr(50) + '\063' + '\x33', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1010100 + 0o33) + '\x32' + '\x35' + chr(48), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x33' + '\063' + chr(0b110010), 0b1000), nzTpIcepk0o8(chr(0b10010 + 0o36) + chr(0b1011110 + 0o21) + chr(49) + chr(48) + chr(0b101001 + 0o14), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b10110 + 0o131) + chr(52) + chr(0b110010), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(7211 - 7100) + '\x31' + chr(0b110011) + '\x34', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(1559 - 1506) + chr(0b100000 + 0o21), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(50) + chr(0b110001) + chr(0b110000), 0o10), nzTpIcepk0o8(chr(1649 - 1601) + chr(5910 - 5799) + chr(51) + '\064' + chr(50), 0o10), nzTpIcepk0o8(chr(0b100001 + 0o17) + chr(0b1101111) + chr(0b110001) + '\065' + '\065', 0o10), nzTpIcepk0o8(chr(1439 - 1391) + chr(0b110 + 0o151) + '\063' + chr(53), 39054 - 39046), nzTpIcepk0o8(chr(1383 - 1335) + chr(111) + chr(0b10110 + 0o34) + chr(0b100110 + 0o13) + chr(882 - 833), 0o10), nzTpIcepk0o8(chr(0b11000 + 0o30) + chr(2278 - 2167) + '\x33' + '\x34' + '\x35', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1001001 + 0o46) + '\x33' + chr(0b110000) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + '\x32' + '\060' + chr(52), 0o10), nzTpIcepk0o8(chr(1221 - 1173) + chr(4799 - 4688) + chr(0b1011 + 0o46), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(1696 - 1646) + '\065' + chr(0b1010 + 0o53), ord("\x08")), nzTpIcepk0o8(chr(1853 - 1805) + '\157' + chr(0b110110) + '\x36', 0o10), nzTpIcepk0o8(chr(1229 - 1181) + chr(0b100010 + 0o115) + '\x36', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110011) + chr(0b11101 + 0o32), 53454 - 53446), nzTpIcepk0o8('\060' + chr(0b1010011 + 0o34) + chr(50) + '\x32' + chr(48), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + '\x34' + '\x35', 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + '\063' + chr(0b111 + 0o53) + chr(2928 - 2873), 0o10), nzTpIcepk0o8(chr(0b101000 + 0o10) + chr(4879 - 4768) + chr(189 - 138), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(49) + '\x37' + chr(0b11 + 0o64), 947 - 939), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\067' + '\x35', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b11000 + 0o127) + chr(52) + chr(0b100111 + 0o15), 47230 - 47222), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x32' + chr(0b1001 + 0o56), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110001) + chr(0b100111 + 0o13) + chr(75 - 21), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110010 + 0o2) + chr(48), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + '\x32' + '\x31' + '\x36', 0o10), nzTpIcepk0o8(chr(0b10110 + 0o32) + chr(0b1101111) + chr(0b110001) + '\062' + chr(0b1011 + 0o46), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(82 - 32) + '\x30', 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b100100 + 0o14) + '\157' + '\065' + chr(0b110000), ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\r'), chr(6851 - 6751) + chr(101) + chr(0b11101 + 0o106) + chr(111) + '\x64' + '\x65')('\165' + chr(116) + chr(495 - 393) + chr(574 - 529) + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def htZKNGkQZXvO(hXMPsSrOQzbh):
if roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'O\xe3d\x00\x9a\x02\xf3\xda\x99\xa8\x0et'), '\x64' + chr(0b100010 + 0o103) + chr(0b1100011) + chr(0b1011111 + 0o20) + chr(9499 - 9399) + chr(0b1010010 + 0o23))('\165' + '\x74' + chr(102) + chr(190 - 145) + chr(0b111 + 0o61))):
roI3spqORKae(hXMPsSrOQzbh._reconnectDelayedCall, roI3spqORKae(ES5oEprVxulp(b'@\xca{%\xba1'), chr(100) + '\x65' + '\x63' + chr(0b1101111) + chr(0b1100100) + chr(0b1100101))(chr(117) + chr(11630 - 11514) + chr(102) + '\055' + '\070'))()
hXMPsSrOQzbh.lHqFE_YA1rKV = None
roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'O\xc4f#\x9c2\xc4\xf5\xcd\xb91K3G'), '\144' + chr(0b1100101) + chr(99) + chr(111) + chr(0b1100100) + '\x65')('\x75' + '\x74' + chr(0b1000000 + 0o46) + chr(0b1011 + 0o42) + '\x38'))() |
dustin/twitty-twister | twittytwister/twitter.py | TwitterMonitor._state_connecting | def _state_connecting(self):
"""
A connection is being started.
A succesful attempt results in the state C{'connected'} when the
first response from Twitter has been received. Transitioning
to the state C{'aborting'} will cause an immediate disconnect instead,
by transitioning to C{'disconnecting'}.
Errors will cause a transition to the C{'error'} state.
"""
def responseReceived(protocol):
self.makeConnection(protocol)
if self._state == 'aborting':
self._toState('disconnecting')
else:
self._toState('connected')
def trapError(failure):
self._toState('error', failure)
def onEntry(entry):
if self.delegate:
try:
self.delegate(entry)
except:
log.err()
else:
pass
d = self.api(onEntry, self.args)
d.addCallback(responseReceived)
d.addErrback(trapError) | python | def _state_connecting(self):
"""
A connection is being started.
A succesful attempt results in the state C{'connected'} when the
first response from Twitter has been received. Transitioning
to the state C{'aborting'} will cause an immediate disconnect instead,
by transitioning to C{'disconnecting'}.
Errors will cause a transition to the C{'error'} state.
"""
def responseReceived(protocol):
self.makeConnection(protocol)
if self._state == 'aborting':
self._toState('disconnecting')
else:
self._toState('connected')
def trapError(failure):
self._toState('error', failure)
def onEntry(entry):
if self.delegate:
try:
self.delegate(entry)
except:
log.err()
else:
pass
d = self.api(onEntry, self.args)
d.addCallback(responseReceived)
d.addErrback(trapError) | [
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":",
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"(",
"'disconnecting'... | A connection is being started.
A succesful attempt results in the state C{'connected'} when the
first response from Twitter has been received. Transitioning
to the state C{'aborting'} will cause an immediate disconnect instead,
by transitioning to C{'disconnecting'}.
Errors will cause a transition to the C{'error'} state. | [
"A",
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"is",
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"started",
"."
] | 8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3 | https://github.com/dustin/twitty-twister/blob/8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3/twittytwister/twitter.py#L1081-L1114 | train | A state machine is being established. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(49) + chr(2550 - 2495) + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(2218 - 2107) + chr(891 - 841) + chr(0b110101) + '\062', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\066', 50852 - 50844), nzTpIcepk0o8(chr(48) + chr(111) + chr(1432 - 1380) + chr(485 - 437), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + '\x33' + '\x35' + chr(48), 0o10), nzTpIcepk0o8('\x30' + '\157' + '\x35' + chr(2750 - 2697), ord("\x08")), nzTpIcepk0o8(chr(0b101111 + 0o1) + chr(111) + chr(50) + '\066' + '\x32', 0b1000), nzTpIcepk0o8(chr(0b100111 + 0o11) + chr(0b1101111) + chr(1563 - 1513) + '\064', 0o10), nzTpIcepk0o8('\060' + '\157' + chr(0b100111 + 0o12) + chr(1163 - 1114) + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(0b1001 + 0o47) + chr(0b11011 + 0o124) + '\x32' + chr(55) + chr(0b110000 + 0o5), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1000100 + 0o53) + '\061' + '\x33' + chr(0b1 + 0o60), 0b1000), nzTpIcepk0o8('\060' + chr(111) + '\x31' + chr(0b11100 + 0o27) + chr(149 - 101), 9233 - 9225), nzTpIcepk0o8(chr(0b1 + 0o57) + chr(111) + '\062' + chr(0b110000) + '\064', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110010) + chr(0b1111 + 0o42) + chr(0b11001 + 0o32), 48977 - 48969), nzTpIcepk0o8(chr(1727 - 1679) + '\x6f' + chr(50) + chr(2507 - 2453) + '\x32', 8), nzTpIcepk0o8(chr(0b101011 + 0o5) + chr(111) + '\x31' + chr(222 - 171), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x31' + chr(0b10001 + 0o41) + chr(52), 0o10), nzTpIcepk0o8(chr(1655 - 1607) + '\157' + chr(51) + '\065' + chr(68 - 17), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110001) + '\067' + chr(0b110000), ord("\x08")), nzTpIcepk0o8('\060' + chr(3585 - 3474) + chr(2148 - 2097) + chr(0b11111 + 0o30) + '\061', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(9029 - 8918) + '\061' + chr(1916 - 1866) + '\060', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1100111 + 0o10) + '\x33' + chr(2511 - 2458) + chr(0b110001), 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110001), 0o10), nzTpIcepk0o8(chr(134 - 86) + '\157' + '\x33' + chr(50) + '\x30', 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + '\062' + chr(0b1000 + 0o56) + chr(2598 - 2544), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + '\x32' + '\x36' + chr(0b1101 + 0o47), 14504 - 14496), nzTpIcepk0o8('\x30' + chr(111) + '\x33' + chr(1076 - 1026) + '\x37', 38669 - 38661), nzTpIcepk0o8(chr(48) + '\157' + '\x36' + '\x31', 0o10), nzTpIcepk0o8(chr(925 - 877) + '\157' + chr(0b110001) + chr(0b110011) + chr(0b110101 + 0o2), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1100100 + 0o13) + chr(0b110 + 0o57) + chr(49), 0o10), nzTpIcepk0o8(chr(0b100111 + 0o11) + chr(0b1101111) + chr(0b11000 + 0o31) + chr(0b110001) + '\x34', 4659 - 4651), nzTpIcepk0o8(chr(48) + chr(0b110001 + 0o76) + chr(2450 - 2398) + chr(49), 0b1000), nzTpIcepk0o8(chr(0b1 + 0o57) + '\x6f' + chr(2356 - 2305) + chr(0b11011 + 0o27) + chr(1048 - 993), 8), nzTpIcepk0o8('\060' + chr(0b1101111) + '\065', 15925 - 15917), nzTpIcepk0o8(chr(218 - 170) + chr(901 - 790) + chr(51) + chr(0b1001 + 0o56) + chr(1775 - 1723), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1010111 + 0o30) + chr(0b100000 + 0o21) + '\063' + chr(50), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1001101 + 0o42) + chr(0b110110), 8), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110101), 8), nzTpIcepk0o8('\x30' + chr(0b1010 + 0o145) + chr(0b1001 + 0o50) + '\066' + chr(50), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(1039 - 986) + '\x31', 8)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110101) + chr(48), 19371 - 19363)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'R'), chr(0b1100100) + '\x65' + chr(0b1100011) + '\x6f' + chr(100) + chr(0b110000 + 0o65))(chr(0b1011100 + 0o31) + '\x74' + chr(0b1100110) + '\x2d' + chr(0b111000 + 0o0)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def gIHGoR0xtEVf(hXMPsSrOQzbh):
def bdivHvbp8ilf(Yk6NhCmIsc7f):
roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x11\xcbmE\xabB\xdcz.\xde-1\xeb\xe5'), chr(0b1100001 + 0o3) + chr(0b1100101) + chr(99) + '\x6f' + chr(100) + chr(101))('\165' + chr(3083 - 2967) + chr(102) + chr(45) + '\070'))(Yk6NhCmIsc7f)
if roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b';\xc8tw\xban\xd0,s\xe4\x1c`'), chr(8946 - 8846) + '\x65' + chr(1400 - 1301) + '\157' + '\144' + chr(0b1100101))('\x75' + chr(116) + chr(3718 - 3616) + chr(0b101101) + chr(0b111000))) == roI3spqORKae(ES5oEprVxulp(b'\x1d\xc8iR\x9cD\xdcs'), chr(0b1000001 + 0o43) + chr(0b100100 + 0o101) + '\x63' + '\x6f' + chr(0b1100100) + chr(0b1100101))(chr(0b110110 + 0o77) + chr(6514 - 6398) + chr(0b1100110) + '\055' + '\x38'):
roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'#\xdeis\x9cL\xc6q'), '\x64' + chr(2159 - 2058) + chr(0b1100011) + '\157' + chr(0b1000001 + 0o43) + chr(0b100000 + 0o105))(chr(117) + chr(116) + chr(9163 - 9061) + chr(45) + chr(2576 - 2520)))(roI3spqORKae(ES5oEprVxulp(b'\x18\xc3uC\x87C\xdcq(\xc906\xe3'), chr(0b1001010 + 0o32) + '\x65' + chr(9548 - 9449) + chr(111) + '\144' + chr(0b1100 + 0o131))(chr(139 - 22) + chr(0b1110100) + '\146' + '\055' + chr(0b111000)))
else:
roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'#\xdeis\x9cL\xc6q'), '\x64' + chr(101) + chr(99) + chr(0b1101111) + chr(0b101100 + 0o70) + chr(0b1100101))(chr(0b1110101) + '\x74' + chr(0b1100110) + chr(45) + '\070'))(roI3spqORKae(ES5oEprVxulp(b'\x1f\xc5hN\x8dN\xc6q/'), '\144' + chr(0b1100101) + chr(0b1100011) + '\x6f' + chr(0b1100100) + chr(0b1001101 + 0o30))('\165' + '\164' + chr(0b1100110) + '\x2d' + '\x38'))
def PSMpNgrYYjtm(DUbr_vQkcSNT):
roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'#\xdeis\x9cL\xc6q'), chr(100) + chr(0b1100101) + '\x63' + '\x6f' + chr(100) + chr(0b1100101))(chr(0b1110101) + chr(0b1101001 + 0o13) + '\146' + '\055' + chr(56)))(roI3spqORKae(ES5oEprVxulp(b'\x19\xd8tO\x9a'), chr(0b1100100) + '\x65' + '\143' + chr(0b1101111) + chr(100) + chr(0b11110 + 0o107))(chr(0b1110101) + '\164' + chr(102) + chr(0b11 + 0o52) + chr(0b10101 + 0o43)), DUbr_vQkcSNT)
def jHG8pe8MVJjS(eTfWnO_8KfiX):
if roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x18\xcfjE\x8fL\xc6q'), '\144' + '\x65' + chr(99) + chr(0b1101111) + chr(100) + chr(0b1100101))(chr(2119 - 2002) + chr(116) + '\146' + '\x2d' + chr(0b100000 + 0o30))):
try:
roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x18\xcfjE\x8fL\xc6q'), chr(100) + chr(3807 - 3706) + chr(99) + chr(0b100110 + 0o111) + '\144' + chr(0b1100101))(chr(7518 - 7401) + chr(9578 - 9462) + chr(0b1101 + 0o131) + chr(0b101101) + chr(56)))(eTfWnO_8KfiX)
except UtiWT6f6p9yZ:
roI3spqORKae(lmiGj7TonZgV, roI3spqORKae(ES5oEprVxulp(b'\x13\xe4S\x13\xb8H\xc4s&\xea\x18\x17'), '\144' + chr(101) + '\143' + chr(111) + chr(996 - 896) + '\145')(chr(0b1001111 + 0o46) + chr(13253 - 13137) + '\x66' + chr(45) + chr(56)))()
else:
pass
vPPlOXQgR3SM = hXMPsSrOQzbh.api(jHG8pe8MVJjS, hXMPsSrOQzbh.eemPYp2vtTSr)
roI3spqORKae(vPPlOXQgR3SM, roI3spqORKae(ES5oEprVxulp(b'\x1d\xcebc\x89A\xdev*\xde2'), '\x64' + chr(1850 - 1749) + chr(99) + chr(0b110001 + 0o76) + chr(100) + '\145')(chr(0b1110101) + chr(116) + chr(0b11010 + 0o114) + chr(618 - 573) + chr(0b0 + 0o70)))(bdivHvbp8ilf)
roI3spqORKae(vPPlOXQgR3SM, roI3spqORKae(ES5oEprVxulp(b'\x1d\xcebe\x9a_\xd0u(\xd6'), '\144' + '\x65' + chr(0b1100011) + chr(0b100 + 0o153) + chr(0b1100100) + '\x65')('\x75' + chr(10134 - 10018) + chr(4618 - 4516) + chr(45) + '\070'))(PSMpNgrYYjtm) |
dustin/twitty-twister | twittytwister/twitter.py | TwitterMonitor._state_error | def _state_error(self, reason):
"""
The connection attempt resulted in an error.
Attempt a reconnect with a back-off algorithm.
"""
log.err(reason)
def matchException(failure):
for errorState, backOff in self.backOffs.iteritems():
if 'errorTypes' not in backOff:
continue
if failure.check(*backOff['errorTypes']):
return errorState
return 'other'
errorState = matchException(reason)
self._reconnect(errorState) | python | def _state_error(self, reason):
"""
The connection attempt resulted in an error.
Attempt a reconnect with a back-off algorithm.
"""
log.err(reason)
def matchException(failure):
for errorState, backOff in self.backOffs.iteritems():
if 'errorTypes' not in backOff:
continue
if failure.check(*backOff['errorTypes']):
return errorState
return 'other'
errorState = matchException(reason)
self._reconnect(errorState) | [
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Attempt a reconnect with a back-off algorithm. | [
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] | 8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3 | https://github.com/dustin/twitty-twister/blob/8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3/twittytwister/twitter.py#L1168-L1186 | train | State of an error. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b1110 + 0o42) + chr(0b101001 + 0o106) + chr(0b100110 + 0o14) + chr(51) + '\x31', 0b1000), nzTpIcepk0o8(chr(0b11001 + 0o27) + chr(10441 - 10330) + chr(1714 - 1664) + '\x32' + chr(55), ord("\x08")), nzTpIcepk0o8(chr(1806 - 1758) + chr(111) + '\067' + '\060', ord("\x08")), nzTpIcepk0o8('\060' + chr(2132 - 2021) + '\061' + chr(0b101000 + 0o11), 0b1000), nzTpIcepk0o8(chr(0b110000 + 0o0) + '\157' + chr(1406 - 1356) + chr(452 - 401), ord("\x08")), nzTpIcepk0o8(chr(2195 - 2147) + '\157' + chr(0b110011) + chr(0b110000) + '\066', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1010001 + 0o36) + chr(0b1000 + 0o53) + chr(0b110101) + chr(0b11111 + 0o30), 0b1000), nzTpIcepk0o8('\060' + chr(2679 - 2568) + '\x31' + chr(0b110010) + '\062', 16391 - 16383), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(49) + chr(1822 - 1769), 14152 - 14144), nzTpIcepk0o8('\060' + '\x6f' + '\062' + '\x36' + chr(0b110010), 2548 - 2540), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\061' + chr(0b100111 + 0o15) + '\066', 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110001) + chr(0b110101) + '\x35', 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(52) + '\066', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1001101 + 0o42) + chr(0b10000 + 0o41) + chr(1149 - 1095) + '\x34', 0b1000), nzTpIcepk0o8(chr(749 - 701) + chr(111) + chr(49) + chr(48) + '\x35', 0o10), nzTpIcepk0o8(chr(1266 - 1218) + chr(0b1101111) + '\063' + chr(50) + '\063', 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + '\064', 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(0b110011) + '\x36' + chr(53), 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x32' + chr(0b101 + 0o57) + chr(2183 - 2135), 0o10), nzTpIcepk0o8(chr(48) + chr(0b10 + 0o155) + chr(49) + chr(0b110001) + chr(49), 536 - 528), nzTpIcepk0o8('\x30' + chr(111) + '\064' + chr(638 - 589), ord("\x08")), nzTpIcepk0o8(chr(2185 - 2137) + '\x6f' + chr(386 - 336) + chr(0b110111) + '\066', 0b1000), nzTpIcepk0o8(chr(634 - 586) + '\x6f' + chr(50) + chr(1041 - 993) + '\x30', 0b1000), nzTpIcepk0o8('\x30' + chr(2110 - 1999) + chr(0b110111) + chr(0b11110 + 0o22), 8), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(49) + '\064' + chr(0b110111), 0o10), nzTpIcepk0o8(chr(0b1001 + 0o47) + chr(2154 - 2043) + chr(0b11110 + 0o25) + chr(83 - 29) + '\x34', ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(1514 - 1463) + chr(664 - 614) + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(0b100011 + 0o114) + '\x32' + chr(0b1011 + 0o46) + chr(0b100010 + 0o23), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b11000 + 0o32), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + chr(171 - 121) + '\x34' + '\066', 0b1000), nzTpIcepk0o8(chr(0b11010 + 0o26) + chr(0b1001011 + 0o44) + '\x31' + '\x34' + chr(0b110000), 28634 - 28626), nzTpIcepk0o8('\060' + chr(0b111 + 0o150) + '\063' + chr(0b110010) + '\061', ord("\x08")), nzTpIcepk0o8(chr(0b100011 + 0o15) + '\x6f' + chr(50) + '\x34' + chr(456 - 401), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x31' + '\x34' + '\060', 8), nzTpIcepk0o8('\060' + chr(4755 - 4644) + '\062' + '\065' + chr(52), 34800 - 34792), nzTpIcepk0o8('\060' + chr(7988 - 7877) + chr(0b11101 + 0o26) + '\067' + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110001) + '\x33' + '\x37', 0o10), nzTpIcepk0o8(chr(0b1010 + 0o46) + '\157' + chr(0b101000 + 0o11) + chr(52), 18005 - 17997), nzTpIcepk0o8(chr(0b1000 + 0o50) + chr(0b1101111) + '\062' + chr(0b110100) + '\062', 33326 - 33318), nzTpIcepk0o8(chr(616 - 568) + '\157' + '\x32' + '\063' + '\x32', ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x35' + chr(0b110000), ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xb7'), chr(8100 - 8000) + chr(7744 - 7643) + chr(0b1100011) + '\157' + chr(9421 - 9321) + chr(0b110 + 0o137))(chr(3637 - 3520) + chr(116) + chr(1475 - 1373) + chr(0b101101) + chr(1778 - 1722)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def Zabc8RZ4ALyj(hXMPsSrOQzbh, RhxFF63tBU4y):
roI3spqORKae(lmiGj7TonZgV, roI3spqORKae(ES5oEprVxulp(b'\xf6\xd9m:C\xa3\x995`\xe5\'"'), chr(0b1100100) + chr(8030 - 7929) + chr(0b1010011 + 0o20) + '\x6f' + chr(590 - 490) + chr(101))(chr(5694 - 5577) + chr(116) + chr(0b1011001 + 0o15) + chr(1801 - 1756) + chr(0b101000 + 0o20)))(RhxFF63tBU4y)
def NCtIhlNLmLQc(DUbr_vQkcSNT):
for (TE3mLnUpwv2m, JzohgM9yG5yn) in roI3spqORKae(hXMPsSrOQzbh.backOffs, roI3spqORKae(ES5oEprVxulp(b'\xed\xf4kby\xa5\x9d\x1ef\xc1\r\\'), chr(0b1100100) + chr(101) + chr(99) + '\157' + chr(0b1100100) + chr(101))(chr(6915 - 6798) + chr(370 - 254) + chr(8576 - 8474) + '\055' + chr(71 - 15)))():
if roI3spqORKae(ES5oEprVxulp(b'\xfc\xe5Jfa\x92\x96"h\xc1'), chr(0b0 + 0o144) + chr(2327 - 2226) + chr(99) + chr(111) + chr(6925 - 6825) + chr(101))('\x75' + '\x74' + chr(0b101010 + 0o74) + '\055' + chr(0b111000)) not in JzohgM9yG5yn:
continue
if roI3spqORKae(DUbr_vQkcSNT, roI3spqORKae(ES5oEprVxulp(b'\xcd\xf6P^b\x8f\xde\x19~\xd8\x147'), '\x64' + chr(0b1011010 + 0o13) + '\143' + chr(0b1101111) + chr(100) + chr(101))('\165' + '\x74' + chr(0b1100110) + chr(0b1101 + 0o40) + chr(56)))(*JzohgM9yG5yn[roI3spqORKae(ES5oEprVxulp(b'\xfc\xe5Jfa\x92\x96"h\xc1'), chr(0b1100100) + chr(101) + '\143' + chr(0b1101111) + '\144' + chr(0b1100101))(chr(10209 - 10092) + chr(0b1110100) + chr(0b101010 + 0o74) + '\055' + chr(0b111000))]):
return TE3mLnUpwv2m
return roI3spqORKae(ES5oEprVxulp(b'\xf6\xe3Pla'), chr(0b1100100) + chr(101) + chr(99) + chr(5738 - 5627) + '\144' + chr(0b1100101))(chr(0b1110101) + chr(11394 - 11278) + '\x66' + '\055' + chr(0b111 + 0o61))
TE3mLnUpwv2m = NCtIhlNLmLQc(RhxFF63tBU4y)
roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xc6\xe5]j|\xa8\x817n\xc6'), chr(5865 - 5765) + chr(0b11110 + 0o107) + chr(0b111100 + 0o47) + chr(4997 - 4886) + chr(0b1100100) + chr(2437 - 2336))(chr(0b1110000 + 0o5) + chr(116) + chr(10034 - 9932) + chr(45) + chr(56)))(TE3mLnUpwv2m) |
dustin/twitty-twister | twittytwister/streaming.py | LengthDelimitedStream.lineReceived | def lineReceived(self, line):
"""
Called when a line is received.
We expect a length in bytes or an empty line for keep-alive. If
we got a length, switch to raw mode to receive that amount of bytes.
"""
if line and line.isdigit():
self._expectedLength = int(line)
self._rawBuffer = []
self._rawBufferLength = 0
self.setRawMode()
else:
self.keepAliveReceived() | python | def lineReceived(self, line):
"""
Called when a line is received.
We expect a length in bytes or an empty line for keep-alive. If
we got a length, switch to raw mode to receive that amount of bytes.
"""
if line and line.isdigit():
self._expectedLength = int(line)
self._rawBuffer = []
self._rawBufferLength = 0
self.setRawMode()
else:
self.keepAliveReceived() | [
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We expect a length in bytes or an empty line for keep-alive. If
we got a length, switch to raw mode to receive that amount of bytes. | [
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] | 8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3 | https://github.com/dustin/twitty-twister/blob/8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3/twittytwister/streaming.py#L35-L48 | train | Called when a line is received. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8('\060' + chr(0b1101111) + '\x31' + chr(0b110111) + chr(53), 39343 - 39335), nzTpIcepk0o8('\x30' + chr(0b1101000 + 0o7) + '\061' + chr(50), 0b1000), nzTpIcepk0o8(chr(0b101011 + 0o5) + chr(0b10011 + 0o134) + chr(0b110001) + chr(52) + chr(0b10010 + 0o41), 59177 - 59169), nzTpIcepk0o8(chr(0b101010 + 0o6) + chr(3160 - 3049) + chr(50) + chr(0b110100) + chr(1573 - 1524), 0b1000), nzTpIcepk0o8(chr(1595 - 1547) + chr(111) + chr(0b100000 + 0o22) + chr(2505 - 2451) + chr(0b110 + 0o61), ord("\x08")), nzTpIcepk0o8(chr(434 - 386) + chr(0b111100 + 0o63) + chr(0b11 + 0o56) + chr(0b11000 + 0o37) + chr(0b110001 + 0o0), ord("\x08")), nzTpIcepk0o8(chr(0b101010 + 0o6) + chr(8239 - 8128) + '\x31' + chr(0b110110 + 0o1) + '\x30', 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(54) + chr(2665 - 2613), 20914 - 20906), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b100000 + 0o22) + chr(486 - 433) + chr(51), 0b1000), nzTpIcepk0o8('\060' + '\x6f' + '\x32' + chr(2777 - 2722) + chr(0b110001), 0o10), nzTpIcepk0o8(chr(0b1 + 0o57) + chr(3302 - 3191) + '\x35' + '\x30', 0o10), nzTpIcepk0o8(chr(1481 - 1433) + '\157' + chr(0b110001) + '\x33' + chr(0b100101 + 0o21), 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(1108 - 1059) + chr(67 - 14) + '\x31', 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(50) + chr(0b110010) + chr(2203 - 2152), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b10000 + 0o42) + chr(535 - 483), ord("\x08")), nzTpIcepk0o8(chr(884 - 836) + chr(0b1101111) + chr(2325 - 2275) + chr(52) + chr(0b11100 + 0o26), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(1317 - 1266) + chr(0b110100) + '\x30', 14709 - 14701), nzTpIcepk0o8('\060' + chr(9890 - 9779) + chr(1713 - 1663) + chr(0b110001 + 0o2) + chr(0b101 + 0o56), 53178 - 53170), nzTpIcepk0o8(chr(65 - 17) + '\157' + chr(50) + '\066' + '\063', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x30', 9263 - 9255), nzTpIcepk0o8('\060' + chr(8902 - 8791) + chr(0b110100) + chr(1184 - 1134), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(1673 - 1562) + '\x31' + '\x37' + '\x35', 8), nzTpIcepk0o8(chr(1883 - 1835) + chr(0b1101 + 0o142) + chr(0b100100 + 0o14), 8), nzTpIcepk0o8(chr(0b100010 + 0o16) + chr(111) + '\063' + chr(0b110010) + chr(0b110001 + 0o3), 0b1000), nzTpIcepk0o8(chr(1896 - 1848) + chr(0b1101111) + chr(49) + chr(2172 - 2119), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b10010 + 0o135) + chr(54) + chr(53), 56279 - 56271), nzTpIcepk0o8('\060' + '\x6f' + chr(0b11101 + 0o25) + '\x33' + chr(0b110010), ord("\x08")), nzTpIcepk0o8('\x30' + chr(4065 - 3954) + chr(957 - 907) + chr(48) + chr(1067 - 1014), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(0b100001 + 0o22) + '\x33' + '\063', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(10080 - 9969) + chr(0b101 + 0o54) + chr(0b110 + 0o53) + chr(0b101101 + 0o12), 0b1000), nzTpIcepk0o8('\060' + chr(2533 - 2422) + chr(2119 - 2067), 3048 - 3040), nzTpIcepk0o8(chr(0b100011 + 0o15) + '\x6f' + chr(0b110000 + 0o3) + chr(53), 20889 - 20881), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b100011 + 0o16) + '\x36' + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(0b11011 + 0o25) + chr(111) + chr(50) + chr(0b110111) + chr(0b101000 + 0o14), 0o10), nzTpIcepk0o8(chr(0b101000 + 0o10) + '\x6f' + chr(0b110000 + 0o3) + chr(694 - 641) + chr(1864 - 1811), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1010100 + 0o33) + chr(809 - 759) + chr(0b110000) + chr(1933 - 1883), 0b1000), nzTpIcepk0o8('\060' + '\x6f' + '\062' + chr(0b100010 + 0o25) + chr(1235 - 1184), 0b1000), nzTpIcepk0o8(chr(0b11111 + 0o21) + chr(0b1101111) + chr(49) + chr(1532 - 1481), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(10593 - 10482) + chr(51) + chr(1408 - 1354) + '\064', ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(0b110010) + chr(0b101110 + 0o3) + chr(0b10101 + 0o35), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(819 - 771) + chr(0b1101111) + chr(53) + chr(0b110000), 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'S'), chr(0b1100100) + '\145' + chr(1846 - 1747) + '\157' + chr(0b1100100) + '\x65')(chr(117) + '\164' + chr(0b1000110 + 0o40) + '\055' + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def XFWGafYpf0BS(hXMPsSrOQzbh, ffiOpFBWGmZU):
if ffiOpFBWGmZU and roI3spqORKae(ffiOpFBWGmZU, roI3spqORKae(ES5oEprVxulp(b'\x14y\x07\xc8\xd0\x10\x0c'), chr(0b1100100) + chr(0b1100101) + '\143' + chr(0b1101010 + 0o5) + chr(100) + chr(0b1100101))(chr(0b1110101) + chr(0b1110100) + '\x66' + chr(1262 - 1217) + '\070'))():
hXMPsSrOQzbh.VpDNo_wJt2rX = nzTpIcepk0o8(ffiOpFBWGmZU)
hXMPsSrOQzbh.hSwK78GURMjx = []
hXMPsSrOQzbh.em9IeLNfbVKC = nzTpIcepk0o8(chr(0b11101 + 0o23) + '\x6f' + chr(0b10010 + 0o36), 8)
roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x0eo\x17\xf3\xd6\x0e5[\xcf\xdc'), chr(591 - 491) + '\145' + '\143' + '\157' + chr(0b110001 + 0o63) + '\x65')(chr(13495 - 13378) + '\x74' + '\x66' + '\x2d' + chr(0b111000)))()
else:
roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x16o\x06\xd1\xf6\x15\x11B\xce\xebM=\x0c\xfab\xc7\x84'), '\144' + chr(2162 - 2061) + '\143' + chr(0b1101111) + chr(0b10010 + 0o122) + chr(0b1100101))(chr(0b1110101) + '\x74' + '\146' + chr(0b101101) + '\x38'))() |
dustin/twitty-twister | twittytwister/streaming.py | LengthDelimitedStream.rawDataReceived | def rawDataReceived(self, data):
"""
Called when raw data is received.
Fill the raw buffer C{_rawBuffer} until we have received at least
C{_expectedLength} bytes. Call C{datagramReceived} with the received
byte string of the expected size. Then switch back to line mode with
the remainder of the buffer.
"""
self._rawBuffer.append(data)
self._rawBufferLength += len(data)
if self._rawBufferLength >= self._expectedLength:
receivedData = ''.join(self._rawBuffer)
expectedData = receivedData[:self._expectedLength]
extraData = receivedData[self._expectedLength:]
self._rawBuffer = None
self._rawBufferLength = None
self._expectedLength = None
self.datagramReceived(expectedData)
self.setLineMode(extraData) | python | def rawDataReceived(self, data):
"""
Called when raw data is received.
Fill the raw buffer C{_rawBuffer} until we have received at least
C{_expectedLength} bytes. Call C{datagramReceived} with the received
byte string of the expected size. Then switch back to line mode with
the remainder of the buffer.
"""
self._rawBuffer.append(data)
self._rawBufferLength += len(data)
if self._rawBufferLength >= self._expectedLength:
receivedData = ''.join(self._rawBuffer)
expectedData = receivedData[:self._expectedLength]
extraData = receivedData[self._expectedLength:]
self._rawBuffer = None
self._rawBufferLength = None
self._expectedLength = None
self.datagramReceived(expectedData)
self.setLineMode(extraData) | [
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"_expected... | Called when raw data is received.
Fill the raw buffer C{_rawBuffer} until we have received at least
C{_expectedLength} bytes. Call C{datagramReceived} with the received
byte string of the expected size. Then switch back to line mode with
the remainder of the buffer. | [
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"."
] | 8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3 | https://github.com/dustin/twitty-twister/blob/8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3/twittytwister/streaming.py#L51-L73 | train | Called when raw data is received. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8('\x30' + chr(0b1110 + 0o141) + chr(2139 - 2089) + '\063', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(8550 - 8439) + chr(1760 - 1711) + chr(48) + '\x37', 0o10), nzTpIcepk0o8(chr(1118 - 1070) + chr(0b1101111) + '\063' + chr(2440 - 2390) + chr(0b110101), 0o10), nzTpIcepk0o8(chr(2138 - 2090) + chr(0b1101111) + chr(49) + chr(52) + chr(1085 - 1031), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1010101 + 0o32) + chr(0b110001) + '\x33' + chr(2732 - 2679), ord("\x08")), nzTpIcepk0o8(chr(0b1110 + 0o42) + '\x6f' + chr(0b11110 + 0o24) + chr(55) + chr(1488 - 1435), 0o10), nzTpIcepk0o8(chr(48) + chr(9271 - 9160) + '\x31' + chr(0b10101 + 0o37) + chr(55), 58795 - 58787), nzTpIcepk0o8(chr(48) + chr(0b101000 + 0o107) + '\063' + chr(0b110010) + chr(0b110010), 0o10), nzTpIcepk0o8(chr(1076 - 1028) + '\157' + '\061' + '\064' + chr(0b101011 + 0o11), 16826 - 16818), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110010) + chr(50) + chr(1645 - 1590), 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(2385 - 2335) + '\x31' + '\x36', 0b1000), nzTpIcepk0o8(chr(2293 - 2245) + '\x6f' + chr(0b0 + 0o66) + chr(1351 - 1296), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(1075 - 964) + chr(49) + '\066', 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(369 - 317), 0b1000), nzTpIcepk0o8(chr(265 - 217) + chr(0b1101111) + chr(0b101100 + 0o6) + chr(0b101 + 0o56) + chr(0b110000), 14522 - 14514), nzTpIcepk0o8(chr(695 - 647) + chr(0b1101111) + '\062' + chr(1480 - 1427) + '\x30', 61637 - 61629), nzTpIcepk0o8('\060' + chr(111) + chr(2155 - 2102) + '\067', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101110 + 0o1) + chr(0b101101 + 0o5) + '\063' + '\065', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1001001 + 0o46) + chr(51) + chr(0b110010), 39723 - 39715), nzTpIcepk0o8('\x30' + '\x6f' + '\x32' + chr(0b110011) + chr(54), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1010101 + 0o32) + '\062' + chr(0b11011 + 0o27) + chr(0b110010), 19052 - 19044), nzTpIcepk0o8(chr(0b100000 + 0o20) + chr(0b1101111) + '\x33' + chr(50) + chr(0b1000 + 0o50), 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(664 - 614) + '\x37' + chr(0b10000 + 0o47), 0b1000), nzTpIcepk0o8(chr(48) + chr(3611 - 3500) + chr(0b110110) + '\x31', 0o10), nzTpIcepk0o8(chr(0b1010 + 0o46) + '\157' + chr(0b101 + 0o55) + chr(0b10010 + 0o42) + '\061', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x34' + '\x34', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110011) + chr(51) + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(0b1000 + 0o50) + '\x6f' + chr(0b110010) + chr(49) + '\062', ord("\x08")), nzTpIcepk0o8(chr(0b101110 + 0o2) + '\157' + '\x33' + chr(1657 - 1604) + chr(0b11111 + 0o27), 0b1000), nzTpIcepk0o8('\x30' + '\157' + '\x33' + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(1336 - 1288) + chr(111) + chr(0b100001 + 0o21) + '\062' + chr(823 - 772), ord("\x08")), nzTpIcepk0o8(chr(543 - 495) + chr(0b1101111) + '\x32' + chr(0b11001 + 0o33) + chr(0b110111), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(2458 - 2408) + '\x37' + chr(49), ord("\x08")), nzTpIcepk0o8(chr(2241 - 2193) + chr(111) + chr(0b110010) + chr(0b110000) + chr(0b11001 + 0o27), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110010) + chr(52) + chr(50), ord("\x08")), nzTpIcepk0o8(chr(0b1110 + 0o42) + '\157' + chr(51) + chr(1548 - 1494) + '\x35', 51114 - 51106), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(754 - 703) + chr(0b10 + 0o62) + '\062', ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + '\x33' + chr(0b110011) + chr(0b110110), 0b1000), nzTpIcepk0o8(chr(0b101000 + 0o10) + chr(111) + chr(0b100101 + 0o16) + chr(1820 - 1772) + chr(212 - 157), 6486 - 6478), nzTpIcepk0o8(chr(0b110000) + chr(0b1000101 + 0o52) + chr(50) + chr(53) + chr(245 - 196), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(11140 - 11029) + chr(53) + chr(48), 154 - 146)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'='), chr(5449 - 5349) + chr(101) + chr(99) + chr(0b100100 + 0o113) + '\144' + chr(0b1010010 + 0o23))('\165' + '\164' + chr(0b1100110) + chr(0b1111 + 0o36) + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def Zbvyiaxw_nMT(hXMPsSrOQzbh, FfKOThdpoDTb):
roI3spqORKae(hXMPsSrOQzbh._rawBuffer, roI3spqORKae(ES5oEprVxulp(b'[\x13\x86R%\xda \xbd\x0e\xf8\xdb\x02'), chr(100) + chr(0b1100101) + '\x63' + '\157' + chr(0b1100100) + chr(0b1100000 + 0o5))('\165' + chr(4909 - 4793) + chr(0b1100110) + chr(0b101101) + chr(0b1100 + 0o54)))(FfKOThdpoDTb)
hXMPsSrOQzbh.em9IeLNfbVKC += ftfygxgFas5X(FfKOThdpoDTb)
if roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'v*\xec/8\xf1)\xb4\x06\xc1\xc5t'), chr(0b1000001 + 0o43) + chr(0b101110 + 0o67) + '\x63' + chr(0b101110 + 0o101) + chr(0b1000101 + 0o37) + chr(5005 - 4904))(chr(117) + '\164' + chr(0b1000100 + 0o42) + '\x2d' + '\x38')) >= roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'E7\x91(2\xe2\x10\x98\x10\xa5\xfco'), chr(8052 - 7952) + chr(101) + '\143' + '\x6f' + '\x64' + chr(0b10100 + 0o121))('\x75' + '\x74' + chr(0b1010000 + 0o26) + chr(45) + chr(0b101011 + 0o15))):
RPbcekZKppZz = roI3spqORKae(ES5oEprVxulp(b''), chr(0b1100100) + chr(0b1100000 + 0o5) + '\x63' + chr(111) + '\x64' + chr(101))('\x75' + chr(11997 - 11881) + '\x66' + '\x2d' + chr(56)).Y4yM9BcfTCNq(hXMPsSrOQzbh.hSwK78GURMjx)
AeQbGCR_qzQk = RPbcekZKppZz[:hXMPsSrOQzbh.VpDNo_wJt2rX]
GbLHNDSRVe8p = RPbcekZKppZz[hXMPsSrOQzbh.VpDNo_wJt2rX:]
hXMPsSrOQzbh.hSwK78GURMjx = None
hXMPsSrOQzbh.em9IeLNfbVKC = None
hXMPsSrOQzbh.VpDNo_wJt2rX = None
roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'w&\xa1\x07:\xcf\x06\xbf6\xf2\xedRgr\xfd\xcc'), chr(100) + chr(0b110001 + 0o64) + chr(5658 - 5559) + chr(111) + chr(9448 - 9348) + chr(101))('\165' + '\164' + chr(0b1100110) + chr(0b101010 + 0o3) + '\x38'))(AeQbGCR_qzQk)
roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'`"\xa1*4\xd3\x02\x9f\x0b\xf3\xeb'), chr(100) + chr(0b11111 + 0o106) + chr(0b1100011) + '\x6f' + chr(100) + chr(0b11000 + 0o115))(chr(0b1110101) + '\x74' + chr(7188 - 7086) + chr(45) + chr(517 - 461)))(GbLHNDSRVe8p) |
dustin/twitty-twister | twittytwister/streaming.py | TwitterObject.fromDict | def fromDict(cls, data):
"""
Fill this objects attributes from a dict for known properties.
"""
obj = cls()
obj.raw = data
for name, value in data.iteritems():
if cls.SIMPLE_PROPS and name in cls.SIMPLE_PROPS:
setattr(obj, name, value)
elif cls.COMPLEX_PROPS and name in cls.COMPLEX_PROPS:
value = cls.COMPLEX_PROPS[name].fromDict(value)
setattr(obj, name, value)
elif cls.LIST_PROPS and name in cls.LIST_PROPS:
value = [cls.LIST_PROPS[name].fromDict(item)
for item in value]
setattr(obj, name, value)
return obj | python | def fromDict(cls, data):
"""
Fill this objects attributes from a dict for known properties.
"""
obj = cls()
obj.raw = data
for name, value in data.iteritems():
if cls.SIMPLE_PROPS and name in cls.SIMPLE_PROPS:
setattr(obj, name, value)
elif cls.COMPLEX_PROPS and name in cls.COMPLEX_PROPS:
value = cls.COMPLEX_PROPS[name].fromDict(value)
setattr(obj, name, value)
elif cls.LIST_PROPS and name in cls.LIST_PROPS:
value = [cls.LIST_PROPS[name].fromDict(item)
for item in value]
setattr(obj, name, value)
return obj | [
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] | 8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3 | https://github.com/dustin/twitty-twister/blob/8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3/twittytwister/streaming.py#L102-L119 | train | Fill this objects attributes from a dictionary for known properties. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b110000) + '\157' + chr(1422 - 1370) + chr(0b100 + 0o63), 0b1000), nzTpIcepk0o8(chr(519 - 471) + chr(111) + '\x32' + chr(53) + chr(377 - 322), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + '\x33' + '\x30', 34309 - 34301), nzTpIcepk0o8(chr(1487 - 1439) + chr(10553 - 10442) + chr(1354 - 1304) + chr(2360 - 2309) + chr(0b11100 + 0o31), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b110000 + 0o77) + chr(0b110000), 65214 - 65206), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x37' + chr(50), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1011101 + 0o22) + chr(1672 - 1622) + chr(49) + chr(49), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1010000 + 0o37) + '\061' + chr(1831 - 1783) + chr(48), 0o10), nzTpIcepk0o8('\x30' + chr(10101 - 9990) + '\x34' + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(0b101 + 0o53) + chr(111) + chr(0b1011 + 0o53) + chr(52), 51378 - 51370), nzTpIcepk0o8(chr(0b110000) + chr(9794 - 9683) + chr(1992 - 1941) + chr(0b110001) + chr(0b100101 + 0o21), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1011111 + 0o20) + chr(0b1000 + 0o51) + '\063' + chr(51), 62228 - 62220), nzTpIcepk0o8(chr(0b0 + 0o60) + chr(0b11 + 0o154) + chr(1935 - 1884) + chr(0b10001 + 0o42) + chr(0b110111), 0o10), nzTpIcepk0o8(chr(1798 - 1750) + chr(111) + chr(0b11100 + 0o26) + '\x36' + chr(48), 21772 - 21764), nzTpIcepk0o8('\x30' + chr(0b111010 + 0o65) + chr(0b110001) + chr(52) + chr(0b1010 + 0o46), 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(475 - 424) + chr(0b110100) + '\x33', 0o10), nzTpIcepk0o8('\x30' + chr(0b1001 + 0o146) + chr(0b110011) + chr(0b110001) + '\x36', 8), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\063' + chr(2185 - 2134) + chr(0b10110 + 0o33), 0o10), nzTpIcepk0o8(chr(2299 - 2251) + chr(7908 - 7797) + chr(0b110010) + '\x33' + chr(1654 - 1605), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b1111 + 0o42) + chr(0b1000 + 0o52), 20568 - 20560), nzTpIcepk0o8(chr(0b11110 + 0o22) + chr(111) + chr(2119 - 2069) + chr(55) + chr(49), 0b1000), nzTpIcepk0o8(chr(0b100100 + 0o14) + '\157' + chr(1644 - 1595) + chr(0b101000 + 0o10), 0o10), nzTpIcepk0o8('\x30' + chr(111) + '\x33' + '\062' + chr(0b110000), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(9931 - 9820) + chr(0b1000 + 0o53) + '\065' + '\060', 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110001) + '\062' + '\x30', 0o10), nzTpIcepk0o8(chr(2051 - 2003) + '\x6f' + chr(51) + '\063' + '\067', 8), nzTpIcepk0o8('\x30' + chr(111) + chr(50) + chr(0b110101) + '\062', 46239 - 46231), nzTpIcepk0o8(chr(0b10 + 0o56) + chr(0b101110 + 0o101) + chr(0b101011 + 0o6) + chr(0b110100) + chr(0b1001 + 0o51), 0b1000), nzTpIcepk0o8(chr(1536 - 1488) + '\x6f' + chr(2089 - 2038) + chr(53), ord("\x08")), nzTpIcepk0o8(chr(1235 - 1187) + chr(111) + '\067' + '\x33', 46770 - 46762), nzTpIcepk0o8('\x30' + '\x6f' + '\x31' + '\062' + '\x31', 47873 - 47865), nzTpIcepk0o8(chr(48) + '\157' + '\062' + chr(2632 - 2580) + chr(690 - 642), 0b1000), nzTpIcepk0o8('\x30' + '\157' + '\062' + '\x35' + '\061', 28852 - 28844), nzTpIcepk0o8(chr(0b100011 + 0o15) + '\157' + chr(54) + '\x35', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(137 - 87) + chr(48), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b10000 + 0o43) + chr(1011 - 962) + chr(1639 - 1591), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(0b10011 + 0o37) + '\062' + '\061', 0o10), nzTpIcepk0o8(chr(633 - 585) + chr(111) + chr(0b1 + 0o60) + chr(2036 - 1981) + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(0b101010 + 0o6) + chr(0b1101101 + 0o2) + chr(1280 - 1232), 8), nzTpIcepk0o8(chr(48) + chr(0b1001 + 0o146) + chr(0b110000 + 0o4) + chr(54), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(53) + '\x30', 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\t'), chr(100) + '\145' + chr(99) + chr(0b1100111 + 0o10) + '\x64' + chr(101))(chr(3499 - 3382) + chr(0b1011110 + 0o26) + chr(102) + chr(0b100101 + 0o10) + chr(0b101000 + 0o20)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def iDj3e8KM29K_(_1vzISbJ_R2i, FfKOThdpoDTb):
kIMfkyypPTcC = _1vzISbJ_R2i()
kIMfkyypPTcC.v3a5CEHPFxU_ = FfKOThdpoDTb
for (SLVB2BPA_mIe, uV9iBiw0y_Mp) in roI3spqORKae(FfKOThdpoDTb, roI3spqORKae(ES5oEprVxulp(b'S\xccK\xf6jY\xfb\x0cNG\xa5j'), '\144' + chr(0b1100101) + chr(0b1100011) + chr(3982 - 3871) + '\144' + '\x65')(chr(0b1110101) + chr(116) + '\146' + '\055' + '\070'))():
if roI3spqORKae(_1vzISbJ_R2i, roI3spqORKae(ES5oEprVxulp(b't\xe6U\xcdL\x7f\xd6\x10w{\x9e\x08'), '\x64' + '\145' + chr(2619 - 2520) + chr(0b101101 + 0o102) + chr(0b1000001 + 0o43) + '\145')(chr(5016 - 4899) + chr(0b1000000 + 0o64) + chr(727 - 625) + chr(0b10100 + 0o31) + chr(56))) and SLVB2BPA_mIe in roI3spqORKae(_1vzISbJ_R2i, roI3spqORKae(ES5oEprVxulp(b't\xe6U\xcdL\x7f\xd6\x10w{\x9e\x08'), chr(0b1100100) + '\145' + '\143' + '\157' + chr(3766 - 3666) + '\x65')('\165' + chr(0b11 + 0o161) + chr(9616 - 9514) + chr(0b100111 + 0o6) + chr(56))):
lCf1uzpaIUMv(kIMfkyypPTcC, SLVB2BPA_mIe, uV9iBiw0y_Mp)
elif roI3spqORKae(_1vzISbJ_R2i, roI3spqORKae(ES5oEprVxulp(b'd\xe0U\xcdL\x7f\xd1\x1fuf\x81\x0b\x8c'), chr(0b1100100) + '\145' + '\143' + chr(111) + chr(0b1100100) + chr(0b1100101))(chr(0b1110101) + '\x74' + chr(0b1100110) + chr(313 - 268) + chr(1947 - 1891))) and SLVB2BPA_mIe in roI3spqORKae(_1vzISbJ_R2i, roI3spqORKae(ES5oEprVxulp(b'd\xe0U\xcdL\x7f\xd1\x1fuf\x81\x0b\x8c'), '\144' + chr(0b1101 + 0o130) + '\x63' + chr(0b1101111) + '\x64' + '\145')('\165' + chr(116) + chr(7331 - 7229) + chr(1876 - 1831) + chr(0b100000 + 0o30))):
uV9iBiw0y_Mp = _1vzISbJ_R2i.COMPLEX_PROPS[SLVB2BPA_mIe].fromDict(uV9iBiw0y_Mp)
lCf1uzpaIUMv(kIMfkyypPTcC, SLVB2BPA_mIe, uV9iBiw0y_Mp)
elif roI3spqORKae(_1vzISbJ_R2i, roI3spqORKae(ES5oEprVxulp(b'k\xe6K\xc9_j\xdb\x0fug'), chr(100) + '\x65' + chr(4898 - 4799) + chr(11861 - 11750) + chr(0b1100100) + '\x65')(chr(0b1110101) + '\164' + '\x66' + chr(0b101101) + chr(56))) and SLVB2BPA_mIe in roI3spqORKae(_1vzISbJ_R2i, roI3spqORKae(ES5oEprVxulp(b'k\xe6K\xc9_j\xdb\x0fug'), chr(100) + chr(0b1100101) + '\x63' + chr(2454 - 2343) + '\144' + chr(0b1100101))('\165' + chr(0b1110100) + '\x66' + '\x2d' + chr(56))):
uV9iBiw0y_Mp = [_1vzISbJ_R2i.LIST_PROPS[SLVB2BPA_mIe].fromDict(IZ1I2J8X1CQz) for IZ1I2J8X1CQz in uV9iBiw0y_Mp]
lCf1uzpaIUMv(kIMfkyypPTcC, SLVB2BPA_mIe, uV9iBiw0y_Mp)
return kIMfkyypPTcC |
dustin/twitty-twister | twittytwister/streaming.py | TwitterStream.datagramReceived | def datagramReceived(self, data):
"""
Decode the JSON-encoded datagram and call the callback.
"""
try:
obj = json.loads(data)
except ValueError, e:
log.err(e, 'Invalid JSON in stream: %r' % data)
return
if u'text' in obj:
obj = Status.fromDict(obj)
else:
log.msg('Unsupported object %r' % obj)
return
self.callback(obj) | python | def datagramReceived(self, data):
"""
Decode the JSON-encoded datagram and call the callback.
"""
try:
obj = json.loads(data)
except ValueError, e:
log.err(e, 'Invalid JSON in stream: %r' % data)
return
if u'text' in obj:
obj = Status.fromDict(obj)
else:
log.msg('Unsupported object %r' % obj)
return
self.callback(obj) | [
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] | 8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3 | https://github.com/dustin/twitty-twister/blob/8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3/twittytwister/streaming.py#L306-L322 | train | Decode the JSON - encoded datagram and call the callback. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8('\060' + chr(111) + '\x32' + chr(54) + chr(2041 - 1990), 22567 - 22559), nzTpIcepk0o8('\060' + chr(0b1101111) + '\063' + chr(0b1001 + 0o47) + '\065', 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x32' + '\x34' + chr(55), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b11111 + 0o120) + '\062' + '\x33' + chr(1298 - 1243), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + '\064' + chr(0b110001), 48896 - 48888), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110 + 0o54) + '\064', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110011) + chr(0b110011) + chr(0b11011 + 0o30), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + '\061' + '\066' + '\067', 45918 - 45910), nzTpIcepk0o8(chr(0b10101 + 0o33) + chr(0b1001111 + 0o40) + chr(0b101110 + 0o3) + '\x30' + chr(54), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(0b10100 + 0o40), 0o10), nzTpIcepk0o8(chr(48) + chr(6080 - 5969) + '\x35' + chr(0b110000 + 0o3), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(1094 - 983) + '\x32' + chr(2470 - 2419) + chr(1011 - 963), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101000 + 0o7) + chr(49) + '\061' + chr(2207 - 2155), 28356 - 28348), nzTpIcepk0o8(chr(1954 - 1906) + '\157' + '\063' + chr(0b101100 + 0o5) + '\060', 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110010) + chr(51) + chr(52), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x33' + chr(53) + chr(0b110111), 30828 - 30820), nzTpIcepk0o8('\x30' + chr(111) + chr(49) + '\x33' + chr(2152 - 2102), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x31' + chr(0b110010) + chr(0b110011), 0o10), nzTpIcepk0o8(chr(416 - 368) + chr(111) + chr(0b110001), 8045 - 8037), nzTpIcepk0o8(chr(0b10010 + 0o36) + chr(7892 - 7781) + chr(50) + '\063' + chr(0b100 + 0o60), 8), nzTpIcepk0o8(chr(0b100010 + 0o16) + '\157' + chr(0b100111 + 0o13) + chr(0b110101) + chr(1001 - 949), 0o10), nzTpIcepk0o8(chr(1227 - 1179) + chr(0b1101111) + '\061' + chr(0b10100 + 0o41) + chr(0b10010 + 0o41), 61113 - 61105), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(51) + chr(0b110001) + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\061' + chr(0b10 + 0o63) + chr(222 - 169), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + '\x33' + chr(1623 - 1569) + chr(615 - 560), ord("\x08")), nzTpIcepk0o8(chr(1508 - 1460) + '\157' + chr(51) + '\060' + '\064', ord("\x08")), nzTpIcepk0o8(chr(0b1101 + 0o43) + chr(0b1101111) + '\067', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1100001 + 0o16) + '\x33' + chr(0b110000) + chr(0b1111 + 0o50), 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110001) + chr(1919 - 1864) + '\066', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110011) + '\063' + chr(0b10001 + 0o37), 63944 - 63936), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x32' + chr(53) + chr(49), 62227 - 62219), nzTpIcepk0o8(chr(2124 - 2076) + '\157' + chr(0b110001) + chr(0b10111 + 0o33) + chr(0b110011), 8), nzTpIcepk0o8('\060' + chr(111) + '\x31' + '\066' + chr(0b110100), 0o10), nzTpIcepk0o8(chr(0b10101 + 0o33) + chr(10079 - 9968) + '\061' + chr(570 - 515) + chr(0b101001 + 0o7), 9678 - 9670), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(1437 - 1384) + chr(0b110011), 8), nzTpIcepk0o8(chr(0b110000) + chr(2233 - 2122) + '\x32' + chr(0b110111) + chr(0b11 + 0o56), 0b1000), nzTpIcepk0o8(chr(2067 - 2019) + chr(2557 - 2446) + chr(276 - 225) + chr(0b110110) + chr(48), ord("\x08")), nzTpIcepk0o8(chr(757 - 709) + chr(9233 - 9122) + '\x32' + chr(48) + chr(0b100100 + 0o14), 57411 - 57403), nzTpIcepk0o8('\x30' + '\x6f' + chr(53) + chr(0b101011 + 0o5), 64424 - 64416), nzTpIcepk0o8(chr(48) + '\157' + chr(0b1010 + 0o50) + '\x33' + chr(49), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + chr(180 - 69) + chr(1682 - 1629) + chr(48), 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x9d'), '\144' + chr(0b100010 + 0o103) + '\x63' + '\157' + chr(0b1011111 + 0o5) + chr(0b11111 + 0o106))(chr(0b1110010 + 0o3) + chr(2759 - 2643) + chr(1146 - 1044) + chr(798 - 753) + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def QxuiIhPV1Khy(hXMPsSrOQzbh, FfKOThdpoDTb):
try:
kIMfkyypPTcC = LNUKEwZDIbyb.OiapAM4bM0Ea(FfKOThdpoDTb)
except WbNHlDKpyPtQ as wgf0sgcu_xPL:
roI3spqORKae(lmiGj7TonZgV, roI3spqORKae(ES5oEprVxulp(b'\xdc\x8b\xf2\xacqq\xad\x10+Sj\xd7'), chr(0b1010 + 0o132) + '\145' + chr(0b10100 + 0o117) + chr(2016 - 1905) + '\144' + chr(101))('\x75' + chr(116) + chr(2710 - 2608) + chr(0b100011 + 0o12) + chr(1020 - 964)))(wgf0sgcu_xPL, roI3spqORKae(ES5oEprVxulp(b"\xfa\xab\xd1\xfeM}\xbfW\x0cWd\xd6l\xa1\xf2\xcf)'s\xf9\xcd\x06\xf1M\xd2\xb6"), '\144' + '\x65' + chr(5269 - 5170) + chr(111) + chr(0b1100100) + '\x65')('\165' + '\x74' + chr(102) + '\055' + chr(1924 - 1868)) % FfKOThdpoDTb)
return
if roI3spqORKae(ES5oEprVxulp(b'\xc7\xa0\xdf\xeb'), chr(4315 - 4215) + '\145' + '\143' + chr(111) + chr(4445 - 4345) + '\145')(chr(0b1000010 + 0o63) + chr(0b1100 + 0o150) + chr(0b11 + 0o143) + chr(45) + chr(1969 - 1913)) in kIMfkyypPTcC:
kIMfkyypPTcC = lJVo3V3OGLki.fromDict(kIMfkyypPTcC)
else:
roI3spqORKae(lmiGj7TonZgV, roI3spqORKae(ES5oEprVxulp(b'\xc0\xa9\xc3\xe5C\\\xad\x12~C\x1a\xcb'), chr(0b1100100) + '\x65' + chr(0b100000 + 0o103) + chr(111) + '\144' + '\x65')(chr(0b1000101 + 0o60) + '\164' + chr(0b1100110) + chr(0b101 + 0o50) + chr(0b111000)))(roI3spqORKae(ES5oEprVxulp(b"\xe6\xab\xd4\xeaQd\xb4\x052aO\xb8#\xaa\xf6\x8a9'!\xb9\xde"), chr(0b1111 + 0o125) + '\x65' + chr(0b101000 + 0o73) + chr(4878 - 4767) + chr(100) + '\145')(chr(0b1110101) + chr(4363 - 4247) + chr(0b1000010 + 0o44) + chr(0b101101) + chr(0b111 + 0o61)) % kIMfkyypPTcC)
return
roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xd9\x82\x92\xd4t \x8e"\x01j@\xad'), chr(100) + chr(664 - 563) + chr(0b1100001 + 0o2) + '\x6f' + chr(100) + '\x65')(chr(0b1110101) + chr(4112 - 3996) + '\146' + chr(45) + chr(56)))(kIMfkyypPTcC) |
dustin/twitty-twister | twittytwister/streaming.py | TwitterStream.connectionLost | def connectionLost(self, reason):
"""
Called when the body is complete or the connection was lost.
@note: As the body length is usually not known at the beginning of the
response we expect a L{PotentialDataLoss} when Twitter closes the
stream, instead of L{ResponseDone}. Other exceptions are treated
as error conditions.
"""
self.setTimeout(None)
if reason.check(ResponseDone, PotentialDataLoss):
self.deferred.callback(None)
else:
self.deferred.errback(reason) | python | def connectionLost(self, reason):
"""
Called when the body is complete or the connection was lost.
@note: As the body length is usually not known at the beginning of the
response we expect a L{PotentialDataLoss} when Twitter closes the
stream, instead of L{ResponseDone}. Other exceptions are treated
as error conditions.
"""
self.setTimeout(None)
if reason.check(ResponseDone, PotentialDataLoss):
self.deferred.callback(None)
else:
self.deferred.errback(reason) | [
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@note: As the body length is usually not known at the beginning of the
response we expect a L{PotentialDataLoss} when Twitter closes the
stream, instead of L{ResponseDone}. Other exceptions are treated
as error conditions. | [
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"lost",
"."
] | 8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3 | https://github.com/dustin/twitty-twister/blob/8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3/twittytwister/streaming.py#L325-L338 | train | Called when the connection is lost. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8('\x30' + chr(0b11011 + 0o124) + chr(2448 - 2394) + chr(0b110001), 6593 - 6585), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110010) + chr(0b110010) + chr(0b101100 + 0o11), ord("\x08")), nzTpIcepk0o8(chr(0b101110 + 0o2) + chr(0b1101111) + chr(311 - 262) + '\063' + chr(2499 - 2448), 0b1000), nzTpIcepk0o8(chr(777 - 729) + chr(0b110100 + 0o73) + chr(1244 - 1195) + chr(0b11100 + 0o32), 18003 - 17995), nzTpIcepk0o8(chr(1957 - 1909) + chr(111) + chr(882 - 833) + chr(0b10001 + 0o37) + chr(0b110101), 61423 - 61415), nzTpIcepk0o8(chr(0b110000) + chr(1779 - 1668) + '\x33' + chr(387 - 339), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110010) + '\061' + chr(0b101011 + 0o7), 49605 - 49597), nzTpIcepk0o8(chr(0b100011 + 0o15) + '\x6f' + chr(0b110010) + '\x37', ord("\x08")), nzTpIcepk0o8(chr(0b101 + 0o53) + chr(0b10010 + 0o135) + chr(0b110001 + 0o1) + chr(53), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1011010 + 0o25) + chr(0b110010) + chr(0b101010 + 0o15) + chr(0b110110), 14205 - 14197), nzTpIcepk0o8(chr(0b110000 + 0o0) + chr(0b1101111) + chr(0b110001) + chr(0b110101) + chr(55), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b100000 + 0o24) + chr(0b1001 + 0o52), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(1381 - 1270) + chr(0b110001) + '\063' + '\067', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1010 + 0o145) + chr(0b101001 + 0o12) + chr(55) + chr(1156 - 1107), 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(0b1010 + 0o52) + chr(0b100010 + 0o20), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b101001 + 0o106) + chr(2447 - 2397) + '\x37' + chr(814 - 762), 30813 - 30805), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b1001 + 0o51) + '\063' + '\065', 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110001) + chr(1474 - 1423) + chr(0b110110), 0b1000), nzTpIcepk0o8('\060' + '\x6f' + '\063' + '\065' + '\063', 0o10), nzTpIcepk0o8(chr(48) + chr(111) + '\x31' + '\064' + chr(1735 - 1680), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + '\062' + chr(53) + chr(1551 - 1503), 0o10), nzTpIcepk0o8(chr(48) + chr(7219 - 7108) + chr(0b10011 + 0o36) + chr(0b110011) + chr(0b110010), 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(1947 - 1896) + chr(0b11101 + 0o30) + chr(0b1101 + 0o47), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + chr(0b110001 + 0o6), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b101111 + 0o2) + chr(0b110011) + chr(51), 8), nzTpIcepk0o8(chr(0b110000) + chr(2147 - 2036) + '\x33' + chr(0b10101 + 0o34) + chr(0b100 + 0o61), 0o10), nzTpIcepk0o8('\x30' + chr(0b1001 + 0o146) + chr(0b110010) + chr(0b1010 + 0o47) + chr(0b110110), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(53) + chr(0b110000), 0o10), nzTpIcepk0o8(chr(0b11011 + 0o25) + '\x6f' + '\x32' + '\066' + chr(0b10101 + 0o41), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(0b100 + 0o55) + '\x34', 0b1000), nzTpIcepk0o8(chr(494 - 446) + chr(419 - 308) + '\064' + chr(0b11100 + 0o31), 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(618 - 567) + chr(0b101 + 0o53) + chr(0b110001), 0b1000), nzTpIcepk0o8(chr(2074 - 2026) + '\157' + chr(0b110011) + chr(0b101101 + 0o5) + chr(51), 0o10), nzTpIcepk0o8(chr(48) + chr(12032 - 11921) + '\066' + chr(0b10011 + 0o35), 12717 - 12709), nzTpIcepk0o8(chr(0b110000 + 0o0) + '\x6f' + chr(51) + chr(52) + chr(54), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(0b11111 + 0o22) + chr(53) + chr(0b100001 + 0o25), 0o10), nzTpIcepk0o8(chr(0b101110 + 0o2) + chr(111) + chr(0b1110 + 0o43) + chr(51) + chr(0b101111 + 0o1), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(0b1111 + 0o44) + '\x33' + chr(0b110001), 47115 - 47107), nzTpIcepk0o8('\060' + '\x6f' + chr(0b10101 + 0o36) + chr(0b110111) + '\066', 0b1000), nzTpIcepk0o8(chr(126 - 78) + chr(1071 - 960) + '\063' + chr(0b110101) + chr(54), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + '\157' + chr(0b110101) + chr(48), 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x1f'), chr(0b1100100) + chr(0b1100101) + chr(1107 - 1008) + chr(0b1101111) + chr(0b1001001 + 0o33) + '\x65')(chr(0b1101010 + 0o13) + '\x74' + chr(7945 - 7843) + chr(0b101101) + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def origEX5kac_R(hXMPsSrOQzbh, RhxFF63tBU4y):
roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'B\xf0/Z,u\xefx`\xca'), '\x64' + '\x65' + chr(99) + chr(111) + '\144' + chr(101))('\165' + chr(116) + chr(0b1100110) + chr(0b101101) + '\070'))(None)
if roI3spqORKae(RhxFF63tBU4y, roI3spqORKae(ES5oEprVxulp(b'e\xf43Y4Q\xbb\\f\xd4\x1dy'), chr(0b1100100) + chr(6621 - 6520) + chr(0b1100011) + chr(0b1000101 + 0o52) + '\144' + chr(4965 - 4864))(chr(117) + '\164' + '\146' + chr(471 - 426) + chr(3024 - 2968)))(qKOxo6E3ditC, ZnkMmyx91390):
roI3spqORKae(hXMPsSrOQzbh.deferred, roI3spqORKae(ES5oEprVxulp(b'[\xd2nE\x10,\xdfBR\xd0\x04\x16'), chr(9371 - 9271) + chr(9616 - 9515) + chr(99) + chr(0b1100010 + 0o15) + chr(0b1100100) + chr(101))('\165' + chr(0b1110100) + chr(9696 - 9594) + chr(0b1100 + 0o41) + chr(0b111 + 0o61)))(None)
else:
roI3spqORKae(hXMPsSrOQzbh.deferred, roI3spqORKae(ES5oEprVxulp(b"y\xf6j6\x03(\xcf'e\xf9 b"), '\144' + chr(5097 - 4996) + chr(1918 - 1819) + chr(919 - 808) + chr(100) + chr(2387 - 2286))('\165' + chr(428 - 312) + chr(0b1010 + 0o134) + '\x2d' + chr(0b111000)))(RhxFF63tBU4y) |
dustin/twitty-twister | twittytwister/txml.py | simpleListFactory | def simpleListFactory(list_type):
"""Used for simple parsers that support only one type of object"""
def create(delegate, extra_args=None):
"""Create a Parser object for the specific tag type, on the fly"""
return listParser(list_type, delegate, extra_args)
return create | python | def simpleListFactory(list_type):
"""Used for simple parsers that support only one type of object"""
def create(delegate, extra_args=None):
"""Create a Parser object for the specific tag type, on the fly"""
return listParser(list_type, delegate, extra_args)
return create | [
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] | 8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3 | https://github.com/dustin/twitty-twister/blob/8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3/twittytwister/txml.py#L305-L310 | train | Used for simple parsers that support only one type of object | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(1797 - 1749) + '\157' + chr(49) + chr(711 - 661), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b101101 + 0o102) + chr(0b10111 + 0o32) + '\064' + chr(49), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + '\x31' + '\x35' + chr(0b10001 + 0o44), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1100110 + 0o11) + chr(2443 - 2393) + '\063' + chr(0b11100 + 0o31), 0o10), nzTpIcepk0o8('\x30' + chr(0b111011 + 0o64) + chr(372 - 321) + chr(0b110100) + chr(0b100101 + 0o21), ord("\x08")), nzTpIcepk0o8(chr(0b1110 + 0o42) + chr(0b1011110 + 0o21) + chr(0b10100 + 0o34), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(1044 - 994) + '\x37' + chr(51), 0o10), nzTpIcepk0o8('\x30' + chr(3954 - 3843) + chr(0b101101 + 0o6) + '\x35' + chr(0b11111 + 0o27), 0b1000), nzTpIcepk0o8(chr(0b101000 + 0o10) + '\x6f' + '\x32' + chr(0b110100) + chr(2352 - 2297), 5361 - 5353), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110001) + '\x33' + '\x36', 0o10), nzTpIcepk0o8(chr(0b11111 + 0o21) + chr(111) + '\x33' + chr(0b110000) + '\065', 0b1000), nzTpIcepk0o8(chr(2095 - 2047) + chr(111) + chr(121 - 69) + '\x37', 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(51) + chr(0b110111) + chr(943 - 892), 0b1000), nzTpIcepk0o8(chr(1286 - 1238) + '\x6f' + chr(0b110011) + chr(1168 - 1115) + chr(53), ord("\x08")), nzTpIcepk0o8(chr(1835 - 1787) + chr(111) + chr(0b110001) + chr(0b110110) + '\063', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b100101 + 0o112) + '\x32' + '\x34' + chr(49), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\061' + chr(0b110010) + '\060', 2402 - 2394), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b101100 + 0o7) + chr(0b10 + 0o64) + chr(0b110000), 19962 - 19954), nzTpIcepk0o8('\060' + chr(11287 - 11176) + chr(52) + '\063', 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(51) + '\x34' + '\x32', 0b1000), nzTpIcepk0o8(chr(0b1010 + 0o46) + '\157' + chr(163 - 112) + '\065' + chr(0b11101 + 0o31), 8), nzTpIcepk0o8(chr(1148 - 1100) + '\x6f' + '\067' + '\x31', ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + '\x32' + '\x32' + chr(0b101110 + 0o10), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110011) + chr(417 - 366) + '\x30', 54913 - 54905), nzTpIcepk0o8(chr(48) + '\157' + '\x31' + chr(855 - 807) + '\063', 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110111) + '\x35', 16227 - 16219), nzTpIcepk0o8(chr(1156 - 1108) + '\157' + chr(55) + '\x37', 0o10), nzTpIcepk0o8('\x30' + chr(111) + '\062' + chr(0b101010 + 0o15) + chr(0b110111), 30094 - 30086), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b100010 + 0o21) + '\x30' + chr(55), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101010 + 0o5) + chr(0b110011) + chr(0b110010) + chr(49), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b101010 + 0o105) + '\x34' + chr(656 - 608), ord("\x08")), nzTpIcepk0o8(chr(0b100110 + 0o12) + chr(7349 - 7238) + chr(0b10001 + 0o40) + chr(271 - 220) + chr(1322 - 1268), 8), nzTpIcepk0o8(chr(1630 - 1582) + chr(9033 - 8922) + '\062' + chr(1406 - 1351) + chr(0b10000 + 0o41), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(50) + chr(48) + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(1679 - 1631) + chr(0b1000001 + 0o56) + chr(114 - 63) + chr(0b100001 + 0o20) + chr(53), ord("\x08")), nzTpIcepk0o8(chr(0b1000 + 0o50) + chr(11491 - 11380) + '\062' + '\x34' + chr(738 - 690), 61311 - 61303), nzTpIcepk0o8(chr(0b11 + 0o55) + chr(111) + '\063' + chr(0b110000) + '\x31', ord("\x08")), nzTpIcepk0o8(chr(1694 - 1646) + chr(111) + chr(1707 - 1657) + chr(704 - 653) + chr(0b110000), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + '\063' + '\062', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b100011 + 0o16) + chr(1879 - 1825) + chr(0b110 + 0o55), 8)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(322 - 274) + chr(111) + chr(337 - 284) + chr(867 - 819), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'$'), chr(0b1100100) + chr(101) + chr(0b1100011) + chr(0b1101111) + chr(7726 - 7626) + '\x65')(chr(11574 - 11457) + chr(2595 - 2479) + chr(0b1100110) + '\055' + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def HNesayeE05Bp(PLuKmt1HSVt6):
def uTw5CPPMOlxD(sl13tsTzFIJl, vsHxRdBONQp3=None):
return HfymcgmzNMe4(PLuKmt1HSVt6, sl13tsTzFIJl, vsHxRdBONQp3)
return uTw5CPPMOlxD |
dustin/twitty-twister | twittytwister/txml.py | BaseXMLHandler.setSubDelegates | def setSubDelegates(self, namelist, before=None, after=None):
"""Set a delegate for a sub-sub-item, according to a list of names"""
if len(namelist) > 1:
def set_sub(i):
i.setSubDelegates(namelist[1:], before, after)
self.setBeforeDelegate(namelist[0], set_sub)
elif len(namelist) == 1:
self.setDelegate(namelist[0], before, after) | python | def setSubDelegates(self, namelist, before=None, after=None):
"""Set a delegate for a sub-sub-item, according to a list of names"""
if len(namelist) > 1:
def set_sub(i):
i.setSubDelegates(namelist[1:], before, after)
self.setBeforeDelegate(namelist[0], set_sub)
elif len(namelist) == 1:
self.setDelegate(namelist[0], before, after) | [
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] | 8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3 | https://github.com/dustin/twitty-twister/blob/8524750ee73adb57bbe14ef0cfd8aa08e1e59fb3/twittytwister/txml.py#L48-L55 | train | Set a delegate for a sub - sub - item according to a list of names | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b111 + 0o52) + '\x37' + '\060', 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x33' + chr(53) + chr(54), 63255 - 63247), nzTpIcepk0o8(chr(0b110000) + chr(0b11001 + 0o126) + chr(1482 - 1432) + chr(2156 - 2101) + chr(0b100000 + 0o23), 19 - 11), nzTpIcepk0o8(chr(0b110000) + '\157' + '\063' + chr(0b110011) + '\x36', ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + '\063' + '\064', 59777 - 59769), nzTpIcepk0o8(chr(264 - 216) + chr(0b1101111) + chr(0b110001) + chr(0b110101) + '\066', 0o10), nzTpIcepk0o8(chr(48) + chr(9832 - 9721) + chr(0b110010) + '\x32' + chr(49), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(54) + '\x30', 0b1000), nzTpIcepk0o8('\060' + chr(0b1010010 + 0o35) + '\x35' + chr(0b10 + 0o57), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(49) + '\062' + '\067', 0o10), nzTpIcepk0o8('\060' + '\157' + '\x32' + chr(1038 - 988) + chr(50), 63000 - 62992), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\066' + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(0b1010 + 0o51) + '\x30' + chr(1705 - 1655), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x31' + chr(0b110010) + '\060', 44708 - 44700), nzTpIcepk0o8(chr(1061 - 1013) + chr(111) + chr(0b110010) + chr(1196 - 1146) + chr(0b110111), 60561 - 60553), nzTpIcepk0o8(chr(2014 - 1966) + chr(0b100 + 0o153) + chr(0b101111 + 0o3) + chr(0b100000 + 0o26) + chr(52), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x31' + chr(55), ord("\x08")), nzTpIcepk0o8(chr(0b11000 + 0o30) + chr(0b1101111) + '\061' + '\x34' + chr(0b110011 + 0o1), ord("\x08")), nzTpIcepk0o8(chr(0b10011 + 0o35) + chr(0b1101111) + '\x31' + chr(0b110001) + chr(1664 - 1612), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1001110 + 0o41) + chr(0b110100) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\063' + '\062' + chr(2048 - 2000), 0o10), nzTpIcepk0o8(chr(0b10000 + 0o40) + chr(662 - 551) + chr(49) + chr(0b110011) + chr(55), ord("\x08")), nzTpIcepk0o8(chr(195 - 147) + '\157' + chr(50) + '\065' + chr(50), 0b1000), nzTpIcepk0o8(chr(0b1110 + 0o42) + '\157' + chr(0b110010) + chr(55) + chr(53), 54772 - 54764), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b101111 + 0o10) + chr(54), 60639 - 60631), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b100001 + 0o20) + '\060' + chr(0b101101 + 0o10), 0o10), nzTpIcepk0o8('\060' + chr(0b101000 + 0o107) + chr(0b101101 + 0o6) + chr(0b100100 + 0o17) + '\062', 0o10), nzTpIcepk0o8(chr(0b101111 + 0o1) + chr(111) + chr(54) + chr(54), 0b1000), nzTpIcepk0o8(chr(0b10010 + 0o36) + chr(111) + '\x34', ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(0b110 + 0o53) + chr(0b110011) + chr(0b101110 + 0o6), 0b1000), nzTpIcepk0o8(chr(0b100 + 0o54) + chr(0b1100111 + 0o10) + chr(0b101101 + 0o4) + chr(859 - 811) + '\x31', 0o10), nzTpIcepk0o8(chr(2216 - 2168) + chr(111) + '\067' + chr(1811 - 1759), 41976 - 41968), nzTpIcepk0o8(chr(0b101010 + 0o6) + chr(0b1101001 + 0o6) + '\063' + chr(1701 - 1647) + '\x32', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(51) + chr(0b11111 + 0o27) + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(1685 - 1637) + '\x6f' + '\061' + chr(1660 - 1611) + '\x30', 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(860 - 810) + chr(0b110110) + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(0b110 + 0o52) + '\x6f' + chr(49) + '\065' + chr(0b100101 + 0o16), 0o10), nzTpIcepk0o8('\060' + chr(1719 - 1608) + chr(0b1000 + 0o52) + '\066', 5076 - 5068), nzTpIcepk0o8(chr(1238 - 1190) + chr(111) + chr(51) + chr(897 - 848) + '\067', 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110010) + '\x36' + '\x31', 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(1727 - 1679) + chr(10869 - 10758) + '\x35' + chr(2142 - 2094), 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'V'), chr(7794 - 7694) + chr(0b1100101) + chr(3381 - 3282) + chr(0b1101111 + 0o0) + chr(100) + chr(0b1100101))(chr(12765 - 12648) + chr(9078 - 8962) + chr(102) + chr(0b1111 + 0o36) + chr(0b11 + 0o65)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def Fw23iGSPeolJ(hXMPsSrOQzbh, SbPDIBbf66wv, OsFA8mB0ZwJd=None, mar_kHe1Xspp=None):
if ftfygxgFas5X(SbPDIBbf66wv) > nzTpIcepk0o8(chr(1980 - 1932) + chr(111) + chr(63 - 14), ord("\x08")):
def YvUdAyavaIBa(ZlbFMSG8gCoF):
roI3spqORKae(ZlbFMSG8gCoF, roI3spqORKae(ES5oEprVxulp(b'\x0b\x8b\xcf\x8di\x0c\xd5UE2\xf5V\xb65\xe4'), chr(0b1010010 + 0o22) + chr(0b1100101) + chr(0b1100011) + chr(9326 - 9215) + chr(100) + '\x65')('\165' + chr(1570 - 1454) + '\x66' + chr(0b101101) + chr(56)))(SbPDIBbf66wv[nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x31', 8):], OsFA8mB0ZwJd, mar_kHe1Xspp)
roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x0b\x8b\xcf\x9cy\x08\xfeBL\x13\xf7[\xa77\xf6\xc0j'), chr(9080 - 8980) + chr(101) + chr(0b101000 + 0o73) + '\x6f' + '\144' + chr(101))(chr(1299 - 1182) + chr(116) + '\146' + '\x2d' + '\070'))(SbPDIBbf66wv[nzTpIcepk0o8(chr(0b110000) + chr(10243 - 10132) + chr(318 - 270), ord("\x08"))], YvUdAyavaIBa)
elif ftfygxgFas5X(SbPDIBbf66wv) == nzTpIcepk0o8(chr(997 - 949) + '\157' + chr(1904 - 1855), 8):
roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x0b\x8b\xcf\x9ay\x02\xf4WH#\xf7'), chr(0b1100100) + '\145' + chr(0b100001 + 0o102) + chr(111) + '\144' + chr(101))('\x75' + chr(116) + chr(0b1100110) + chr(0b101101) + chr(0b111000)))(SbPDIBbf66wv[nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110000), 8)], OsFA8mB0ZwJd, mar_kHe1Xspp) |
jupyter/jupyter-drive | jupyterdrive/mixednbmanager.py | _split_path | def _split_path(path):
"""split a path return by the api
return
- the sentinel:
- the rest of the path as a list.
- the original path stripped of / for normalisation.
"""
path = path.strip('/')
list_path = path.split('/')
sentinel = list_path.pop(0)
return sentinel, list_path, path | python | def _split_path(path):
"""split a path return by the api
return
- the sentinel:
- the rest of the path as a list.
- the original path stripped of / for normalisation.
"""
path = path.strip('/')
list_path = path.split('/')
sentinel = list_path.pop(0)
return sentinel, list_path, path | [
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] | 545813377cb901235e8ea81f83b0ac7755dbd7a9 | https://github.com/jupyter/jupyter-drive/blob/545813377cb901235e8ea81f83b0ac7755dbd7a9/jupyterdrive/mixednbmanager.py#L21-L32 | train | split a path into sentinel list_path and path | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b101 + 0o56) + chr(0b110111) + chr(922 - 868), ord("\x08")), nzTpIcepk0o8('\060' + chr(6137 - 6026) + chr(0b11001 + 0o30) + chr(53) + '\x30', 39316 - 39308), nzTpIcepk0o8(chr(0b1111 + 0o41) + chr(8815 - 8704) + chr(49) + '\x30', 4103 - 4095), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110010) + '\x37' + chr(0b1010 + 0o47), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b10111 + 0o33) + chr(2230 - 2179) + chr(2472 - 2417), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + '\064' + chr(1435 - 1385), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + '\x31' + chr(0b1000 + 0o56) + chr(49), ord("\x08")), nzTpIcepk0o8(chr(0b1010 + 0o46) + chr(0b1101111) + '\063' + chr(0b11111 + 0o23) + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b100100 + 0o113) + '\061' + chr(54) + '\x30', 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + '\x31' + chr(0b110101) + '\x32', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\063' + chr(2137 - 2084) + chr(711 - 656), 47220 - 47212), nzTpIcepk0o8('\x30' + chr(5581 - 5470) + chr(0b1110 + 0o50) + '\x33', 51963 - 51955), nzTpIcepk0o8('\060' + chr(111) + chr(0b110001) + chr(899 - 846) + chr(0b101 + 0o57), 53368 - 53360), nzTpIcepk0o8(chr(0b11010 + 0o26) + chr(111) + chr(970 - 921) + chr(0b10100 + 0o40) + chr(0b10100 + 0o41), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(813 - 764) + chr(53) + chr(0b110000), 8), nzTpIcepk0o8(chr(0b10001 + 0o37) + chr(0b1101111) + chr(0b110001 + 0o1) + chr(51) + chr(214 - 166), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(52) + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110011) + '\x31', 0o10), nzTpIcepk0o8('\060' + '\x6f' + '\x31' + chr(0b1 + 0o57) + '\060', 0b1000), nzTpIcepk0o8(chr(1638 - 1590) + '\x6f' + chr(0b110011) + chr(0b110001) + chr(0b100100 + 0o17), 54242 - 54234), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(51) + '\x37' + chr(55), ord("\x08")), nzTpIcepk0o8(chr(0b1101 + 0o43) + chr(0b1101111) + chr(0b111 + 0o52) + chr(52) + '\060', ord("\x08")), nzTpIcepk0o8(chr(1237 - 1189) + '\157' + chr(50) + chr(0b100110 + 0o13) + chr(1328 - 1276), 0b1000), nzTpIcepk0o8(chr(2068 - 2020) + chr(111) + chr(50) + chr(0b11100 + 0o30), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110011) + chr(1202 - 1154) + chr(2956 - 2901), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b101011 + 0o104) + chr(54) + chr(51), 8), nzTpIcepk0o8('\x30' + chr(3161 - 3050) + chr(336 - 286) + chr(527 - 475) + '\x32', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b111 + 0o150) + chr(55) + chr(0b110001), 54115 - 54107), nzTpIcepk0o8(chr(2238 - 2190) + '\x6f' + '\067' + chr(52), ord("\x08")), nzTpIcepk0o8(chr(0b101110 + 0o2) + chr(8602 - 8491) + chr(397 - 347) + '\x32' + chr(1625 - 1575), ord("\x08")), nzTpIcepk0o8(chr(491 - 443) + '\x6f' + chr(771 - 722) + chr(0b110010) + chr(0b110011), 0o10), nzTpIcepk0o8(chr(1288 - 1240) + chr(0b1101100 + 0o3) + chr(442 - 393) + '\065' + chr(0b10000 + 0o42), 8), nzTpIcepk0o8('\x30' + chr(111) + chr(0b1010 + 0o47) + chr(0b101010 + 0o10) + '\x33', 8), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b111 + 0o54) + chr(0b100000 + 0o20) + chr(0b100111 + 0o13), 41641 - 41633), nzTpIcepk0o8(chr(0b10110 + 0o32) + chr(11552 - 11441) + chr(1676 - 1625) + chr(0b110001 + 0o6) + chr(0b110110), 8), nzTpIcepk0o8(chr(2290 - 2242) + chr(5065 - 4954) + '\066' + '\064', 35454 - 35446), nzTpIcepk0o8('\060' + '\x6f' + chr(0b100 + 0o56) + '\066' + chr(0b110101), 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(404 - 349) + chr(151 - 103), 47585 - 47577), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110011) + chr(2995 - 2940) + chr(48), 57267 - 57259), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(51) + '\x37' + chr(0b100100 + 0o21), 49187 - 49179)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + chr(8664 - 8553) + chr(2664 - 2611) + chr(0b110000), 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xd0'), '\x64' + chr(712 - 611) + chr(0b110101 + 0o56) + '\157' + '\144' + chr(0b1001101 + 0o30))(chr(0b1110101) + chr(116) + chr(0b1011001 + 0o15) + chr(45) + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def wKRV0gI3uDSm(_pSYqrosNb95):
_pSYqrosNb95 = _pSYqrosNb95.kdIDrcwZTCs5(roI3spqORKae(ES5oEprVxulp(b'\xd1'), chr(100) + chr(101) + chr(0b10011 + 0o120) + chr(111) + chr(0b1001 + 0o133) + '\x65')(chr(117) + chr(0b1011011 + 0o31) + chr(0b111000 + 0o56) + chr(1542 - 1497) + chr(0b11 + 0o65)))
WmnenMQCSCdQ = _pSYqrosNb95.LfRrQOxuDvnC(roI3spqORKae(ES5oEprVxulp(b'\xd1'), '\x64' + '\x65' + chr(99) + chr(111) + '\x64' + '\x65')(chr(10420 - 10303) + chr(116) + '\x66' + chr(1697 - 1652) + '\x38'))
lUJPb6OgnhJi = WmnenMQCSCdQ.uC_Yoybx7J0I(nzTpIcepk0o8(chr(0b110000) + chr(0b1001110 + 0o41) + chr(0b100010 + 0o16), 0b1000))
return (lUJPb6OgnhJi, WmnenMQCSCdQ, _pSYqrosNb95) |
jupyter/jupyter-drive | jupyterdrive/mixednbmanager.py | MixedContentsManager.path_dispatch_rename | def path_dispatch_rename(rename_like_method):
"""
decorator for rename-like function, that need dispatch on 2 arguments
"""
def _wrapper_method(self, old_path, new_path):
old_path, _old_path, old_sentinel = _split_path(old_path);
new_path, _new_path, new_sentinel = _split_path(new_path);
if old_sentinel != new_sentinel:
raise ValueError('Does not know how to move things across contents manager mountpoints')
else:
sentinel = new_sentinel
man = self.managers.get(sentinel, None)
if man is not None:
rename_meth = getattr(man, rename_like_method.__name__)
sub = rename_meth('/'.join(_old_path), '/'.join(_new_path))
return sub
else :
return rename_meth(self, old_path, new_path)
return _wrapper_method | python | def path_dispatch_rename(rename_like_method):
"""
decorator for rename-like function, that need dispatch on 2 arguments
"""
def _wrapper_method(self, old_path, new_path):
old_path, _old_path, old_sentinel = _split_path(old_path);
new_path, _new_path, new_sentinel = _split_path(new_path);
if old_sentinel != new_sentinel:
raise ValueError('Does not know how to move things across contents manager mountpoints')
else:
sentinel = new_sentinel
man = self.managers.get(sentinel, None)
if man is not None:
rename_meth = getattr(man, rename_like_method.__name__)
sub = rename_meth('/'.join(_old_path), '/'.join(_new_path))
return sub
else :
return rename_meth(self, old_path, new_path)
return _wrapper_method | [
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] | 545813377cb901235e8ea81f83b0ac7755dbd7a9 | https://github.com/jupyter/jupyter-drive/blob/545813377cb901235e8ea81f83b0ac7755dbd7a9/jupyterdrive/mixednbmanager.py#L186-L208 | train | Decorator for rename - like method that need dispatch on 2 arguments
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ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(667 - 618) + chr(0b110100) + chr(440 - 391), 6351 - 6343), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x33' + '\x37' + chr(1469 - 1419), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(55) + chr(0b101010 + 0o7), 23703 - 23695), nzTpIcepk0o8('\060' + chr(111) + chr(51) + chr(2320 - 2270) + chr(0b110011), 27630 - 27622), nzTpIcepk0o8(chr(0b110000) + chr(11595 - 11484) + chr(50) + '\060' + '\x31', 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + '\061' + '\x32', 9975 - 9967), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x32' + chr(0b101100 + 0o12) + chr(1490 - 1435), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x33' + chr(2547 - 2496) + chr(1291 - 1238), 0b1000), nzTpIcepk0o8('\x30' + chr(10453 - 10342) + chr(0b101101 + 0o6) + chr(0b110011) + chr(0b110001), ord("\x08")), nzTpIcepk0o8(chr(0b111 + 0o51) + chr(0b1101111) + chr(0b110110) + chr(494 - 444), 29004 - 28996), nzTpIcepk0o8(chr(0b10110 + 0o32) + chr(0b1010110 + 0o31) + '\061' + chr(0b10000 + 0o43) + chr(177 - 129), 0b1000), nzTpIcepk0o8(chr(994 - 946) + chr(111) + chr(51) + '\x31' + chr(1958 - 1906), 1648 - 1640), nzTpIcepk0o8('\060' + chr(762 - 651) + '\061' + '\x34' + chr(0b0 + 0o67), 0b1000), nzTpIcepk0o8(chr(1815 - 1767) + '\x6f' + chr(49) + '\x30' + '\x33', 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(0b10000 + 0o41) + '\x37' + chr(0b100 + 0o63), 0o10), nzTpIcepk0o8(chr(0b11111 + 0o21) + '\x6f' + '\062' + '\x35' + '\x36', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110010) + chr(0b101110 + 0o5) + chr(0b100101 + 0o13), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101101 + 0o2) + '\x31' + chr(0b110000) + '\x34', 40724 - 40716), nzTpIcepk0o8(chr(48) + chr(0b1001000 + 0o47) + chr(0b110011) + '\064' + chr(51), ord("\x08")), nzTpIcepk0o8(chr(949 - 901) + chr(0b1101111) + '\x32' + '\066' + chr(609 - 555), 13546 - 13538), nzTpIcepk0o8(chr(384 - 336) + '\157' + '\062' + chr(694 - 644) + chr(0b10001 + 0o46), 0o10), nzTpIcepk0o8('\060' + chr(0b110010 + 0o75) + '\062' + chr(52) + '\x34', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(3401 - 3290) + '\x32' + chr(0b110011) + '\x32', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(5632 - 5521) + chr(50) + chr(2556 - 2504) + chr(0b11000 + 0o35), 0o10), nzTpIcepk0o8(chr(0b110 + 0o52) + chr(0b1101111) + chr(835 - 784) + chr(0b101010 + 0o10), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110001) + chr(0b110011 + 0o0) + chr(49), ord("\x08")), nzTpIcepk0o8(chr(0b110000 + 0o0) + chr(11186 - 11075) + chr(0b10001 + 0o41) + '\066' + chr(0b110111), 8), nzTpIcepk0o8('\x30' + chr(0b110011 + 0o74) + chr(587 - 536) + chr(2060 - 2012) + chr(0b10001 + 0o41), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(50) + chr(50), 62440 - 62432), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(1226 - 1177) + chr(0b110000 + 0o7) + chr(48), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101100 + 0o3) + chr(1855 - 1805) + chr(48) + chr(0b1111 + 0o42), 8), nzTpIcepk0o8(chr(1997 - 1949) + chr(341 - 230) + chr(303 - 253) + chr(351 - 301) + chr(55), 8), nzTpIcepk0o8('\x30' + chr(7521 - 7410) + chr(0b101110 + 0o5) + '\x33' + '\063', 13143 - 13135), nzTpIcepk0o8(chr(0b10100 + 0o34) + '\157' + chr(51) + chr(1126 - 1074) + '\062', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b10110 + 0o131) + chr(599 - 545) + chr(1711 - 1660), 0o10), nzTpIcepk0o8(chr(0b101011 + 0o5) + '\157' + chr(684 - 634) + '\062' + chr(0b110011), 30974 - 30966), nzTpIcepk0o8(chr(1395 - 1347) + chr(0b11000 + 0o127) + '\062' + '\060' + '\x33', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110001) + chr(55), 0b1000), nzTpIcepk0o8('\x30' + chr(6833 - 6722) + '\062' + chr(54) + chr(54), 8), nzTpIcepk0o8(chr(0b1001 + 0o47) + '\157' + chr(50) + chr(0b110010) + chr(154 - 104), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + chr(0b10100 + 0o133) + chr(0b10110 + 0o37) + chr(0b101 + 0o53), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'O'), chr(100) + chr(0b1100101) + chr(217 - 118) + '\157' + chr(2919 - 2819) + chr(0b1011101 + 0o10))(chr(1377 - 1260) + chr(835 - 719) + chr(9587 - 9485) + '\055' + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def kR4wJNakmtft(nEPbPtmhJbhW):
def FMXSq2WX3OBd(hXMPsSrOQzbh, c8Xk69MAHINc, F6o1qlXVb1rn):
(c8Xk69MAHINc, m16vRVNSIvLZ, M4Li8IuxZ7lR) = wKRV0gI3uDSm(c8Xk69MAHINc)
(F6o1qlXVb1rn, SPPbflJp2xU4, e7nIBI8ArxJM) = wKRV0gI3uDSm(F6o1qlXVb1rn)
if M4Li8IuxZ7lR != e7nIBI8ArxJM:
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'%\x95\\\xa0\xa1d\xd8\xa9\xf9Y6\xa3\x10c\x17\xc1\xefd\x97\xd9\xb7\xc9\xf5\xd3\x7fy\xc3\xaa{\x16\xe6\xe4\xfb\x83P\xe1\xec|\xc5\xb2\x02\x95W\xa7\xe4d\xc3\xae\xf9_9\xa2\x06$\x1a\xdc\xb8)\x8c\xc3\xf9\xd0\xea\xcas7\xc3\xb1'), chr(0b1011011 + 0o11) + '\x65' + chr(0b1100011) + chr(0b1101111) + chr(0b1100100) + '\145')('\165' + '\164' + chr(102) + chr(45) + chr(56)))
else:
lUJPb6OgnhJi = e7nIBI8ArxJM
NYd4bvAQ8GZ9 = hXMPsSrOQzbh.managers.GUKetu4xaGsJ(lUJPb6OgnhJi, None)
if NYd4bvAQ8GZ9 is not None:
WDw0ffAOTyHt = roI3spqORKae(NYd4bvAQ8GZ9, nEPbPtmhJbhW.AYtDRlqeP0tq)
_zPndKq6xMgp = WDw0ffAOTyHt(roI3spqORKae(ES5oEprVxulp(b'N'), '\x64' + chr(9829 - 9728) + chr(99) + '\157' + chr(3646 - 3546) + chr(0b10110 + 0o117))('\x75' + '\164' + '\x66' + chr(232 - 187) + chr(0b111000)).Y4yM9BcfTCNq(m16vRVNSIvLZ), roI3spqORKae(ES5oEprVxulp(b'N'), chr(100) + chr(4412 - 4311) + chr(0b1000100 + 0o37) + chr(111) + chr(7746 - 7646) + chr(0b1000010 + 0o43))(chr(0b1110101) + chr(0b1110100) + chr(5500 - 5398) + '\x2d' + '\x38').Y4yM9BcfTCNq(SPPbflJp2xU4))
return _zPndKq6xMgp
else:
return WDw0ffAOTyHt(hXMPsSrOQzbh, c8Xk69MAHINc, F6o1qlXVb1rn)
return FMXSq2WX3OBd |
jupyter/jupyter-drive | jupyterdrive/__init__.py | deactivate | def deactivate(profile='default'):
"""should be a matter of just unsetting the above keys
"""
with jconfig(profile) as config:
deact = True;
if not getattr(config.NotebookApp.contents_manager_class, 'startswith',lambda x:False)('jupyterdrive'):
deact=False
if 'gdrive' not in getattr(config.NotebookApp.tornado_settings,'get', lambda _,__:'')('contents_js_source',''):
deact=False
if deact:
del config['NotebookApp']['tornado_settings']['contents_js_source']
del config['NotebookApp']['contents_manager_class'] | python | def deactivate(profile='default'):
"""should be a matter of just unsetting the above keys
"""
with jconfig(profile) as config:
deact = True;
if not getattr(config.NotebookApp.contents_manager_class, 'startswith',lambda x:False)('jupyterdrive'):
deact=False
if 'gdrive' not in getattr(config.NotebookApp.tornado_settings,'get', lambda _,__:'')('contents_js_source',''):
deact=False
if deact:
del config['NotebookApp']['tornado_settings']['contents_js_source']
del config['NotebookApp']['contents_manager_class'] | [
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] | 545813377cb901235e8ea81f83b0ac7755dbd7a9 | https://github.com/jupyter/jupyter-drive/blob/545813377cb901235e8ea81f83b0ac7755dbd7a9/jupyterdrive/__init__.py#L111-L122 | train | deactivate the contents manager class | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b10111 + 0o31) + '\x6f' + chr(2261 - 2212) + chr(0b110101) + chr(0b110010), 0b1000), nzTpIcepk0o8(chr(1129 - 1081) + chr(0b101000 + 0o107) + chr(0b10100 + 0o37) + chr(0b1100 + 0o45) + chr(0b110100), 0o10), nzTpIcepk0o8(chr(2237 - 2189) + '\x6f' + '\x32' + chr(49) + chr(0b11001 + 0o33), 62661 - 62653), nzTpIcepk0o8('\060' + '\157' + chr(1023 - 973) + chr(54) + chr(53), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + '\x31' + chr(929 - 878), 0o10), nzTpIcepk0o8(chr(48) + chr(11465 - 11354) + chr(1799 - 1749) + '\x32', 0b1000), nzTpIcepk0o8(chr(1581 - 1533) + chr(111) + '\x32' + '\x32' + chr(0b110001), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + '\061' + '\065' + chr(0b110100), 53719 - 53711), nzTpIcepk0o8(chr(882 - 834) + chr(111) + chr(1240 - 1191) + '\062' + chr(0b101101 + 0o7), ord("\x08")), nzTpIcepk0o8(chr(1451 - 1403) + chr(9476 - 9365) + '\x33' + chr(0b110100) + chr(1495 - 1440), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110010) + chr(1506 - 1452) + chr(48), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x31' + chr(55) + '\x32', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b110011 + 0o74) + chr(51) + chr(0b110101) + chr(1116 - 1066), 33684 - 33676), nzTpIcepk0o8('\060' + chr(0b1011000 + 0o27) + chr(464 - 415) + chr(0b110011) + chr(0b11010 + 0o32), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(50) + chr(0b1110 + 0o50) + '\064', ord("\x08")), nzTpIcepk0o8('\060' + chr(11221 - 11110) + '\063' + chr(0b110110) + chr(53), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110111) + chr(0b11101 + 0o31), 38996 - 38988), nzTpIcepk0o8(chr(0b101 + 0o53) + '\157' + chr(0b11100 + 0o26) + chr(0b110110) + '\x34', 8), nzTpIcepk0o8(chr(112 - 64) + chr(1477 - 1366) + '\061' + chr(0b110110) + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(8581 - 8470) + chr(208 - 159) + '\x34' + '\063', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x33' + chr(0b100110 + 0o20) + chr(2258 - 2208), 37776 - 37768), nzTpIcepk0o8('\060' + chr(0b1101111) + '\063' + '\066' + '\065', 8), nzTpIcepk0o8(chr(48) + '\157' + '\x32' + chr(0b100101 + 0o17) + chr(0b110010 + 0o4), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + '\x33' + chr(0b11010 + 0o34) + chr(0b110110), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + '\063' + chr(0b110000) + '\060', 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110010) + chr(600 - 551) + '\x36', 61689 - 61681), nzTpIcepk0o8(chr(1666 - 1618) + chr(111) + '\x33' + chr(55) + chr(0b110001), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110010) + '\x32' + '\x37', ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(0b100001 + 0o20) + chr(55) + '\062', 8), nzTpIcepk0o8('\x30' + '\157' + chr(49) + chr(2620 - 2567) + chr(0b110101), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b11000 + 0o127) + chr(0b110011) + chr(49) + chr(1174 - 1126), ord("\x08")), nzTpIcepk0o8(chr(141 - 93) + chr(0b1100111 + 0o10) + chr(0b10110 + 0o35) + chr(0b1011 + 0o47) + chr(48), ord("\x08")), nzTpIcepk0o8('\060' + chr(8613 - 8502) + chr(1287 - 1238) + chr(0b110010) + chr(3021 - 2966), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(0b110101 + 0o0) + chr(49), 0b1000), nzTpIcepk0o8(chr(958 - 910) + chr(0b1101111) + chr(0b101000 + 0o12) + '\x37' + '\x32', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(2380 - 2330) + chr(50) + chr(1027 - 972), 8), nzTpIcepk0o8(chr(696 - 648) + '\x6f' + chr(0b110001) + '\060' + chr(306 - 256), 46600 - 46592), nzTpIcepk0o8('\060' + '\157' + '\062' + chr(0b10011 + 0o35) + '\063', 23358 - 23350), nzTpIcepk0o8('\060' + chr(0b101111 + 0o100) + '\x32' + chr(0b110010) + '\067', 8), nzTpIcepk0o8('\x30' + '\x6f' + chr(2426 - 2376) + '\066' + chr(0b110110), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110101) + chr(48), 29433 - 29425)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'D'), chr(0b1100100) + '\x65' + chr(0b1100010 + 0o1) + chr(0b1101111) + chr(100) + chr(0b110000 + 0o65))(chr(117) + chr(0b1110100) + chr(496 - 394) + chr(0b11111 + 0o16) + chr(0b110110 + 0o2)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def kza7CQNKuCNA(nQ8dle22Rrpj=roI3spqORKae(ES5oEprVxulp(b'\x0e\xa9\xea\xd4~~\xe5'), chr(0b1100100) + chr(0b1100101) + chr(3291 - 3192) + '\x6f' + chr(4444 - 4344) + chr(101))(chr(0b110101 + 0o100) + '\164' + '\x66' + '\x2d' + chr(56))):
with _qYSwB3WkWQj(nQ8dle22Rrpj) as kgkKUcD36lls:
tOXcYdYc915w = nzTpIcepk0o8('\060' + chr(6221 - 6110) + chr(1867 - 1818), ord("\x08"))
if not roI3spqORKae(roI3spqORKae(kgkKUcD36lls.NotebookApp, roI3spqORKae(ES5oEprVxulp(b'\t\xa3\xe2\xc1n|\xe5\x1f\x0b\x8a\xd1\x14\x8b;\xd1\x87a\xd7\x1c\x02\x81\x86'), chr(7427 - 7327) + chr(9002 - 8901) + '\143' + '\157' + chr(0b100110 + 0o76) + chr(0b1100101))(chr(117) + chr(0b10 + 0o162) + '\x66' + chr(0b111 + 0o46) + chr(56))), roI3spqORKae(ES5oEprVxulp(b'\x19\xb8\xed\xc7\x7fa\xe6\x05 \x8f'), '\x64' + chr(101) + '\143' + '\157' + chr(1514 - 1414) + chr(101))('\x75' + chr(4271 - 4155) + chr(102) + chr(0b101101) + '\070'), lambda bI5jsQ9OkQtj: nzTpIcepk0o8(chr(0b100010 + 0o16) + '\x6f' + chr(0b0 + 0o60), ord("\x08")))(roI3spqORKae(ES5oEprVxulp(b'\x00\xb9\xfc\xcc\x7fw\xe3\x08&\x8e\xc6\x1f'), '\x64' + '\x65' + chr(1417 - 1318) + chr(0b1101111) + chr(0b1100100) + chr(5969 - 5868))(chr(117) + '\x74' + '\x66' + chr(0b101101) + chr(0b111000))):
tOXcYdYc915w = nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b100110 + 0o12), 8)
if roI3spqORKae(ES5oEprVxulp(b'\r\xa8\xfe\xdc}w'), '\144' + '\x65' + chr(0b100001 + 0o102) + chr(0b1101111) + chr(0b1100100) + '\x65')('\165' + '\164' + '\x66' + '\x2d' + '\070') not in roI3spqORKae(roI3spqORKae(kgkKUcD36lls.NotebookApp, roI3spqORKae(ES5oEprVxulp(b"\x1e\xa3\xfe\xdbjv\xfe3'\x82\xc4\x0e\x832\xd3\x86"), '\x64' + chr(0b1100101) + chr(0b1100011) + chr(9655 - 9544) + '\144' + '\x65')('\x75' + '\164' + '\146' + chr(0b100 + 0o51) + '\x38')), roI3spqORKae(ES5oEprVxulp(b'\r\xa9\xf8'), '\x64' + chr(0b1100101) + chr(0b1100011) + '\x6f' + chr(0b1000000 + 0o44) + '\x65')(chr(0b1110101) + chr(0b1010000 + 0o44) + chr(2921 - 2819) + '\055' + '\070'), lambda zIqcgNgQ9U6F, U5tbVIuvdqYi: roI3spqORKae(ES5oEprVxulp(b''), '\144' + '\145' + chr(0b110111 + 0o54) + chr(4367 - 4256) + chr(0b1100100) + chr(4730 - 4629))(chr(0b111011 + 0o72) + '\164' + chr(0b1100000 + 0o6) + chr(0b100 + 0o51) + '\070'))(roI3spqORKae(ES5oEprVxulp(b'\t\xa3\xe2\xc1n|\xe5\x1f\x0b\x8d\xc3%\x993\xc1\x87]\xd1'), '\x64' + chr(0b1100101) + chr(99) + '\x6f' + '\144' + '\145')(chr(0b1110101) + chr(0b1110100) + '\146' + '\x2d' + '\070'), roI3spqORKae(ES5oEprVxulp(b''), chr(0b100001 + 0o103) + chr(0b1100101) + chr(4229 - 4130) + chr(0b110101 + 0o72) + chr(100) + '\145')(chr(0b1110101) + '\164' + '\146' + chr(1776 - 1731) + '\070')):
tOXcYdYc915w = nzTpIcepk0o8('\x30' + chr(0b1110 + 0o141) + chr(0b110000), 8)
if tOXcYdYc915w:
del kgkKUcD36lls[roI3spqORKae(ES5oEprVxulp(b'$\xa3\xf8\xd0i}\xfe\x07\x15\x97\xc0'), chr(0b1101 + 0o127) + chr(2277 - 2176) + chr(0b11000 + 0o113) + chr(5593 - 5482) + '\144' + chr(101))(chr(3720 - 3603) + chr(0b1110010 + 0o2) + '\x66' + chr(45) + chr(1197 - 1141))][roI3spqORKae(ES5oEprVxulp(b"\x1e\xa3\xfe\xdbjv\xfe3'\x82\xc4\x0e\x832\xd3\x86"), chr(100) + chr(2017 - 1916) + '\x63' + '\x6f' + '\144' + chr(2548 - 2447))(chr(117) + chr(116) + chr(4213 - 4111) + chr(45) + chr(0b11101 + 0o33))][roI3spqORKae(ES5oEprVxulp(b'\t\xa3\xe2\xc1n|\xe5\x1f\x0b\x8d\xc3%\x993\xc1\x87]\xd1'), chr(0b101111 + 0o65) + '\145' + chr(0b1010100 + 0o17) + '\x6f' + '\x64' + chr(0b1100101))(chr(8652 - 8535) + chr(12840 - 12724) + chr(0b1000011 + 0o43) + chr(0b1010 + 0o43) + chr(0b111000))]
del kgkKUcD36lls[roI3spqORKae(ES5oEprVxulp(b'$\xa3\xf8\xd0i}\xfe\x07\x15\x97\xc0'), chr(5219 - 5119) + '\x65' + chr(99) + chr(8930 - 8819) + chr(9882 - 9782) + chr(3347 - 3246))(chr(117) + chr(116) + '\146' + chr(0b100 + 0o51) + '\070')][roI3spqORKae(ES5oEprVxulp(b'\t\xa3\xe2\xc1n|\xe5\x1f\x0b\x8a\xd1\x14\x8b;\xd1\x87a\xd7\x1c\x02\x81\x86'), chr(0b11011 + 0o111) + '\145' + chr(6092 - 5993) + chr(0b1101111) + chr(0b110100 + 0o60) + chr(0b1010 + 0o133))(chr(0b1110101) + chr(13097 - 12981) + chr(102) + chr(0b101101) + chr(0b1 + 0o67))] |
klavinslab/coral | coral/analysis/utils.py | sequence_type | def sequence_type(seq):
'''Validates a coral.sequence data type.
:param sequence_in: input DNA sequence.
:type sequence_in: any
:returns: The material - 'dna', 'rna', or 'peptide'.
:rtype: str
:raises: ValueError
'''
if isinstance(seq, coral.DNA):
material = 'dna'
elif isinstance(seq, coral.RNA):
material = 'rna'
elif isinstance(seq, coral.Peptide):
material = 'peptide'
else:
raise ValueError('Input was not a recognized coral.sequence object.')
return material | python | def sequence_type(seq):
'''Validates a coral.sequence data type.
:param sequence_in: input DNA sequence.
:type sequence_in: any
:returns: The material - 'dna', 'rna', or 'peptide'.
:rtype: str
:raises: ValueError
'''
if isinstance(seq, coral.DNA):
material = 'dna'
elif isinstance(seq, coral.RNA):
material = 'rna'
elif isinstance(seq, coral.Peptide):
material = 'peptide'
else:
raise ValueError('Input was not a recognized coral.sequence object.')
return material | [
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/analysis/utils.py#L5-L23 | train | Validates a coral. sequence data type. Returns the material - dna rna or peptide. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b1101 + 0o43) + '\x6f' + '\x31' + '\060' + chr(0b110110), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(989 - 878) + chr(0b110011) + '\064' + chr(0b101000 + 0o17), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x31' + chr(53) + chr(0b110000), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(7644 - 7533) + '\x33' + chr(0b1110 + 0o43) + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(1306 - 1258) + chr(9271 - 9160) + '\x32' + chr(0b11011 + 0o26) + chr(0b10110 + 0o34), ord("\x08")), nzTpIcepk0o8(chr(0b10111 + 0o31) + '\157' + '\x33' + chr(49) + chr(1702 - 1650), 8), nzTpIcepk0o8(chr(1371 - 1323) + chr(111) + chr(1588 - 1538) + '\x31' + chr(49), 64632 - 64624), nzTpIcepk0o8(chr(48) + chr(111) + '\061' + chr(0b100111 + 0o20) + '\063', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(875 - 825) + chr(0b101101 + 0o6) + chr(0b100110 + 0o16), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(51) + chr(0b110001) + chr(0b111 + 0o57), 34978 - 34970), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\061' + chr(0b110 + 0o57) + chr(0b100101 + 0o15), 0b1000), nzTpIcepk0o8(chr(0b101001 + 0o7) + chr(111) + chr(0b110110) + '\062', ord("\x08")), nzTpIcepk0o8(chr(0b110000 + 0o0) + '\x6f' + chr(0b110011) + '\x33' + chr(50), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(1512 - 1463) + chr(0b11101 + 0o27) + chr(0b110101), 22830 - 22822), nzTpIcepk0o8(chr(1184 - 1136) + '\157' + chr(50) + chr(1835 - 1780) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110010) + chr(537 - 484) + '\065', 0o10), nzTpIcepk0o8(chr(1541 - 1493) + '\x6f' + chr(0b110001) + '\x30' + chr(1647 - 1599), ord("\x08")), nzTpIcepk0o8(chr(0b10110 + 0o32) + chr(111) + '\x32' + chr(0b10011 + 0o42) + '\x32', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x32' + chr(0b110010) + chr(0b110001), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110001) + chr(0b110111) + chr(0b110010), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(53) + '\x33', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b11101 + 0o31) + '\x31', 25585 - 25577), nzTpIcepk0o8(chr(0b1010 + 0o46) + '\x6f' + chr(0b110001) + chr(0b1101 + 0o52) + '\065', 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110001) + '\x30' + '\066', 8), nzTpIcepk0o8(chr(1708 - 1660) + chr(0b1000000 + 0o57) + chr(49) + chr(0b11011 + 0o30), 39433 - 39425), nzTpIcepk0o8('\x30' + chr(3655 - 3544) + '\x31' + '\x37' + chr(51), 8), nzTpIcepk0o8('\x30' + chr(111) + '\x33' + chr(49) + '\067', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110010) + chr(0b10011 + 0o36) + chr(53), 0b1000), nzTpIcepk0o8(chr(412 - 364) + chr(111) + '\x34' + chr(52), 24178 - 24170), nzTpIcepk0o8(chr(0b110000) + chr(0b110000 + 0o77) + chr(0b101010 + 0o11) + chr(0b11110 + 0o23) + chr(2384 - 2331), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b101100 + 0o103) + '\x33' + chr(54) + '\061', 61774 - 61766), nzTpIcepk0o8(chr(903 - 855) + chr(0b1101111) + chr(50) + '\x33' + '\x31', 25860 - 25852), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b10110 + 0o41) + chr(50), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(49) + chr(50) + chr(0b110101 + 0o1), 43389 - 43381), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b11100 + 0o25) + '\x36' + chr(0b10010 + 0o41), 32500 - 32492), nzTpIcepk0o8(chr(0b1110 + 0o42) + '\x6f' + chr(49) + chr(0b1111 + 0o47) + chr(642 - 593), 0b1000), nzTpIcepk0o8(chr(1436 - 1388) + chr(111) + chr(0b110001) + chr(1020 - 969) + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(2187 - 2076) + chr(0b110010) + '\064' + chr(49), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\062' + chr(684 - 631) + '\062', 8), nzTpIcepk0o8(chr(48) + '\x6f' + chr(51) + chr(90 - 37) + chr(320 - 272), 51265 - 51257)][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + chr(1784 - 1673) + '\x35' + chr(0b100001 + 0o17), 41056 - 41048)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'h'), chr(6269 - 6169) + '\x65' + '\143' + '\x6f' + chr(0b1100100) + chr(101))(chr(8789 - 8672) + '\x74' + '\146' + chr(1701 - 1656) + chr(0b100 + 0o64)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def sgqfshs0FZxF(ftk9lc7G5FOo):
if suIjIS24Zkqw(ftk9lc7G5FOo, roI3spqORKae(_bFWSozA7z0G, roI3spqORKae(ES5oEprVxulp(b'\x02\xa9)'), chr(8348 - 8248) + chr(7952 - 7851) + '\x63' + chr(0b110000 + 0o77) + chr(8350 - 8250) + chr(9869 - 9768))('\x75' + chr(0b1001001 + 0o53) + chr(0b11 + 0o143) + chr(683 - 638) + '\070'))):
P6MCancmTVIW = roI3spqORKae(ES5oEprVxulp(b'"\x89\t'), '\144' + chr(0b101011 + 0o72) + chr(0b1100011) + chr(0b1101000 + 0o7) + chr(0b10000 + 0o124) + chr(0b101 + 0o140))(chr(0b1110001 + 0o4) + chr(436 - 320) + chr(0b1100110) + '\055' + chr(0b10010 + 0o46))
elif suIjIS24Zkqw(ftk9lc7G5FOo, roI3spqORKae(_bFWSozA7z0G, roI3spqORKae(ES5oEprVxulp(b'\x14\xa9)'), chr(100) + chr(101) + '\x63' + chr(0b1101111) + '\144' + chr(0b10001 + 0o124))(chr(0b1101111 + 0o6) + chr(6766 - 6650) + chr(0b1010111 + 0o17) + chr(0b11101 + 0o20) + '\x38'))):
P6MCancmTVIW = roI3spqORKae(ES5oEprVxulp(b'4\x89\t'), '\x64' + chr(101) + '\x63' + chr(0b1101111) + chr(100) + '\x65')(chr(7659 - 7542) + chr(0b1000010 + 0o62) + chr(3575 - 3473) + chr(936 - 891) + chr(0b110111 + 0o1))
elif suIjIS24Zkqw(ftk9lc7G5FOo, roI3spqORKae(_bFWSozA7z0G, roI3spqORKae(ES5oEprVxulp(b'\x16\x82\x18\xb8\xe3\xa8\xec'), chr(6114 - 6014) + chr(7863 - 7762) + '\x63' + chr(0b1101111) + '\144' + chr(8458 - 8357))('\x75' + chr(0b1110100) + chr(0b111101 + 0o51) + chr(0b1001 + 0o44) + chr(0b111000)))):
P6MCancmTVIW = roI3spqORKae(ES5oEprVxulp(b'6\x82\x18\xb8\xe3\xa8\xec'), chr(100) + chr(101) + chr(0b1100011) + chr(0b1010011 + 0o34) + chr(0b1100100) + chr(1221 - 1120))(chr(117) + '\x74' + '\x66' + chr(494 - 449) + '\x38')
else:
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'\x0f\x89\x18\xb9\xfe\xec\xfe\x1a\xef\xee\x04]\xaeE\xdd\x8d2\xcf\xf2\x15L_\x14<n\x1f\xef\xeeK\xbf\x90\xf5\x14%\x16\x00*\xc4\xc4\x8b#\xc7\x07\xae\xe0\xa9\xea\x0f\xb2'), chr(0b1100100) + chr(0b110101 + 0o60) + '\x63' + chr(0b100100 + 0o113) + '\144' + '\x65')(chr(6457 - 6340) + chr(116) + '\x66' + chr(45) + chr(56)))
return P6MCancmTVIW |
klavinslab/coral | coral/reaction/_pcr.py | pcr | def pcr(template, primer1, primer2, min_tm=50.0, min_primer_len=14):
'''Simulate a PCR.
:param template: DNA template from which to PCR.
:type template: coral.DNA
:param primer1: First PCR primer.
:type primer1: coral.Primer
:param primer2: First PCR primer.
:type primer2: coral.Primer
:param min_tm: Minimum melting temperature (Tm) at which primers must bind
to the template.
:type min_tm: float
:param min_primer_len: Minimum amount of template homology required at the
3' end of each primer.
:type min_primer_len: int
:returns: A dsDNA Amplicon.
:rtype: coral.DNA
:raises: PrimingError if a primer binds more than once on the template,
primers bind in overlapping sequence of the template, there are no
forward primer binding sites or reverse priming sites, or if the
PCR would work only on a circular version of the template (if
template is linear).
'''
# Find match in top or bottom strands for each primer
p1_matches = coral.analysis.anneal(template, primer1, min_tm=min_tm,
min_len=min_primer_len)
p2_matches = coral.analysis.anneal(template, primer2, min_tm=min_tm,
min_len=min_primer_len)
p1_binding_locations = [m[0] for strand in p1_matches for m in strand]
p2_binding_locations = [m[0] for strand in p2_matches for m in strand]
# Ensure unique top and bottom matches
if len(p1_binding_locations) > 1:
primer_msg = 'Multiple primer 1 binding locations: {}'
raise PrimingError(primer_msg.format(p1_binding_locations))
if len(p2_binding_locations) > 1:
primer_msg = 'Multiple primer 2 binding locations: {}'
raise PrimingError(primer_msg.format(p2_binding_locations))
if not p1_binding_locations and not p2_binding_locations:
raise PrimingError('Neither primer binds the template')
if not p1_binding_locations:
raise PrimingError('Primer 1 does not bind the template')
if not p2_binding_locations:
raise PrimingError('Primer 2 does not bind the template')
# Check that primers bind on opposite strands of the template
tops = p1_matches[0] + p2_matches[0]
bottoms = p1_matches[1] + p2_matches[1]
if not tops:
raise PrimingError('No primers bind the template\'s top strand.')
if not bottoms:
raise PrimingError('No primers bind the template\'s bottom strand.')
# Figure out which primer matches the top strand
if p1_matches[0]:
# primer1 is top
fwd = primer1
rev = primer2
else:
# primer2 matches top strand
fwd = primer2
rev = primer1
# Now we can simulate the PCR. If primer locations are overlapping, we
# throw an error. If the primers won't amplify a product (e.g. a linear
# template with primers facing away from one another), throw a different
# error. Otherwise, amplify the product, including any overhangs.
# 3' locations, annealing region length
fwd_3, fwd_len = tops[0]
rev_3, rev_len = bottoms[0]
# 5' locations
fwd_5 = fwd_3 - fwd_len
rev_5 = rev_3 - rev_len
# location on the top strand where the 'reverse' primer ends (its 3' end)
rev_3_top = len(template) - rev_3
rev_5_top = len(template) - rev_5
# TODO: Use % operator?
if rev_5_top > len(template):
rev_5_top = rev_5_top - len(template)
# overhangs
fwd_overhang = fwd.primer()[:-fwd_len]
rev_overhang = rev.primer()[:-rev_len]
# TODO: what about searching substrings over circulate templates?
# Cases:
# 1) Primers point towards one another - overlapping is fine
# -> isolate region between 5' annealing regions and tack on the
# rest of the overhang.
# 2) Primers point away from one another, template is linear
# -> error
# 3) Primers point away from one another, template is circular
# a) Primers don't overlap
# -> rotate to 'top' primer start, extract sequence
# b) Primers overlap
# -> Extract whole sequence as linear fragment, tack on rest of
# 'bottom' primer. May disrupt features.
if template.circular:
# Circular template - primers always point towards one another
if rev_3_top > fwd_3:
# Inter-primer region doesn't go over the origin (index 0)
# However, the 'anneal' region may extend over it.
# FIXME: handle case where 'anneal' region extends over origin
# FIXME: simplify - just generate 'before' and 'after', then
# combine with preamplicon later
if rev_3_top + rev_len > len(template):
# Reverse primer extends over the origin
if fwd_5 - fwd_len < 0:
# Forward primer extends over the origin
preamplicon = template.linearize()
# Add extra anneal regions
before = template[fwd_5:]
after = template[:rev_5_top]
preamplicon = before + preamplicon + after
else:
# Only the reverse primer extends over the origin
preamplicon = template[fwd_5:]
after = template[:rev_5_top]
preamplicon = preamplicon + after
elif fwd_5 - fwd_len < 0:
# Only the forward primer extends over the origin
before = template[fwd_5:]
preamplicon = before + template[:rev_5_top]
else:
# Extract like normal
preamplicon = template[fwd_5:len(template) - rev_5]
else:
# Inter-primer region goes over the origin (index 0)
preamplicon_len = len(template) - fwd_5 + rev_5_top
preamplicon = template.rotate(-fwd_5)[:preamplicon_len]
else:
# Linear template
if rev_3_top < fwd_5 or fwd_3 > rev_5_top:
# Primers point away from one another.
raise PrimingError('Primers point away from one another.')
else:
# Primers point towards each other.
preamplicon = template[fwd_5:len(template) - rev_5]
# Add overhangs
amplicon = (fwd_overhang.to_ds() +
preamplicon +
rev_overhang.to_ds().reverse_complement())
return amplicon | python | def pcr(template, primer1, primer2, min_tm=50.0, min_primer_len=14):
'''Simulate a PCR.
:param template: DNA template from which to PCR.
:type template: coral.DNA
:param primer1: First PCR primer.
:type primer1: coral.Primer
:param primer2: First PCR primer.
:type primer2: coral.Primer
:param min_tm: Minimum melting temperature (Tm) at which primers must bind
to the template.
:type min_tm: float
:param min_primer_len: Minimum amount of template homology required at the
3' end of each primer.
:type min_primer_len: int
:returns: A dsDNA Amplicon.
:rtype: coral.DNA
:raises: PrimingError if a primer binds more than once on the template,
primers bind in overlapping sequence of the template, there are no
forward primer binding sites or reverse priming sites, or if the
PCR would work only on a circular version of the template (if
template is linear).
'''
# Find match in top or bottom strands for each primer
p1_matches = coral.analysis.anneal(template, primer1, min_tm=min_tm,
min_len=min_primer_len)
p2_matches = coral.analysis.anneal(template, primer2, min_tm=min_tm,
min_len=min_primer_len)
p1_binding_locations = [m[0] for strand in p1_matches for m in strand]
p2_binding_locations = [m[0] for strand in p2_matches for m in strand]
# Ensure unique top and bottom matches
if len(p1_binding_locations) > 1:
primer_msg = 'Multiple primer 1 binding locations: {}'
raise PrimingError(primer_msg.format(p1_binding_locations))
if len(p2_binding_locations) > 1:
primer_msg = 'Multiple primer 2 binding locations: {}'
raise PrimingError(primer_msg.format(p2_binding_locations))
if not p1_binding_locations and not p2_binding_locations:
raise PrimingError('Neither primer binds the template')
if not p1_binding_locations:
raise PrimingError('Primer 1 does not bind the template')
if not p2_binding_locations:
raise PrimingError('Primer 2 does not bind the template')
# Check that primers bind on opposite strands of the template
tops = p1_matches[0] + p2_matches[0]
bottoms = p1_matches[1] + p2_matches[1]
if not tops:
raise PrimingError('No primers bind the template\'s top strand.')
if not bottoms:
raise PrimingError('No primers bind the template\'s bottom strand.')
# Figure out which primer matches the top strand
if p1_matches[0]:
# primer1 is top
fwd = primer1
rev = primer2
else:
# primer2 matches top strand
fwd = primer2
rev = primer1
# Now we can simulate the PCR. If primer locations are overlapping, we
# throw an error. If the primers won't amplify a product (e.g. a linear
# template with primers facing away from one another), throw a different
# error. Otherwise, amplify the product, including any overhangs.
# 3' locations, annealing region length
fwd_3, fwd_len = tops[0]
rev_3, rev_len = bottoms[0]
# 5' locations
fwd_5 = fwd_3 - fwd_len
rev_5 = rev_3 - rev_len
# location on the top strand where the 'reverse' primer ends (its 3' end)
rev_3_top = len(template) - rev_3
rev_5_top = len(template) - rev_5
# TODO: Use % operator?
if rev_5_top > len(template):
rev_5_top = rev_5_top - len(template)
# overhangs
fwd_overhang = fwd.primer()[:-fwd_len]
rev_overhang = rev.primer()[:-rev_len]
# TODO: what about searching substrings over circulate templates?
# Cases:
# 1) Primers point towards one another - overlapping is fine
# -> isolate region between 5' annealing regions and tack on the
# rest of the overhang.
# 2) Primers point away from one another, template is linear
# -> error
# 3) Primers point away from one another, template is circular
# a) Primers don't overlap
# -> rotate to 'top' primer start, extract sequence
# b) Primers overlap
# -> Extract whole sequence as linear fragment, tack on rest of
# 'bottom' primer. May disrupt features.
if template.circular:
# Circular template - primers always point towards one another
if rev_3_top > fwd_3:
# Inter-primer region doesn't go over the origin (index 0)
# However, the 'anneal' region may extend over it.
# FIXME: handle case where 'anneal' region extends over origin
# FIXME: simplify - just generate 'before' and 'after', then
# combine with preamplicon later
if rev_3_top + rev_len > len(template):
# Reverse primer extends over the origin
if fwd_5 - fwd_len < 0:
# Forward primer extends over the origin
preamplicon = template.linearize()
# Add extra anneal regions
before = template[fwd_5:]
after = template[:rev_5_top]
preamplicon = before + preamplicon + after
else:
# Only the reverse primer extends over the origin
preamplicon = template[fwd_5:]
after = template[:rev_5_top]
preamplicon = preamplicon + after
elif fwd_5 - fwd_len < 0:
# Only the forward primer extends over the origin
before = template[fwd_5:]
preamplicon = before + template[:rev_5_top]
else:
# Extract like normal
preamplicon = template[fwd_5:len(template) - rev_5]
else:
# Inter-primer region goes over the origin (index 0)
preamplicon_len = len(template) - fwd_5 + rev_5_top
preamplicon = template.rotate(-fwd_5)[:preamplicon_len]
else:
# Linear template
if rev_3_top < fwd_5 or fwd_3 > rev_5_top:
# Primers point away from one another.
raise PrimingError('Primers point away from one another.')
else:
# Primers point towards each other.
preamplicon = template[fwd_5:len(template) - rev_5]
# Add overhangs
amplicon = (fwd_overhang.to_ds() +
preamplicon +
rev_overhang.to_ds().reverse_complement())
return amplicon | [
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"primer2",
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"min_tm",
"=",
"50.0",
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"# Find match in top or bottom strands for each primer",
"p1_matches",
"=",
"coral",
".",
"analysis",
".",
"anneal",
"(",
"temp... | Simulate a PCR.
:param template: DNA template from which to PCR.
:type template: coral.DNA
:param primer1: First PCR primer.
:type primer1: coral.Primer
:param primer2: First PCR primer.
:type primer2: coral.Primer
:param min_tm: Minimum melting temperature (Tm) at which primers must bind
to the template.
:type min_tm: float
:param min_primer_len: Minimum amount of template homology required at the
3' end of each primer.
:type min_primer_len: int
:returns: A dsDNA Amplicon.
:rtype: coral.DNA
:raises: PrimingError if a primer binds more than once on the template,
primers bind in overlapping sequence of the template, there are no
forward primer binding sites or reverse priming sites, or if the
PCR would work only on a circular version of the template (if
template is linear). | [
"Simulate",
"a",
"PCR",
"."
] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/reaction/_pcr.py#L9-L161 | train | Simulate a PCR. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(974 - 926) + chr(0b1101111) + chr(0b110011) + chr(0b110101 + 0o1) + '\x35', 51354 - 51346), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x33' + chr(0b110001 + 0o6) + chr(0b100000 + 0o24), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(51) + chr(243 - 192), 0o10), nzTpIcepk0o8(chr(0b10011 + 0o35) + chr(0b1000011 + 0o54) + chr(52) + '\062', 0o10), nzTpIcepk0o8('\060' + chr(0b111110 + 0o61) + chr(2214 - 2165) + '\x37', ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110001) + chr(0b110010) + '\x33', 62156 - 62148), nzTpIcepk0o8(chr(2134 - 2086) + '\x6f' + chr(0b110010 + 0o0) + '\x30' + '\x32', 41577 - 41569), nzTpIcepk0o8(chr(0b1010 + 0o46) + '\157' + '\x31' + chr(752 - 703), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110110) + chr(828 - 779), 0o10), nzTpIcepk0o8(chr(401 - 353) + chr(6492 - 6381) + chr(0b1000 + 0o52) + chr(0b110111) + chr(49), 0o10), nzTpIcepk0o8(chr(1380 - 1332) + chr(111) + chr(50) + '\066' + chr(0b110111), 27805 - 27797), nzTpIcepk0o8(chr(48) + chr(0b1101101 + 0o2) + chr(0b110111) + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(989 - 941) + chr(111) + chr(0b1000 + 0o51) + chr(0b100000 + 0o21) + chr(0b11 + 0o56), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + '\x33' + '\062' + chr(808 - 754), 0o10), nzTpIcepk0o8(chr(637 - 589) + '\157' + chr(0b11010 + 0o30) + chr(50) + chr(280 - 227), 46070 - 46062), nzTpIcepk0o8(chr(0b110000) + chr(0b11001 + 0o126) + '\x31' + chr(0b110101) + chr(0b10000 + 0o40), 0b1000), nzTpIcepk0o8('\x30' + chr(0b10110 + 0o131) + chr(2271 - 2221) + '\x30' + '\x37', 17418 - 17410), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(51) + chr(0b110000 + 0o5) + '\x33', 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b100110 + 0o15) + '\062' + chr(2639 - 2586), ord("\x08")), nzTpIcepk0o8(chr(0b100010 + 0o16) + '\x6f' + chr(0b101110 + 0o5) + chr(1343 - 1295) + chr(0b110101), 26149 - 26141), nzTpIcepk0o8(chr(991 - 943) + '\x6f' + chr(0b110001) + chr(51) + chr(2428 - 2376), 419 - 411), nzTpIcepk0o8(chr(48) + chr(9479 - 9368) + chr(0b1011 + 0o46) + '\066', 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(49) + chr(2311 - 2261) + chr(53), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(10897 - 10786) + chr(0b110011), 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(797 - 744) + chr(415 - 360), 24484 - 24476), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110001) + '\067' + chr(50), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + '\062' + chr(0b100011 + 0o22) + chr(0b100101 + 0o20), 57316 - 57308), nzTpIcepk0o8('\x30' + chr(868 - 757) + chr(0b1110 + 0o46) + chr(459 - 409), 8), nzTpIcepk0o8(chr(0b110000) + chr(3274 - 3163) + '\x34' + '\x35', 55128 - 55120), nzTpIcepk0o8('\x30' + chr(111) + '\x32' + '\061' + '\x33', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1000100 + 0o53) + chr(838 - 788) + '\064' + chr(0b1001 + 0o52), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(50) + '\063' + chr(0b110011), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(50) + '\061' + chr(0b101111 + 0o4), 8), nzTpIcepk0o8(chr(48) + chr(0b1100110 + 0o11) + '\x32' + chr(48), 0o10), nzTpIcepk0o8(chr(1413 - 1365) + chr(11190 - 11079) + chr(0b110111) + chr(1679 - 1625), ord("\x08")), nzTpIcepk0o8(chr(55 - 7) + chr(2028 - 1917) + chr(0b10101 + 0o36) + chr(0b110110) + chr(851 - 798), 8), nzTpIcepk0o8(chr(1091 - 1043) + chr(0b1101111) + chr(152 - 103) + '\x36' + chr(106 - 58), ord("\x08")), nzTpIcepk0o8(chr(0b10101 + 0o33) + '\157' + chr(0b11011 + 0o27) + chr(52) + '\064', 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(49) + chr(0b110011) + chr(0b100101 + 0o21), 0b1000), nzTpIcepk0o8(chr(1357 - 1309) + chr(111) + chr(1267 - 1212) + '\061', 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + chr(0b1001010 + 0o45) + chr(207 - 154) + '\x30', 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xdb'), '\x64' + chr(0b1100101) + '\143' + chr(2359 - 2248) + '\144' + chr(5383 - 5282))(chr(117) + '\x74' + chr(0b11111 + 0o107) + chr(0b101101) + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def s0cavndkPfj6(Pe8smzX7Gsur, QEHoVbpEj8nx, PG1U_Og1H3qR, _xMdwXUWHWlj=50.0, N_uoyLD6y7xr=nzTpIcepk0o8(chr(0b110000) + chr(1825 - 1714) + chr(49) + chr(0b110110), 8)):
r62uiW4NAbW9 = _bFWSozA7z0G.analysis.anneal(Pe8smzX7Gsur, QEHoVbpEj8nx, min_tm=_xMdwXUWHWlj, min_len=N_uoyLD6y7xr)
pgnbestRHt1O = _bFWSozA7z0G.analysis.anneal(Pe8smzX7Gsur, PG1U_Og1H3qR, min_tm=_xMdwXUWHWlj, min_len=N_uoyLD6y7xr)
fS1sbOg_FE57 = [tF75nqoNENFL[nzTpIcepk0o8('\060' + chr(0b1101111) + '\060', ord("\x08"))] for sOvPdpw6JkD6 in r62uiW4NAbW9 for tF75nqoNENFL in sOvPdpw6JkD6]
lnKjRro3MWpZ = [tF75nqoNENFL[nzTpIcepk0o8('\x30' + chr(111) + chr(0b1000 + 0o50), 8)] for sOvPdpw6JkD6 in pgnbestRHt1O for tF75nqoNENFL in sOvPdpw6JkD6]
if ftfygxgFas5X(fS1sbOg_FE57) > nzTpIcepk0o8(chr(1678 - 1630) + chr(0b1101111) + chr(0b1000 + 0o51), 0b1000):
W8oPIVPwtc2W = roI3spqORKae(ES5oEprVxulp(b'\xb8\x89wVf#\xeel\x11\xc9\xc5U$\xb3\xe7H\xb6\xcb\xb7\xac2j<mHZ\xc1MF\xea\xd7\xf2\xe4~M\xcfP\xdf#'), chr(100) + chr(101) + chr(0b1100011) + '\157' + '\144' + chr(101))(chr(117) + chr(0b1011 + 0o151) + chr(0b1010 + 0o134) + chr(0b101101) + '\x38')
raise aBVfwyHamCon(roI3spqORKae(W8oPIVPwtc2W, roI3spqORKae(ES5oEprVxulp(b'\x84\xcf(iH`\xe4f`\xe6\xf4v'), chr(100) + '\x65' + '\x63' + '\157' + '\144' + chr(0b1100101))(chr(0b1110101) + chr(0b1010011 + 0o41) + chr(0b1100110) + '\055' + '\070'))(fS1sbOg_FE57))
if ftfygxgFas5X(lnKjRro3MWpZ) > nzTpIcepk0o8(chr(0b110000) + chr(0b1000000 + 0o57) + chr(0b110001), 8):
W8oPIVPwtc2W = roI3spqORKae(ES5oEprVxulp(b'\xb8\x89wVf#\xeel\x11\xc9\xc5U$\xb3\xe7H\xb5\xcb\xb7\xac2j<mHZ\xc1MF\xea\xd7\xf2\xe4~M\xcfP\xdf#'), '\x64' + '\x65' + chr(4500 - 4401) + chr(6636 - 6525) + '\x64' + chr(0b1100101))('\165' + '\164' + chr(102) + chr(0b101101) + chr(0b100000 + 0o30))
raise aBVfwyHamCon(roI3spqORKae(W8oPIVPwtc2W, roI3spqORKae(ES5oEprVxulp(b'\x84\xcf(iH`\xe4f`\xe6\xf4v'), chr(0b1100100) + '\145' + chr(4272 - 4173) + chr(111) + chr(0b100 + 0o140) + chr(8857 - 8756))(chr(0b1110101) + '\x74' + '\146' + chr(45) + chr(56)))(lnKjRro3MWpZ))
if not fS1sbOg_FE57 and (not lnKjRro3MWpZ):
raise aBVfwyHamCon(roI3spqORKae(ES5oEprVxulp(b'\xbb\x99rVg6\xf0)A\xcb\xdeQ,\xa4\xb5\n\xee\x85\xb1\xb6|z=f\x0f\x0e\xc8OU\xe7\xc2\xef\xee'), '\144' + chr(101) + '\x63' + chr(0b1000100 + 0o53) + chr(100) + '\x65')('\165' + '\x74' + chr(102) + '\055' + '\x38'))
if not fS1sbOg_FE57:
raise aBVfwyHamCon(roI3spqORKae(ES5oEprVxulp(b'\xa5\x8erOj!\xa28\x11\xdd\xd8Y:\xf6\xfb\x07\xf3\xcb\xb7\xac2juwG\x1f\x8dV@\xe6\xd3\xf7\xead['), chr(0b10 + 0o142) + '\x65' + chr(0b101 + 0o136) + chr(7018 - 6907) + chr(4334 - 4234) + chr(101))('\x75' + chr(0b1001111 + 0o45) + chr(0b1010100 + 0o22) + chr(0b101101) + chr(56)))
if not lnKjRro3MWpZ:
raise aBVfwyHamCon(roI3spqORKae(ES5oEprVxulp(b'\xa5\x8erOj!\xa2;\x11\xdd\xd8Y:\xf6\xfb\x07\xf3\xcb\xb7\xac2juwG\x1f\x8dV@\xe6\xd3\xf7\xead['), chr(100) + '\x65' + '\143' + chr(0b1101111) + chr(0b1100100) + chr(0b1100101))('\x75' + chr(116) + chr(102) + chr(0b101101) + chr(0b1 + 0o67)))
DOgyC50tt5XW = r62uiW4NAbW9[nzTpIcepk0o8(chr(809 - 761) + chr(9029 - 8918) + chr(0b110000), 8)] + pgnbestRHt1O[nzTpIcepk0o8('\x30' + '\157' + chr(71 - 23), 8)]
VD7VwQ7fTAYZ = r62uiW4NAbW9[nzTpIcepk0o8(chr(0b1110 + 0o42) + chr(111) + '\061', 8)] + pgnbestRHt1O[nzTpIcepk0o8(chr(2073 - 2025) + chr(0b1101111) + '\x31', 8)]
if not DOgyC50tt5XW:
raise aBVfwyHamCon(roI3spqORKae(ES5oEprVxulp(b'\xbb\x93;R}:\xeflC\xca\x97^ \xb8\xf1H\xf3\x83\xb0\xe5(k8sC\x1b\xd9G\x02\xf8\x83\xef\xe4`\x1e\x86\x04\xd6?W\x91\xd2'), '\x64' + '\x65' + '\x63' + '\x6f' + chr(4009 - 3909) + '\145')('\165' + chr(116) + '\146' + '\055' + chr(56)))
if not VD7VwQ7fTAYZ:
raise aBVfwyHamCon(roI3spqORKae(ES5oEprVxulp(b'\xbb\x93;R}:\xeflC\xca\x97^ \xb8\xf1H\xf3\x83\xb0\xe5(k8sC\x1b\xd9G\x02\xf8\x83\xf9\xe4dJ\x9a\x1d\x84-M\x87\x9duF!'), chr(346 - 246) + '\x65' + chr(0b11011 + 0o110) + '\x6f' + '\x64' + chr(8428 - 8327))('\165' + chr(116) + chr(102) + chr(0b101010 + 0o3) + chr(0b111000)))
if r62uiW4NAbW9[nzTpIcepk0o8(chr(0b110000) + chr(2001 - 1890) + chr(0b110000), 8)]:
f6ucHbZL4GdI = QEHoVbpEj8nx
dizdA8h9BTE_ = PG1U_Og1H3qR
else:
f6ucHbZL4GdI = PG1U_Og1H3qR
dizdA8h9BTE_ = QEHoVbpEj8nx
(ITrXoJDrmnFD, S8Y2CJk47RdA) = DOgyC50tt5XW[nzTpIcepk0o8('\060' + chr(0b1101111) + '\x30', 8)]
(tfM98wCHo1NA, aSBObqkJ4htr) = VD7VwQ7fTAYZ[nzTpIcepk0o8(chr(48) + chr(0b1001111 + 0o40) + '\060', 8)]
jRWbzzeatuPB = ITrXoJDrmnFD - S8Y2CJk47RdA
QRREY9FCiKOo = tfM98wCHo1NA - aSBObqkJ4htr
t50e_0QPgXW3 = ftfygxgFas5X(Pe8smzX7Gsur) - tfM98wCHo1NA
VPTgxpWILZhU = ftfygxgFas5X(Pe8smzX7Gsur) - QRREY9FCiKOo
if VPTgxpWILZhU > ftfygxgFas5X(Pe8smzX7Gsur):
VPTgxpWILZhU = VPTgxpWILZhU - ftfygxgFas5X(Pe8smzX7Gsur)
mlwSKwkTxZBP = f6ucHbZL4GdI.primer()[:-S8Y2CJk47RdA]
VU2zc5rCdloJ = dizdA8h9BTE_.primer()[:-aSBObqkJ4htr]
if roI3spqORKae(Pe8smzX7Gsur, roI3spqORKae(ES5oEprVxulp(b'\x96\x95iAz?\xe3{'), '\144' + '\145' + '\x63' + '\157' + chr(0b1100100) + '\145')(chr(117) + '\164' + chr(0b11101 + 0o111) + chr(0b11100 + 0o21) + '\070')):
if t50e_0QPgXW3 > ITrXoJDrmnFD:
if t50e_0QPgXW3 + aSBObqkJ4htr > ftfygxgFas5X(Pe8smzX7Gsur):
if jRWbzzeatuPB - S8Y2CJk47RdA < nzTpIcepk0o8(chr(144 - 96) + chr(0b1101111) + '\x30', 8):
KelKHnfKg55t = Pe8smzX7Gsur.linearize()
OsFA8mB0ZwJd = Pe8smzX7Gsur[jRWbzzeatuPB:]
mar_kHe1Xspp = Pe8smzX7Gsur[:VPTgxpWILZhU]
KelKHnfKg55t = OsFA8mB0ZwJd + KelKHnfKg55t + mar_kHe1Xspp
else:
KelKHnfKg55t = Pe8smzX7Gsur[jRWbzzeatuPB:]
mar_kHe1Xspp = Pe8smzX7Gsur[:VPTgxpWILZhU]
KelKHnfKg55t = KelKHnfKg55t + mar_kHe1Xspp
elif jRWbzzeatuPB - S8Y2CJk47RdA < nzTpIcepk0o8('\x30' + chr(111) + chr(0b1101 + 0o43), 8):
OsFA8mB0ZwJd = Pe8smzX7Gsur[jRWbzzeatuPB:]
KelKHnfKg55t = OsFA8mB0ZwJd + Pe8smzX7Gsur[:VPTgxpWILZhU]
else:
KelKHnfKg55t = Pe8smzX7Gsur[jRWbzzeatuPB:ftfygxgFas5X(Pe8smzX7Gsur) - QRREY9FCiKOo]
else:
d5Ub2h9S4rjj = ftfygxgFas5X(Pe8smzX7Gsur) - jRWbzzeatuPB + VPTgxpWILZhU
KelKHnfKg55t = Pe8smzX7Gsur.rotate(-jRWbzzeatuPB)[:d5Ub2h9S4rjj]
elif t50e_0QPgXW3 < jRWbzzeatuPB or ITrXoJDrmnFD > VPTgxpWILZhU:
raise aBVfwyHamCon(roI3spqORKae(ES5oEprVxulp(b'\xa5\x8erOj!\xf1)A\xd6\xdeR=\xf6\xf4\x1f\xe6\x92\xf5\xa3.a8#@\x14\xc8\x02D\xe5\xcc\xef\xe3uL\xdb'), '\x64' + '\x65' + chr(0b1100011) + chr(7461 - 7350) + chr(0b1100100) + chr(0b11011 + 0o112))(chr(0b1110101) + chr(0b1011001 + 0o33) + chr(102) + chr(726 - 681) + '\070'))
else:
KelKHnfKg55t = Pe8smzX7Gsur[jRWbzzeatuPB:ftfygxgFas5X(Pe8smzX7Gsur) - QRREY9FCiKOo]
BTiGDmDJ_m5N = mlwSKwkTxZBP.to_ds() + KelKHnfKg55t + VU2zc5rCdloJ.to_ds().reverse_complement()
return BTiGDmDJ_m5N |
klavinslab/coral | coral/reaction/_restriction.py | digest | def digest(dna, restriction_enzyme):
'''Restriction endonuclease reaction.
:param dna: DNA template to digest.
:type dna: coral.DNA
:param restriction_site: Restriction site to use.
:type restriction_site: RestrictionSite
:returns: list of digested DNA fragments.
:rtype: coral.DNA list
'''
pattern = restriction_enzyme.recognition_site
located = dna.locate(pattern)
if not located[0] and not located[1]:
return [dna]
# Bottom strand indices are relative to the bottom strand 5' end.
# Convert to same type as top strand
pattern_len = len(pattern)
r_indices = [len(dna) - index - pattern_len for index in
located[1]]
# If sequence is palindrome, remove redundant results
if pattern.is_palindrome():
r_indices = [index for index in r_indices if index not in
located[0]]
# Flatten cut site indices
cut_sites = sorted(located[0] + r_indices)
# Go through each cut site starting at highest one
# Cut remaining template once, generating remaining + new
current = [dna]
for cut_site in cut_sites[::-1]:
new = _cut(current, cut_site, restriction_enzyme)
current.append(new[1])
current.append(new[0])
current.reverse()
# Combine first and last back together if digest was circular
if dna.circular:
current[0] = current.pop() + current[0]
return current | python | def digest(dna, restriction_enzyme):
'''Restriction endonuclease reaction.
:param dna: DNA template to digest.
:type dna: coral.DNA
:param restriction_site: Restriction site to use.
:type restriction_site: RestrictionSite
:returns: list of digested DNA fragments.
:rtype: coral.DNA list
'''
pattern = restriction_enzyme.recognition_site
located = dna.locate(pattern)
if not located[0] and not located[1]:
return [dna]
# Bottom strand indices are relative to the bottom strand 5' end.
# Convert to same type as top strand
pattern_len = len(pattern)
r_indices = [len(dna) - index - pattern_len for index in
located[1]]
# If sequence is palindrome, remove redundant results
if pattern.is_palindrome():
r_indices = [index for index in r_indices if index not in
located[0]]
# Flatten cut site indices
cut_sites = sorted(located[0] + r_indices)
# Go through each cut site starting at highest one
# Cut remaining template once, generating remaining + new
current = [dna]
for cut_site in cut_sites[::-1]:
new = _cut(current, cut_site, restriction_enzyme)
current.append(new[1])
current.append(new[0])
current.reverse()
# Combine first and last back together if digest was circular
if dna.circular:
current[0] = current.pop() + current[0]
return current | [
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"[",... | Restriction endonuclease reaction.
:param dna: DNA template to digest.
:type dna: coral.DNA
:param restriction_site: Restriction site to use.
:type restriction_site: RestrictionSite
:returns: list of digested DNA fragments.
:rtype: coral.DNA list | [
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"endonuclease",
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/reaction/_restriction.py#L5-L42 | train | Given a DNA template and a restriction endonuclease reaction return a list of digested DNA fragments. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(243 - 195) + chr(0b1101000 + 0o7) + chr(50) + '\066' + chr(765 - 710), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1001001 + 0o46) + '\061' + chr(0b10000 + 0o41) + '\x33', 0b1000), nzTpIcepk0o8(chr(0b10000 + 0o40) + chr(111) + chr(0b110100) + '\060', 0o10), nzTpIcepk0o8(chr(0b11110 + 0o22) + '\x6f' + chr(813 - 763) + chr(2339 - 2284) + chr(1415 - 1360), 0o10), nzTpIcepk0o8(chr(0b100111 + 0o11) + '\157' + chr(2907 - 2852) + chr(0b110010 + 0o5), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x31' + '\x35' + chr(0b110110), 0b1000), nzTpIcepk0o8('\060' + chr(2581 - 2470) + chr(79 - 30) + chr(53) + '\064', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1011111 + 0o20) + chr(50) + chr(52), 21967 - 21959), nzTpIcepk0o8(chr(2237 - 2189) + chr(111) + '\065' + chr(49), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110011) + chr(51) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x33' + '\065' + chr(0b110000), 0b1000), nzTpIcepk0o8(chr(1703 - 1655) + chr(0b111100 + 0o63) + chr(0b1100 + 0o46) + chr(49) + '\x34', 57824 - 57816), nzTpIcepk0o8('\x30' + chr(0b1100110 + 0o11) + '\063' + chr(1892 - 1839) + '\066', ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110001) + chr(745 - 695) + chr(0b1010 + 0o46), 5168 - 5160), nzTpIcepk0o8(chr(138 - 90) + '\x6f' + chr(0b1101 + 0o44) + '\x32' + '\062', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b111 + 0o53) + chr(188 - 135) + chr(0b10111 + 0o37), 19882 - 19874), nzTpIcepk0o8(chr(0b1000 + 0o50) + chr(6227 - 6116) + '\061' + chr(54) + '\x35', ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b1010 + 0o50) + chr(0b110010), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1000111 + 0o50) + '\063' + chr(49), ord("\x08")), nzTpIcepk0o8(chr(1581 - 1533) + chr(0b1101111) + '\062' + chr(0b110100), 8), nzTpIcepk0o8(chr(0b10011 + 0o35) + '\157' + '\063' + chr(0b101001 + 0o15) + chr(50), 0o10), nzTpIcepk0o8('\060' + '\x6f' + '\x31' + chr(0b110111) + '\x34', 0b1000), nzTpIcepk0o8(chr(1874 - 1826) + '\157' + chr(50) + chr(339 - 290), ord("\x08")), nzTpIcepk0o8(chr(695 - 647) + '\157' + chr(76 - 27) + chr(0b110111) + '\061', 47788 - 47780), nzTpIcepk0o8(chr(48) + chr(10280 - 10169) + '\062' + '\064' + chr(2916 - 2862), 31099 - 31091), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b0 + 0o63) + chr(0b11001 + 0o30) + chr(1889 - 1838), 35529 - 35521), nzTpIcepk0o8(chr(48) + chr(350 - 239) + '\062' + chr(51) + '\x35', 20083 - 20075), nzTpIcepk0o8('\x30' + chr(1680 - 1569) + chr(0b101000 + 0o12) + chr(49) + '\065', 9202 - 9194), nzTpIcepk0o8('\x30' + chr(0b1010001 + 0o36) + chr(1666 - 1611) + chr(0b110110), 0b1000), nzTpIcepk0o8(chr(0b10000 + 0o40) + '\x6f' + '\x31' + chr(0b1111 + 0o43) + '\063', ord("\x08")), nzTpIcepk0o8(chr(969 - 921) + chr(111) + chr(0b110011) + '\x31' + chr(0b101011 + 0o12), 58341 - 58333), nzTpIcepk0o8(chr(48) + '\157' + '\x32' + chr(0b110001) + '\x36', 51749 - 51741), nzTpIcepk0o8(chr(1761 - 1713) + '\157' + chr(0b101011 + 0o10) + '\x30' + chr(0b100111 + 0o12), 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(0b110011) + chr(52) + chr(49), 0b1000), nzTpIcepk0o8(chr(0b1101 + 0o43) + chr(111) + chr(1807 - 1757) + chr(0b110110) + '\x32', 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b11010 + 0o30) + chr(1635 - 1584) + chr(51), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110011) + chr(0b110101) + '\x34', 0b1000), nzTpIcepk0o8('\x30' + chr(4303 - 4192) + chr(0b10001 + 0o42) + chr(48) + chr(0b10001 + 0o40), 8), nzTpIcepk0o8('\x30' + chr(0b1011010 + 0o25) + '\062' + chr(2433 - 2379) + '\062', 8), nzTpIcepk0o8('\x30' + chr(0b10011 + 0o134) + chr(0b11001 + 0o30) + chr(470 - 418) + chr(0b11 + 0o63), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b100010 + 0o16) + chr(0b1101111) + chr(0b110101) + chr(929 - 881), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x99'), '\x64' + chr(237 - 136) + chr(99) + '\x6f' + chr(3298 - 3198) + chr(7351 - 7250))(chr(117) + '\164' + chr(8801 - 8699) + chr(0b1011 + 0o42) + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def CikyTeQ_2JKj(z3lWtzdILzgZ, XccBG0Au3H4O):
UYtHA0XyNB9C = XccBG0Au3H4O.recognition_site
F88Ik6gDrBth = z3lWtzdILzgZ.locate(UYtHA0XyNB9C)
if not F88Ik6gDrBth[nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b1 + 0o57), ord("\x08"))] and (not F88Ik6gDrBth[nzTpIcepk0o8(chr(48) + chr(7016 - 6905) + chr(49), 0b1000)]):
return [z3lWtzdILzgZ]
YLQ1wQU3lR6a = ftfygxgFas5X(UYtHA0XyNB9C)
OfWKW3pldms2 = [ftfygxgFas5X(z3lWtzdILzgZ) - ZpfN5tSLaZze - YLQ1wQU3lR6a for ZpfN5tSLaZze in F88Ik6gDrBth[nzTpIcepk0o8(chr(0b10111 + 0o31) + chr(0b10011 + 0o134) + '\061', 8)]]
if roI3spqORKae(UYtHA0XyNB9C, roI3spqORKae(ES5oEprVxulp(b'\xde8\x7f\xcf^\x02\x05zM\xa9\x87\xe1\x8b'), chr(7109 - 7009) + chr(2393 - 2292) + chr(99) + '\157' + chr(0b1100100) + chr(0b1100101))(chr(117) + chr(0b1110100) + chr(5917 - 5815) + '\x2d' + chr(601 - 545)))():
OfWKW3pldms2 = [ZpfN5tSLaZze for ZpfN5tSLaZze in OfWKW3pldms2 if ZpfN5tSLaZze not in F88Ik6gDrBth[nzTpIcepk0o8('\x30' + chr(111) + chr(0b100101 + 0o13), 8)]]
UfLg7KSeGhGD = V3OlOVg98A85(F88Ik6gDrBth[nzTpIcepk0o8(chr(0b101010 + 0o6) + chr(9158 - 9047) + '\x30', 8)] + OfWKW3pldms2)
btnZMuSDwyyx = [z3lWtzdILzgZ]
for Wpm33MqnmnpS in UfLg7KSeGhGD[::-nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110001), 8)]:
bZWmgf4GjgvH = IFykXeEhhbdF(btnZMuSDwyyx, Wpm33MqnmnpS, XccBG0Au3H4O)
roI3spqORKae(btnZMuSDwyyx, roI3spqORKae(ES5oEprVxulp(b'\xff\x1fs\x8bG\t+{C\xb4\xbd\xb9'), chr(100) + chr(101) + chr(99) + chr(111) + chr(0b101011 + 0o71) + chr(0b1011000 + 0o15))(chr(0b1110101) + chr(0b1110100) + chr(0b1100110) + chr(0b101101) + chr(171 - 115)))(bZWmgf4GjgvH[nzTpIcepk0o8('\x30' + chr(4085 - 3974) + chr(49), 8)])
roI3spqORKae(btnZMuSDwyyx, roI3spqORKae(ES5oEprVxulp(b'\xff\x1fs\x8bG\t+{C\xb4\xbd\xb9'), chr(1322 - 1222) + chr(3879 - 3778) + '\143' + chr(0b1101111) + chr(0b1000110 + 0o36) + '\x65')(chr(0b111100 + 0o71) + '\164' + '\146' + '\055' + chr(0b111000)))(bZWmgf4GjgvH[nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110000), 8)])
roI3spqORKae(btnZMuSDwyyx, roI3spqORKae(ES5oEprVxulp(b'\xd0~U\xf8Y ]|^\x98\x9e\xef'), chr(0b11 + 0o141) + chr(131 - 30) + chr(0b110011 + 0o60) + chr(11972 - 11861) + '\x64' + chr(101))(chr(117) + '\164' + chr(0b1100110) + chr(45) + chr(0b111000)))()
if roI3spqORKae(z3lWtzdILzgZ, roI3spqORKae(ES5oEprVxulp(b'\xd4"R\xdcJ\x02\rf'), chr(8108 - 8008) + chr(3032 - 2931) + chr(0b1100011) + '\157' + chr(0b10111 + 0o115) + '\x65')(chr(0b110101 + 0o100) + '\164' + chr(6078 - 5976) + chr(0b101101) + '\x38')):
btnZMuSDwyyx[nzTpIcepk0o8('\060' + chr(0b1101111) + chr(374 - 326), 8)] = btnZMuSDwyyx.uC_Yoybx7J0I() + btnZMuSDwyyx[nzTpIcepk0o8(chr(0b101111 + 0o1) + chr(111) + chr(0b101110 + 0o2), 8)]
return btnZMuSDwyyx |
klavinslab/coral | coral/reaction/_restriction.py | _cut | def _cut(dna, index, restriction_enzyme):
'''Cuts template once at the specified index.
:param dna: DNA to cut
:type dna: coral.DNA
:param index: index at which to cut
:type index: int
:param restriction_enzyme: Enzyme with which to cut
:type restriction_enzyme: coral.RestrictionSite
:returns: 2-element list of digested sequence, including any overhangs.
:rtype: list
'''
# TODO: handle case where cut site is outside of recognition sequence,
# for both circular and linear cases where site is at index 0
# Find absolute indices at which to cut
cut_site = restriction_enzyme.cut_site
top_cut = index + cut_site[0]
bottom_cut = index + cut_site[1]
# Isolate left and ride sequences
to_cut = dna.pop()
max_cut = max(top_cut, bottom_cut)
min_cut = min(top_cut, bottom_cut)
left = to_cut[:max_cut]
right = to_cut[min_cut:]
# If applicable, leave overhangs
diff = top_cut - bottom_cut
if not diff:
# Blunt-end cutter, no adjustment necessary
pass
elif diff > 0:
# 3' overhangs
left = coral.reaction.five_resect(left.flip(), diff).flip()
right = coral.reaction.five_resect(right, diff)
else:
# 5' overhangs
left = coral.reaction.three_resect(left, abs(diff))
right = coral.reaction.three_resect(right.flip(), abs(diff)).flip()
return [left, right] | python | def _cut(dna, index, restriction_enzyme):
'''Cuts template once at the specified index.
:param dna: DNA to cut
:type dna: coral.DNA
:param index: index at which to cut
:type index: int
:param restriction_enzyme: Enzyme with which to cut
:type restriction_enzyme: coral.RestrictionSite
:returns: 2-element list of digested sequence, including any overhangs.
:rtype: list
'''
# TODO: handle case where cut site is outside of recognition sequence,
# for both circular and linear cases where site is at index 0
# Find absolute indices at which to cut
cut_site = restriction_enzyme.cut_site
top_cut = index + cut_site[0]
bottom_cut = index + cut_site[1]
# Isolate left and ride sequences
to_cut = dna.pop()
max_cut = max(top_cut, bottom_cut)
min_cut = min(top_cut, bottom_cut)
left = to_cut[:max_cut]
right = to_cut[min_cut:]
# If applicable, leave overhangs
diff = top_cut - bottom_cut
if not diff:
# Blunt-end cutter, no adjustment necessary
pass
elif diff > 0:
# 3' overhangs
left = coral.reaction.five_resect(left.flip(), diff).flip()
right = coral.reaction.five_resect(right, diff)
else:
# 5' overhangs
left = coral.reaction.three_resect(left, abs(diff))
right = coral.reaction.three_resect(right.flip(), abs(diff)).flip()
return [left, right] | [
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:param restriction_enzyme: Enzyme with which to cut
:type restriction_enzyme: coral.RestrictionSite
:returns: 2-element list of digested sequence, including any overhangs.
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ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(48) + chr(0b11 + 0o154) + chr(0b110011) + chr(48) + '\062', 62358 - 62350), nzTpIcepk0o8(chr(0b10011 + 0o35) + chr(0b1101111) + '\062' + chr(0b110111) + chr(2062 - 2008), 0b1000), nzTpIcepk0o8(chr(0b11101 + 0o23) + '\x6f' + '\x31' + '\060' + '\x33', 52531 - 52523), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x37' + '\x35', 60546 - 60538), nzTpIcepk0o8(chr(1026 - 978) + chr(111) + chr(50) + chr(1055 - 1001), 0o10), nzTpIcepk0o8(chr(778 - 730) + '\x6f' + chr(0b1111 + 0o44) + '\x30', 0b1000), nzTpIcepk0o8(chr(0b100100 + 0o14) + chr(0b1101111) + '\x33' + '\062' + chr(0b110011), 28896 - 28888), nzTpIcepk0o8(chr(0b110000) + chr(0b11101 + 0o122) + '\063' + '\066' + chr(940 - 890), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\066', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(50) + chr(334 - 285) + '\x33', 45819 - 45811), nzTpIcepk0o8('\x30' + '\157' + chr(51) + chr(0b11001 + 0o31) + chr(767 - 712), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(49) + chr(54) + chr(551 - 498), 0o10), nzTpIcepk0o8(chr(592 - 544) + chr(0b1101111) + '\063' + chr(50) + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b10000 + 0o44) + '\060', 0o10), nzTpIcepk0o8(chr(2126 - 2078) + chr(0b1101111) + '\x32' + chr(0b100000 + 0o26) + chr(0b10000 + 0o40), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x32' + '\x30' + '\061', 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(51), 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(1994 - 1943) + chr(0b101100 + 0o12) + chr(0b100100 + 0o22), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b111011 + 0o64) + '\x35' + chr(0b1001 + 0o51), 5411 - 5403), nzTpIcepk0o8('\060' + chr(111) + chr(53) + chr(0b110110), 0o10), nzTpIcepk0o8(chr(1372 - 1324) + '\x6f' + chr(0b110010) + chr(0b1100 + 0o52) + chr(54), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1100111 + 0o10) + chr(0b110111) + '\x34', 10392 - 10384), nzTpIcepk0o8('\x30' + '\157' + chr(1448 - 1398) + chr(1568 - 1515) + chr(581 - 529), 3790 - 3782), nzTpIcepk0o8('\060' + '\x6f' + chr(1395 - 1346) + '\x37' + '\x35', ord("\x08")), nzTpIcepk0o8('\x30' + chr(683 - 572) + '\x33' + chr(49) + '\063', 0o10), nzTpIcepk0o8('\060' + chr(5743 - 5632) + '\061' + chr(49) + chr(0b100101 + 0o21), 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110001) + chr(0b10111 + 0o31) + chr(0b110111), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + '\x32' + chr(0b110001), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(0b1110 + 0o45) + '\061' + '\061', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b100110 + 0o15) + chr(0b110100) + chr(0b11100 + 0o33), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110101) + '\x34', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(4195 - 4084) + '\065', 0b1000), nzTpIcepk0o8(chr(1401 - 1353) + '\157' + chr(0b100010 + 0o20) + chr(0b110011) + '\067', 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(1378 - 1329) + chr(1633 - 1578) + '\x30', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110010) + chr(0b110000) + '\061', 8), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x35' + '\061', 21437 - 21429), nzTpIcepk0o8(chr(0b1010 + 0o46) + chr(0b1010111 + 0o30) + chr(51) + chr(2645 - 2593) + chr(55), 8), nzTpIcepk0o8('\x30' + chr(0b101101 + 0o102) + chr(0b110001) + '\060', 0b1000), nzTpIcepk0o8(chr(2236 - 2188) + chr(5319 - 5208) + chr(0b101011 + 0o10) + chr(0b110101) + chr(0b110000 + 0o1), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(2053 - 1942) + '\x32' + chr(0b11111 + 0o22) + chr(282 - 229), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + '\x6f' + chr(0b110101) + chr(0b110000), ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xec'), chr(0b1011110 + 0o6) + chr(101) + '\x63' + chr(111) + '\x64' + chr(3392 - 3291))(chr(0b1110101) + chr(2688 - 2572) + chr(0b1100110) + chr(0b101101) + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def IFykXeEhhbdF(z3lWtzdILzgZ, ZpfN5tSLaZze, XccBG0Au3H4O):
Wpm33MqnmnpS = XccBG0Au3H4O.cut_site
fCFhOJBtEaV8 = ZpfN5tSLaZze + Wpm33MqnmnpS[nzTpIcepk0o8(chr(436 - 388) + chr(0b111000 + 0o67) + chr(48), 0b1000)]
ErcOarRrxJiQ = ZpfN5tSLaZze + Wpm33MqnmnpS[nzTpIcepk0o8(chr(0b0 + 0o60) + '\x6f' + '\x31', 34205 - 34197)]
yhNEKo4AuxHk = z3lWtzdILzgZ.uC_Yoybx7J0I()
f2PCvcS7hbhj = KV9ckIhroIia(fCFhOJBtEaV8, ErcOarRrxJiQ)
a225GEXCuMQn = XURpmPuEWCNF(fCFhOJBtEaV8, ErcOarRrxJiQ)
ZJRgJr1hTjIz = yhNEKo4AuxHk[:f2PCvcS7hbhj]
HDutv6NlG_yf = yhNEKo4AuxHk[a225GEXCuMQn:]
H5XQ4iF_jpSm = fCFhOJBtEaV8 - ErcOarRrxJiQ
if not H5XQ4iF_jpSm:
pass
elif H5XQ4iF_jpSm > nzTpIcepk0o8('\060' + '\x6f' + chr(0b11100 + 0o24), 8):
ZJRgJr1hTjIz = _bFWSozA7z0G.reaction.five_resect(ZJRgJr1hTjIz.flip(), H5XQ4iF_jpSm).flip()
HDutv6NlG_yf = _bFWSozA7z0G.reaction.five_resect(HDutv6NlG_yf, H5XQ4iF_jpSm)
else:
ZJRgJr1hTjIz = _bFWSozA7z0G.reaction.three_resect(ZJRgJr1hTjIz, zQBGwUT7UU8L(H5XQ4iF_jpSm))
HDutv6NlG_yf = _bFWSozA7z0G.reaction.three_resect(HDutv6NlG_yf.flip(), zQBGwUT7UU8L(H5XQ4iF_jpSm)).flip()
return [ZJRgJr1hTjIz, HDutv6NlG_yf] |
klavinslab/coral | bin/ipynb2rst.py | ipynb_to_rst | def ipynb_to_rst(directory, filename):
"""Converts a given file in a directory to an rst in the same directory."""
print(filename)
os.chdir(directory)
subprocess.Popen(["ipython", "nbconvert", "--to", "rst",
filename],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
cwd=directory) | python | def ipynb_to_rst(directory, filename):
"""Converts a given file in a directory to an rst in the same directory."""
print(filename)
os.chdir(directory)
subprocess.Popen(["ipython", "nbconvert", "--to", "rst",
filename],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
cwd=directory) | [
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/bin/ipynb2rst.py#L13-L21 | train | Converts a given file in a directory to an rst in the same directory. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110010) + chr(0b10111 + 0o36), 0o10), nzTpIcepk0o8(chr(2012 - 1964) + chr(0b1100001 + 0o16) + '\x33' + chr(0b10 + 0o61) + chr(0b101100 + 0o5), ord("\x08")), nzTpIcepk0o8(chr(1536 - 1488) + chr(0b111 + 0o150) + '\065' + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(8451 - 8340) + '\x33' + '\x31' + chr(53), 29975 - 29967), nzTpIcepk0o8(chr(0b110000) + chr(0b100100 + 0o113) + '\062' + '\062' + chr(0b10 + 0o56), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(49) + '\065' + chr(0b110010), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(396 - 347) + chr(0b110010) + chr(0b101111 + 0o10), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + '\061' + chr(55) + chr(2331 - 2276), 48242 - 48234), nzTpIcepk0o8(chr(48) + chr(111) + '\063' + '\067' + chr(54), 34267 - 34259), nzTpIcepk0o8('\x30' + chr(111) + chr(2370 - 2321) + chr(0b110011) + chr(0b110010), 0o10), nzTpIcepk0o8(chr(0b1111 + 0o41) + '\157' + '\066' + '\064', 19012 - 19004), nzTpIcepk0o8('\060' + '\x6f' + chr(1377 - 1326) + '\x37' + chr(0b110001), 0b1000), nzTpIcepk0o8(chr(0b101001 + 0o7) + chr(0b1100101 + 0o12) + '\x33' + '\x33' + '\x30', 50516 - 50508), nzTpIcepk0o8(chr(0b10010 + 0o36) + chr(111) + chr(0b1011 + 0o46) + chr(52) + '\x31', 60118 - 60110), nzTpIcepk0o8(chr(0b101 + 0o53) + '\x6f' + chr(0b110010) + chr(2494 - 2440), 7509 - 7501), nzTpIcepk0o8(chr(0b1011 + 0o45) + '\157' + chr(2006 - 1951) + chr(53), 0o10), nzTpIcepk0o8(chr(0b11000 + 0o30) + chr(111) + chr(0b11111 + 0o23) + chr(0b1011 + 0o46) + '\060', 0o10), nzTpIcepk0o8(chr(48) + chr(111) + '\x33' + chr(552 - 503) + '\067', 36499 - 36491), nzTpIcepk0o8(chr(1194 - 1146) + chr(8600 - 8489) + '\063' + chr(0b110101) + chr(0b11110 + 0o30), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1010011 + 0o34) + chr(0b110010) + chr(0b110100) + '\064', 0b1000), nzTpIcepk0o8(chr(1523 - 1475) + chr(111) + '\x33' + chr(2337 - 2282) + chr(901 - 852), 8), nzTpIcepk0o8(chr(1197 - 1149) + chr(0b100000 + 0o117) + chr(0b100111 + 0o13) + chr(0b1111 + 0o45) + chr(1928 - 1878), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1010101 + 0o32) + chr(51) + chr(53) + chr(1777 - 1728), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(50 - 0) + '\061' + chr(0b110111), 0o10), nzTpIcepk0o8('\x30' + chr(6895 - 6784) + chr(0b110001) + '\063' + chr(596 - 547), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101110 + 0o1) + chr(0b100101 + 0o14) + chr(0b110101) + '\064', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b111 + 0o150) + '\061' + chr(0b101110 + 0o6) + chr(50), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + '\x33' + '\x35' + chr(1554 - 1502), 0o10), nzTpIcepk0o8(chr(48) + '\157' + '\x31' + '\065', 13436 - 13428), nzTpIcepk0o8(chr(1865 - 1817) + chr(111) + chr(55) + chr(0b11 + 0o61), 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(0b101100 + 0o5) + chr(0b101011 + 0o13) + chr(0b110011), ord("\x08")), nzTpIcepk0o8(chr(0b110 + 0o52) + '\x6f' + chr(1779 - 1730) + '\067' + chr(49), 40916 - 40908), nzTpIcepk0o8(chr(0b100000 + 0o20) + chr(0b1010000 + 0o37) + chr(0b110001) + chr(0b11 + 0o56) + '\x34', 0o10), nzTpIcepk0o8(chr(1186 - 1138) + chr(0b1000101 + 0o52) + '\x33' + chr(0b100010 + 0o20) + chr(1360 - 1306), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110011) + chr(52) + '\x36', 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(50) + '\x31' + '\064', 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(51) + '\066' + chr(51), 62434 - 62426), nzTpIcepk0o8(chr(0b100011 + 0o15) + chr(0b1100101 + 0o12) + chr(1441 - 1392) + chr(0b110111) + '\x37', 8), nzTpIcepk0o8(chr(0b101010 + 0o6) + chr(9373 - 9262) + chr(0b110011) + chr(50) + '\x36', 8), nzTpIcepk0o8(chr(787 - 739) + chr(0b110011 + 0o74) + chr(0b110001) + '\x37' + chr(0b110110), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + '\157' + chr(2694 - 2641) + chr(621 - 573), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b';'), '\144' + '\145' + chr(0b1100011) + chr(2749 - 2638) + chr(4529 - 4429) + chr(101))(chr(0b1010100 + 0o41) + chr(116) + '\146' + chr(0b101101) + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def DdziiETI9Vqd(InVoWQwNBeGF, FxZHtXEolYsL):
v8jsMqaYV6U2(FxZHtXEolYsL)
roI3spqORKae(aHUqKstZLeS6, roI3spqORKae(ES5oEprVxulp(b'v\xb1O\xa4\xe2'), chr(100) + chr(0b1100101) + '\143' + chr(111) + chr(0b1011011 + 0o11) + chr(101))(chr(0b1000010 + 0o63) + chr(4429 - 4313) + chr(0b100100 + 0o102) + chr(0b101101) + chr(0b111000)))(InVoWQwNBeGF)
roI3spqORKae(eT8Y087E_kfd, roI3spqORKae(ES5oEprVxulp(b'E\xb6[\xa8\xfe'), chr(0b1100100) + chr(6403 - 6302) + chr(7943 - 7844) + chr(1279 - 1168) + chr(3351 - 3251) + chr(0b110011 + 0o62))('\165' + chr(0b1110100) + '\x66' + '\055' + '\070'))([roI3spqORKae(ES5oEprVxulp(b'|\xa9R\xb9\xf8\x059'), chr(100) + '\145' + chr(0b11101 + 0o106) + '\x6f' + chr(0b1000000 + 0o44) + '\x65')(chr(0b1010100 + 0o41) + chr(5337 - 5221) + chr(0b10101 + 0o121) + '\x2d' + '\070'), roI3spqORKae(ES5oEprVxulp(b'{\xbbH\xa2\xfe\x1c2\r\x8a'), '\144' + chr(0b1100101) + chr(0b1001100 + 0o27) + '\157' + chr(0b10000 + 0o124) + chr(101))(chr(6103 - 5986) + '\164' + chr(102) + chr(45) + chr(0b111000)), roI3spqORKae(ES5oEprVxulp(b'8\xf4_\xa2'), '\144' + chr(0b1100001 + 0o4) + chr(99) + chr(0b1101111) + chr(0b100001 + 0o103) + chr(5525 - 5424))(chr(117) + chr(0b1110100) + chr(0b1011100 + 0o12) + chr(0b1101 + 0o40) + '\070'), roI3spqORKae(ES5oEprVxulp(b'g\xaa_'), '\x64' + chr(101) + '\143' + chr(0b11011 + 0o124) + chr(0b1000001 + 0o43) + chr(0b101 + 0o140))(chr(0b1110101) + chr(116) + '\146' + chr(927 - 882) + chr(56)), FxZHtXEolYsL], stdout=roI3spqORKae(eT8Y087E_kfd, roI3spqORKae(ES5oEprVxulp(b'E\x90{\x88'), chr(0b1100100) + chr(7673 - 7572) + chr(99) + chr(0b1101101 + 0o2) + chr(0b1011000 + 0o14) + chr(101))('\x75' + '\164' + chr(0b1100110) + '\x2d' + chr(0b110 + 0o62))), stderr=roI3spqORKae(eT8Y087E_kfd, roI3spqORKae(ES5oEprVxulp(b'E\x90{\x88'), '\144' + chr(0b100011 + 0o102) + chr(1884 - 1785) + chr(0b1000110 + 0o51) + chr(0b111101 + 0o47) + '\145')('\165' + chr(116) + chr(0b1100100 + 0o2) + '\x2d' + chr(0b111000))), cwd=InVoWQwNBeGF) |
klavinslab/coral | bin/ipynb2rst.py | convert_ipynbs | def convert_ipynbs(directory):
"""Recursively converts all ipynb files in a directory into rst files in
the same directory."""
# The ipython_examples dir has to be in the same dir as this script
for root, subfolders, files in os.walk(os.path.abspath(directory)):
for f in files:
if ".ipynb_checkpoints" not in root:
if f.endswith("ipynb"):
ipynb_to_rst(root, f) | python | def convert_ipynbs(directory):
"""Recursively converts all ipynb files in a directory into rst files in
the same directory."""
# The ipython_examples dir has to be in the same dir as this script
for root, subfolders, files in os.walk(os.path.abspath(directory)):
for f in files:
if ".ipynb_checkpoints" not in root:
if f.endswith("ipynb"):
ipynb_to_rst(root, f) | [
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"."
] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/bin/ipynb2rst.py#L24-L32 | train | Recursively converts all ipynb files in a directory into rst files in
the same directory. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b100 + 0o54) + chr(0b1101111) + '\065', 35650 - 35642), nzTpIcepk0o8(chr(0b101 + 0o53) + chr(111) + chr(0b110011) + chr(0b101100 + 0o10) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(535 - 485) + chr(1820 - 1768) + '\x34', 0b1000), nzTpIcepk0o8(chr(48) + chr(10890 - 10779) + chr(531 - 481) + chr(2176 - 2128) + chr(0b10111 + 0o34), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110011) + chr(0b110001) + chr(2473 - 2420), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(0b1 + 0o57), ord("\x08")), nzTpIcepk0o8(chr(1619 - 1571) + '\x6f' + chr(0b10 + 0o65) + chr(0b100100 + 0o22), 5631 - 5623), nzTpIcepk0o8('\060' + '\157' + chr(0b101110 + 0o5) + chr(0b101011 + 0o12) + chr(0b1110 + 0o51), 54247 - 54239), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x33' + '\067' + chr(0b10100 + 0o35), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(0b101 + 0o54) + chr(1378 - 1328) + chr(1392 - 1344), 22451 - 22443), nzTpIcepk0o8('\x30' + chr(111) + chr(0b101110 + 0o7) + '\062', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1011 + 0o144) + chr(0b110100) + chr(0b11111 + 0o27), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(0b11011 + 0o30) + chr(0b110110) + chr(0b100101 + 0o15), 0b1000), nzTpIcepk0o8(chr(0b10 + 0o56) + chr(0b1101111) + '\065' + '\x33', 0b1000), nzTpIcepk0o8('\x30' + chr(111) + '\063' + chr(0b110011) + chr(0b110100), 0b1000), nzTpIcepk0o8('\x30' + chr(111) + '\x32' + chr(2017 - 1969) + '\x35', 0b1000), nzTpIcepk0o8(chr(461 - 413) + chr(0b111011 + 0o64) + '\x33' + chr(0b110010) + chr(0b11001 + 0o27), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(661 - 611) + '\x37' + chr(0b110000), 3591 - 3583), nzTpIcepk0o8(chr(2009 - 1961) + chr(0b1101111) + chr(2263 - 2212) + chr(0b11101 + 0o27) + chr(0b110110), 0o10), nzTpIcepk0o8(chr(2059 - 2011) + '\x6f' + chr(2136 - 2086) + chr(49) + '\061', 0o10), nzTpIcepk0o8('\x30' + chr(2539 - 2428) + chr(0b11010 + 0o30) + '\064', 28605 - 28597), nzTpIcepk0o8('\x30' + '\157' + '\063' + '\063' + '\x35', 37299 - 37291), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110001) + '\062' + '\067', 0b1000), nzTpIcepk0o8(chr(2281 - 2233) + chr(0b1101111) + chr(0b110111) + chr(1785 - 1736), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(0b1010 + 0o50) + chr(461 - 407) + chr(49), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1011010 + 0o25) + chr(809 - 759) + '\x31' + '\063', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b1101 + 0o45) + chr(0b100100 + 0o14) + chr(0b110100), 9266 - 9258), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x33' + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1010110 + 0o31) + chr(50) + chr(50) + chr(1121 - 1070), 8367 - 8359), nzTpIcepk0o8('\x30' + chr(0b1000010 + 0o55) + '\062' + chr(0b101011 + 0o5) + chr(1148 - 1097), 8), nzTpIcepk0o8('\x30' + chr(8523 - 8412) + '\062' + chr(49) + chr(0b110101), 0o10), nzTpIcepk0o8(chr(48) + chr(5934 - 5823) + chr(50) + '\066' + chr(515 - 466), 8), nzTpIcepk0o8(chr(223 - 175) + chr(111) + '\x37' + '\x31', 8), nzTpIcepk0o8(chr(0b110000) + chr(0b1010100 + 0o33) + chr(51) + '\x35' + '\x32', 23525 - 23517), nzTpIcepk0o8(chr(0b10101 + 0o33) + '\x6f' + chr(1041 - 990) + '\063' + '\066', 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110001) + chr(0b110110) + chr(0b100101 + 0o22), 14504 - 14496), nzTpIcepk0o8('\060' + '\157' + chr(0b10111 + 0o32) + chr(554 - 502) + chr(54), 8940 - 8932), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110010) + chr(0b110000), 0b1000), nzTpIcepk0o8(chr(0b101100 + 0o4) + '\157' + '\x33' + '\065' + chr(0b110011), 64923 - 64915), nzTpIcepk0o8('\060' + chr(8797 - 8686) + chr(49) + '\067' + chr(0b100110 + 0o15), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b1101 + 0o50) + chr(0b110000), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'+'), chr(0b1100100) + chr(8418 - 8317) + '\143' + chr(1648 - 1537) + chr(100) + chr(4667 - 4566))(chr(0b1110101) + chr(0b110101 + 0o77) + chr(0b11010 + 0o114) + chr(1570 - 1525) + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def mvx9ateS8w11(InVoWQwNBeGF):
for (kF9CWBi2ucGu, iHALFe2PTvS5, wR5_YWECjaY7) in roI3spqORKae(aHUqKstZLeS6, roI3spqORKae(ES5oEprVxulp(b'O\xae\xf2\xf0\xa71{\xbe\xad%E|'), '\144' + chr(0b101000 + 0o75) + '\x63' + '\x6f' + '\144' + chr(0b10010 + 0o123))('\165' + '\x74' + chr(102) + chr(45) + chr(702 - 646)))(roI3spqORKae(aHUqKstZLeS6.path, roI3spqORKae(ES5oEprVxulp(b'd\x81\xd7\xf3\xactV'), chr(605 - 505) + '\145' + chr(3701 - 3602) + '\157' + chr(100) + chr(0b1011111 + 0o6))(chr(10746 - 10629) + chr(7139 - 7023) + chr(0b1100110) + '\055' + chr(0b110 + 0o62)))(InVoWQwNBeGF)):
for _R8IKF5IwAfX in wR5_YWECjaY7:
if roI3spqORKae(ES5oEprVxulp(b'+\x8a\xd4\xfa\xa3ba\x8c\x915IM\x82D\xb5\xeb\xa4\xcb'), chr(100) + chr(6763 - 6662) + chr(6517 - 6418) + '\157' + '\x64' + '\145')(chr(0b1110101) + '\164' + chr(102) + chr(1395 - 1350) + '\070') not in kF9CWBi2ucGu:
if roI3spqORKae(_R8IKF5IwAfX, roI3spqORKae(ES5oEprVxulp(b'L\xda\xc2\xc8\x84C\x7f\xa3\x98%`T'), chr(0b1100100) + chr(829 - 728) + chr(99) + chr(0b1000001 + 0o56) + '\144' + chr(1357 - 1256))(chr(11402 - 11285) + chr(116) + chr(654 - 552) + '\x2d' + '\x38'))(roI3spqORKae(ES5oEprVxulp(b'l\x93\xdd\xed\xaf'), chr(100) + chr(0b1000000 + 0o45) + chr(0b1100011) + chr(111) + '\144' + '\x65')(chr(0b1011100 + 0o31) + '\x74' + '\146' + chr(45) + '\070')):
DdziiETI9Vqd(kF9CWBi2ucGu, _R8IKF5IwAfX) |
klavinslab/coral | coral/analysis/_structure/structure_windows.py | _context_walk | def _context_walk(dna, window_size, context_len, step):
'''Generate context-dependent 'non-boundedness' scores for a DNA sequence.
:param dna: Sequence to score.
:type dna: coral.DNA
:param window_size: Window size in base pairs.
:type window_size: int
:param context_len: The number of bases of context to use when analyzing
each window.
:type context_len: int
:param step: The number of base pairs to move for each new window.
:type step: int
'''
# Generate window indices
window_start_ceiling = len(dna) - context_len - window_size
window_starts = range(context_len - 1, window_start_ceiling, step)
window_ends = [start + window_size for start in window_starts]
# Generate left and right in-context subsequences
l_starts = [step * i for i in range(len(window_starts))]
l_seqs = [dna[start:end] for start, end in zip(l_starts, window_ends)]
r_ends = [x + window_size + context_len for x in window_starts]
r_seqs = [dna[start:end].reverse_complement() for start, end in
zip(window_starts, r_ends)]
# Combine and calculate nupack pair probabilities
seqs = l_seqs + r_seqs
pairs_run = coral.analysis.nupack_multi(seqs, 'dna', 'pairs', {'index': 0})
# Focus on pair probabilities that matter - those in the window
pairs = [run[-window_size:] for run in pairs_run]
# Score by average pair probability
lr_scores = [sum(pair) / len(pair) for pair in pairs]
# Split into left-right contexts again and sum for each window
l_scores = lr_scores[0:len(seqs) / 2]
r_scores = lr_scores[len(seqs) / 2:]
scores = [(l + r) / 2 for l, r in zip(l_scores, r_scores)]
# Summarize and return window indices and score
summary = zip(window_starts, window_ends, scores)
return summary | python | def _context_walk(dna, window_size, context_len, step):
'''Generate context-dependent 'non-boundedness' scores for a DNA sequence.
:param dna: Sequence to score.
:type dna: coral.DNA
:param window_size: Window size in base pairs.
:type window_size: int
:param context_len: The number of bases of context to use when analyzing
each window.
:type context_len: int
:param step: The number of base pairs to move for each new window.
:type step: int
'''
# Generate window indices
window_start_ceiling = len(dna) - context_len - window_size
window_starts = range(context_len - 1, window_start_ceiling, step)
window_ends = [start + window_size for start in window_starts]
# Generate left and right in-context subsequences
l_starts = [step * i for i in range(len(window_starts))]
l_seqs = [dna[start:end] for start, end in zip(l_starts, window_ends)]
r_ends = [x + window_size + context_len for x in window_starts]
r_seqs = [dna[start:end].reverse_complement() for start, end in
zip(window_starts, r_ends)]
# Combine and calculate nupack pair probabilities
seqs = l_seqs + r_seqs
pairs_run = coral.analysis.nupack_multi(seqs, 'dna', 'pairs', {'index': 0})
# Focus on pair probabilities that matter - those in the window
pairs = [run[-window_size:] for run in pairs_run]
# Score by average pair probability
lr_scores = [sum(pair) / len(pair) for pair in pairs]
# Split into left-right contexts again and sum for each window
l_scores = lr_scores[0:len(seqs) / 2]
r_scores = lr_scores[len(seqs) / 2:]
scores = [(l + r) / 2 for l, r in zip(l_scores, r_scores)]
# Summarize and return window indices and score
summary = zip(window_starts, window_ends, scores)
return summary | [
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:param context_len: The number of bases of context to use when analyzing
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/analysis/_structure/structure_windows.py#L56-L98 | train | Generate a context - dependent non - boundedness score for a DNA sequence. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b1001 + 0o47) + chr(0b1011000 + 0o27) + chr(0b100100 + 0o15) + chr(0b110010) + chr(2324 - 2271), 19863 - 19855), nzTpIcepk0o8('\x30' + '\x6f' + chr(49) + chr(0b110110), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x31' + '\x32' + '\064', 49778 - 49770), nzTpIcepk0o8('\x30' + chr(2377 - 2266) + '\x31' + chr(2565 - 2511) + chr(0b100100 + 0o17), 0o10), nzTpIcepk0o8(chr(1857 - 1809) + chr(111) + '\x31' + '\060' + chr(2627 - 2573), 32959 - 32951), nzTpIcepk0o8('\060' + '\157' + chr(1024 - 973) + chr(49), 0o10), nzTpIcepk0o8('\060' + chr(0b1001111 + 0o40) + chr(50) + chr(892 - 843), ord("\x08")), nzTpIcepk0o8(chr(1255 - 1207) + chr(0b1101111) + chr(1573 - 1523) + chr(0b101111 + 0o7), 0b1000), nzTpIcepk0o8(chr(48) + chr(7290 - 7179) + '\x33' + chr(0b110001) + chr(0b111 + 0o51), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(55), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110010) + chr(2576 - 2524), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b101111 + 0o100) + chr(0b110011) + chr(0b10110 + 0o35) + chr(0b10001 + 0o46), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(2405 - 2352) + '\064', 0b1000), nzTpIcepk0o8('\060' + '\157' + '\062' + chr(0b1110 + 0o45) + '\x33', 0b1000), nzTpIcepk0o8(chr(0b101111 + 0o1) + chr(0b1101111) + '\x31' + '\064' + '\064', 44364 - 44356), nzTpIcepk0o8('\x30' + chr(111) + chr(0b100 + 0o57) + chr(0b110100) + chr(53), 53050 - 53042), nzTpIcepk0o8('\060' + '\157' + chr(0b10 + 0o57) + '\x35' + '\x31', 0b1000), nzTpIcepk0o8(chr(2158 - 2110) + '\x6f' + '\x33' + chr(2550 - 2496) + chr(654 - 599), 43484 - 43476), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110010) + '\066' + chr(359 - 306), 0o10), nzTpIcepk0o8(chr(0b11000 + 0o30) + chr(0b111111 + 0o60) + '\065' + chr(0b100110 + 0o12), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(3285 - 3174) + '\062' + chr(54) + '\061', 0b1000), nzTpIcepk0o8(chr(1823 - 1775) + chr(0b1010010 + 0o35) + '\x32' + '\x33' + '\x36', 0b1000), nzTpIcepk0o8(chr(48) + chr(9113 - 9002) + '\063' + chr(0b110001) + chr(0b11 + 0o57), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b10101 + 0o34) + chr(735 - 680), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1010100 + 0o33) + chr(49) + '\x31' + '\063', ord("\x08")), nzTpIcepk0o8(chr(776 - 728) + chr(0b1101010 + 0o5) + chr(49) + '\065' + chr(54), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b10101 + 0o42) + '\064', ord("\x08")), nzTpIcepk0o8(chr(0b100010 + 0o16) + chr(0b1101111) + chr(50) + chr(53), 0o10), nzTpIcepk0o8(chr(1898 - 1850) + '\x6f' + '\062' + '\067' + chr(1743 - 1693), 0o10), nzTpIcepk0o8(chr(48) + chr(4082 - 3971) + chr(0b110011) + chr(0b110100) + '\x37', 0o10), nzTpIcepk0o8(chr(0b1111 + 0o41) + chr(0b10000 + 0o137) + chr(1432 - 1379) + '\x34', 8), nzTpIcepk0o8(chr(357 - 309) + '\157' + '\062' + chr(1675 - 1623), 8), nzTpIcepk0o8(chr(0b101001 + 0o7) + chr(1770 - 1659) + chr(51) + chr(2231 - 2182) + chr(0b110100), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1100100 + 0o13) + chr(599 - 549) + chr(55) + chr(0b110011), 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(50) + chr(50) + chr(52), 49645 - 49637), nzTpIcepk0o8(chr(820 - 772) + chr(0b1101111) + '\061' + chr(2275 - 2222) + chr(52), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x31' + chr(1039 - 990) + chr(0b110011), 8), nzTpIcepk0o8(chr(1479 - 1431) + '\x6f' + chr(49), ord("\x08")), nzTpIcepk0o8('\x30' + chr(909 - 798) + '\062' + '\x32', 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b10100 + 0o37) + '\061', 8)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(2926 - 2815) + '\x35' + chr(0b11 + 0o55), 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'{'), '\144' + '\145' + '\x63' + chr(209 - 98) + chr(6346 - 6246) + chr(0b1100101))(chr(117) + '\x74' + chr(0b1000000 + 0o46) + chr(0b10 + 0o53) + chr(122 - 66)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def MQkxG9TEJg08(z3lWtzdILzgZ, sr1jcqYH2Bwu, bnBrzmMDCqOX, ZiKB99Xs91Lo):
JaWfapJaErl6 = ftfygxgFas5X(z3lWtzdILzgZ) - bnBrzmMDCqOX - sr1jcqYH2Bwu
MKGMn0wNXFB2 = bbT2xIe5pzk7(bnBrzmMDCqOX - nzTpIcepk0o8(chr(2120 - 2072) + chr(7571 - 7460) + chr(0b101111 + 0o2), 8), JaWfapJaErl6, ZiKB99Xs91Lo)
jDPoTQI3tqFV = [KQbHFTcl_LKy + sr1jcqYH2Bwu for KQbHFTcl_LKy in MKGMn0wNXFB2]
EdP4yJKcB1V1 = [ZiKB99Xs91Lo * ZlbFMSG8gCoF for ZlbFMSG8gCoF in bbT2xIe5pzk7(ftfygxgFas5X(MKGMn0wNXFB2))]
YOLqTM8egJQU = [z3lWtzdILzgZ[KQbHFTcl_LKy:NiWVjAWn0l6T] for (KQbHFTcl_LKy, NiWVjAWn0l6T) in TxMFWa_Xzviv(EdP4yJKcB1V1, jDPoTQI3tqFV)]
AmizuBea_rBo = [bI5jsQ9OkQtj + sr1jcqYH2Bwu + bnBrzmMDCqOX for bI5jsQ9OkQtj in MKGMn0wNXFB2]
_RcX5VnZBTBE = [z3lWtzdILzgZ[KQbHFTcl_LKy:NiWVjAWn0l6T].reverse_complement() for (KQbHFTcl_LKy, NiWVjAWn0l6T) in TxMFWa_Xzviv(MKGMn0wNXFB2, AmizuBea_rBo)]
LmTSN4iJgDMb = YOLqTM8egJQU + _RcX5VnZBTBE
dF9AMURgl6MX = _bFWSozA7z0G.analysis.nupack_multi(LmTSN4iJgDMb, roI3spqORKae(ES5oEprVxulp(b'1`5'), '\x64' + chr(0b1100101) + '\143' + '\x6f' + chr(1146 - 1046) + chr(101))('\x75' + '\x74' + '\146' + chr(0b100011 + 0o12) + '\x38'), roI3spqORKae(ES5oEprVxulp(b'%o=\x015'), chr(0b1001011 + 0o31) + '\145' + chr(0b1100011) + '\157' + chr(100) + chr(0b1001101 + 0o30))(chr(0b1110101) + chr(2968 - 2852) + '\x66' + chr(0b10010 + 0o33) + chr(267 - 211)), {roI3spqORKae(ES5oEprVxulp(b'<`0\x16>'), chr(0b101110 + 0o66) + chr(101) + chr(2256 - 2157) + '\x6f' + chr(100) + chr(0b1100101))(chr(0b1101111 + 0o6) + chr(116) + chr(0b1100110) + chr(45) + chr(0b111000)): nzTpIcepk0o8(chr(0b110000) + chr(0b1010000 + 0o37) + '\x30', ord("\x08"))})
VxbmnfX6T_2s = [qnPOIdBQJdzY[-sr1jcqYH2Bwu:] for qnPOIdBQJdzY in dF9AMURgl6MX]
qD82t1Cl1_kU = [oclC8DLjA_lV(YhzVz4aO0FLl) / ftfygxgFas5X(YhzVz4aO0FLl) for YhzVz4aO0FLl in VxbmnfX6T_2s]
es2rIUnSEUak = qD82t1Cl1_kU[nzTpIcepk0o8(chr(0b10011 + 0o35) + chr(0b1101111) + chr(48), 8):ftfygxgFas5X(LmTSN4iJgDMb) / nzTpIcepk0o8(chr(1626 - 1578) + chr(0b1001 + 0o146) + '\x32', 0b1000)]
dQDELe3LKveS = qD82t1Cl1_kU[ftfygxgFas5X(LmTSN4iJgDMb) / nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x32', 8):]
EZCjrKz8Dzwm = [(fPrVrKACaFCC + LCrwg7lcbmU9) / nzTpIcepk0o8('\060' + chr(7385 - 7274) + chr(809 - 759), 8) for (fPrVrKACaFCC, LCrwg7lcbmU9) in TxMFWa_Xzviv(es2rIUnSEUak, dQDELe3LKveS)]
QEXp0HPqz7Se = TxMFWa_Xzviv(MKGMn0wNXFB2, jDPoTQI3tqFV, EZCjrKz8Dzwm)
return QEXp0HPqz7Se |
klavinslab/coral | coral/analysis/_structure/structure_windows.py | StructureWindows.windows | def windows(self, window_size=60, context_len=90, step=10):
'''Walk through the sequence of interest in windows of window_size,
evaluate free (unbound) pair probabilities.
:param window_size: Window size in base pairs.
:type window_size: int
:param context_len: The number of bases of context to use when
analyzing each window.
:type context_len: int
:param step: The number of base pairs to move for each new window.
:type step: int
'''
self.walked = _context_walk(self.template, window_size, context_len,
step)
self.core_starts, self.core_ends, self.scores = zip(*self.walked)
return self.walked | python | def windows(self, window_size=60, context_len=90, step=10):
'''Walk through the sequence of interest in windows of window_size,
evaluate free (unbound) pair probabilities.
:param window_size: Window size in base pairs.
:type window_size: int
:param context_len: The number of bases of context to use when
analyzing each window.
:type context_len: int
:param step: The number of base pairs to move for each new window.
:type step: int
'''
self.walked = _context_walk(self.template, window_size, context_len,
step)
self.core_starts, self.core_ends, self.scores = zip(*self.walked)
return self.walked | [
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/analysis/_structure/structure_windows.py#L20-L36 | train | Walk through the sequence of interest in windows of window_size evaluate free pair probabilities. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(263 - 215) + chr(111) + chr(52) + '\x31', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(1130 - 1080) + chr(0b1011 + 0o52) + chr(0b110010), 0b1000), nzTpIcepk0o8(chr(0b11100 + 0o24) + chr(0b1101111) + '\x32' + '\067' + '\067', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x33' + chr(0b110001) + chr(1534 - 1481), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101110 + 0o1) + chr(50) + '\x31' + '\067', 10209 - 10201), nzTpIcepk0o8('\060' + '\x6f' + chr(0b1 + 0o62) + chr(55) + chr(0b101100 + 0o12), 27618 - 27610), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x32' + '\x31' + '\065', 0b1000), nzTpIcepk0o8('\x30' + chr(0b11010 + 0o125) + chr(0b110011) + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110011) + chr(54) + chr(1239 - 1186), 16970 - 16962), nzTpIcepk0o8(chr(2072 - 2024) + chr(0b1101111) + chr(381 - 332) + chr(51) + chr(0b110111), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b111 + 0o150) + chr(109 - 60) + chr(52) + chr(53), 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(2122 - 2071) + chr(0b110101) + chr(1173 - 1120), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + '\063' + chr(0b110101) + '\x37', 22611 - 22603), nzTpIcepk0o8('\x30' + chr(111) + chr(50) + chr(0b110110) + '\x31', 0b1000), nzTpIcepk0o8('\x30' + '\157' + '\x31' + chr(52) + chr(55), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(49) + chr(0b110101) + '\060', 0o10), nzTpIcepk0o8('\060' + '\157' + chr(371 - 318) + chr(1542 - 1492), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101101 + 0o2) + chr(0b101111 + 0o4) + chr(53), 0o10), nzTpIcepk0o8('\x30' + chr(0b111101 + 0o62) + chr(0b110011) + chr(50) + '\065', 12321 - 12313), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110001) + chr(0b100011 + 0o21) + '\x34', 0b1000), nzTpIcepk0o8('\060' + chr(0b1100000 + 0o17) + chr(704 - 653) + chr(52) + '\x35', ord("\x08")), nzTpIcepk0o8('\060' + chr(3159 - 3048) + chr(0b11100 + 0o25) + chr(54) + chr(406 - 352), 0b1000), nzTpIcepk0o8(chr(0b1011 + 0o45) + chr(111) + '\061' + chr(0b110100) + '\x37', 8), nzTpIcepk0o8('\060' + chr(0b1 + 0o156) + chr(52) + chr(60 - 7), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110010) + chr(0b10011 + 0o44), 0b1000), nzTpIcepk0o8(chr(991 - 943) + chr(0b1101111) + chr(1526 - 1476) + '\061', 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(49) + chr(50) + chr(1347 - 1296), 0o10), nzTpIcepk0o8('\060' + chr(510 - 399) + '\066', ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110001) + chr(0b10 + 0o64) + chr(959 - 909), 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(50) + chr(0b11101 + 0o26) + chr(0b110100 + 0o2), 0b1000), nzTpIcepk0o8('\x30' + chr(2524 - 2413) + chr(0b1 + 0o60) + chr(0b100010 + 0o23) + '\x32', 0o10), nzTpIcepk0o8(chr(48) + chr(10440 - 10329) + chr(0b100111 + 0o14) + chr(118 - 65), 8), nzTpIcepk0o8('\060' + chr(111) + chr(2567 - 2516) + chr(51) + chr(0b110111), 0o10), nzTpIcepk0o8('\x30' + chr(6203 - 6092) + chr(2029 - 1979) + chr(0b110110) + '\x35', ord("\x08")), nzTpIcepk0o8(chr(2064 - 2016) + chr(0b1101111) + chr(711 - 662) + chr(709 - 661) + chr(53), 44545 - 44537), nzTpIcepk0o8(chr(48) + chr(0b110 + 0o151) + chr(0b10011 + 0o36) + chr(0b110100) + '\x31', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1010011 + 0o34) + '\061' + chr(54) + chr(0b11110 + 0o23), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(4763 - 4652) + chr(0b110100) + chr(52), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110011) + chr(0b11010 + 0o27) + chr(55), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\065' + chr(51), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + '\157' + '\x35' + chr(0b11110 + 0o22), ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x0f'), chr(0b1100100) + '\145' + chr(2445 - 2346) + chr(0b1101111) + chr(0b110000 + 0o64) + '\x65')('\165' + chr(11925 - 11809) + chr(9568 - 9466) + '\055' + chr(2853 - 2797)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def hVZaXHr1SthH(hXMPsSrOQzbh, sr1jcqYH2Bwu=nzTpIcepk0o8(chr(290 - 242) + chr(1317 - 1206) + chr(0b110111) + chr(0b110100), 0o10), bnBrzmMDCqOX=nzTpIcepk0o8(chr(48) + chr(111) + chr(49) + chr(0b110011) + chr(1654 - 1604), ord("\x08")), ZiKB99Xs91Lo=nzTpIcepk0o8(chr(1988 - 1940) + chr(111) + chr(0b110001) + chr(883 - 833), 0o10)):
hXMPsSrOQzbh.yA55TqxNVw05 = MQkxG9TEJg08(hXMPsSrOQzbh.Pe8smzX7Gsur, sr1jcqYH2Bwu, bnBrzmMDCqOX, ZiKB99Xs91Lo)
(hXMPsSrOQzbh.U7FPsLY5vHOs, hXMPsSrOQzbh.b_dTXIfaRSn4, hXMPsSrOQzbh.EZCjrKz8Dzwm) = TxMFWa_Xzviv(*hXMPsSrOQzbh.yA55TqxNVw05)
return roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'X\xeb\x8a\xf8\xdb\x8f\xf5Q\xa3(U\xd8'), chr(0b101101 + 0o67) + chr(101) + '\143' + chr(111) + chr(0b101000 + 0o74) + '\x65')(chr(117) + chr(116) + chr(0b1100110) + chr(45) + '\070')) |
klavinslab/coral | coral/analysis/_structure/structure_windows.py | StructureWindows.plot | def plot(self):
'''Plot the results of the run method.'''
try:
from matplotlib import pylab
except ImportError:
raise ImportError('Optional dependency matplotlib not installed.')
if self.walked:
fig = pylab.figure()
ax1 = fig.add_subplot(111)
ax1.plot(self.core_starts, self.scores, 'bo-')
pylab.xlabel('Core sequence start position (base pairs).')
pylab.ylabel('Score - Probability of being unbound.')
pylab.show()
else:
raise Exception('Run calculate() first so there\'s data to plot!') | python | def plot(self):
'''Plot the results of the run method.'''
try:
from matplotlib import pylab
except ImportError:
raise ImportError('Optional dependency matplotlib not installed.')
if self.walked:
fig = pylab.figure()
ax1 = fig.add_subplot(111)
ax1.plot(self.core_starts, self.scores, 'bo-')
pylab.xlabel('Core sequence start position (base pairs).')
pylab.ylabel('Score - Probability of being unbound.')
pylab.show()
else:
raise Exception('Run calculate() first so there\'s data to plot!') | [
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"."
] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/analysis/_structure/structure_windows.py#L38-L53 | train | Plot the results of the run method. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8('\060' + '\x6f' + chr(0b11001 + 0o35) + '\x31', 0o10), nzTpIcepk0o8('\x30' + chr(111) + '\x35' + chr(0b110000), 0b1000), nzTpIcepk0o8(chr(2010 - 1962) + '\157' + chr(0b11 + 0o57) + chr(52), 0b1000), nzTpIcepk0o8(chr(0b101000 + 0o10) + chr(384 - 273) + '\063' + '\061' + chr(0b11 + 0o55), 50033 - 50025), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b100100 + 0o16) + chr(1828 - 1778), 0b1000), nzTpIcepk0o8(chr(0b110000 + 0o0) + '\x6f' + '\x32' + '\065' + '\067', 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(0b11 + 0o60) + chr(54), 62488 - 62480), nzTpIcepk0o8(chr(383 - 335) + chr(11795 - 11684) + chr(51) + chr(0b110110), 8), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b100110 + 0o16) + chr(183 - 128), ord("\x08")), nzTpIcepk0o8(chr(986 - 938) + chr(0b1111 + 0o140) + chr(420 - 369) + chr(0b110111) + chr(0b100011 + 0o16), 0o10), nzTpIcepk0o8(chr(50 - 2) + chr(0b1101111) + chr(55), 0b1000), nzTpIcepk0o8(chr(804 - 756) + chr(0b1101111) + chr(2159 - 2110) + '\060' + chr(49), 0b1000), nzTpIcepk0o8('\x30' + chr(3508 - 3397) + '\x31' + chr(50) + chr(0b10 + 0o57), 0o10), nzTpIcepk0o8(chr(460 - 412) + chr(8904 - 8793) + chr(2339 - 2288) + '\x31' + '\x33', 0b1000), nzTpIcepk0o8('\060' + '\157' + '\x32' + chr(0b101111 + 0o1) + chr(996 - 947), 34138 - 34130), nzTpIcepk0o8('\060' + '\157' + chr(0b100110 + 0o13) + chr(0b110110) + chr(53), 0o10), nzTpIcepk0o8(chr(2107 - 2059) + '\x6f' + chr(1640 - 1590) + '\060' + chr(0b110111), 0o10), nzTpIcepk0o8('\x30' + '\157' + '\062' + chr(53), 0b1000), nzTpIcepk0o8(chr(2019 - 1971) + chr(0b111010 + 0o65) + chr(0b1 + 0o60) + '\x30' + '\x30', 0o10), nzTpIcepk0o8(chr(0b110 + 0o52) + chr(111) + chr(54) + chr(48), 6256 - 6248), nzTpIcepk0o8(chr(78 - 30) + chr(6263 - 6152) + chr(1391 - 1340) + chr(0b11001 + 0o27) + chr(50), 0b1000), nzTpIcepk0o8(chr(48) + chr(417 - 306) + chr(0b100011 + 0o17) + chr(0b110011 + 0o0) + chr(0b110011), 11554 - 11546), nzTpIcepk0o8(chr(48) + chr(0b1100011 + 0o14) + '\061' + chr(0b101110 + 0o10) + chr(1918 - 1868), 0o10), nzTpIcepk0o8('\x30' + chr(111) + '\065' + chr(0b1101 + 0o43), 8), nzTpIcepk0o8('\x30' + chr(796 - 685) + chr(0b10001 + 0o40) + chr(0b110110) + '\x31', 50398 - 50390), nzTpIcepk0o8(chr(1378 - 1330) + chr(111) + chr(51) + chr(621 - 572) + chr(1218 - 1168), ord("\x08")), nzTpIcepk0o8(chr(1901 - 1853) + chr(0b10010 + 0o135) + chr(51) + chr(1056 - 1008) + chr(52), 32974 - 32966), nzTpIcepk0o8(chr(0b11001 + 0o27) + '\x6f' + chr(50) + '\x36' + chr(1144 - 1096), 38015 - 38007), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b11000 + 0o32) + chr(0b110010) + '\066', 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + '\x34' + chr(52), 59400 - 59392), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\067' + chr(51), 23269 - 23261), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x33' + chr(0b1 + 0o57) + chr(50), 8), nzTpIcepk0o8(chr(0b110000) + chr(11255 - 11144) + chr(55) + '\x30', 60091 - 60083), nzTpIcepk0o8(chr(48) + chr(111) + chr(1892 - 1841) + chr(0b110010 + 0o3), 0b1000), nzTpIcepk0o8(chr(589 - 541) + '\x6f' + chr(51) + chr(0b110011) + chr(0b100000 + 0o20), 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110 + 0o53) + chr(0b101111 + 0o3) + chr(0b110010), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110001) + '\x35' + chr(737 - 688), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(1351 - 1301) + chr(1563 - 1513) + chr(0b110111), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(989 - 938) + chr(0b10011 + 0o41) + '\064', ord("\x08")), nzTpIcepk0o8('\060' + chr(8810 - 8699) + '\061' + chr(0b110110), 45537 - 45529)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b11100 + 0o24) + chr(0b1101111) + '\065' + chr(48), 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x1f'), '\144' + '\x65' + '\x63' + chr(3490 - 3379) + chr(0b1100100) + '\145')(chr(0b1110011 + 0o2) + chr(0b1110100) + '\x66' + chr(45) + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def mocO8sWgkzH7(hXMPsSrOQzbh):
try:
(s895axJpHMpz,) = (roI3spqORKae(rFFUeiYWzOhx(roI3spqORKae(ES5oEprVxulp(b'\\I`\xb8~\xc0jrN\x9b'), chr(100) + chr(0b10 + 0o143) + chr(2024 - 1925) + chr(0b1000111 + 0o50) + '\x64' + chr(2314 - 2213))(chr(11529 - 11412) + chr(2698 - 2582) + chr(0b1100110) + chr(0b101101) + chr(56)), roI3spqORKae(ES5oEprVxulp(b'AQx\xa9p'), '\144' + chr(101) + chr(99) + '\x6f' + chr(100) + chr(741 - 640))('\x75' + '\164' + chr(0b11011 + 0o113) + chr(0b100000 + 0o15) + chr(1466 - 1410))), roI3spqORKae(ES5oEprVxulp(b'AQx\xa9p'), chr(0b1100100) + chr(0b1100101) + chr(0b1100011 + 0o0) + chr(0b110000 + 0o77) + chr(0b1100100) + chr(0b1100101))(chr(0b11101 + 0o130) + chr(9193 - 9077) + chr(0b10111 + 0o117) + '\055' + chr(0b111000))),)
except fPFTJxVnGShv:
raise fPFTJxVnGShv(roI3spqORKae(ES5oEprVxulp(b'~X`\xa1}\xc1\x7fr\x07\x9db14\xa5\xe5\x10\xe9v9\x10\xaf\xfa\x06X\x1d\xa5\xb0\xdc\xffF\x1b\xacWi\xf8;\x07\xe4\x90o]Dq\xac<'), chr(100) + chr(0b1100101) + chr(99) + chr(0b1101001 + 0o6) + chr(4568 - 4468) + chr(0b1000000 + 0o45))('\165' + chr(0b1101001 + 0o13) + chr(10033 - 9931) + '\x2d' + chr(951 - 895)))
if roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'Hi!\xfdF\xdefPq\x8e7t'), chr(0b1100100) + chr(6441 - 6340) + chr(4473 - 4374) + '\157' + chr(0b1100100) + chr(0b1100101))('\165' + '\x74' + chr(0b11101 + 0o111) + chr(0b101101) + chr(0b101100 + 0o14))):
ux0XlXMUdKbX = s895axJpHMpz.es0Z6dzChSL5()
zKeNdjqvSKqz = ux0XlXMUdKbX.add_subplot(nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110001) + chr(0b1 + 0o64) + chr(55), ord("\x08")))
roI3spqORKae(zKeNdjqvSKqz, roI3spqORKae(ES5oEprVxulp(b'AD{\xbc'), chr(0b1100100) + '\x65' + '\x63' + chr(0b111111 + 0o60) + '\x64' + chr(101))('\x75' + '\x74' + chr(0b101111 + 0o67) + chr(0b10010 + 0o33) + '\x38'))(roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'd\x1fR\x98a\xe3G+Q\xb1H2'), chr(6487 - 6387) + '\145' + '\143' + chr(0b1101111) + '\x64' + chr(0b1101 + 0o130))(chr(0b1000101 + 0o60) + chr(0b1110100) + chr(102) + '\055' + chr(2550 - 2494))), roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'trW\xa2`\xe4d&c\x83p,'), chr(443 - 343) + '\x65' + chr(0b1010001 + 0o22) + chr(11037 - 10926) + chr(0b1100100) + chr(101))(chr(117) + chr(9501 - 9385) + chr(102) + '\x2d' + '\070')), roI3spqORKae(ES5oEprVxulp(b'SG9'), chr(0b11101 + 0o107) + chr(0b1100101) + '\143' + '\x6f' + chr(0b1100100) + '\x65')('\165' + chr(0b1101001 + 0o13) + chr(102) + '\x2d' + chr(0b111000)))
roI3spqORKae(s895axJpHMpz, roI3spqORKae(ES5oEprVxulp(b'IDu\xaaw\xc3'), chr(4746 - 4646) + chr(101) + chr(0b110011 + 0o60) + '\x6f' + '\144' + chr(0b1100101))('\165' + '\164' + chr(0b10100 + 0o122) + chr(0b100001 + 0o14) + chr(56)))(roI3spqORKae(ES5oEprVxulp(b'rGf\xad2\xdc{oR\x9ci"4\xeb\xf2\x01\xe6g4\x10\xb2\xf4\x01A\x05\xa3\xab\xde\xb6\x0cY\xa3Kx\xf8"\x08\xfe\x96}\x18\x06'), chr(0b1100100) + chr(0b1100101) + chr(0b1001 + 0o132) + chr(0b1001 + 0o146) + '\x64' + chr(101))(chr(117) + '\x74' + chr(102) + chr(0b101101) + '\070'))
roI3spqORKae(s895axJpHMpz, roI3spqORKae(ES5oEprVxulp(b'HDu\xaaw\xc3'), chr(100) + chr(0b10001 + 0o124) + '\143' + chr(8079 - 7968) + chr(0b111010 + 0o52) + '\145')('\x75' + '\164' + '\146' + chr(0b1111 + 0o36) + chr(56)))(roI3spqORKae(ES5oEprVxulp(b'bK{\xbaw\x8f3>w\x8bh#0\xa9\xe8\x19\xeea9\x10\xad\xfdRJ\x14\xa3\xaa\xd7\xb6QU\xa0Wh\xb66G'), '\x64' + chr(0b1 + 0o144) + '\x63' + chr(0b110001 + 0o76) + chr(0b1100100) + '\x65')('\x75' + chr(116) + chr(0b11 + 0o143) + chr(0b10011 + 0o32) + '\070'))
roI3spqORKae(s895axJpHMpz, roI3spqORKae(ES5oEprVxulp(b'W\x7fQ\xa5w\xe7Ijx\xa6K;'), '\x64' + chr(0b111111 + 0o46) + '\x63' + chr(0b1101111) + '\x64' + chr(986 - 885))(chr(5471 - 5354) + chr(0b1110100) + chr(9771 - 9669) + chr(45) + chr(56)))()
else:
raise zfo2Sgkz3IVJ(roI3spqORKae(ES5oEprVxulp(b'c]z\xe8q\xcer}R\x95f54\xe3\xa8U\xe1|2C\xb6\xbb\x01GQ\xbe\xac\xd5\xe4A\x1c\xb1\x18y\xb9&\x08\xb7\x90a\x11Xx\xa7f\x8e'), chr(0b1001101 + 0o27) + chr(6138 - 6037) + chr(0b1001111 + 0o24) + chr(111) + chr(100) + '\x65')('\x75' + chr(116) + '\146' + chr(0b101010 + 0o3) + chr(0b111000))) |
klavinslab/coral | coral/analysis/_sequence/anneal.py | anneal | def anneal(template, primer, min_tm=50.0, min_len=10):
'''Simulates a primer binding event. Will find the maximum subset
of bases in the primer that binds to the template, including overhang
sequences. **Note**: Primer binding locations indicate the 3' end of the
primer, not the begining of the annealing sequence.
:param template: DNA template for which to bind a primer.
:type template: coral.DNA
:param primer: Primer to bind to template.
:type primer: coral.Primer
:param min_tm: The cutoff melting temperature for primer binding - a binder
with a lower Tm will be rejected.
:type min_tm: float
:param min_len: The cutoff for bases required for binding - a binder with
fewer bases will be rejected.
:type min_len: int
:returns: A length 2 list (top and bottom strands) of matches. Each
match is itself a 2-tuple indicating (1) the location on the
template of the 3' end of the primer binding site and (2) the
length of the match (number of bases), e.g. [[(25, 15)],[]] would
indicate a single top-strand match at template position 25 with
15 bases of 3' primer homology.
:rtype: list
:raises: PrimerLengthError if primer length is too small.
AnnealError if inputs are of the wrong type.
'''
# TODO: add possibility for primer basepair mismatch
if len(primer) < min_len:
msg = 'Primer length is shorter than min_len argument.'
raise PrimerLengthError(msg)
if len(template) < min_len:
msg = 'Template is shorter than the min_len argument.'
raise AnnealError(msg)
# Strategy: locate all min-length matches, then extend them until they
# no longer match. This provides an advantage over the previous strategy of
# updating a dictionary with indices from coral.DNA.locate() as keys, as
# the latter's indices may actually move for a given primer as it passes
# over the origin
def update_match_linear(base, location_length, anneal_seq):
'''Increase the location and length of binding site, if applicable.'''
# TODO: this is very inefficient - should stop updating once the first
# mismatch occurs.
location, length = location_length
if location == 0:
return location_length
location_next = location - 1
length_next = length + 1
seq = base[location_next:location_next + length_next]
if seq == anneal_seq:
return (location_next, length_next)
else:
return location_length
def update_match_circular(base, location_length, anneal_seq):
'''Increase the location and length of binding site, if applicable.'''
# TODO: this is very inefficient - should stop updating once the first
# mismatch occurs.
base_len = len(base)
location, length = location_length
if location == 0:
location_next = base_len - 1
else:
location_next = location - 1
length_next = length + 1
if (location_next + length_next) > base_len:
upstream = base[location_next:]
downstream = base[:length_next - (base_len - location_next)]
seq = upstream + downstream
else:
# No need to 'rotate' sequence
seq = base[location_next:location_next + length_next]
if seq == anneal_seq:
return (location_next, length_next)
else:
return location_length
if template.circular:
update_fun = update_match_circular
else:
update_fun = update_match_linear
# Maximum annealing length to test (can't exceed template length)
max_len = min(len(template), len(primer))
primer_dna = primer.to_ds()
anneal_len = min_len
anneal_seq = primer_dna[-anneal_len:]
binding_data = []
for k, strand_locs in enumerate(template.locate(anneal_seq)):
matches = zip(strand_locs, [min_len] * len(strand_locs))
for i in range(anneal_len + 1, max_len + 1):
anneal_seq = primer_dna[-i:]
for j, match in enumerate(matches):
if k == 0:
matches[j] = update_fun(template.top, match, anneal_seq)
else:
matches[j] = update_fun(template.bottom, match,
anneal_seq)
binding_data.append(matches)
# Now, filter out all the matches that are too short
for i in reversed(range(len(primer_dna) + 1)):
min_len = i + 1
tm = primer_dna[-min_len:].tm()
if tm < min_tm:
break
for strand in binding_data:
for i in reversed(range(len(strand))):
if strand[i][1] < min_len:
strand.pop(i)
# Finally, adjust the position to be the 3' end
for strand in binding_data:
for i, match in enumerate(strand):
length = match[1]
loc_new = match[0] + length
if loc_new > len(template):
# Circularly permute
loc_new = loc_new - len(template)
strand[i] = [loc_new, length]
# Overwriting dictionary keys ensures uniqueness
# fwd_matches = {}
# rev_matches = {}
# for i in range(len(primer) - min_len + 1)[::-1]:
# primer_dna = primer.overhang + primer.anneal
# annealing = primer_dna[i:]
# anneal_temp = annealing.tm()
# anneal_len = len(annealing)
# if anneal_temp > min_tm:
# p_matches = template.locate(annealing)
# for match in p_matches[0]:
# fwd_matches[match + anneal_len] = anneal_len
# for match in p_matches[1]:
# rev_matches[match + anneal_len] = anneal_len
# # Convert dictionaries to lists
# fwds = [[key, val] for key, val in fwd_matches.iteritems()]
# revs = [[key, val] for key, val in rev_matches.iteritems()]
return binding_data | python | def anneal(template, primer, min_tm=50.0, min_len=10):
'''Simulates a primer binding event. Will find the maximum subset
of bases in the primer that binds to the template, including overhang
sequences. **Note**: Primer binding locations indicate the 3' end of the
primer, not the begining of the annealing sequence.
:param template: DNA template for which to bind a primer.
:type template: coral.DNA
:param primer: Primer to bind to template.
:type primer: coral.Primer
:param min_tm: The cutoff melting temperature for primer binding - a binder
with a lower Tm will be rejected.
:type min_tm: float
:param min_len: The cutoff for bases required for binding - a binder with
fewer bases will be rejected.
:type min_len: int
:returns: A length 2 list (top and bottom strands) of matches. Each
match is itself a 2-tuple indicating (1) the location on the
template of the 3' end of the primer binding site and (2) the
length of the match (number of bases), e.g. [[(25, 15)],[]] would
indicate a single top-strand match at template position 25 with
15 bases of 3' primer homology.
:rtype: list
:raises: PrimerLengthError if primer length is too small.
AnnealError if inputs are of the wrong type.
'''
# TODO: add possibility for primer basepair mismatch
if len(primer) < min_len:
msg = 'Primer length is shorter than min_len argument.'
raise PrimerLengthError(msg)
if len(template) < min_len:
msg = 'Template is shorter than the min_len argument.'
raise AnnealError(msg)
# Strategy: locate all min-length matches, then extend them until they
# no longer match. This provides an advantage over the previous strategy of
# updating a dictionary with indices from coral.DNA.locate() as keys, as
# the latter's indices may actually move for a given primer as it passes
# over the origin
def update_match_linear(base, location_length, anneal_seq):
'''Increase the location and length of binding site, if applicable.'''
# TODO: this is very inefficient - should stop updating once the first
# mismatch occurs.
location, length = location_length
if location == 0:
return location_length
location_next = location - 1
length_next = length + 1
seq = base[location_next:location_next + length_next]
if seq == anneal_seq:
return (location_next, length_next)
else:
return location_length
def update_match_circular(base, location_length, anneal_seq):
'''Increase the location and length of binding site, if applicable.'''
# TODO: this is very inefficient - should stop updating once the first
# mismatch occurs.
base_len = len(base)
location, length = location_length
if location == 0:
location_next = base_len - 1
else:
location_next = location - 1
length_next = length + 1
if (location_next + length_next) > base_len:
upstream = base[location_next:]
downstream = base[:length_next - (base_len - location_next)]
seq = upstream + downstream
else:
# No need to 'rotate' sequence
seq = base[location_next:location_next + length_next]
if seq == anneal_seq:
return (location_next, length_next)
else:
return location_length
if template.circular:
update_fun = update_match_circular
else:
update_fun = update_match_linear
# Maximum annealing length to test (can't exceed template length)
max_len = min(len(template), len(primer))
primer_dna = primer.to_ds()
anneal_len = min_len
anneal_seq = primer_dna[-anneal_len:]
binding_data = []
for k, strand_locs in enumerate(template.locate(anneal_seq)):
matches = zip(strand_locs, [min_len] * len(strand_locs))
for i in range(anneal_len + 1, max_len + 1):
anneal_seq = primer_dna[-i:]
for j, match in enumerate(matches):
if k == 0:
matches[j] = update_fun(template.top, match, anneal_seq)
else:
matches[j] = update_fun(template.bottom, match,
anneal_seq)
binding_data.append(matches)
# Now, filter out all the matches that are too short
for i in reversed(range(len(primer_dna) + 1)):
min_len = i + 1
tm = primer_dna[-min_len:].tm()
if tm < min_tm:
break
for strand in binding_data:
for i in reversed(range(len(strand))):
if strand[i][1] < min_len:
strand.pop(i)
# Finally, adjust the position to be the 3' end
for strand in binding_data:
for i, match in enumerate(strand):
length = match[1]
loc_new = match[0] + length
if loc_new > len(template):
# Circularly permute
loc_new = loc_new - len(template)
strand[i] = [loc_new, length]
# Overwriting dictionary keys ensures uniqueness
# fwd_matches = {}
# rev_matches = {}
# for i in range(len(primer) - min_len + 1)[::-1]:
# primer_dna = primer.overhang + primer.anneal
# annealing = primer_dna[i:]
# anneal_temp = annealing.tm()
# anneal_len = len(annealing)
# if anneal_temp > min_tm:
# p_matches = template.locate(annealing)
# for match in p_matches[0]:
# fwd_matches[match + anneal_len] = anneal_len
# for match in p_matches[1]:
# rev_matches[match + anneal_len] = anneal_len
# # Convert dictionaries to lists
# fwds = [[key, val] for key, val in fwd_matches.iteritems()]
# revs = [[key, val] for key, val in rev_matches.iteritems()]
return binding_data | [
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"'Primer length is shorter... | Simulates a primer binding event. Will find the maximum subset
of bases in the primer that binds to the template, including overhang
sequences. **Note**: Primer binding locations indicate the 3' end of the
primer, not the begining of the annealing sequence.
:param template: DNA template for which to bind a primer.
:type template: coral.DNA
:param primer: Primer to bind to template.
:type primer: coral.Primer
:param min_tm: The cutoff melting temperature for primer binding - a binder
with a lower Tm will be rejected.
:type min_tm: float
:param min_len: The cutoff for bases required for binding - a binder with
fewer bases will be rejected.
:type min_len: int
:returns: A length 2 list (top and bottom strands) of matches. Each
match is itself a 2-tuple indicating (1) the location on the
template of the 3' end of the primer binding site and (2) the
length of the match (number of bases), e.g. [[(25, 15)],[]] would
indicate a single top-strand match at template position 25 with
15 bases of 3' primer homology.
:rtype: list
:raises: PrimerLengthError if primer length is too small.
AnnealError if inputs are of the wrong type. | [
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"... | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/analysis/_sequence/anneal.py#L12-L160 | train | Simulates a primer binding event. Will find the maximum subset of basepairs in the primer that binds to the template and extend them until the maximum basepair is found. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x31' + chr(0b10101 + 0o40) + '\x33', 0b1000), nzTpIcepk0o8('\060' + chr(0b1001000 + 0o47) + chr(954 - 905) + chr(0b110110) + chr(0b101101 + 0o4), 33224 - 33216), nzTpIcepk0o8('\x30' + chr(111) + chr(0b0 + 0o61) + chr(52) + chr(0b110110), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\067' + chr(1403 - 1350), 0o10), nzTpIcepk0o8(chr(1117 - 1069) + chr(0b1100011 + 0o14) + chr(0b110011) + chr(1538 - 1484) + '\x35', 0b1000), nzTpIcepk0o8(chr(0b11000 + 0o30) + '\157' + chr(53) + chr(53), 0o10), nzTpIcepk0o8(chr(0b100110 + 0o12) + chr(4032 - 3921) + chr(0b110 + 0o55) + chr(0b110000) + chr(55), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + '\061' + '\064' + '\x31', 21314 - 21306), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110011) + '\067' + '\x30', 54857 - 54849), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110010) + chr(0b10000 + 0o44) + chr(50), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(0b110001) + '\x30' + chr(244 - 192), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + '\x33' + chr(50) + '\063', ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(0b11001 + 0o32) + '\x32' + '\064', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110010) + chr(50), 0b1000), nzTpIcepk0o8('\x30' + chr(2126 - 2015) + chr(0b11100 + 0o26) + chr(0b110101) + '\067', ord("\x08")), nzTpIcepk0o8(chr(0b101000 + 0o10) + '\157' + chr(2319 - 2269) + chr(52) + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(0b1011 + 0o45) + chr(111) + chr(2487 - 2436) + chr(0b110011) + '\061', 4830 - 4822), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(51) + chr(1351 - 1300), 0o10), nzTpIcepk0o8(chr(1292 - 1244) + chr(0b1101111) + chr(0b100110 + 0o14) + chr(0b110101) + chr(0b10101 + 0o42), 8), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110001) + chr(0b110110) + '\061', 8), nzTpIcepk0o8(chr(48) + chr(9556 - 9445) + '\x33' + '\060' + chr(0b110110), 49556 - 49548), nzTpIcepk0o8(chr(48) + '\x6f' + '\x32' + '\064', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110010) + '\063' + chr(0b110101), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1011111 + 0o20) + chr(0b100011 + 0o16) + chr(0b100011 + 0o23) + '\065', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(53) + chr(0b101100 + 0o6), 53122 - 53114), nzTpIcepk0o8(chr(535 - 487) + '\157' + '\x32' + '\x34' + chr(49), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(51) + '\066' + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(0b1001 + 0o47) + '\x6f' + chr(0b11111 + 0o27) + '\x32', 19245 - 19237), nzTpIcepk0o8('\x30' + '\157' + chr(1925 - 1875) + '\x35', 45829 - 45821), nzTpIcepk0o8('\x30' + '\157' + chr(1889 - 1839) + chr(0b110000 + 0o1) + '\060', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1000111 + 0o50) + chr(50) + chr(1380 - 1325) + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110001) + '\061' + chr(54), 33734 - 33726), nzTpIcepk0o8(chr(1323 - 1275) + '\157' + chr(974 - 924) + '\x36' + chr(1213 - 1163), 0b1000), nzTpIcepk0o8(chr(2070 - 2022) + '\x6f' + '\x31' + chr(52) + '\065', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(2387 - 2338) + '\x34' + chr(185 - 134), ord("\x08")), nzTpIcepk0o8(chr(0b100101 + 0o13) + chr(0b1101111) + chr(355 - 304) + '\065' + chr(2157 - 2105), 51317 - 51309), nzTpIcepk0o8(chr(0b100010 + 0o16) + chr(0b101111 + 0o100) + '\061' + chr(0b110000 + 0o1), 6088 - 6080), nzTpIcepk0o8('\x30' + chr(0b10000 + 0o137) + '\x31' + chr(0b110100) + chr(128 - 75), 8), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(50) + '\065' + chr(2290 - 2240), ord("\x08")), nzTpIcepk0o8(chr(99 - 51) + chr(2212 - 2101) + chr(0b100011 + 0o17) + '\x34', 8)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(111) + '\065' + '\x30', ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'E'), chr(0b1100100) + chr(0b1100101) + '\x63' + chr(111) + '\x64' + chr(0b1100101))('\165' + chr(0b111110 + 0o66) + '\x66' + chr(45) + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def p0Q1fRxPswvI(Pe8smzX7Gsur, thHp9mlDSVMt, _xMdwXUWHWlj=50.0, Lif6FAYA6nmJ=nzTpIcepk0o8(chr(48) + chr(4703 - 4592) + chr(0b110001) + chr(50), ord("\x08"))):
if ftfygxgFas5X(thHp9mlDSVMt) < Lif6FAYA6nmJ:
sldzbHve8G1S = roI3spqORKae(ES5oEprVxulp(b";\x03\x0fP\x90_\xe7\r\x9d\xcc#\xa7\xbc2\xc6\xd4\xf9h\xc7\x1e\xb4`\xf8\x07\n\xd5\x9fS{\xa8\xd2'\xdc:\x0f\x89gE\xcbf\x0c\x04\x0bX\x9bY\xe9"), '\x64' + chr(101) + chr(99) + chr(1224 - 1113) + '\x64' + chr(597 - 496))(chr(0b1110101) + '\164' + '\x66' + '\x2d' + chr(0b111000))
raise MO5KRu_kOMX4(sldzbHve8G1S)
if ftfygxgFas5X(Pe8smzX7Gsur) < Lif6FAYA6nmJ:
sldzbHve8G1S = roI3spqORKae(ES5oEprVxulp(b'?\x14\x0bM\x99L\xb3\x04\xd8\xcb7\xf3\xa7z\xc0\xd5\xad~\xddQ\xb2|\xfc\x1b\n\xd5\x9fW5\xe5\xd6 \xed\t\x06\x82)\x04\xd8s\x1e\x1c\x03S\x81\x03'), '\x64' + chr(0b1100101) + chr(0b1100011) + chr(0b110111 + 0o70) + chr(0b1100100) + '\145')(chr(0b1 + 0o164) + '\x74' + chr(0b1100110) + chr(0b101101) + chr(0b1101 + 0o53))
raise Mv1K_HFUeokR(sldzbHve8G1S)
def ZmjzRf72UxjD(xvptlew7LsBo, oym1CzAmE4cd, w9JbS6N8ub9R):
(y87dwGy_Qoj4, a1RCQZREo3Kd) = oym1CzAmE4cd
if y87dwGy_Qoj4 == nzTpIcepk0o8(chr(0b10001 + 0o37) + '\157' + chr(0b10101 + 0o33), ord("\x08")):
return oym1CzAmE4cd
G1rWfvtArtx6 = y87dwGy_Qoj4 - nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(1197 - 1148), 0b1000)
xltktxb4esnm = a1RCQZREo3Kd + nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\061', 8)
ftk9lc7G5FOo = xvptlew7LsBo[G1rWfvtArtx6:G1rWfvtArtx6 + xltktxb4esnm]
if ftk9lc7G5FOo == w9JbS6N8ub9R:
return (G1rWfvtArtx6, xltktxb4esnm)
else:
return oym1CzAmE4cd
def pJ8rG8d1tNgU(xvptlew7LsBo, oym1CzAmE4cd, w9JbS6N8ub9R):
lOOTjb4Zchyc = ftfygxgFas5X(xvptlew7LsBo)
(y87dwGy_Qoj4, a1RCQZREo3Kd) = oym1CzAmE4cd
if y87dwGy_Qoj4 == nzTpIcepk0o8(chr(664 - 616) + chr(111) + chr(2099 - 2051), 8):
G1rWfvtArtx6 = lOOTjb4Zchyc - nzTpIcepk0o8('\x30' + chr(1453 - 1342) + chr(49), 8)
else:
G1rWfvtArtx6 = y87dwGy_Qoj4 - nzTpIcepk0o8(chr(0b110000 + 0o0) + '\x6f' + chr(0b110001), 8)
xltktxb4esnm = a1RCQZREo3Kd + nzTpIcepk0o8('\x30' + '\x6f' + '\061', 8)
if G1rWfvtArtx6 + xltktxb4esnm > lOOTjb4Zchyc:
WTOmH_cKH_WR = xvptlew7LsBo[G1rWfvtArtx6:]
aYhWa46FHcnf = xvptlew7LsBo[:xltktxb4esnm - (lOOTjb4Zchyc - G1rWfvtArtx6)]
ftk9lc7G5FOo = WTOmH_cKH_WR + aYhWa46FHcnf
else:
ftk9lc7G5FOo = xvptlew7LsBo[G1rWfvtArtx6:G1rWfvtArtx6 + xltktxb4esnm]
if ftk9lc7G5FOo == w9JbS6N8ub9R:
return (G1rWfvtArtx6, xltktxb4esnm)
else:
return oym1CzAmE4cd
if roI3spqORKae(Pe8smzX7Gsur, roI3spqORKae(ES5oEprVxulp(b'\x08\x18\x14^\x80A\xa6\x13'), chr(0b110000 + 0o64) + chr(0b10100 + 0o121) + chr(0b10001 + 0o122) + chr(0b1000 + 0o147) + '\x64' + chr(2256 - 2155))('\165' + chr(12251 - 12135) + chr(0b11110 + 0o110) + '\x2d' + chr(0b111000))):
N7VRPTVBydPa = pJ8rG8d1tNgU
else:
N7VRPTVBydPa = ZmjzRf72UxjD
JVxan5ttzsBT = XURpmPuEWCNF(ftfygxgFas5X(Pe8smzX7Gsur), ftfygxgFas5X(thHp9mlDSVMt))
Md7iQpLY4j_N = thHp9mlDSVMt.to_ds()
tlAltg9307NG = Lif6FAYA6nmJ
w9JbS6N8ub9R = Md7iQpLY4j_N[-tlAltg9307NG:]
SGKzfUQil5Tx = []
for (B6UAF1zReOyJ, OJNmYNEvZ4BF) in _kV_Bomx8PZ4(roI3spqORKae(Pe8smzX7Gsur, roI3spqORKae(ES5oEprVxulp(b'\x07\x1e\x05\\\x81H'), chr(0b101 + 0o137) + chr(101) + chr(0b1100011) + '\157' + chr(100) + chr(9815 - 9714))(chr(0b1110101) + chr(549 - 433) + chr(102) + '\055' + chr(56)))(w9JbS6N8ub9R)):
ONopK8INb53O = TxMFWa_Xzviv(OJNmYNEvZ4BF, [Lif6FAYA6nmJ] * ftfygxgFas5X(OJNmYNEvZ4BF))
for ZlbFMSG8gCoF in bbT2xIe5pzk7(tlAltg9307NG + nzTpIcepk0o8(chr(0b110000) + chr(4477 - 4366) + chr(0b100 + 0o55), 8), JVxan5ttzsBT + nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110001), 8)):
w9JbS6N8ub9R = Md7iQpLY4j_N[-ZlbFMSG8gCoF:]
for (sChW4gUsXrIC, hk9OijmiC_zA) in _kV_Bomx8PZ4(ONopK8INb53O):
if B6UAF1zReOyJ == nzTpIcepk0o8(chr(2091 - 2043) + '\157' + '\x30', 8):
ONopK8INb53O[sChW4gUsXrIC] = N7VRPTVBydPa(Pe8smzX7Gsur.A2AC7Zsqx_Vf, hk9OijmiC_zA, w9JbS6N8ub9R)
else:
ONopK8INb53O[sChW4gUsXrIC] = N7VRPTVBydPa(Pe8smzX7Gsur.bottom, hk9OijmiC_zA, w9JbS6N8ub9R)
roI3spqORKae(SGKzfUQil5Tx, roI3spqORKae(ES5oEprVxulp(b'#%5\t\x8dJ\x80\x0e\x92\xcd\x11\xe6'), chr(2696 - 2596) + '\x65' + chr(0b11011 + 0o110) + '\x6f' + chr(0b110110 + 0o56) + chr(101))(chr(0b1110101) + chr(0b1110100) + '\x66' + chr(45) + '\x38'))(ONopK8INb53O)
for ZlbFMSG8gCoF in DoS4vLAglV8A(bbT2xIe5pzk7(ftfygxgFas5X(Md7iQpLY4j_N) + nzTpIcepk0o8(chr(1040 - 992) + chr(111) + '\061', 8))):
Lif6FAYA6nmJ = ZlbFMSG8gCoF + nzTpIcepk0o8(chr(1123 - 1075) + chr(0b1010100 + 0o33) + '\061', 8)
VH5NUDuH5Da3 = Md7iQpLY4j_N[-Lif6FAYA6nmJ:].VH5NUDuH5Da3()
if VH5NUDuH5Da3 < _xMdwXUWHWlj:
break
for sOvPdpw6JkD6 in SGKzfUQil5Tx:
for ZlbFMSG8gCoF in DoS4vLAglV8A(bbT2xIe5pzk7(ftfygxgFas5X(sOvPdpw6JkD6))):
if sOvPdpw6JkD6[ZlbFMSG8gCoF][nzTpIcepk0o8(chr(48) + chr(111) + chr(1896 - 1847), 8)] < Lif6FAYA6nmJ:
roI3spqORKae(sOvPdpw6JkD6, roI3spqORKae(ES5oEprVxulp(b'\x1e29d\x9aT\xa5\x19\xcf\xe8t\x9a'), chr(0b101001 + 0o73) + chr(0b1100101) + chr(2420 - 2321) + '\x6f' + '\144' + '\145')('\165' + chr(0b1110100) + '\x66' + chr(0b11101 + 0o20) + '\x38'))(ZlbFMSG8gCoF)
for sOvPdpw6JkD6 in SGKzfUQil5Tx:
for (ZlbFMSG8gCoF, hk9OijmiC_zA) in _kV_Bomx8PZ4(sOvPdpw6JkD6):
a1RCQZREo3Kd = hk9OijmiC_zA[nzTpIcepk0o8(chr(0b100001 + 0o17) + chr(111) + chr(0b1011 + 0o46), 8)]
UsIhzNz0w3aB = hk9OijmiC_zA[nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\060', 8)] + a1RCQZREo3Kd
if UsIhzNz0w3aB > ftfygxgFas5X(Pe8smzX7Gsur):
UsIhzNz0w3aB = UsIhzNz0w3aB - ftfygxgFas5X(Pe8smzX7Gsur)
sOvPdpw6JkD6[ZlbFMSG8gCoF] = [UsIhzNz0w3aB, a1RCQZREo3Kd]
return SGKzfUQil5Tx |
klavinslab/coral | coral/design/_primers.py | primer | def primer(dna, tm=65, min_len=10, tm_undershoot=1, tm_overshoot=3,
end_gc=False, tm_parameters='cloning', overhang=None,
structure=False):
'''Design primer to a nearest-neighbor Tm setpoint.
:param dna: Sequence for which to design a primer.
:type dna: coral.DNA
:param tm: Ideal primer Tm in degrees C.
:type tm: float
:param min_len: Minimum primer length.
:type min_len: int
:param tm_undershoot: Allowed Tm undershoot.
:type tm_undershoot: float
:param tm_overshoot: Allowed Tm overshoot.
:type tm_overshoot: float
:param end_gc: Obey the 'end on G or C' rule.
:type end_gc: bool
:param tm_parameters: Melting temp calculator method to use.
:type tm_parameters: string
:param overhang: Append the primer to this overhang sequence.
:type overhang: str
:param structure: Evaluate primer for structure, with warning for high
structure.
:type structure: bool
:returns: A primer.
:rtype: coral.Primer
:raises: ValueError if the input sequence is lower than the Tm settings
allow.
ValueError if a primer ending with G or C can't be found given
the Tm settings.
'''
# Check Tm of input sequence to see if it's already too low
seq_tm = coral.analysis.tm(dna, parameters=tm_parameters)
if seq_tm < (tm - tm_undershoot):
msg = 'Input sequence Tm is lower than primer Tm setting'
raise ValueError(msg)
# Focus on first 90 bases - shouldn't need more than 90bp to anneal
dna = dna[0:90]
# Generate primers from min_len to 'tm' + tm_overshoot
# TODO: this is a good place for optimization. Only calculate as many
# primers as are needed. Use binary search.
primers_tms = []
last_tm = 0
bases = min_len
while last_tm <= tm + tm_overshoot and bases != len(dna):
next_primer = dna[0:bases]
last_tm = coral.analysis.tm(next_primer, parameters=tm_parameters)
primers_tms.append((next_primer, last_tm))
bases += 1
# Trim primer list based on tm_undershoot and end_gc
primers_tms = [(primer, melt) for primer, melt in primers_tms if
melt >= tm - tm_undershoot]
if end_gc:
primers_tms = [pair for pair in primers_tms if
pair[0][-1] == coral.DNA('C') or
pair[0][-1] == coral.DNA('G')]
if not primers_tms:
raise ValueError('No primers could be generated using these settings')
# Find the primer closest to the set Tm, make it single stranded
tm_diffs = [abs(melt - tm) for primer, melt in primers_tms]
best_index = tm_diffs.index(min(tm_diffs))
best_primer, best_tm = primers_tms[best_index]
best_primer = best_primer.top
# Apply overhang
if overhang:
overhang = overhang.top
output_primer = coral.Primer(best_primer, best_tm, overhang=overhang)
def _structure(primer):
'''Check annealing sequence for structure.
:param primer: Primer for which to evaluate structure
:type primer: sequence.Primer
'''
# Check whole primer for high-probability structure, focus in on
# annealing sequence, report average
nupack = coral.analysis.Nupack(primer.primer())
pairs = nupack.pairs(0)
anneal_len = len(primer.anneal)
pairs_mean = sum(pairs[-anneal_len:]) / anneal_len
if pairs_mean < 0.5:
warnings.warn('High probability structure', Warning)
return pairs_mean
if structure:
_structure(output_primer)
return output_primer | python | def primer(dna, tm=65, min_len=10, tm_undershoot=1, tm_overshoot=3,
end_gc=False, tm_parameters='cloning', overhang=None,
structure=False):
'''Design primer to a nearest-neighbor Tm setpoint.
:param dna: Sequence for which to design a primer.
:type dna: coral.DNA
:param tm: Ideal primer Tm in degrees C.
:type tm: float
:param min_len: Minimum primer length.
:type min_len: int
:param tm_undershoot: Allowed Tm undershoot.
:type tm_undershoot: float
:param tm_overshoot: Allowed Tm overshoot.
:type tm_overshoot: float
:param end_gc: Obey the 'end on G or C' rule.
:type end_gc: bool
:param tm_parameters: Melting temp calculator method to use.
:type tm_parameters: string
:param overhang: Append the primer to this overhang sequence.
:type overhang: str
:param structure: Evaluate primer for structure, with warning for high
structure.
:type structure: bool
:returns: A primer.
:rtype: coral.Primer
:raises: ValueError if the input sequence is lower than the Tm settings
allow.
ValueError if a primer ending with G or C can't be found given
the Tm settings.
'''
# Check Tm of input sequence to see if it's already too low
seq_tm = coral.analysis.tm(dna, parameters=tm_parameters)
if seq_tm < (tm - tm_undershoot):
msg = 'Input sequence Tm is lower than primer Tm setting'
raise ValueError(msg)
# Focus on first 90 bases - shouldn't need more than 90bp to anneal
dna = dna[0:90]
# Generate primers from min_len to 'tm' + tm_overshoot
# TODO: this is a good place for optimization. Only calculate as many
# primers as are needed. Use binary search.
primers_tms = []
last_tm = 0
bases = min_len
while last_tm <= tm + tm_overshoot and bases != len(dna):
next_primer = dna[0:bases]
last_tm = coral.analysis.tm(next_primer, parameters=tm_parameters)
primers_tms.append((next_primer, last_tm))
bases += 1
# Trim primer list based on tm_undershoot and end_gc
primers_tms = [(primer, melt) for primer, melt in primers_tms if
melt >= tm - tm_undershoot]
if end_gc:
primers_tms = [pair for pair in primers_tms if
pair[0][-1] == coral.DNA('C') or
pair[0][-1] == coral.DNA('G')]
if not primers_tms:
raise ValueError('No primers could be generated using these settings')
# Find the primer closest to the set Tm, make it single stranded
tm_diffs = [abs(melt - tm) for primer, melt in primers_tms]
best_index = tm_diffs.index(min(tm_diffs))
best_primer, best_tm = primers_tms[best_index]
best_primer = best_primer.top
# Apply overhang
if overhang:
overhang = overhang.top
output_primer = coral.Primer(best_primer, best_tm, overhang=overhang)
def _structure(primer):
'''Check annealing sequence for structure.
:param primer: Primer for which to evaluate structure
:type primer: sequence.Primer
'''
# Check whole primer for high-probability structure, focus in on
# annealing sequence, report average
nupack = coral.analysis.Nupack(primer.primer())
pairs = nupack.pairs(0)
anneal_len = len(primer.anneal)
pairs_mean = sum(pairs[-anneal_len:]) / anneal_len
if pairs_mean < 0.5:
warnings.warn('High probability structure', Warning)
return pairs_mean
if structure:
_structure(output_primer)
return output_primer | [
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:param dna: Sequence for which to design a primer.
:type dna: coral.DNA
:param tm: Ideal primer Tm in degrees C.
:type tm: float
:param min_len: Minimum primer length.
:type min_len: int
:param tm_undershoot: Allowed Tm undershoot.
:type tm_undershoot: float
:param tm_overshoot: Allowed Tm overshoot.
:type tm_overshoot: float
:param end_gc: Obey the 'end on G or C' rule.
:type end_gc: bool
:param tm_parameters: Melting temp calculator method to use.
:type tm_parameters: string
:param overhang: Append the primer to this overhang sequence.
:type overhang: str
:param structure: Evaluate primer for structure, with warning for high
structure.
:type structure: bool
:returns: A primer.
:rtype: coral.Primer
:raises: ValueError if the input sequence is lower than the Tm settings
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"."
] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/design/_primers.py#L6-L98 | train | Design a primer to a nearest - neighbor Tm setpoint. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b10011 + 0o36) + chr(1171 - 1122), ord("\x08")), nzTpIcepk0o8(chr(0b11011 + 0o25) + chr(111) + '\062' + chr(50) + '\x31', 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110 + 0o54) + '\x35' + chr(1047 - 994), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(480 - 431) + chr(2536 - 2483) + chr(135 - 87), 0o10), nzTpIcepk0o8(chr(712 - 664) + '\x6f' + chr(0b110011) + '\x37' + chr(0b110010 + 0o1), 0o10), nzTpIcepk0o8(chr(625 - 577) + '\157' + chr(0b1011 + 0o51) + chr(52), 0b1000), nzTpIcepk0o8(chr(633 - 585) + chr(9948 - 9837) + '\065' + '\x30', 37086 - 37078), nzTpIcepk0o8('\060' + chr(729 - 618) + '\062' + '\063' + chr(49), 0b1000), nzTpIcepk0o8(chr(2277 - 2229) + '\x6f' + chr(0b11010 + 0o35) + chr(50), 0o10), nzTpIcepk0o8('\x30' + chr(4661 - 4550) + '\x31' + '\060' + chr(49), 1913 - 1905), nzTpIcepk0o8('\x30' + '\x6f' + chr(51) + chr(0b110100 + 0o2) + chr(0b11111 + 0o30), 0b1000), nzTpIcepk0o8(chr(1917 - 1869) + chr(0b1101111) + chr(0b101010 + 0o11) + chr(871 - 823) + '\066', 0b1000), nzTpIcepk0o8(chr(48) + chr(3728 - 3617) + '\x32' + '\x35' + chr(53), 8), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\061' + '\064' + '\x35', ord("\x08")), nzTpIcepk0o8(chr(0b0 + 0o60) + chr(0b1000100 + 0o53) + chr(493 - 442) + '\x32' + chr(0b101010 + 0o6), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110001) + chr(1704 - 1656) + chr(325 - 272), ord("\x08")), nzTpIcepk0o8(chr(1535 - 1487) + '\157' + chr(0b10101 + 0o34) + '\060' + chr(721 - 667), 0o10), nzTpIcepk0o8('\x30' + chr(0b111100 + 0o63) + '\x31' + '\x35' + chr(0b110000), 8), nzTpIcepk0o8(chr(1189 - 1141) + chr(4743 - 4632) + chr(517 - 467) + '\063' + chr(2294 - 2242), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x33' + chr(0b110000) + chr(53), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x32' + chr(0b110000) + chr(0b110010), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1000110 + 0o51) + '\064' + chr(0b110001), 0b1000), nzTpIcepk0o8(chr(430 - 382) + chr(0b1101111) + chr(0b110010) + chr(0b100010 + 0o16), 0b1000), nzTpIcepk0o8('\x30' + chr(4336 - 4225) + chr(0b110 + 0o54) + '\067' + chr(48), ord("\x08")), nzTpIcepk0o8(chr(0b10001 + 0o37) + '\x6f' + chr(50) + '\x32' + chr(0b1010 + 0o50), 0o10), nzTpIcepk0o8(chr(48) + chr(0b111000 + 0o67) + chr(0b110011) + chr(48) + chr(48), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(50) + chr(2332 - 2280) + chr(0b110100), 2880 - 2872), nzTpIcepk0o8(chr(48) + '\157' + '\x35' + chr(2192 - 2140), 42089 - 42081), nzTpIcepk0o8(chr(48) + chr(0b111010 + 0o65) + chr(2154 - 2104) + chr(1997 - 1949) + chr(0b11100 + 0o30), 45407 - 45399), nzTpIcepk0o8('\060' + chr(111) + chr(2388 - 2339) + chr(51) + chr(48), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(1022 - 971) + chr(49) + chr(54), ord("\x08")), nzTpIcepk0o8(chr(827 - 779) + chr(0b1101111) + chr(1881 - 1832) + chr(55) + chr(53), 0b1000), nzTpIcepk0o8(chr(48) + chr(3358 - 3247) + '\061' + chr(0b110100) + '\x35', 8), nzTpIcepk0o8('\060' + chr(0b1001011 + 0o44) + chr(0b10010 + 0o37) + chr(0b10110 + 0o36) + chr(0b101001 + 0o13), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(51) + '\062' + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b110010 + 0o75) + '\x36' + chr(52), 30149 - 30141), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x31' + chr(53) + chr(48), 8), nzTpIcepk0o8(chr(0b1111 + 0o41) + chr(0b1101111) + '\x32' + chr(0b110000) + '\062', 8), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110011) + chr(0b110010) + chr(0b110001), 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(816 - 767) + chr(49), 8)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(182 - 134) + '\x6f' + chr(53) + '\060', 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b"'"), chr(100) + '\x65' + chr(0b1100011) + chr(0b100110 + 0o111) + '\x64' + '\x65')(chr(0b101000 + 0o115) + chr(8577 - 8461) + chr(102) + chr(0b101101) + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def thHp9mlDSVMt(z3lWtzdILzgZ, VH5NUDuH5Da3=nzTpIcepk0o8(chr(603 - 555) + chr(0b11001 + 0o126) + chr(0b100 + 0o55) + '\060' + chr(0b10100 + 0o35), 8), Lif6FAYA6nmJ=nzTpIcepk0o8(chr(0b1011 + 0o45) + '\x6f' + '\x31' + '\062', 9377 - 9369), TYlt6fBRg5m3=nzTpIcepk0o8('\060' + '\x6f' + chr(0b11100 + 0o25), 0o10), ZDL9iZHCcdFN=nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x33', ord("\x08")), Yos4XoSuc0dt=nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110000), ord("\x08")), JGIG9UHwpmNR=roI3spqORKae(ES5oEprVxulp(b'j\xfd\xc2\x06\x92JO'), '\x64' + '\145' + chr(99) + '\157' + chr(100) + chr(8490 - 8389))(chr(0b1110101) + chr(12684 - 12568) + chr(102) + '\x2d' + chr(0b11000 + 0o40)), W3dAi1GDJXNe=None, YHBL8s40WpmM=nzTpIcepk0o8(chr(48) + '\157' + chr(0b10011 + 0o35), 8)):
nom3QAohoBR8 = _bFWSozA7z0G.analysis.VH5NUDuH5Da3(z3lWtzdILzgZ, parameters=JGIG9UHwpmNR)
if nom3QAohoBR8 < VH5NUDuH5Da3 - TYlt6fBRg5m3:
sldzbHve8G1S = roI3spqORKae(ES5oEprVxulp(b'@\xff\xdd\x1d\x8f\x04[\xfcK4\x92\xa8\xce\x00\xf0\x11+H\xf5\xb6\xa2M\x7f\xcf\xf7\xb2\x84X\xec9\xa0]\x15\x16\xbbY\r\xf0\xf1]d\xb1\xde\r\x8fPA\xf7]'), chr(100) + chr(0b1101 + 0o130) + chr(99) + chr(0b101000 + 0o107) + chr(100) + chr(0b1100101 + 0o0))(chr(117) + '\164' + '\146' + chr(0b100011 + 0o12) + chr(722 - 666))
raise WbNHlDKpyPtQ(sldzbHve8G1S)
z3lWtzdILzgZ = z3lWtzdILzgZ[nzTpIcepk0o8(chr(0b110000) + chr(10625 - 10514) + chr(0b110000), 8):nzTpIcepk0o8(chr(2106 - 2058) + chr(0b101001 + 0o106) + chr(1943 - 1894) + chr(0b110011) + chr(50), 0o10)]
e7fetqjXue9e = []
_ZXSxwMI1YaK = nzTpIcepk0o8('\x30' + chr(11295 - 11184) + '\x30', 8)
kVd35VdQTInh = Lif6FAYA6nmJ
while _ZXSxwMI1YaK <= VH5NUDuH5Da3 + ZDL9iZHCcdFN and kVd35VdQTInh != ftfygxgFas5X(z3lWtzdILzgZ):
yzfyQz__QXCE = z3lWtzdILzgZ[nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110000), 8):kVd35VdQTInh]
_ZXSxwMI1YaK = _bFWSozA7z0G.analysis.VH5NUDuH5Da3(yzfyQz__QXCE, parameters=JGIG9UHwpmNR)
roI3spqORKae(e7fetqjXue9e, roI3spqORKae(ES5oEprVxulp(b'A\xc5\xfe\\\x83Co\xf6P.\xa2\xf3'), '\x64' + chr(9237 - 9136) + chr(4993 - 4894) + chr(0b1101111) + chr(4691 - 4591) + chr(0b100110 + 0o77))(chr(0b1100011 + 0o22) + chr(116) + chr(0b1100110) + '\x2d' + chr(2785 - 2729)))((yzfyQz__QXCE, _ZXSxwMI1YaK))
kVd35VdQTInh += nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x31', 8)
e7fetqjXue9e = [(thHp9mlDSVMt, Kgeufh4yaujL) for (thHp9mlDSVMt, Kgeufh4yaujL) in e7fetqjXue9e if Kgeufh4yaujL >= VH5NUDuH5Da3 - TYlt6fBRg5m3]
if Yos4XoSuc0dt:
e7fetqjXue9e = [YhzVz4aO0FLl for YhzVz4aO0FLl in e7fetqjXue9e if YhzVz4aO0FLl[nzTpIcepk0o8(chr(1563 - 1515) + '\157' + chr(0b110000), 8)][-nzTpIcepk0o8(chr(0b11011 + 0o25) + '\157' + '\061', 8)] == _bFWSozA7z0G.DNA(roI3spqORKae(ES5oEprVxulp(b'J'), chr(0b1000011 + 0o41) + chr(5576 - 5475) + '\143' + '\x6f' + chr(0b1100100) + '\x65')(chr(0b101 + 0o160) + chr(3708 - 3592) + chr(102) + chr(1181 - 1136) + '\x38')) or YhzVz4aO0FLl[nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(825 - 777), 8)][-nzTpIcepk0o8(chr(48) + chr(111) + '\x31', 8)] == _bFWSozA7z0G.DNA(roI3spqORKae(ES5oEprVxulp(b'N'), chr(7114 - 7014) + chr(0b111 + 0o136) + '\143' + '\157' + chr(100) + '\x65')(chr(2520 - 2403) + '\x74' + chr(0b1100010 + 0o4) + chr(45) + chr(2770 - 2714)))]
if not e7fetqjXue9e:
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'G\xfe\x8d\x18\x89ME\xfcH2\xd7\xa5\xc2\x10\xbc!f\n\xf9\xe5\xe5D~\xdd\xe0\xa1\xd0I\xe0x\xbb\x0e\x0c\n\xb5\x14\x1c\xea\xb4zl\xb1\xde\r\x8fPA\xf7]2'), chr(0b111 + 0o135) + '\x65' + '\143' + chr(111) + chr(0b100011 + 0o101) + chr(5107 - 5006))(chr(0b1110101) + chr(0b1110100) + chr(0b1100110) + '\055' + '\070'))
__yOinuFPO9R = [zQBGwUT7UU8L(Kgeufh4yaujL - VH5NUDuH5Da3) for (thHp9mlDSVMt, Kgeufh4yaujL) in e7fetqjXue9e]
gqPYegDmN1nD = __yOinuFPO9R.ZpfN5tSLaZze(XURpmPuEWCNF(__yOinuFPO9R))
(G71BsYTG2siL, RsM1DvODafzK) = e7fetqjXue9e[gqPYegDmN1nD]
G71BsYTG2siL = G71BsYTG2siL.A2AC7Zsqx_Vf
if W3dAi1GDJXNe:
W3dAi1GDJXNe = W3dAi1GDJXNe.A2AC7Zsqx_Vf
eQftV1rxx570 = _bFWSozA7z0G.Primer(G71BsYTG2siL, RsM1DvODafzK, overhang=W3dAi1GDJXNe)
def XpwUptRXQlqi(thHp9mlDSVMt):
zPs0RBqzFue6 = _bFWSozA7z0G.analysis.Nupack(thHp9mlDSVMt.primer())
VxbmnfX6T_2s = zPs0RBqzFue6.pairs(nzTpIcepk0o8('\x30' + chr(1208 - 1097) + chr(0b110000), 8))
tlAltg9307NG = ftfygxgFas5X(thHp9mlDSVMt.anneal)
aJN9ryhQWj09 = oclC8DLjA_lV(VxbmnfX6T_2s[-tlAltg9307NG:]) / tlAltg9307NG
if aJN9ryhQWj09 < 0.5:
roI3spqORKae(EyN62Frii5S5, roI3spqORKae(ES5oEprVxulp(b"z\xdb\xfc>\xa4lY\xca\x03'\x90\xbc"), chr(0b1001011 + 0o31) + chr(0b1100101) + '\x63' + chr(11071 - 10960) + '\144' + chr(0b110 + 0o137))(chr(0b111111 + 0o66) + chr(116) + chr(0b10101 + 0o121) + chr(45) + '\070'))(roI3spqORKae(ES5oEprVxulp(b'A\xf8\xca\x00\xdbTZ\xf6X \x95\xaf\xc1\x0c\xa4<f\x1b\xe8\xb7\xf7Bd\xcd\xe0\xa5'), chr(100) + chr(5015 - 4914) + chr(0b1100011) + chr(0b1101111) + '\144' + chr(0b1010010 + 0o23))(chr(0b1000101 + 0o60) + chr(0b1110100) + chr(0b1000000 + 0o46) + '\055' + '\070'), z18h6aCn31dg)
return aJN9ryhQWj09
if YHBL8s40WpmM:
XpwUptRXQlqi(eQftV1rxx570)
return eQftV1rxx570 |
klavinslab/coral | coral/design/_primers.py | primers | def primers(dna, tm=65, min_len=10, tm_undershoot=1, tm_overshoot=3,
end_gc=False, tm_parameters='cloning', overhangs=None,
structure=False):
'''Design primers for PCR amplifying any arbitrary sequence.
:param dna: Input sequence.
:type dna: coral.DNA
:param tm: Ideal primer Tm in degrees C.
:type tm: float
:param min_len: Minimum primer length.
:type min_len: int
:param tm_undershoot: Allowed Tm undershoot.
:type tm_undershoot: float
:param tm_overshoot: Allowed Tm overshoot.
:type tm_overshoot: float
:param end_gc: Obey the 'end on G or C' rule.
:type end_gc: bool
:param tm_parameters: Melting temp calculator method to use.
:type tm_parameters: string
:param overhangs: 2-tuple of overhang sequences.
:type overhangs: tuple
:param structure: Evaluate each primer for structure, with warning for high
structure.
:type structure: bool
:returns: A list primers (the output of primer).
:rtype: list
'''
if not overhangs:
overhangs = [None, None]
templates = [dna, dna.reverse_complement()]
primer_list = []
for template, overhang in zip(templates, overhangs):
primer_i = primer(template, tm=tm, min_len=min_len,
tm_undershoot=tm_undershoot,
tm_overshoot=tm_overshoot, end_gc=end_gc,
tm_parameters=tm_parameters,
overhang=overhang, structure=structure)
primer_list.append(primer_i)
return primer_list | python | def primers(dna, tm=65, min_len=10, tm_undershoot=1, tm_overshoot=3,
end_gc=False, tm_parameters='cloning', overhangs=None,
structure=False):
'''Design primers for PCR amplifying any arbitrary sequence.
:param dna: Input sequence.
:type dna: coral.DNA
:param tm: Ideal primer Tm in degrees C.
:type tm: float
:param min_len: Minimum primer length.
:type min_len: int
:param tm_undershoot: Allowed Tm undershoot.
:type tm_undershoot: float
:param tm_overshoot: Allowed Tm overshoot.
:type tm_overshoot: float
:param end_gc: Obey the 'end on G or C' rule.
:type end_gc: bool
:param tm_parameters: Melting temp calculator method to use.
:type tm_parameters: string
:param overhangs: 2-tuple of overhang sequences.
:type overhangs: tuple
:param structure: Evaluate each primer for structure, with warning for high
structure.
:type structure: bool
:returns: A list primers (the output of primer).
:rtype: list
'''
if not overhangs:
overhangs = [None, None]
templates = [dna, dna.reverse_complement()]
primer_list = []
for template, overhang in zip(templates, overhangs):
primer_i = primer(template, tm=tm, min_len=min_len,
tm_undershoot=tm_undershoot,
tm_overshoot=tm_overshoot, end_gc=end_gc,
tm_parameters=tm_parameters,
overhang=overhang, structure=structure)
primer_list.append(primer_i)
return primer_list | [
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"st... | Design primers for PCR amplifying any arbitrary sequence.
:param dna: Input sequence.
:type dna: coral.DNA
:param tm: Ideal primer Tm in degrees C.
:type tm: float
:param min_len: Minimum primer length.
:type min_len: int
:param tm_undershoot: Allowed Tm undershoot.
:type tm_undershoot: float
:param tm_overshoot: Allowed Tm overshoot.
:type tm_overshoot: float
:param end_gc: Obey the 'end on G or C' rule.
:type end_gc: bool
:param tm_parameters: Melting temp calculator method to use.
:type tm_parameters: string
:param overhangs: 2-tuple of overhang sequences.
:type overhangs: tuple
:param structure: Evaluate each primer for structure, with warning for high
structure.
:type structure: bool
:returns: A list primers (the output of primer).
:rtype: list | [
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/design/_primers.py#L101-L140 | train | Design primers for PCR amplifying any arbitrary sequence. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b101101 + 0o3) + '\x6f' + '\062' + '\x36' + chr(0b100011 + 0o16), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110011) + chr(0b110010 + 0o1) + '\066', 0b1000), nzTpIcepk0o8(chr(48) + chr(8134 - 8023) + chr(0b110010) + '\x35' + chr(53), 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(0b101101 + 0o5) + '\060' + chr(0b110111), 54271 - 54263), nzTpIcepk0o8(chr(48) + chr(111) + chr(1137 - 1087) + chr(49) + chr(54), 0o10), nzTpIcepk0o8(chr(1090 - 1042) + '\x6f' + '\062' + '\x34' + chr(49), 13169 - 13161), nzTpIcepk0o8(chr(0b110000) + chr(11015 - 10904) + chr(50) + '\066' + chr(0b110010), 0b1000), nzTpIcepk0o8(chr(0b100110 + 0o12) + '\x6f' + chr(1137 - 1087) + chr(0b110010) + chr(1238 - 1189), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110010) + chr(0b10100 + 0o40), 0b1000), nzTpIcepk0o8('\060' + chr(0b10000 + 0o137) + chr(1153 - 1104) + '\067' + '\064', 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(1675 - 1626) + chr(0b101101 + 0o6), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1000111 + 0o50) + chr(49) + chr(1527 - 1473) + '\066', 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\062' + chr(2000 - 1950) + '\060', 32727 - 32719), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110110), 29416 - 29408), nzTpIcepk0o8(chr(0b110000) + chr(0b1010111 + 0o30) + chr(1251 - 1202) + '\060' + chr(0b110000), 0b1000), nzTpIcepk0o8('\x30' + chr(2662 - 2551) + chr(575 - 524) + chr(0b110111) + chr(0b110110), 0b1000), nzTpIcepk0o8(chr(664 - 616) + '\157' + chr(0b110011) + '\x34' + '\x35', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1001100 + 0o43) + chr(0b101101 + 0o4) + '\x32' + chr(0b110110), ord("\x08")), nzTpIcepk0o8(chr(0b10011 + 0o35) + chr(0b111 + 0o150) + chr(54) + '\x33', 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x32' + chr(0b110001) + '\063', 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(1923 - 1872) + chr(0b110111), 38880 - 38872), nzTpIcepk0o8(chr(0b10010 + 0o36) + chr(7446 - 7335) + chr(0b100000 + 0o20), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110001) + chr(0b11101 + 0o30) + chr(0b10110 + 0o32), 0b1000), nzTpIcepk0o8('\060' + chr(0b111100 + 0o63) + chr(853 - 802) + chr(747 - 693) + '\x31', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b11110 + 0o25) + chr(0b11000 + 0o30) + chr(0b10010 + 0o45), 59468 - 59460), nzTpIcepk0o8(chr(905 - 857) + chr(0b110001 + 0o76) + chr(0b101010 + 0o13), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(51) + chr(0b110110) + chr(0b110000), 0o10), nzTpIcepk0o8('\x30' + chr(0b110110 + 0o71) + '\063' + '\066' + chr(2064 - 2014), 0b1000), nzTpIcepk0o8(chr(1515 - 1467) + chr(0b1101111) + '\062' + chr(0b110011) + chr(0b100000 + 0o22), 0o10), nzTpIcepk0o8(chr(1642 - 1594) + chr(111) + chr(0b10011 + 0o40) + chr(55), 8), nzTpIcepk0o8(chr(0b10111 + 0o31) + chr(0b1101111) + chr(0b110001) + chr(0b110101) + '\x32', 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(49) + '\x37' + chr(1593 - 1540), 19857 - 19849), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110001) + chr(400 - 346) + chr(0b110010), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110010) + '\x32' + '\064', 0o10), nzTpIcepk0o8(chr(996 - 948) + '\157' + chr(0b110011) + '\x32', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(660 - 609) + '\x32' + chr(1265 - 1212), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b1101 + 0o45) + '\x30' + chr(54), 56122 - 56114), nzTpIcepk0o8('\x30' + '\x6f' + chr(998 - 947) + chr(1189 - 1140) + chr(0b10001 + 0o37), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(0b10 + 0o61) + chr(2641 - 2586) + chr(0b10011 + 0o43), 8), nzTpIcepk0o8(chr(0b0 + 0o60) + chr(0b1010101 + 0o32) + chr(690 - 641) + chr(0b110001) + chr(0b110011), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(0b1001010 + 0o45) + chr(2411 - 2358) + chr(1181 - 1133), 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x9f'), chr(0b111110 + 0o46) + '\x65' + '\x63' + chr(0b1010001 + 0o36) + chr(0b110000 + 0o64) + '\x65')('\x75' + chr(116) + chr(102) + chr(45) + chr(0b1011 + 0o55)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def yFt7KjQREd_F(z3lWtzdILzgZ, VH5NUDuH5Da3=nzTpIcepk0o8('\x30' + chr(3682 - 3571) + chr(49) + chr(0b11001 + 0o27) + chr(49), 0b1000), Lif6FAYA6nmJ=nzTpIcepk0o8(chr(1166 - 1118) + chr(5416 - 5305) + '\061' + '\x32', ord("\x08")), TYlt6fBRg5m3=nzTpIcepk0o8('\x30' + chr(0b110101 + 0o72) + '\061', 0b1000), ZDL9iZHCcdFN=nzTpIcepk0o8('\060' + '\x6f' + chr(1671 - 1620), 41927 - 41919), Yos4XoSuc0dt=nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b100100 + 0o14), 8), JGIG9UHwpmNR=roI3spqORKae(ES5oEprVxulp(b'\xd2\xb2\xc2\xe9\xe7\xcf\xd5'), chr(100) + chr(0b110011 + 0o62) + '\143' + chr(111) + chr(0b1110 + 0o126) + chr(3152 - 3051))(chr(117) + '\x74' + chr(0b110001 + 0o65) + '\x2d' + chr(0b1 + 0o67)), dlNnLyFN6g7A=None, YHBL8s40WpmM=nzTpIcepk0o8(chr(2183 - 2135) + chr(0b1101111) + '\060', 8)):
if not dlNnLyFN6g7A:
dlNnLyFN6g7A = [None, None]
np8PxOtHhpST = [z3lWtzdILzgZ, z3lWtzdILzgZ.reverse_complement()]
aB0brEPgy33p = []
for (Pe8smzX7Gsur, W3dAi1GDJXNe) in TxMFWa_Xzviv(np8PxOtHhpST, dlNnLyFN6g7A):
xb0p2C1KkAwW = thHp9mlDSVMt(Pe8smzX7Gsur, tm=VH5NUDuH5Da3, min_len=Lif6FAYA6nmJ, tm_undershoot=TYlt6fBRg5m3, tm_overshoot=ZDL9iZHCcdFN, end_gc=Yos4XoSuc0dt, tm_parameters=JGIG9UHwpmNR, overhang=W3dAi1GDJXNe, structure=YHBL8s40WpmM)
roI3spqORKae(aB0brEPgy33p, roI3spqORKae(ES5oEprVxulp(b'\xf9\x8a\xfe\xb3\xf6\xc6\xf5\xfe~\x13^C'), chr(0b1100100) + chr(0b1000011 + 0o42) + chr(7346 - 7247) + chr(111) + '\x64' + '\145')(chr(117) + '\x74' + chr(0b1100110) + chr(0b1111 + 0o36) + '\x38'))(xb0p2C1KkAwW)
return aB0brEPgy33p |
klavinslab/coral | coral/reaction/_oligo_assembly.py | assemble_oligos | def assemble_oligos(dna_list, reference=None):
'''Given a list of DNA sequences, assemble into a single construct.
:param dna_list: List of DNA sequences - they must be single-stranded.
:type dna_list: coral.DNA list
:param reference: Expected sequence - once assembly completed, this will
be used to reorient the DNA (assembly could potentially occur from either
side of a linear DNA construct if oligos are in a random order). If this
fails, an AssemblyError is raised.
:type reference: coral.DNA
:raises: AssemblyError if it can't assemble for any reason.
:returns: A single assembled DNA sequence
:rtype: coral.DNA
'''
# FIXME: this protocol currently only supports 5' ends on the assembly
# Find all matches for every oligo. If more than 2 per side, error.
# Self-oligo is included in case the 3' end is self-complementary.
# 1) Find all unique 3' binders (and non-binders).
match_3 = [bind_unique(seq, dna_list, right=True) for i, seq in
enumerate(dna_list)]
# 2) Find all unique 5' binders (and non-binders).
match_5 = [bind_unique(seq, dna_list, right=False) for i, seq in
enumerate(dna_list)]
# Assemble into 2-tuple
zipped = zip(match_5, match_3)
# 3) If none found, error out with 'oligo n has no binders'
for i, oligo_match in enumerate(zipped):
if not any(oligo_match):
error = 'Oligo {} has no binding partners.'.format(i + 1)
raise AssemblyError(error)
# 4) There should be exactly 2 oligos that bind at 3' end but
# not 5'.
ends = []
for i, (five, three) in enumerate(zipped):
if five is None and three is not None:
ends.append(i)
# 5) If more than 2, error with 'too many ends'.
if len(ends) > 2:
raise AssemblyError('Too many (>2) end oligos found.')
# 6) If more than 2, error with 'not enough ends'.
if len(ends) < 2:
raise AssemblyError('Not enough (<2) end oligos found.')
# NOTE:If 1-4 are satisfied, unique linear assembly has been found (proof?)
# 8) Start with first end and build iteratively
last_index = ends[0]
assembly = dna_list[last_index]
flip = True
# This would be slightly less complicated if the sequences were tied to
# their match info in a tuple
# Append next region n - 1 times
for i in range(len(dna_list) - 1):
if flip:
# Next oligo needs to be flipped before concatenation
# Grab 3' match from last oligo's info
current_index, matchlen = zipped[last_index][1]
# Get new oligo sequence, make double-stranded for concatenation
next_oligo = dna_list[current_index].to_ds()
# Reverse complement for concatenation
next_oligo = next_oligo.reverse_complement()
# Don't reverse complement the next one
flip = False
else:
# Grab 5' match from last oligo's info
current_index, matchlen = zipped[last_index][0]
# Get new oligo sequence, make double-stranded for concatenation
next_oligo = dna_list[current_index].to_ds()
# Reverse complement the next one
flip = True
# Trim overlap from new sequence
next_oligo = next_oligo[(matchlen - 1):]
# Concatenate and update last oligo's information
assembly += next_oligo
last_index = current_index
if reference:
if assembly == reference or assembly == reference.reverse_complement():
return assembly
else:
raise AssemblyError('Assembly did not match reference')
else:
return assembly | python | def assemble_oligos(dna_list, reference=None):
'''Given a list of DNA sequences, assemble into a single construct.
:param dna_list: List of DNA sequences - they must be single-stranded.
:type dna_list: coral.DNA list
:param reference: Expected sequence - once assembly completed, this will
be used to reorient the DNA (assembly could potentially occur from either
side of a linear DNA construct if oligos are in a random order). If this
fails, an AssemblyError is raised.
:type reference: coral.DNA
:raises: AssemblyError if it can't assemble for any reason.
:returns: A single assembled DNA sequence
:rtype: coral.DNA
'''
# FIXME: this protocol currently only supports 5' ends on the assembly
# Find all matches for every oligo. If more than 2 per side, error.
# Self-oligo is included in case the 3' end is self-complementary.
# 1) Find all unique 3' binders (and non-binders).
match_3 = [bind_unique(seq, dna_list, right=True) for i, seq in
enumerate(dna_list)]
# 2) Find all unique 5' binders (and non-binders).
match_5 = [bind_unique(seq, dna_list, right=False) for i, seq in
enumerate(dna_list)]
# Assemble into 2-tuple
zipped = zip(match_5, match_3)
# 3) If none found, error out with 'oligo n has no binders'
for i, oligo_match in enumerate(zipped):
if not any(oligo_match):
error = 'Oligo {} has no binding partners.'.format(i + 1)
raise AssemblyError(error)
# 4) There should be exactly 2 oligos that bind at 3' end but
# not 5'.
ends = []
for i, (five, three) in enumerate(zipped):
if five is None and three is not None:
ends.append(i)
# 5) If more than 2, error with 'too many ends'.
if len(ends) > 2:
raise AssemblyError('Too many (>2) end oligos found.')
# 6) If more than 2, error with 'not enough ends'.
if len(ends) < 2:
raise AssemblyError('Not enough (<2) end oligos found.')
# NOTE:If 1-4 are satisfied, unique linear assembly has been found (proof?)
# 8) Start with first end and build iteratively
last_index = ends[0]
assembly = dna_list[last_index]
flip = True
# This would be slightly less complicated if the sequences were tied to
# their match info in a tuple
# Append next region n - 1 times
for i in range(len(dna_list) - 1):
if flip:
# Next oligo needs to be flipped before concatenation
# Grab 3' match from last oligo's info
current_index, matchlen = zipped[last_index][1]
# Get new oligo sequence, make double-stranded for concatenation
next_oligo = dna_list[current_index].to_ds()
# Reverse complement for concatenation
next_oligo = next_oligo.reverse_complement()
# Don't reverse complement the next one
flip = False
else:
# Grab 5' match from last oligo's info
current_index, matchlen = zipped[last_index][0]
# Get new oligo sequence, make double-stranded for concatenation
next_oligo = dna_list[current_index].to_ds()
# Reverse complement the next one
flip = True
# Trim overlap from new sequence
next_oligo = next_oligo[(matchlen - 1):]
# Concatenate and update last oligo's information
assembly += next_oligo
last_index = current_index
if reference:
if assembly == reference or assembly == reference.reverse_complement():
return assembly
else:
raise AssemblyError('Assembly did not match reference')
else:
return assembly | [
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"# FIXME: this protocol currently only supports 5' ends on the assembly",
"# Find all matches for every oligo. If more than 2 per side, error.",
"# Self-oligo is included in case the 3' end is self-complement... | Given a list of DNA sequences, assemble into a single construct.
:param dna_list: List of DNA sequences - they must be single-stranded.
:type dna_list: coral.DNA list
:param reference: Expected sequence - once assembly completed, this will
be used to reorient the DNA (assembly could potentially occur from either
side of a linear DNA construct if oligos are in a random order). If this
fails, an AssemblyError is raised.
:type reference: coral.DNA
:raises: AssemblyError if it can't assemble for any reason.
:returns: A single assembled DNA sequence
:rtype: coral.DNA | [
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":",... | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/reaction/_oligo_assembly.py#L12-L92 | train | Given a list of DNA sequences assemble into a single construct. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8('\060' + chr(111) + '\062' + '\066' + chr(48), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + '\062' + chr(2675 - 2623) + '\066', ord("\x08")), nzTpIcepk0o8('\060' + chr(10943 - 10832) + chr(0b101101 + 0o5) + chr(0b110110) + chr(48), 8), nzTpIcepk0o8(chr(48) + chr(0b10111 + 0o130) + '\x33' + '\066' + chr(54), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + '\063' + chr(0b100 + 0o55) + chr(0b110100), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b10 + 0o155) + '\x31' + '\x37' + chr(0b101000 + 0o16), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(1724 - 1675) + chr(0b110010) + chr(0b10111 + 0o36), 42194 - 42186), nzTpIcepk0o8(chr(48) + '\x6f' + chr(49) + '\x33' + chr(54), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b101000 + 0o12) + chr(49), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110111) + chr(0b110111), 0o10), nzTpIcepk0o8('\x30' + chr(3900 - 3789) + chr(0b10 + 0o60), 26914 - 26906), nzTpIcepk0o8(chr(0b110000) + chr(0b111111 + 0o60) + chr(52) + '\x32', 0o10), nzTpIcepk0o8('\x30' + '\157' + '\x32' + chr(0b11 + 0o57) + chr(148 - 96), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(761 - 710) + '\x30' + chr(1275 - 1222), 0o10), nzTpIcepk0o8(chr(0b100001 + 0o17) + '\x6f' + chr(0b110010) + chr(0b110001 + 0o3) + chr(2014 - 1960), 8), nzTpIcepk0o8('\060' + chr(0b111110 + 0o61) + chr(0b1111 + 0o42) + chr(0b110001) + chr(48), 42327 - 42319), nzTpIcepk0o8('\060' + '\157' + chr(474 - 419) + chr(0b110011), 55860 - 55852), nzTpIcepk0o8('\060' + chr(111) + '\x31', 0b1000), nzTpIcepk0o8(chr(1043 - 995) + chr(0b110010 + 0o75) + chr(0b11111 + 0o30), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + '\063' + '\x34' + chr(54), 0o10), nzTpIcepk0o8('\060' + '\157' + '\065' + '\x34', ord("\x08")), nzTpIcepk0o8(chr(676 - 628) + chr(0b1101111) + chr(0b110010 + 0o0) + chr(2288 - 2240) + chr(0b100110 + 0o17), 46423 - 46415), nzTpIcepk0o8(chr(0b101100 + 0o4) + '\157' + '\062' + '\062' + chr(0b110110), 0b1000), nzTpIcepk0o8(chr(1908 - 1860) + '\x6f' + '\x32' + '\x33' + '\x30', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110010) + '\062' + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x32' + '\063' + chr(53), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(1992 - 1943) + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b101100 + 0o103) + chr(0b101001 + 0o10) + '\x37' + '\x35', 0b1000), nzTpIcepk0o8(chr(0b11111 + 0o21) + chr(8977 - 8866) + chr(0b101110 + 0o5) + chr(2282 - 2233) + '\x35', 0o10), nzTpIcepk0o8('\060' + chr(9026 - 8915) + chr(50) + chr(51) + '\x33', ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(49) + chr(0b1 + 0o63) + chr(55), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + '\x36' + chr(48), 0b1000), nzTpIcepk0o8(chr(1033 - 985) + chr(0b1010000 + 0o37) + '\x31' + '\x35' + chr(54), 0o10), nzTpIcepk0o8(chr(1201 - 1153) + chr(0b1101111) + '\063' + chr(0b110000) + chr(2070 - 2022), 29319 - 29311), nzTpIcepk0o8('\060' + chr(8227 - 8116) + chr(51) + chr(51) + '\x30', 3353 - 3345), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(49) + chr(0b10011 + 0o43) + chr(0b1101 + 0o50), 0b1000), nzTpIcepk0o8(chr(713 - 665) + chr(295 - 184) + '\x32' + chr(1209 - 1155) + '\x34', ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110010) + chr(93 - 44) + chr(48), 0o10), nzTpIcepk0o8(chr(912 - 864) + '\157' + chr(0b1001 + 0o55) + chr(49), 7307 - 7299), nzTpIcepk0o8('\x30' + '\157' + chr(0b110011) + chr(0b110111) + chr(0b11011 + 0o32), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(600 - 552) + '\x6f' + chr(0b110101) + chr(0b11110 + 0o22), 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x9e'), '\x64' + chr(0b1100101) + chr(99) + '\x6f' + chr(0b1100100) + '\145')('\x75' + chr(0b1110100) + chr(0b1000111 + 0o37) + chr(0b101000 + 0o5) + chr(0b1101 + 0o53)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def ykpKtSPh1j3W(t234amCEzgDj, USoNBjlAQ1w9=None):
E61wyQfnp5a7 = [qoeFBmfoIjV5(ftk9lc7G5FOo, t234amCEzgDj, right=nzTpIcepk0o8(chr(48) + '\x6f' + chr(49), 8)) for (ZlbFMSG8gCoF, ftk9lc7G5FOo) in _kV_Bomx8PZ4(t234amCEzgDj)]
E6xp1l7RZNvg = [qoeFBmfoIjV5(ftk9lc7G5FOo, t234amCEzgDj, right=nzTpIcepk0o8('\060' + chr(0b1000100 + 0o53) + '\060', 52627 - 52619)) for (ZlbFMSG8gCoF, ftk9lc7G5FOo) in _kV_Bomx8PZ4(t234amCEzgDj)]
gLZq1HDvlClS = TxMFWa_Xzviv(E6xp1l7RZNvg, E61wyQfnp5a7)
for (ZlbFMSG8gCoF, JITbOwy9szUI) in _kV_Bomx8PZ4(gLZq1HDvlClS):
if not VF4pKOObtlPc(JITbOwy9szUI):
qi1wipPVvEKd = roI3spqORKae(ES5oEprVxulp(b'\xff\xca\xd9\x91\xa3^.#1WcQ\xb4\xab\xc9hYhi\x82E\xeb\xf1\xb8\xe0\xfc\x7f\t\xa3\xfe\x15C@'), chr(8236 - 8136) + '\x65' + '\x63' + '\157' + chr(0b1110 + 0o126) + '\145')(chr(2556 - 2439) + chr(0b1110100) + chr(102) + '\x2d' + '\x38').q33KG3foQ_CJ(ZlbFMSG8gCoF + nzTpIcepk0o8('\060' + '\x6f' + chr(0b110001), 8))
raise vrWXJ6oZDsg3(qi1wipPVvEKd)
ZrTYOwwszwjW = []
for (ZlbFMSG8gCoF, (XK3KWpgZlpcX, eunyxHv2D4rT)) in _kV_Bomx8PZ4(gLZq1HDvlClS):
if XK3KWpgZlpcX is None and eunyxHv2D4rT is not None:
roI3spqORKae(ZrTYOwwszwjW, roI3spqORKae(ES5oEprVxulp(b'\xf8\xf2\xe3\xc2\xb4\x19\x121{PW\x17'), '\144' + '\x65' + chr(0b1100011) + '\157' + chr(0b1010011 + 0o21) + '\x65')(chr(0b1110101) + '\164' + chr(1550 - 1448) + '\055' + chr(56)))(ZlbFMSG8gCoF)
if ftfygxgFas5X(ZrTYOwwszwjW) > nzTpIcepk0o8(chr(298 - 250) + chr(111) + chr(822 - 772), 8):
raise vrWXJ6oZDsg3(roI3spqORKae(ES5oEprVxulp(b"\xe4\xc9\xdf\xd6\xa1\x1f;'1\x17<\x10\xbd\xe5\xc3&_!h\x8aE\xe2\xf9\xeb\xb0\xfbb\x08\xa3\xffI"), chr(0b110010 + 0o62) + '\145' + '\143' + chr(2865 - 2754) + '\144' + chr(0b1100101))('\x75' + chr(13374 - 13258) + chr(6058 - 5956) + '\x2d' + chr(0b110010 + 0o6)))
if ftfygxgFas5X(ZrTYOwwszwjW) < nzTpIcepk0o8(chr(48) + chr(6368 - 6257) + '\x32', 8):
raise vrWXJ6oZDsg3(roI3spqORKae(ES5oEprVxulp(b'\xfe\xc9\xc4\xd6\xa9\x10:+vW"\n\xa8\xf7\x8fh^oc\xc6C\xe9\xff\xff\xff\xee-\x1b\xa2\xee\tT@'), chr(0b1000010 + 0o42) + '\145' + chr(0b1100011) + '\x6f' + '\144' + chr(0b111110 + 0o47))(chr(117) + '\164' + chr(102) + chr(45) + chr(0b10101 + 0o43)))
H6eidouYyOI8 = ZrTYOwwszwjW[nzTpIcepk0o8(chr(0b101000 + 0o10) + chr(111) + chr(0b110000), 8)]
Tni7tuYwJ8I1 = t234amCEzgDj[H6eidouYyOI8]
LeuPzfhzM9U8 = nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(1058 - 1009), 8)
for ZlbFMSG8gCoF in bbT2xIe5pzk7(ftfygxgFas5X(t234amCEzgDj) - nzTpIcepk0o8('\x30' + chr(1863 - 1752) + chr(591 - 542), 8)):
if LeuPzfhzM9U8:
(JwWuUFxG49ge, g2ILF2ZMugLZ) = gLZq1HDvlClS[H6eidouYyOI8][nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110001), 8)]
qqhqsQHhNCt5 = t234amCEzgDj[JwWuUFxG49ge].to_ds()
qqhqsQHhNCt5 = qqhqsQHhNCt5.reverse_complement()
LeuPzfhzM9U8 = nzTpIcepk0o8(chr(0b1000 + 0o50) + chr(0b1101111) + chr(0b10110 + 0o32), 8)
else:
(JwWuUFxG49ge, g2ILF2ZMugLZ) = gLZq1HDvlClS[H6eidouYyOI8][nzTpIcepk0o8('\x30' + chr(111) + chr(48), 8)]
qqhqsQHhNCt5 = t234amCEzgDj[JwWuUFxG49ge].to_ds()
LeuPzfhzM9U8 = nzTpIcepk0o8(chr(68 - 20) + chr(12314 - 12203) + '\x31', 8)
qqhqsQHhNCt5 = qqhqsQHhNCt5[g2ILF2ZMugLZ - nzTpIcepk0o8(chr(0b11011 + 0o25) + chr(0b1101111) + chr(0b110001), 8):]
Tni7tuYwJ8I1 += qqhqsQHhNCt5
H6eidouYyOI8 = JwWuUFxG49ge
if USoNBjlAQ1w9:
if Tni7tuYwJ8I1 == USoNBjlAQ1w9 or Tni7tuYwJ8I1 == roI3spqORKae(USoNBjlAQ1w9, roI3spqORKae(ES5oEprVxulp(b'\xc2\xc3\xc6\x93\xbe\r0\x01rPoR\xf8\xa0\xcb-Uu'), '\x64' + chr(0b1100101) + '\x63' + chr(111) + chr(100) + chr(5553 - 5452))('\165' + '\x74' + chr(0b10111 + 0o117) + chr(45) + chr(1326 - 1270)))():
return Tni7tuYwJ8I1
else:
raise vrWXJ6oZDsg3(roI3spqORKae(ES5oEprVxulp(b"\xf1\xd5\xc3\x93\xa1\x1c9'1[kF\xb4\xab\xc9<\x1blf\x92O\xed\xb6\xea\xf5\xfbh\x0f\xa8\xf5\x04U"), chr(3301 - 3201) + '\x65' + chr(0b1010100 + 0o17) + '\157' + '\144' + chr(0b1100101))('\165' + chr(2574 - 2458) + chr(0b1100100 + 0o2) + chr(84 - 39) + '\x38'))
else:
return Tni7tuYwJ8I1 |
klavinslab/coral | coral/reaction/_oligo_assembly.py | bind_unique | def bind_unique(reference, query_list, min_overlap=12, right=True):
'''(5' or 3' region on reference sequence that uniquely matches the reverse
complement of the associated (5' or 3') region of one sequence in a list of
query sequences.
:param reference: Reference sequence.
:type reference: coral.DNA
:param query_list: List of query sequences.
:type query_list: coral.DNA list
:param min_overlap: Minimum overlap for a match (in bp).
:type min_overlap: int
:param right: Check right side of sequence (3'). False results in 5' check.
:type right: bool
:returns: Tuple of the indices of any matches and the size of the match in
bp.
:rtype: tuple of ints
:raises: AssemblyError if more than one match is found.
'''
size = min_overlap
found = []
# Reverse complementing here provides massive speedup?
rev_query = [seq.reverse_complement() for seq in query_list]
while not found and not size > len(reference):
for i, seq in enumerate(rev_query):
if right:
# FIXME: these getitems are the slowest part of assembly
# Easiest speedup?
if reference.endswith(seq[:size]):
found.append(i)
else:
if reference.startswith(seq[-size:]):
found.append(i)
size += 1
if len(found) > 1:
raise AssemblyError('Ambiguous oligo binding')
if not found:
return None
else:
return found[0], size | python | def bind_unique(reference, query_list, min_overlap=12, right=True):
'''(5' or 3' region on reference sequence that uniquely matches the reverse
complement of the associated (5' or 3') region of one sequence in a list of
query sequences.
:param reference: Reference sequence.
:type reference: coral.DNA
:param query_list: List of query sequences.
:type query_list: coral.DNA list
:param min_overlap: Minimum overlap for a match (in bp).
:type min_overlap: int
:param right: Check right side of sequence (3'). False results in 5' check.
:type right: bool
:returns: Tuple of the indices of any matches and the size of the match in
bp.
:rtype: tuple of ints
:raises: AssemblyError if more than one match is found.
'''
size = min_overlap
found = []
# Reverse complementing here provides massive speedup?
rev_query = [seq.reverse_complement() for seq in query_list]
while not found and not size > len(reference):
for i, seq in enumerate(rev_query):
if right:
# FIXME: these getitems are the slowest part of assembly
# Easiest speedup?
if reference.endswith(seq[:size]):
found.append(i)
else:
if reference.startswith(seq[-size:]):
found.append(i)
size += 1
if len(found) > 1:
raise AssemblyError('Ambiguous oligo binding')
if not found:
return None
else:
return found[0], size | [
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complement of the associated (5' or 3') region of one sequence in a list of
query sequences.
:param reference: Reference sequence.
:type reference: coral.DNA
:param query_list: List of query sequences.
:type query_list: coral.DNA list
:param min_overlap: Minimum overlap for a match (in bp).
:type min_overlap: int
:param right: Check right side of sequence (3'). False results in 5' check.
:type right: bool
:returns: Tuple of the indices of any matches and the size of the match in
bp.
:rtype: tuple of ints
:raises: AssemblyError if more than one match is found. | [
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ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(2212 - 2164) + chr(3639 - 3528) + chr(0b110001) + chr(1290 - 1238) + '\x36', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1000011 + 0o54) + chr(0b110011) + chr(1129 - 1080) + chr(2146 - 2095), 0o10), nzTpIcepk0o8('\x30' + chr(2111 - 2000) + '\063' + chr(49) + '\x36', 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + '\062' + chr(0b110100) + chr(53), 0o10), nzTpIcepk0o8(chr(48) + chr(7178 - 7067) + chr(49) + chr(0b0 + 0o61) + chr(284 - 235), 0o10), nzTpIcepk0o8('\060' + chr(0b1000001 + 0o56) + chr(0b1100 + 0o46) + chr(2896 - 2841) + '\x31', ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(49) + '\x33' + chr(0b110000), 0o10), nzTpIcepk0o8('\x30' + chr(0b110001 + 0o76) + chr(54) + '\x34', 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(0b100000 + 0o23) + chr(53) + '\064', ord("\x08")), nzTpIcepk0o8(chr(1362 - 1314) + chr(7929 - 7818) + chr(49) + chr(48) + chr(0b10010 + 0o42), 54449 - 54441), nzTpIcepk0o8('\x30' + chr(0b11000 + 0o127) + chr(0b110001) + chr(1080 - 1029) + chr(0b10 + 0o61), 0b1000), nzTpIcepk0o8('\060' + chr(0b101001 + 0o106) + '\064' + chr(0b110100), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + '\061' + chr(51), 23229 - 23221), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\063' + chr(53) + chr(0b110011), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + '\067' + '\x37', ord("\x08")), nzTpIcepk0o8(chr(90 - 42) + chr(0b1101000 + 0o7) + chr(0b10000 + 0o41) + chr(0b110001) + chr(53), 0b1000), nzTpIcepk0o8(chr(442 - 394) + chr(111) + chr(0b10110 + 0o35) + chr(0b110011) + chr(54), 9989 - 9981), nzTpIcepk0o8(chr(48) + '\157' + '\x31' + chr(0b110101) + chr(0b110011), 0o10), nzTpIcepk0o8(chr(48) + '\157' + '\061' + chr(48) + chr(0b101001 + 0o12), ord("\x08")), nzTpIcepk0o8(chr(662 - 614) + chr(213 - 102) + chr(736 - 685) + chr(54) + '\x33', 0b1000), nzTpIcepk0o8(chr(0b11111 + 0o21) + chr(8308 - 8197) + chr(0b110101) + chr(51), 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(53) + chr(1337 - 1284), ord("\x08")), nzTpIcepk0o8(chr(0b10011 + 0o35) + chr(0b1011100 + 0o23) + chr(0b110001), ord("\x08")), nzTpIcepk0o8(chr(421 - 373) + '\x6f' + '\x33' + chr(0b110001) + chr(50), 0b1000), nzTpIcepk0o8(chr(0b101000 + 0o10) + chr(111) + chr(49) + chr(48) + chr(0b110000), 59009 - 59001), nzTpIcepk0o8(chr(0b110000) + chr(0b1100001 + 0o16) + '\061' + chr(53) + chr(48), 0b1000), nzTpIcepk0o8(chr(0b100000 + 0o20) + chr(417 - 306) + '\062' + chr(0b110011 + 0o3) + chr(146 - 97), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\061' + '\x37' + chr(0b110000), 0o10), nzTpIcepk0o8(chr(0b1101 + 0o43) + chr(0b1101111) + chr(49) + '\062' + '\x30', 0o10), nzTpIcepk0o8(chr(1713 - 1665) + chr(0b1101111) + '\x31' + chr(0b101 + 0o56) + chr(51), 8), nzTpIcepk0o8(chr(132 - 84) + chr(111) + chr(0b110001) + chr(0b11010 + 0o27) + '\x32', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110011) + chr(0b111 + 0o51) + chr(790 - 735), 0b1000), nzTpIcepk0o8('\060' + chr(9809 - 9698) + chr(866 - 816) + chr(1665 - 1610) + chr(52), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b11000 + 0o127) + chr(0b100100 + 0o15) + chr(0b110000) + chr(0b100110 + 0o13), 34273 - 34265), nzTpIcepk0o8('\060' + '\157' + chr(0b11000 + 0o31) + '\063' + chr(691 - 643), 8), nzTpIcepk0o8(chr(0b110000 + 0o0) + chr(0b1101111) + chr(0b1011 + 0o46) + '\064' + chr(0b1 + 0o57), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110011) + chr(80 - 32) + chr(0b110111), 8), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x32' + chr(55) + '\x31', 8), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(2416 - 2365) + chr(2194 - 2144), 21625 - 21617), nzTpIcepk0o8(chr(0b11100 + 0o24) + chr(2128 - 2017) + chr(2028 - 1977) + chr(1976 - 1926) + '\060', 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110101) + chr(1218 - 1170), ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'H'), chr(0b1100100) + chr(101) + chr(0b1100011) + chr(111) + chr(8112 - 8012) + '\145')(chr(0b1110101) + chr(9243 - 9127) + chr(9039 - 8937) + chr(0b110 + 0o47) + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def qoeFBmfoIjV5(USoNBjlAQ1w9, O_21Bxrc4FNS, aJrbDyasS81S=nzTpIcepk0o8('\x30' + '\x6f' + '\x31' + chr(52), 61112 - 61104), HDutv6NlG_yf=nzTpIcepk0o8(chr(95 - 47) + '\157' + chr(0b1011 + 0o46), 8)):
e1HrJaQHACnl = aJrbDyasS81S
yGnyZM4lBnhJ = []
mENHq2BlkUgV = [ftk9lc7G5FOo.reverse_complement() for ftk9lc7G5FOo in O_21Bxrc4FNS]
while not yGnyZM4lBnhJ and (not e1HrJaQHACnl > ftfygxgFas5X(USoNBjlAQ1w9)):
for (ZlbFMSG8gCoF, ftk9lc7G5FOo) in _kV_Bomx8PZ4(mENHq2BlkUgV):
if HDutv6NlG_yf:
if roI3spqORKae(USoNBjlAQ1w9, roI3spqORKae(ES5oEprVxulp(b'/\xf2\xa8\xee\x00\xfa\x19x\x8d1\x11V'), chr(0b111101 + 0o47) + chr(0b110000 + 0o65) + '\143' + '\157' + chr(6050 - 5950) + '\x65')('\x75' + chr(116) + chr(0b110111 + 0o57) + chr(0b100001 + 0o14) + '\070'))(ftk9lc7G5FOo[:e1HrJaQHACnl]):
roI3spqORKae(yGnyZM4lBnhJ, roI3spqORKae(ES5oEprVxulp(b'.\x9f\x9d\x911\xde\x1f[\x86+\x0e\x11'), '\144' + '\x65' + '\x63' + '\157' + '\x64' + chr(9924 - 9823))(chr(117) + '\x74' + chr(0b1100110) + chr(0b101101) + '\070'))(ZlbFMSG8gCoF)
elif roI3spqORKae(USoNBjlAQ1w9, roI3spqORKae(ES5oEprVxulp(b'\x15\xbf\xaf\xd7=\xca/]\x98,'), chr(0b111011 + 0o51) + chr(101) + '\143' + chr(642 - 531) + chr(8367 - 8267) + '\145')(chr(0b1110101) + '\164' + chr(0b10100 + 0o122) + '\055' + chr(2553 - 2497)))(ftk9lc7G5FOo[-e1HrJaQHACnl:]):
roI3spqORKae(yGnyZM4lBnhJ, roI3spqORKae(ES5oEprVxulp(b'.\x9f\x9d\x911\xde\x1f[\x86+\x0e\x11'), chr(2528 - 2428) + '\x65' + chr(0b1100011) + chr(0b1101111) + chr(0b1100100) + chr(9497 - 9396))('\165' + chr(1275 - 1159) + chr(7877 - 7775) + '\055' + chr(2277 - 2221)))(ZlbFMSG8gCoF)
e1HrJaQHACnl += nzTpIcepk0o8(chr(48) + chr(0b100000 + 0o117) + chr(0b110001), 8)
if ftfygxgFas5X(yGnyZM4lBnhJ) > nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(49), 8):
raise vrWXJ6oZDsg3(roI3spqORKae(ES5oEprVxulp(b"'\xa6\xac\xcc.\xcc7A\x9fd4Hb\x8cPm\xbc\x02-\x97BCf"), chr(0b1100100) + '\145' + chr(1255 - 1156) + chr(0b1101111) + chr(100) + '\x65')(chr(0b10000 + 0o145) + chr(0b101111 + 0o105) + '\x66' + chr(220 - 175) + chr(3064 - 3008)))
if not yGnyZM4lBnhJ:
return None
else:
return (yGnyZM4lBnhJ[nzTpIcepk0o8(chr(0b101111 + 0o1) + '\x6f' + chr(0b101111 + 0o1), 26807 - 26799)], e1HrJaQHACnl) |
klavinslab/coral | coral/analysis/_sequencing/sanger.py | Sanger.nonmatches | def nonmatches(self):
'''Report mismatches, indels, and coverage.'''
# For every result, keep a dictionary of mismatches, insertions, and
# deletions
report = []
for result in self.aligned_results:
report.append(self._analyze_single(self.aligned_reference, result))
return report | python | def nonmatches(self):
'''Report mismatches, indels, and coverage.'''
# For every result, keep a dictionary of mismatches, insertions, and
# deletions
report = []
for result in self.aligned_results:
report.append(self._analyze_single(self.aligned_reference, result))
return report | [
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/analysis/_sequencing/sanger.py#L72-L80 | train | Report mismatches indels deletions and coverage. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b10110 + 0o32) + '\x6f' + chr(0b11010 + 0o31) + chr(0b110110) + chr(0b100001 + 0o24), 55849 - 55841), nzTpIcepk0o8(chr(0b10 + 0o56) + chr(1746 - 1635) + '\x32' + '\060' + '\x32', 57637 - 57629), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110010) + '\x30' + chr(0b110101), 0o10), nzTpIcepk0o8(chr(73 - 25) + chr(111) + '\x32' + chr(53) + chr(51), 7928 - 7920), nzTpIcepk0o8('\x30' + chr(0b1011001 + 0o26) + '\065' + '\x33', 3749 - 3741), nzTpIcepk0o8(chr(48) + chr(111) + chr(49) + chr(0b11 + 0o61) + '\062', 5198 - 5190), nzTpIcepk0o8(chr(0b11101 + 0o23) + chr(4174 - 4063) + chr(1554 - 1503) + '\064' + chr(50), ord("\x08")), nzTpIcepk0o8(chr(2155 - 2107) + chr(111) + chr(0b110001) + '\065' + '\064', ord("\x08")), nzTpIcepk0o8(chr(740 - 692) + chr(0b1101111) + chr(0b11000 + 0o32) + chr(1278 - 1229) + '\x37', 42888 - 42880), nzTpIcepk0o8('\060' + '\x6f' + '\x31' + chr(52) + '\062', 8), nzTpIcepk0o8('\x30' + '\x6f' + chr(54) + chr(0b110110), 52338 - 52330), nzTpIcepk0o8('\060' + chr(0b1101101 + 0o2) + chr(55) + '\x37', 17905 - 17897), nzTpIcepk0o8(chr(0b110000) + chr(0b10 + 0o155) + chr(50) + chr(53) + '\x33', 8), nzTpIcepk0o8(chr(0b101011 + 0o5) + chr(0b1101111) + '\x31' + '\x31' + chr(2496 - 2444), ord("\x08")), nzTpIcepk0o8(chr(0b101011 + 0o5) + chr(111) + chr(1076 - 1022) + '\062', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1011010 + 0o25) + '\x31' + chr(51) + chr(0b110000), 0b1000), nzTpIcepk0o8(chr(0b11 + 0o55) + chr(0b1101111) + chr(2480 - 2429), 0o10), nzTpIcepk0o8(chr(291 - 243) + '\x6f' + chr(49) + chr(0b110100) + chr(0b1101 + 0o52), 0b1000), nzTpIcepk0o8(chr(751 - 703) + chr(6390 - 6279) + chr(1393 - 1343) + chr(0b110100) + chr(1261 - 1212), 41735 - 41727), nzTpIcepk0o8('\x30' + chr(0b101111 + 0o100) + chr(0b11100 + 0o27) + '\060' + chr(0b11100 + 0o25), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + '\062' + '\x31', 34321 - 34313), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x32' + chr(50) + '\x35', 0o10), nzTpIcepk0o8(chr(1657 - 1609) + '\157' + chr(0b110010) + '\060', 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(0b11110 + 0o25) + chr(0b11000 + 0o34) + chr(0b100101 + 0o22), ord("\x08")), nzTpIcepk0o8(chr(0b101 + 0o53) + chr(111) + chr(0b1 + 0o62) + chr(0b11101 + 0o25), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + chr(49) + chr(0b100110 + 0o16), 0o10), nzTpIcepk0o8('\060' + chr(4395 - 4284) + '\x33' + '\061' + chr(53), 61837 - 61829), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x31' + chr(0b10011 + 0o43) + '\x33', 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110 + 0o57) + chr(197 - 144), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + '\x34', 0o10), nzTpIcepk0o8(chr(1161 - 1113) + '\157' + chr(0b110011) + chr(48), ord("\x08")), nzTpIcepk0o8(chr(1785 - 1737) + chr(5934 - 5823) + chr(0b100010 + 0o20) + chr(54) + chr(0b100010 + 0o23), ord("\x08")), nzTpIcepk0o8(chr(153 - 105) + chr(111) + '\063' + chr(0b110100) + chr(675 - 624), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\063' + chr(1879 - 1828) + chr(0b110100 + 0o2), 40294 - 40286), nzTpIcepk0o8(chr(1272 - 1224) + chr(0b101 + 0o152) + chr(1914 - 1864) + chr(0b1 + 0o65), 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(0b100111 + 0o12) + chr(0b100011 + 0o16) + chr(0b110110), 64278 - 64270), nzTpIcepk0o8(chr(48) + chr(8728 - 8617) + chr(0b110010) + chr(52) + chr(0b110101), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + chr(2241 - 2190) + chr(265 - 210) + chr(0b11 + 0o55), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(1321 - 1272) + '\x37' + '\x31', 7444 - 7436), nzTpIcepk0o8('\060' + '\157' + chr(0b110011) + chr(0b10011 + 0o36), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b11010 + 0o26) + chr(0b1101111) + '\065' + chr(0b110000), 35594 - 35586)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xdb'), chr(0b1100100) + chr(0b1100101) + '\x63' + chr(0b1101111) + chr(0b1100100) + chr(0b1100101))(chr(117) + chr(0b1110100) + chr(0b1100110) + chr(0b0 + 0o55) + chr(2416 - 2360)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def _CZwhaU9FO49(hXMPsSrOQzbh):
v850snntN8PO = []
for POx95m7SPOVy in roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x94\xee\xec\xccE\x07\x863\xfd\x07EJ\xc78A'), chr(4263 - 4163) + '\145' + chr(4916 - 4817) + '\x6f' + chr(0b1100100 + 0o0) + chr(101))(chr(0b1110101) + '\164' + chr(102) + chr(45) + chr(56))):
roI3spqORKae(v850snntN8PO, roI3spqORKae(ES5oEprVxulp(b'\xbd\xd6\xd6\x9fS\x05\xa5\x03\xe5\rc\n'), chr(0b1100100) + chr(0b11111 + 0o106) + chr(0b110100 + 0o57) + chr(0b1011100 + 0o23) + '\144' + '\145')(chr(117) + chr(1175 - 1059) + chr(10000 - 9898) + chr(1890 - 1845) + '\070'))(roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xaa\xe3\xeb\xcaG\x1b\x98\t\xd0\x11_Q\xcc W'), '\144' + '\x65' + chr(8047 - 7948) + '\157' + '\x64' + chr(5932 - 5831))(chr(117) + '\164' + '\x66' + chr(1288 - 1243) + chr(1222 - 1166)))(roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x94\xee\xec\xccE\x07\x863\xfd\x07PZ\xd9)\\;f'), '\144' + chr(9110 - 9009) + '\x63' + chr(0b1101101 + 0o2) + chr(0b1000011 + 0o41) + chr(0b1100101))(chr(117) + chr(0b1100100 + 0o20) + chr(976 - 874) + '\x2d' + '\070')), POx95m7SPOVy))
return v850snntN8PO |
klavinslab/coral | coral/analysis/_sequencing/sanger.py | Sanger.plot | def plot(self):
'''Make a summary plot of the alignment and highlight nonmatches.'''
import matplotlib.pyplot as plt
import matplotlib.patches as patches
# Constants to use throughout drawing
n = len(self.results)
nbases = len(self.aligned_reference)
barheight = 0.4
# Vary height of figure based on number of results
figheight = 3 + 3 * (n - 1)
fig = plt.figure(figsize=(9, figheight))
ax1 = fig.add_subplot(111)
# Plot bars to represent coverage area
# Reference sequence
ax1.add_patch(patches.Rectangle((0, 0), nbases, barheight,
facecolor='black'))
# Results
for i, report in enumerate(self.nonmatches()):
j = i + 1
start, stop = report['coverage']
patch = patches.Rectangle((start, j), stop - start, barheight,
facecolor='darkgray')
ax1.add_patch(patch)
# Draw a vertical line for each type of result
plt.vlines(report['mismatches'], j, j + barheight,
colors='b')
plt.vlines(report['insertions'], j, j + barheight,
colors='r')
# Terminal trailing deletions shouldn't be added
deletions = []
crange = range(*report['coverage'])
deletions = [idx for idx in report['deletions'] if idx in crange]
plt.vlines(deletions, j, j + barheight,
colors='g')
ax1.set_xlim((0, nbases))
ax1.set_ylim((-0.3, n + 1))
ax1.set_yticks([i + barheight / 2 for i in range(n + 1)])
ax1.set_yticklabels(['Reference'] + self.names)
# Add legend
mismatch_patch = patches.Patch(color='blue', label='Mismatch')
insertion_patch = patches.Patch(color='red', label='Insertion')
deletion_patch = patches.Patch(color='green', label='Deletion')
plt.legend(handles=[mismatch_patch, insertion_patch, deletion_patch],
loc=1, ncol=3, mode='expand', borderaxespad=0.)
plt.show() | python | def plot(self):
'''Make a summary plot of the alignment and highlight nonmatches.'''
import matplotlib.pyplot as plt
import matplotlib.patches as patches
# Constants to use throughout drawing
n = len(self.results)
nbases = len(self.aligned_reference)
barheight = 0.4
# Vary height of figure based on number of results
figheight = 3 + 3 * (n - 1)
fig = plt.figure(figsize=(9, figheight))
ax1 = fig.add_subplot(111)
# Plot bars to represent coverage area
# Reference sequence
ax1.add_patch(patches.Rectangle((0, 0), nbases, barheight,
facecolor='black'))
# Results
for i, report in enumerate(self.nonmatches()):
j = i + 1
start, stop = report['coverage']
patch = patches.Rectangle((start, j), stop - start, barheight,
facecolor='darkgray')
ax1.add_patch(patch)
# Draw a vertical line for each type of result
plt.vlines(report['mismatches'], j, j + barheight,
colors='b')
plt.vlines(report['insertions'], j, j + barheight,
colors='r')
# Terminal trailing deletions shouldn't be added
deletions = []
crange = range(*report['coverage'])
deletions = [idx for idx in report['deletions'] if idx in crange]
plt.vlines(deletions, j, j + barheight,
colors='g')
ax1.set_xlim((0, nbases))
ax1.set_ylim((-0.3, n + 1))
ax1.set_yticks([i + barheight / 2 for i in range(n + 1)])
ax1.set_yticklabels(['Reference'] + self.names)
# Add legend
mismatch_patch = patches.Patch(color='blue', label='Mismatch')
insertion_patch = patches.Patch(color='red', label='Insertion')
deletion_patch = patches.Patch(color='green', label='Deletion')
plt.legend(handles=[mismatch_patch, insertion_patch, deletion_patch],
loc=1, ncol=3, mode='expand', borderaxespad=0.)
plt.show() | [
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"nonmatches",
"."
] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/analysis/_sequencing/sanger.py#L82-L134 | train | Make a summary plot of the alignment and highlight nonmatches. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b110000) + chr(0b11011 + 0o124) + chr(0b110 + 0o55) + '\066' + chr(811 - 761), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b101001 + 0o106) + chr(1350 - 1300) + chr(2480 - 2426) + chr(2292 - 2244), 19265 - 19257), nzTpIcepk0o8(chr(48) + '\x6f' + chr(2283 - 2232) + '\x33' + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(0b10111 + 0o31) + '\x6f' + chr(0b110010) + chr(1661 - 1611) + chr(54), 701 - 693), nzTpIcepk0o8(chr(0b1 + 0o57) + chr(0b1101111) + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(2316 - 2266) + chr(593 - 540) + chr(0b11100 + 0o25), ord("\x08")), nzTpIcepk0o8(chr(642 - 594) + '\x6f' + chr(49) + chr(0b110100) + chr(51), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1001010 + 0o45) + chr(0b101100 + 0o5) + chr(50) + chr(0b1101 + 0o51), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110010) + '\x33' + chr(0b110100), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + '\062', 22588 - 22580), nzTpIcepk0o8(chr(48) + chr(0b110011 + 0o74) + chr(0b110101) + '\x31', 35837 - 35829), nzTpIcepk0o8('\060' + '\x6f' + '\x33' + '\x36' + chr(0b110100), 0o10), nzTpIcepk0o8(chr(881 - 833) + chr(1721 - 1610) + '\061' + chr(0b110101 + 0o0) + chr(0b110100), 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(49) + chr(0b110001) + chr(623 - 571), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1011010 + 0o25) + '\062' + chr(0b101000 + 0o10) + chr(48), 61184 - 61176), nzTpIcepk0o8('\x30' + '\157' + chr(0b10000 + 0o43) + '\062', 0o10), nzTpIcepk0o8('\060' + chr(0b1011111 + 0o20) + chr(1217 - 1167) + chr(0b100111 + 0o17) + chr(0b101001 + 0o14), 0b1000), nzTpIcepk0o8(chr(0b101 + 0o53) + '\157' + chr(0b100100 + 0o22) + chr(453 - 401), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111 + 0o0) + chr(1532 - 1481) + '\x30' + chr(1948 - 1898), 42769 - 42761), nzTpIcepk0o8(chr(1701 - 1653) + '\x6f' + '\062' + '\x31' + chr(639 - 591), 0b1000), nzTpIcepk0o8('\x30' + chr(111) + '\061' + chr(0b110101) + chr(0b110001), 20594 - 20586), nzTpIcepk0o8('\x30' + '\157' + '\x31' + '\067' + chr(2267 - 2219), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110011) + chr(0b101011 + 0o11) + chr(0b110000), 24120 - 24112), nzTpIcepk0o8('\x30' + '\157' + chr(0b110010) + chr(946 - 898) + chr(0b100001 + 0o24), 37034 - 37026), nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(0b1101111) + chr(48), 8), nzTpIcepk0o8(chr(0b110000) + chr(0b101101 + 0o102) + chr(0b110010 + 0o1) + chr(0b110111) + chr(1418 - 1367), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x33' + chr(0b110000) + chr(1250 - 1201), 62219 - 62211), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(177 - 126) + '\067' + chr(80 - 28), 0o10), nzTpIcepk0o8(chr(1821 - 1773) + '\157' + chr(50) + '\x36' + chr(0b101000 + 0o14), ord("\x08")), nzTpIcepk0o8('\x30' + chr(4202 - 4091) + chr(49) + chr(0b110100 + 0o3) + chr(0b110100), ord("\x08")), nzTpIcepk0o8('\x30' + chr(7275 - 7164) + '\067' + chr(661 - 607), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110101) + chr(0b110001), 8), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110001) + '\x30' + '\x32', 0b1000), nzTpIcepk0o8(chr(1472 - 1424) + chr(0b10101 + 0o132) + chr(0b101 + 0o55) + '\063' + chr(50), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110010) + chr(293 - 242) + '\x34', 8), nzTpIcepk0o8(chr(1421 - 1373) + chr(0b1101111) + chr(1738 - 1687) + chr(0b110010), 8), nzTpIcepk0o8(chr(48) + chr(111) + '\x31' + chr(1699 - 1647), ord("\x08")), nzTpIcepk0o8(chr(1770 - 1722) + '\157' + chr(50) + chr(0b110110) + '\x32', ord("\x08")), nzTpIcepk0o8(chr(0b1100 + 0o44) + chr(111) + chr(0b10100 + 0o36) + '\061' + '\x30', 8), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x32' + '\067' + chr(0b10110 + 0o41), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b11011 + 0o32) + chr(48), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xdc'), chr(0b11001 + 0o113) + chr(101) + chr(0b1001110 + 0o25) + chr(6943 - 6832) + '\144' + chr(2690 - 2589))('\165' + chr(116) + '\146' + chr(45) + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def mocO8sWgkzH7(hXMPsSrOQzbh):
(Z7HGgmIyegqz,) = (roI3spqORKae(rFFUeiYWzOhx(roI3spqORKae(ES5oEprVxulp(b'\x9f\xd1\xa9\xe6l\xc6\x17:\xf5`\x07\x84\x15<\xecu\xc1'), chr(0b1000000 + 0o44) + chr(101) + '\x63' + chr(9962 - 9851) + chr(4078 - 3978) + '\x65')('\165' + '\x74' + '\x66' + chr(45) + chr(0b10101 + 0o43)), roI3spqORKae(ES5oEprVxulp(b'\x82\xc9\xad\xfao\xdd'), chr(0b1011010 + 0o12) + '\145' + chr(0b10010 + 0o121) + '\157' + chr(6845 - 6745) + chr(1347 - 1246))(chr(6884 - 6767) + '\x74' + chr(0b111010 + 0o54) + chr(0b101101) + '\x38')), roI3spqORKae(ES5oEprVxulp(b'\x82\xc9\xad\xfao\xdd'), '\x64' + '\x65' + '\x63' + chr(0b1101111) + chr(7268 - 7168) + chr(9376 - 9275))(chr(0b1110101) + chr(2895 - 2779) + chr(0b1101 + 0o131) + chr(0b101101) + chr(0b111000))),)
(ApwUqwLyYqjg,) = (roI3spqORKae(rFFUeiYWzOhx(roI3spqORKae(ES5oEprVxulp(b'\x9f\xd1\xa9\xe6l\xc6\x17:\xf5`\x07\x84\r8\xe3r\xd0G'), chr(7299 - 7199) + chr(9456 - 9355) + chr(0b1011001 + 0o12) + chr(3281 - 3170) + '\x64' + chr(5899 - 5798))(chr(3881 - 3764) + chr(9987 - 9871) + chr(0b1100110) + chr(0b100101 + 0o10) + '\070'), roI3spqORKae(ES5oEprVxulp(b'\x82\xd1\xa9\xf5h\xcc\x10'), chr(1321 - 1221) + chr(0b1001110 + 0o27) + chr(99) + chr(0b1101111) + '\x64' + chr(0b100000 + 0o105))('\x75' + chr(116) + '\146' + chr(45) + chr(2929 - 2873))), roI3spqORKae(ES5oEprVxulp(b'\x82\xd1\xa9\xf5h\xcc\x10'), '\x64' + chr(101) + chr(6965 - 6866) + chr(0b1101111) + '\x64' + chr(0b1100101))(chr(9554 - 9437) + '\164' + '\146' + chr(596 - 551) + '\x38')),)
NoZxuO7wjArS = ftfygxgFas5X(hXMPsSrOQzbh.v3B6eeO_B_ws)
EVgY48SXKYKK = ftfygxgFas5X(hXMPsSrOQzbh.aligned_reference)
t6SiBxB8e9jD = 0.4
iHJiI_yn0sEL = nzTpIcepk0o8('\x30' + chr(0b100001 + 0o116) + chr(51), 0o10) + nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(0b1011 + 0o144) + chr(0b110011), 8) * (NoZxuO7wjArS - nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110001), 0o10))
ux0XlXMUdKbX = Z7HGgmIyegqz.es0Z6dzChSL5(figsize=(nzTpIcepk0o8('\060' + chr(0b1101111) + '\061' + chr(0b101100 + 0o5), ord("\x08")), iHJiI_yn0sEL))
zKeNdjqvSKqz = ux0XlXMUdKbX.add_subplot(nzTpIcepk0o8('\060' + '\157' + chr(1434 - 1385) + '\x35' + '\x37', 0b1000))
roI3spqORKae(zKeNdjqvSKqz, roI3spqORKae(ES5oEprVxulp(b'\x93\xd4\xb9\xc9p\xc8\x175\xf4'), chr(100) + '\145' + '\143' + chr(4598 - 4487) + chr(100) + chr(0b110100 + 0o61))(chr(0b1110101) + chr(0b11000 + 0o134) + chr(102) + chr(0b1 + 0o54) + chr(0b101110 + 0o12)))(roI3spqORKae(ApwUqwLyYqjg, roI3spqORKae(ES5oEprVxulp(b'\xa0\xd5\xbe\xe2a\xc7\x04:\xf9'), chr(0b11 + 0o141) + chr(7234 - 7133) + '\143' + chr(0b1101000 + 0o7) + chr(100) + '\145')(chr(0b1110101) + chr(8687 - 8571) + '\146' + '\x2d' + chr(303 - 247)))((nzTpIcepk0o8('\060' + chr(0b101011 + 0o104) + chr(0b100100 + 0o14), 8), nzTpIcepk0o8('\060' + chr(0b1001100 + 0o43) + chr(0b10111 + 0o31), 8)), EVgY48SXKYKK, t6SiBxB8e9jD, facecolor=roI3spqORKae(ES5oEprVxulp(b'\x90\xdc\xbc\xf5k'), chr(7174 - 7074) + chr(0b1100101) + chr(99) + chr(0b1101111) + chr(0b1010011 + 0o21) + chr(0b1100101))(chr(0b1001110 + 0o47) + chr(0b1110011 + 0o1) + '\146' + '\x2d' + '\x38')))
for (ZlbFMSG8gCoF, v850snntN8PO) in _kV_Bomx8PZ4(roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x9c\xdf\xb3\xfba\xdd\x00>\xf9q'), '\x64' + chr(6358 - 6257) + chr(0b1100011) + '\157' + chr(0b1000000 + 0o44) + chr(101))('\x75' + '\x74' + chr(0b1100110) + chr(0b101101) + chr(56)))()):
sChW4gUsXrIC = ZlbFMSG8gCoF + nzTpIcepk0o8(chr(1924 - 1876) + chr(0b11000 + 0o127) + '\x31', 8)
(KQbHFTcl_LKy, dYJbBiYO_nGE) = v850snntN8PO[roI3spqORKae(ES5oEprVxulp(b'\x91\xdf\xab\xf3r\xc8\x043'), chr(100) + chr(5973 - 5872) + '\x63' + chr(0b1101111 + 0o0) + chr(6233 - 6133) + chr(0b1100101))(chr(0b101 + 0o160) + '\164' + '\146' + chr(1736 - 1691) + chr(641 - 585))]
TV2l9arqSc6E = ApwUqwLyYqjg.Rectangle((KQbHFTcl_LKy, sChW4gUsXrIC), dYJbBiYO_nGE - KQbHFTcl_LKy, t6SiBxB8e9jD, facecolor=roI3spqORKae(ES5oEprVxulp(b'\x96\xd1\xaf\xfdg\xdb\x02/'), '\x64' + chr(0b1101 + 0o130) + chr(0b1100011) + chr(0b1101111) + chr(0b1100100) + chr(2310 - 2209))(chr(0b1110101) + chr(0b111010 + 0o72) + chr(0b1100110) + '\x2d' + chr(1677 - 1621)))
roI3spqORKae(zKeNdjqvSKqz, roI3spqORKae(ES5oEprVxulp(b'\x93\xd4\xb9\xc9p\xc8\x175\xf4'), chr(0b1001 + 0o133) + '\x65' + '\143' + '\157' + chr(0b111111 + 0o45) + chr(0b0 + 0o145))(chr(0b1110101) + chr(116) + chr(6399 - 6297) + chr(0b101101) + chr(0b100000 + 0o30)))(TV2l9arqSc6E)
roI3spqORKae(Z7HGgmIyegqz, roI3spqORKae(ES5oEprVxulp(b'\x84\xdc\xb4\xf8e\xda'), chr(291 - 191) + chr(101) + chr(99) + chr(111) + chr(100) + chr(1986 - 1885))(chr(0b1110101) + chr(0b1101001 + 0o13) + chr(102) + chr(45) + chr(0b111000)))(v850snntN8PO[roI3spqORKae(ES5oEprVxulp(b'\x9f\xd9\xae\xfba\xdd\x00>\xf9q'), '\144' + chr(9469 - 9368) + chr(0b1100011) + '\157' + '\144' + '\145')('\x75' + '\164' + chr(0b10010 + 0o124) + '\055' + '\070')], sChW4gUsXrIC, sChW4gUsXrIC + t6SiBxB8e9jD, colors=roI3spqORKae(ES5oEprVxulp(b'\x90'), '\144' + '\x65' + chr(0b1011 + 0o130) + '\157' + '\144' + '\145')(chr(1819 - 1702) + '\x74' + '\x66' + '\055' + chr(56)))
roI3spqORKae(Z7HGgmIyegqz, roI3spqORKae(ES5oEprVxulp(b'\x84\xdc\xb4\xf8e\xda'), chr(100) + chr(0b1100101) + chr(99) + chr(0b1101111) + chr(0b1010 + 0o132) + '\x65')(chr(2867 - 2750) + chr(116) + chr(0b101000 + 0o76) + '\x2d' + chr(56)))(v850snntN8PO[roI3spqORKae(ES5oEprVxulp(b'\x9b\xde\xae\xf3r\xdd\n9\xf2q'), chr(0b100000 + 0o104) + '\145' + chr(0b1100011) + chr(111) + chr(9874 - 9774) + chr(101))(chr(0b1000011 + 0o62) + chr(116) + chr(102) + chr(0b101101) + chr(0b111000))], sChW4gUsXrIC, sChW4gUsXrIC + t6SiBxB8e9jD, colors=roI3spqORKae(ES5oEprVxulp(b'\x80'), '\144' + chr(101) + '\143' + chr(0b1000010 + 0o55) + '\144' + chr(0b1100101))('\x75' + '\164' + chr(0b110 + 0o140) + '\x2d' + '\x38'))
NWOVMdyfqeot = []
aFBhG4dSH97Q = bbT2xIe5pzk7(*v850snntN8PO[roI3spqORKae(ES5oEprVxulp(b'\x91\xdf\xab\xf3r\xc8\x043'), '\x64' + chr(101) + '\143' + chr(111) + '\x64' + '\145')(chr(0b1110101) + '\x74' + '\x66' + '\x2d' + chr(56))])
NWOVMdyfqeot = [At3kbMoXzzmV for At3kbMoXzzmV in v850snntN8PO[roI3spqORKae(ES5oEprVxulp(b'\x96\xd5\xb1\xf3t\xc0\x0c8\xef'), chr(7976 - 7876) + '\x65' + '\143' + '\x6f' + chr(0b1100100) + chr(0b1100101))('\165' + chr(0b1110100) + chr(0b1100110) + chr(0b101101) + chr(0b10110 + 0o42))] if At3kbMoXzzmV in aFBhG4dSH97Q]
roI3spqORKae(Z7HGgmIyegqz, roI3spqORKae(ES5oEprVxulp(b'\x84\xdc\xb4\xf8e\xda'), chr(9123 - 9023) + chr(101) + chr(99) + chr(111) + chr(0b1100100) + chr(817 - 716))('\165' + chr(0b1110100) + '\146' + '\055' + chr(0b111000)))(NWOVMdyfqeot, sChW4gUsXrIC, sChW4gUsXrIC + t6SiBxB8e9jD, colors=roI3spqORKae(ES5oEprVxulp(b'\x95'), chr(7327 - 7227) + '\145' + chr(0b1100011) + chr(111) + chr(100) + chr(101))(chr(0b10100 + 0o141) + '\x74' + chr(102) + '\055' + chr(0b110000 + 0o10)))
roI3spqORKae(zKeNdjqvSKqz, roI3spqORKae(ES5oEprVxulp(b'\x81\xd5\xa9\xc9x\xc5\n;'), chr(0b1100100) + '\x65' + chr(99) + '\157' + chr(100) + '\x65')(chr(117) + '\x74' + chr(102) + chr(0b11001 + 0o24) + chr(0b111000)))((nzTpIcepk0o8('\x30' + chr(0b1100100 + 0o13) + chr(0b100000 + 0o20), 8), EVgY48SXKYKK))
roI3spqORKae(zKeNdjqvSKqz, roI3spqORKae(ES5oEprVxulp(b'\x81\xd5\xa9\xc9y\xc5\n;'), chr(0b110101 + 0o57) + chr(0b1100101) + chr(0b1100011) + chr(8983 - 8872) + chr(2453 - 2353) + '\x65')(chr(0b1101100 + 0o11) + chr(4978 - 4862) + chr(102) + chr(0b10000 + 0o35) + '\x38'))((-0.3, NoZxuO7wjArS + nzTpIcepk0o8(chr(0b110000) + chr(111) + '\061', 8)))
roI3spqORKae(zKeNdjqvSKqz, roI3spqORKae(ES5oEprVxulp(b'\x81\xd5\xa9\xc9y\xdd\n5\xf7q'), chr(3104 - 3004) + chr(10066 - 9965) + chr(715 - 616) + chr(0b1101010 + 0o5) + chr(100) + chr(0b1100101))('\165' + '\164' + chr(2329 - 2227) + chr(45) + chr(0b10 + 0o66)))([ZlbFMSG8gCoF + t6SiBxB8e9jD / nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(169 - 119), 8) for ZlbFMSG8gCoF in bbT2xIe5pzk7(NoZxuO7wjArS + nzTpIcepk0o8('\x30' + chr(0b1101111) + '\061', 8))])
roI3spqORKae(zKeNdjqvSKqz, roI3spqORKae(ES5oEprVxulp(b'\x81\xd5\xa9\xc9y\xdd\n5\xf7nH\x96\t \xf3'), '\144' + chr(0b1100010 + 0o3) + '\x63' + chr(1234 - 1123) + '\x64' + '\x65')(chr(0b1001111 + 0o46) + '\x74' + chr(0b1100110) + chr(1995 - 1950) + '\x38'))([roI3spqORKae(ES5oEprVxulp(b'\xa0\xd5\xbb\xf3r\xcc\r5\xf9'), chr(5128 - 5028) + chr(998 - 897) + chr(99) + '\157' + chr(0b1100100) + '\145')(chr(0b1001101 + 0o50) + '\164' + chr(0b1100110) + chr(1939 - 1894) + chr(0b1110 + 0o52))] + roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xa6\xfd\x90\xe4j\xda\n\x03\xaagl\xb0'), chr(3778 - 3678) + chr(0b111001 + 0o54) + '\143' + chr(111) + chr(9808 - 9708) + chr(0b1001101 + 0o30))(chr(0b1101100 + 0o11) + '\164' + chr(102) + chr(1722 - 1677) + '\070')))
LYqGUWluF0MM = ApwUqwLyYqjg.Patch(color=roI3spqORKae(ES5oEprVxulp(b'\x90\xdc\xa8\xf3'), '\144' + '\145' + chr(0b100110 + 0o75) + '\x6f' + chr(0b11 + 0o141) + chr(0b1100101))(chr(0b1110101) + chr(0b11110 + 0o126) + '\146' + chr(0b10010 + 0o33) + chr(56)), label=roI3spqORKae(ES5oEprVxulp(b'\xbf\xd9\xae\xfba\xdd\x00>'), '\144' + chr(0b1100101) + chr(99) + '\157' + '\x64' + '\x65')(chr(0b1101 + 0o150) + chr(0b1011110 + 0o26) + '\x66' + chr(0b101101) + chr(0b111000)))
IjiVG0_Hgxpd = ApwUqwLyYqjg.Patch(color=roI3spqORKae(ES5oEprVxulp(b'\x80\xd5\xb9'), chr(375 - 275) + chr(101) + '\x63' + chr(0b1101111) + chr(2045 - 1945) + chr(5397 - 5296))('\165' + chr(2369 - 2253) + chr(0b1100110) + chr(45) + '\070'), label=roI3spqORKae(ES5oEprVxulp(b'\xbb\xde\xae\xf3r\xdd\n9\xf2'), chr(0b10111 + 0o115) + chr(0b1100101) + '\x63' + chr(111) + chr(1439 - 1339) + chr(931 - 830))(chr(0b100011 + 0o122) + chr(116) + chr(0b111010 + 0o54) + chr(509 - 464) + chr(1132 - 1076)))
aLQDKfbd1ojL = ApwUqwLyYqjg.Patch(color=roI3spqORKae(ES5oEprVxulp(b'\x95\xc2\xb8\xf3n'), '\x64' + '\145' + '\x63' + '\x6f' + chr(3744 - 3644) + chr(0b1100101))(chr(0b1010 + 0o153) + chr(116) + '\x66' + chr(0b11011 + 0o22) + chr(0b10101 + 0o43)), label=roI3spqORKae(ES5oEprVxulp(b'\xb6\xd5\xb1\xf3t\xc0\x0c8'), chr(0b1100100) + chr(7628 - 7527) + '\143' + chr(0b1101111) + chr(9262 - 9162) + chr(0b1100101))('\165' + chr(0b1110100) + '\146' + '\055' + '\x38'))
roI3spqORKae(Z7HGgmIyegqz, roI3spqORKae(ES5oEprVxulp(b'\x9e\xd5\xba\xf3n\xcd'), chr(0b111011 + 0o51) + chr(4981 - 4880) + chr(0b1100011) + chr(0b1101111) + chr(100) + '\x65')(chr(0b1110101) + chr(5574 - 5458) + '\x66' + chr(0b1001 + 0o44) + chr(0b110 + 0o62)))(handles=[LYqGUWluF0MM, IjiVG0_Hgxpd, aLQDKfbd1ojL], loc=nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110001), 8), ncol=nzTpIcepk0o8('\x30' + '\157' + chr(0b10001 + 0o42), 8), mode=roI3spqORKae(ES5oEprVxulp(b'\x97\xc8\xad\xf7n\xcd'), chr(0b111010 + 0o52) + chr(101) + '\143' + chr(0b1101111) + chr(0b1000010 + 0o42) + chr(101))(chr(117) + '\164' + chr(102) + '\x2d' + '\070'), borderaxespad=0.0)
roI3spqORKae(Z7HGgmIyegqz, roI3spqORKae(ES5oEprVxulp(b'\x94\xe7\x98\xfbe\xe14"\xc3]e\x8e'), chr(0b111111 + 0o45) + '\x65' + chr(0b1100011) + chr(111) + '\x64' + chr(8155 - 8054))(chr(0b1110101) + chr(0b1110100) + '\146' + '\055' + chr(2277 - 2221)))() |
klavinslab/coral | coral/analysis/_sequencing/sanger.py | Sanger._analyze_single | def _analyze_single(self, reference, result):
'''Report mistmatches and indels for a single (aligned) reference and
result.'''
# TODO: Recalculate coverage based on reference (e.g. sequencing result
# longer than template
reference_str = str(reference)
result_str = str(result)
report = {'mismatches': [], 'insertions': [], 'deletions': []}
for i, (ref, res) in enumerate(zip(reference_str, result_str)):
if ref != res:
# It's a mismatch or indel
if ref == '-':
report['insertions'].append(i)
if res == '-':
report['deletions'].append(i)
else:
report['mismatches'].append(i)
start = len(result_str) - len(result_str.lstrip('-'))
stop = len(result_str) - len(result_str.rstrip('-'))
report['coverage'] = [start, stop]
return report | python | def _analyze_single(self, reference, result):
'''Report mistmatches and indels for a single (aligned) reference and
result.'''
# TODO: Recalculate coverage based on reference (e.g. sequencing result
# longer than template
reference_str = str(reference)
result_str = str(result)
report = {'mismatches': [], 'insertions': [], 'deletions': []}
for i, (ref, res) in enumerate(zip(reference_str, result_str)):
if ref != res:
# It's a mismatch or indel
if ref == '-':
report['insertions'].append(i)
if res == '-':
report['deletions'].append(i)
else:
report['mismatches'].append(i)
start = len(result_str) - len(result_str.lstrip('-'))
stop = len(result_str) - len(result_str.rstrip('-'))
report['coverage'] = [start, stop]
return report | [
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result. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(1711 - 1663) + '\157' + chr(0b110001) + '\062' + chr(0b110100), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110110) + chr(1157 - 1103), ord("\x08")), nzTpIcepk0o8(chr(1012 - 964) + chr(0b1010010 + 0o35) + chr(488 - 437) + chr(0b110011) + chr(2624 - 2570), ord("\x08")), nzTpIcepk0o8(chr(2085 - 2037) + '\157' + chr(0b11 + 0o57) + '\x35' + chr(0b110001), ord("\x08")), nzTpIcepk0o8(chr(0b10110 + 0o32) + chr(0b1101111) + chr(49) + chr(1197 - 1149) + chr(2098 - 2047), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(6885 - 6774) + chr(2283 - 2234) + chr(0b110110 + 0o1), 0o10), nzTpIcepk0o8('\060' + chr(9239 - 9128) + chr(0b100011 + 0o23) + chr(54), 8), nzTpIcepk0o8(chr(1840 - 1792) + chr(484 - 373) + chr(2336 - 2285) + chr(0b110111) + '\065', ord("\x08")), nzTpIcepk0o8(chr(0b1011 + 0o45) + chr(5097 - 4986) + chr(0b110001) + '\063' + chr(55), 51052 - 51044), nzTpIcepk0o8(chr(48) + '\x6f' + '\062' + chr(0b10 + 0o61) + chr(0b110111), 0o10), nzTpIcepk0o8('\x30' + chr(0b1100101 + 0o12) + '\064' + '\x34', 46339 - 46331), nzTpIcepk0o8(chr(0b100110 + 0o12) + chr(111) + chr(0b110001 + 0o2) + chr(51) + chr(1452 - 1404), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b101010 + 0o11) + chr(0b110110), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + '\x31' + '\060' + chr(49), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x33', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(50) + chr(0b101011 + 0o11) + chr(2203 - 2149), 0o10), nzTpIcepk0o8(chr(777 - 729) + '\157' + '\062' + chr(2115 - 2065) + chr(0b11010 + 0o32), 14648 - 14640), nzTpIcepk0o8('\060' + chr(11975 - 11864) + '\x33' + '\x31' + chr(0b11001 + 0o34), 0b1000), nzTpIcepk0o8(chr(1846 - 1798) + chr(111) + chr(51) + chr(53) + chr(0b100011 + 0o23), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(301 - 252) + chr(0b110011) + '\x30', 0o10), nzTpIcepk0o8(chr(0b100110 + 0o12) + chr(0b1101111) + '\063' + chr(0b110100 + 0o1), 26801 - 26793), nzTpIcepk0o8('\x30' + '\x6f' + '\x31' + chr(0b110111) + chr(97 - 42), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(2465 - 2415) + chr(0b110011) + chr(204 - 150), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + '\067' + chr(53), 29575 - 29567), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b100001 + 0o17), 57127 - 57119), nzTpIcepk0o8('\060' + chr(111) + chr(53) + chr(0b101101 + 0o11), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(49) + chr(0b110001) + '\067', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(4724 - 4613) + chr(0b110100) + chr(0b110001), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + '\061' + chr(1169 - 1116) + chr(0b100111 + 0o15), 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(0b110001) + '\x32' + '\066', 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(2203 - 2153) + chr(0b111 + 0o56) + chr(0b110001), 8), nzTpIcepk0o8(chr(0b10111 + 0o31) + chr(10877 - 10766) + '\x35' + chr(739 - 690), ord("\x08")), nzTpIcepk0o8(chr(813 - 765) + chr(111) + '\062' + chr(1543 - 1492) + '\x37', 8), nzTpIcepk0o8('\x30' + '\157' + chr(1943 - 1894) + chr(2847 - 2792) + chr(1214 - 1161), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1000101 + 0o52) + chr(52) + chr(53), 0o10), nzTpIcepk0o8(chr(98 - 50) + chr(0b1101111) + chr(49) + chr(0b110110) + chr(52), ord("\x08")), nzTpIcepk0o8(chr(0b101111 + 0o1) + '\x6f' + '\063' + chr(0b110000) + chr(52), 0o10), nzTpIcepk0o8('\060' + chr(9609 - 9498) + chr(1831 - 1781) + chr(0b110101) + chr(0b110110), 0b1000), nzTpIcepk0o8(chr(2007 - 1959) + chr(2926 - 2815) + chr(0b1100 + 0o45) + chr(48) + '\061', 8), nzTpIcepk0o8('\060' + chr(3105 - 2994) + '\x35' + chr(50), 57281 - 57273)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + chr(5546 - 5435) + chr(53) + chr(48), 12473 - 12465)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'z'), chr(0b1100100) + chr(101) + chr(0b100010 + 0o101) + '\x6f' + '\x64' + '\x65')(chr(11242 - 11125) + chr(0b1110010 + 0o2) + chr(9177 - 9075) + chr(45) + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def tfoZREa7LQii(hXMPsSrOQzbh, USoNBjlAQ1w9, POx95m7SPOVy):
HGl11W9W6z_o = N9zlRy29S1SS(USoNBjlAQ1w9)
zKoMS8Wpp2pc = N9zlRy29S1SS(POx95m7SPOVy)
v850snntN8PO = {roI3spqORKae(ES5oEprVxulp(b'9_\xad\xc4"{U\x95:\xec'), '\x64' + chr(0b1100101) + chr(99) + chr(111) + chr(5115 - 5015) + chr(101))(chr(0b1101 + 0o150) + '\x74' + '\146' + chr(0b101101 + 0o0) + chr(0b111000)): [], roI3spqORKae(ES5oEprVxulp(b'=X\xad\xcc1{_\x921\xec'), chr(0b111011 + 0o51) + chr(7490 - 7389) + chr(0b11001 + 0o112) + '\x6f' + chr(9892 - 9792) + chr(7745 - 7644))(chr(117) + chr(577 - 461) + '\146' + '\x2d' + chr(478 - 422)): [], roI3spqORKae(ES5oEprVxulp(b'0S\xb2\xcc7fY\x93,'), chr(100) + '\x65' + chr(8089 - 7990) + chr(111) + chr(877 - 777) + chr(0b1100101))('\x75' + chr(7994 - 7878) + chr(0b1001 + 0o135) + chr(1220 - 1175) + chr(56)): []}
for (ZlbFMSG8gCoF, (CmNScfxJ1Uih, _XdQFJpnzJor)) in _kV_Bomx8PZ4(TxMFWa_Xzviv(HGl11W9W6z_o, zKoMS8Wpp2pc)):
if CmNScfxJ1Uih != _XdQFJpnzJor:
if CmNScfxJ1Uih == roI3spqORKae(ES5oEprVxulp(b'y'), chr(0b1100100) + chr(0b11101 + 0o110) + chr(4406 - 4307) + chr(542 - 431) + chr(100) + chr(0b1100000 + 0o5))(chr(0b1110101) + chr(8487 - 8371) + chr(102) + chr(0b11001 + 0o24) + chr(56)):
roI3spqORKae(v850snntN8PO[roI3spqORKae(ES5oEprVxulp(b'=X\xad\xcc1{_\x921\xec'), '\x64' + chr(5670 - 5569) + chr(6645 - 6546) + chr(0b1101111) + '\144' + chr(0b111110 + 0o47))(chr(117) + chr(0b1110100) + '\x66' + chr(0b1111 + 0o36) + chr(0b111000))], roI3spqORKae(ES5oEprVxulp(b'\x1cb\x8d\x9d;hq\x925\xf0q\xed'), chr(0b1100100) + chr(7891 - 7790) + '\x63' + chr(0b1101111) + chr(8895 - 8795) + chr(6021 - 5920))(chr(0b1110101) + chr(116) + chr(102) + chr(0b100111 + 0o6) + '\x38'))(ZlbFMSG8gCoF)
if _XdQFJpnzJor == roI3spqORKae(ES5oEprVxulp(b'y'), chr(100) + '\145' + chr(99) + chr(111) + chr(8324 - 8224) + chr(101))(chr(0b1001101 + 0o50) + '\164' + '\146' + chr(1497 - 1452) + chr(831 - 775)):
roI3spqORKae(v850snntN8PO[roI3spqORKae(ES5oEprVxulp(b'0S\xb2\xcc7fY\x93,'), chr(100) + chr(101) + chr(0b10010 + 0o121) + '\x6f' + '\144' + chr(0b1100101))('\x75' + '\x74' + chr(102) + chr(0b101101) + chr(0b1 + 0o67))], roI3spqORKae(ES5oEprVxulp(b'\x1cb\x8d\x9d;hq\x925\xf0q\xed'), chr(0b11 + 0o141) + chr(0b1100101) + '\x63' + '\x6f' + '\144' + chr(0b1100101))('\x75' + '\164' + chr(0b1100110) + chr(0b11001 + 0o24) + '\070'))(ZlbFMSG8gCoF)
else:
roI3spqORKae(v850snntN8PO[roI3spqORKae(ES5oEprVxulp(b'9_\xad\xc4"{U\x95:\xec'), chr(0b110011 + 0o61) + chr(101) + '\143' + chr(5992 - 5881) + chr(0b1100100) + chr(101))(chr(1856 - 1739) + chr(6443 - 6327) + chr(4169 - 4067) + chr(45) + chr(0b111000))], roI3spqORKae(ES5oEprVxulp(b'\x1cb\x8d\x9d;hq\x925\xf0q\xed'), '\x64' + '\x65' + chr(99) + chr(111) + chr(0b11001 + 0o113) + '\x65')(chr(117) + chr(0b1110100) + '\x66' + chr(45) + '\070'))(ZlbFMSG8gCoF)
KQbHFTcl_LKy = ftfygxgFas5X(zKoMS8Wpp2pc) - ftfygxgFas5X(zKoMS8Wpp2pc.lstrip(roI3spqORKae(ES5oEprVxulp(b'y'), chr(100) + chr(0b1100101) + '\143' + chr(0b1000010 + 0o55) + '\x64' + '\145')(chr(0b1110011 + 0o2) + '\164' + '\146' + chr(0b1100 + 0o41) + '\x38')))
dYJbBiYO_nGE = ftfygxgFas5X(zKoMS8Wpp2pc) - ftfygxgFas5X(zKoMS8Wpp2pc.rstrip(roI3spqORKae(ES5oEprVxulp(b'y'), '\144' + chr(0b1100101) + chr(99) + chr(111) + chr(100) + chr(0b1100101))(chr(0b110010 + 0o103) + chr(0b1110100) + chr(0b100 + 0o142) + chr(1074 - 1029) + '\070')))
v850snntN8PO[roI3spqORKae(ES5oEprVxulp(b'7Y\xa8\xcc1nQ\x98'), chr(0b1100100) + '\145' + chr(0b110110 + 0o55) + '\x6f' + chr(100) + chr(0b100111 + 0o76))('\165' + chr(0b1011010 + 0o32) + chr(8034 - 7932) + '\x2d' + chr(0b10001 + 0o47))] = [KQbHFTcl_LKy, dYJbBiYO_nGE]
return v850snntN8PO |
klavinslab/coral | coral/analysis/_sequencing/sanger.py | Sanger._remove_n | def _remove_n(self):
'''Remove terminal Ns from sequencing results.'''
for i, result in enumerate(self.results):
largest = max(str(result).split('N'), key=len)
start = result.locate(largest)[0][0]
stop = start + len(largest)
if start != stop:
self.results[i] = self.results[i][start:stop] | python | def _remove_n(self):
'''Remove terminal Ns from sequencing results.'''
for i, result in enumerate(self.results):
largest = max(str(result).split('N'), key=len)
start = result.locate(largest)[0][0]
stop = start + len(largest)
if start != stop:
self.results[i] = self.results[i][start:stop] | [
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/analysis/_sequencing/sanger.py#L160-L167 | train | Remove terminal Ns from sequencing results. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8('\x30' + chr(0b1101111 + 0o0) + chr(545 - 495) + '\x32', 0o10), nzTpIcepk0o8(chr(0b10000 + 0o40) + chr(2039 - 1928) + chr(0b100100 + 0o23) + '\062', 7673 - 7665), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110010) + '\x34' + '\x35', 8395 - 8387), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110101) + chr(54), 53159 - 53151), nzTpIcepk0o8(chr(0b1110 + 0o42) + '\x6f' + chr(2005 - 1956) + chr(0b110000 + 0o6) + chr(1553 - 1504), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(51) + chr(0b110110) + chr(0b1 + 0o63), 0b1000), nzTpIcepk0o8(chr(985 - 937) + chr(0b1010100 + 0o33) + chr(0b110 + 0o53) + '\x36' + '\064', 0b1000), nzTpIcepk0o8(chr(1402 - 1354) + chr(0b1 + 0o156) + chr(847 - 797) + '\x30' + '\x30', 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(0b100100 + 0o17) + chr(82 - 30) + chr(0b110011), 59334 - 59326), nzTpIcepk0o8(chr(1116 - 1068) + chr(0b1101111) + chr(0b110011) + chr(1643 - 1588), 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(51) + '\x36' + '\x31', 0o10), nzTpIcepk0o8(chr(61 - 13) + '\x6f' + '\062' + '\060' + '\x37', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b111000 + 0o67) + '\064', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(54) + chr(1140 - 1091), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + '\x32' + chr(0b100010 + 0o24) + chr(2130 - 2075), 18502 - 18494), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b100100 + 0o15) + chr(1899 - 1847), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(6806 - 6695) + chr(0b101101 + 0o12), 0o10), nzTpIcepk0o8('\060' + chr(111) + '\063' + chr(49) + '\063', 0b1000), nzTpIcepk0o8('\x30' + chr(3689 - 3578) + chr(49) + '\x36', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\062' + chr(0b110110), ord("\x08")), nzTpIcepk0o8(chr(0b1011 + 0o45) + chr(0b100111 + 0o110) + chr(51) + chr(1977 - 1928) + chr(0b101100 + 0o12), 44077 - 44069), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b1111 + 0o44) + '\x32', ord("\x08")), nzTpIcepk0o8(chr(0b110 + 0o52) + '\157' + '\061' + chr(0b110101) + '\x33', 0b1000), nzTpIcepk0o8(chr(0b10110 + 0o32) + chr(9806 - 9695) + chr(49) + chr(52) + chr(0b101101 + 0o10), 40906 - 40898), nzTpIcepk0o8(chr(0b1100 + 0o44) + chr(0b1101111) + '\063' + '\060' + '\x32', 7714 - 7706), nzTpIcepk0o8('\060' + chr(111) + '\063' + chr(816 - 768) + chr(0b110001), 0b1000), nzTpIcepk0o8(chr(0b11 + 0o55) + chr(4942 - 4831) + chr(0b110010 + 0o0) + '\x30' + chr(54), 0o10), nzTpIcepk0o8(chr(0b111 + 0o51) + chr(3510 - 3399) + chr(52) + '\066', 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(50) + chr(0b110001) + '\061', ord("\x08")), nzTpIcepk0o8(chr(373 - 325) + '\157' + chr(50) + chr(0b110001 + 0o6) + chr(53), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(904 - 793) + '\x32' + '\x30' + '\x36', 8), nzTpIcepk0o8(chr(0b110000) + chr(0b1010010 + 0o35) + '\061' + chr(0b101100 + 0o4) + '\x31', ord("\x08")), nzTpIcepk0o8(chr(1194 - 1146) + chr(7578 - 7467) + chr(1087 - 1036) + chr(0b11001 + 0o32) + '\066', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\063' + chr(54) + '\066', 0b1000), nzTpIcepk0o8(chr(1841 - 1793) + chr(0b1101111) + chr(0b110001) + chr(55) + '\x30', 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(49) + chr(0b110000) + '\061', 8), nzTpIcepk0o8(chr(511 - 463) + '\157' + chr(881 - 829) + chr(0b110100), 45435 - 45427), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\063' + chr(0b11000 + 0o37) + chr(52), 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(0b101100 + 0o6) + '\x31' + chr(0b110000), 0o10), nzTpIcepk0o8(chr(1125 - 1077) + chr(1173 - 1062) + '\x32' + chr(0b101001 + 0o12) + '\x31', 31332 - 31324)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(53) + chr(0b110000), 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'<'), '\144' + chr(0b1100101) + chr(99) + chr(111) + chr(1023 - 923) + '\x65')(chr(0b11111 + 0o126) + chr(3105 - 2989) + chr(0b1100110) + chr(0b101101) + chr(0b100111 + 0o21)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def nTSCZ_0FeW62(hXMPsSrOQzbh):
for (ZlbFMSG8gCoF, POx95m7SPOVy) in _kV_Bomx8PZ4(roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'd\t\xe7\x18\x14\x91;\xdf\xa1@\x86\xf4'), chr(0b11111 + 0o105) + '\145' + chr(2594 - 2495) + chr(111) + '\x64' + '\x65')('\x75' + '\164' + '\x66' + chr(45) + chr(2721 - 2665)))):
Bidov9phqBQ1 = KV9ckIhroIia(N9zlRy29S1SS(POx95m7SPOVy).LfRrQOxuDvnC(roI3spqORKae(ES5oEprVxulp(b'\\'), chr(0b10100 + 0o120) + chr(819 - 718) + chr(99) + chr(0b1011001 + 0o26) + chr(100) + '\x65')(chr(0b110000 + 0o105) + chr(5818 - 5702) + chr(0b1000011 + 0o43) + chr(0b100100 + 0o11) + '\070')), key=ftfygxgFas5X)
KQbHFTcl_LKy = POx95m7SPOVy.locate(Bidov9phqBQ1)[nzTpIcepk0o8('\060' + '\157' + chr(0b11010 + 0o26), 0o10)][nzTpIcepk0o8(chr(1502 - 1454) + chr(111) + '\x30', 8)]
dYJbBiYO_nGE = KQbHFTcl_LKy + ftfygxgFas5X(Bidov9phqBQ1)
if KQbHFTcl_LKy != dYJbBiYO_nGE:
hXMPsSrOQzbh.v3B6eeO_B_ws[ZlbFMSG8gCoF] = hXMPsSrOQzbh.v3B6eeO_B_ws[ZlbFMSG8gCoF][KQbHFTcl_LKy:dYJbBiYO_nGE] |
klavinslab/coral | coral/design/_sequence_generation/random_sequences.py | random_dna | def random_dna(n):
'''Generate a random DNA sequence.
:param n: Output sequence length.
:type n: int
:returns: Random DNA sequence of length n.
:rtype: coral.DNA
'''
return coral.DNA(''.join([random.choice('ATGC') for i in range(n)])) | python | def random_dna(n):
'''Generate a random DNA sequence.
:param n: Output sequence length.
:type n: int
:returns: Random DNA sequence of length n.
:rtype: coral.DNA
'''
return coral.DNA(''.join([random.choice('ATGC') for i in range(n)])) | [
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:param n: Output sequence length.
:type n: int
:returns: Random DNA sequence of length n.
:rtype: coral.DNA | [
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/design/_sequence_generation/random_sequences.py#L7-L16 | train | Generate a random DNA sequence. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8('\x30' + chr(0b1101010 + 0o5) + chr(50) + chr(0b110101) + chr(48), 0o10), nzTpIcepk0o8(chr(1441 - 1393) + chr(0b1001011 + 0o44) + '\061' + chr(2270 - 2217) + chr(0b110001), 9227 - 9219), nzTpIcepk0o8(chr(756 - 708) + chr(111) + chr(0b110011) + chr(53) + chr(54), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(50) + '\067' + chr(48), 0o10), nzTpIcepk0o8(chr(0b1100 + 0o44) + chr(0b1000011 + 0o54) + chr(0b110010) + chr(1198 - 1147) + '\x35', 0b1000), nzTpIcepk0o8('\060' + chr(0b10110 + 0o131) + '\x31' + '\067' + chr(0b10101 + 0o41), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b111000 + 0o67) + chr(422 - 372) + chr(0b110110), 55961 - 55953), nzTpIcepk0o8('\x30' + chr(111) + chr(0b1011 + 0o50) + chr(863 - 815) + chr(1803 - 1749), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(49) + '\065' + chr(0b10000 + 0o41), 8), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(49) + chr(0b101100 + 0o5), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110011) + chr(0b110001) + chr(0b110001), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(9689 - 9578) + chr(1847 - 1796) + '\064', 6021 - 6013), nzTpIcepk0o8(chr(48) + chr(1853 - 1742) + '\x32' + chr(52) + '\066', 0o10), nzTpIcepk0o8(chr(0b100001 + 0o17) + '\157' + chr(0b100111 + 0o13) + chr(0b11011 + 0o32) + chr(0b100111 + 0o16), 1637 - 1629), nzTpIcepk0o8('\x30' + chr(5610 - 5499) + '\062' + '\062' + chr(0b110110), 53122 - 53114), nzTpIcepk0o8('\x30' + '\157' + '\x31' + chr(0b101100 + 0o6) + '\062', 0o10), nzTpIcepk0o8(chr(0b100 + 0o54) + '\x6f' + chr(0b110011) + '\065' + chr(0b110010 + 0o2), 0b1000), nzTpIcepk0o8(chr(0b100110 + 0o12) + chr(111) + chr(49) + chr(0b1001 + 0o54) + chr(0b110101), 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110001) + chr(0b110010) + chr(1728 - 1676), 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(2307 - 2257) + chr(50) + chr(49), 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(0b1111 + 0o42) + chr(50) + chr(0b110100), 8), nzTpIcepk0o8(chr(1619 - 1571) + chr(111) + '\x31' + '\x35' + chr(2588 - 2537), 0o10), nzTpIcepk0o8(chr(0b100000 + 0o20) + chr(0b1101111) + chr(0b100010 + 0o21) + '\x33' + chr(50), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(341 - 288), 57734 - 57726), nzTpIcepk0o8('\x30' + '\157' + chr(2244 - 2194) + chr(0b110011) + '\x37', 54353 - 54345), nzTpIcepk0o8('\060' + '\157' + chr(0b10010 + 0o41) + chr(0b110010), 18426 - 18418), nzTpIcepk0o8(chr(48) + chr(0b1011101 + 0o22) + chr(51) + chr(0b100 + 0o62) + '\x36', 58449 - 58441), nzTpIcepk0o8(chr(1102 - 1054) + chr(111) + chr(49) + chr(1042 - 991) + chr(49), 20869 - 20861), nzTpIcepk0o8(chr(48) + '\157' + '\x33' + '\066' + chr(0b100111 + 0o11), 0o10), nzTpIcepk0o8('\x30' + chr(254 - 143) + '\x32' + '\x32' + '\x32', 28805 - 28797), nzTpIcepk0o8(chr(48) + '\157' + '\x31' + chr(719 - 670) + chr(1095 - 1040), 0b1000), nzTpIcepk0o8(chr(0b1100 + 0o44) + chr(0b11001 + 0o126) + chr(728 - 679) + chr(1867 - 1812) + chr(867 - 814), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b10000 + 0o41) + '\060' + chr(292 - 239), 37072 - 37064), nzTpIcepk0o8('\x30' + chr(7706 - 7595) + chr(0b110011) + chr(48) + '\x36', 8), nzTpIcepk0o8('\060' + chr(111) + '\061' + '\x36' + chr(2235 - 2180), 0o10), nzTpIcepk0o8(chr(0b1010 + 0o46) + chr(8753 - 8642) + chr(0b101011 + 0o6) + chr(223 - 168) + chr(542 - 489), 8), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(621 - 572) + chr(2468 - 2418) + chr(0b110110), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(11832 - 11721) + '\x35' + chr(52), 0o10), nzTpIcepk0o8(chr(1576 - 1528) + chr(4913 - 4802) + chr(0b110001) + chr(54) + chr(0b100100 + 0o14), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\061' + '\065' + chr(0b100100 + 0o20), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + chr(5302 - 5191) + chr(0b110101) + chr(0b11111 + 0o21), 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x86'), chr(8190 - 8090) + chr(0b1001001 + 0o34) + chr(99) + chr(111) + chr(2643 - 2543) + chr(0b1100101))('\165' + '\164' + chr(0b1100110) + chr(1104 - 1059) + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def cGvzZCWsncko(NoZxuO7wjArS):
return roI3spqORKae(_bFWSozA7z0G, roI3spqORKae(ES5oEprVxulp(b"\xec'\xaf"), chr(100) + chr(101) + chr(99) + '\x6f' + chr(100) + chr(2540 - 2439))(chr(4546 - 4429) + chr(0b1011101 + 0o27) + chr(0b1100110) + '\x2d' + chr(0b111000)))(roI3spqORKae(roI3spqORKae(ES5oEprVxulp(b''), chr(0b1000000 + 0o44) + '\145' + chr(99) + '\157' + chr(7441 - 7341) + '\145')(chr(117) + chr(0b1000011 + 0o61) + chr(0b1001011 + 0o33) + chr(0b101101) + chr(56)), roI3spqORKae(ES5oEprVxulp(b'\xf1]\x97\xf5\xa4<u\xa0=J\x87m'), chr(0b10 + 0o142) + '\145' + '\x63' + '\157' + chr(0b1001011 + 0o31) + chr(101))(chr(0b1101000 + 0o15) + '\164' + chr(102) + chr(45) + chr(56)))([roI3spqORKae(PNI8nORkWcyJ, roI3spqORKae(ES5oEprVxulp(b'\xcb\x01\x81\xd1\xfe\x1b'), chr(0b1100100) + chr(101) + chr(0b101100 + 0o67) + chr(7488 - 7377) + chr(100) + chr(869 - 768))('\x75' + '\x74' + chr(0b110101 + 0o61) + '\x2d' + chr(404 - 348)))(roI3spqORKae(ES5oEprVxulp(b'\xe9=\xa9\xfb'), chr(100) + chr(0b1100001 + 0o4) + chr(2506 - 2407) + chr(0b110100 + 0o73) + '\144' + chr(9537 - 9436))(chr(12909 - 12792) + '\x74' + chr(0b1100110) + chr(0b100000 + 0o15) + '\070')) for ZlbFMSG8gCoF in bbT2xIe5pzk7(NoZxuO7wjArS)])) |
klavinslab/coral | coral/design/_sequence_generation/random_sequences.py | random_codons | def random_codons(peptide, frequency_cutoff=0.0, weighted=False, table=None):
'''Generate randomized codons given a peptide sequence.
:param peptide: Peptide sequence for which to generate randomized
codons.
:type peptide: coral.Peptide
:param frequency_cutoff: Relative codon usage cutoff - codons that
are rarer will not be used. Frequency is
relative to average over all codons for a
given amino acid.
:param frequency_cutoff: Codon frequency table to use.
:param weighted: Use codon table
:type weighted: bool
:param table: Codon frequency table to use. Table should be organized
by amino acid, then be a dict of codon: frequency.
Only relevant if weighted=True or frequency_cutoff > 0.
Tables available:
constants.molecular_bio.CODON_FREQ_BY_AA['sc'] (default)
:type table: dict
:returns: Randomized sequence of codons (DNA) that code for the input
peptide.
:rtype: coral.DNA
:raises: ValueError if frequency_cutoff is set so high that there are no
codons available for an amino acid in the input peptide.
'''
if table is None:
table = CODON_FREQ_BY_AA['sc']
# Process codon table using frequency_cutoff
new_table = _cutoff(table, frequency_cutoff)
# Select codons randomly or using weighted distribution
rna = ''
for amino_acid in str(peptide):
codons = new_table[amino_acid.upper()]
if not codons:
raise ValueError('No {} codons at freq cutoff'.format(amino_acid))
if weighted:
cumsum = []
running_sum = 0
for codon, frequency in codons.iteritems():
running_sum += frequency
cumsum.append(running_sum)
random_num = random.uniform(0, max(cumsum))
for codon, value in zip(codons, cumsum):
if value > random_num:
selection = codon
break
else:
selection = random.choice(codons.keys())
rna += selection
return coral.RNA(rna) | python | def random_codons(peptide, frequency_cutoff=0.0, weighted=False, table=None):
'''Generate randomized codons given a peptide sequence.
:param peptide: Peptide sequence for which to generate randomized
codons.
:type peptide: coral.Peptide
:param frequency_cutoff: Relative codon usage cutoff - codons that
are rarer will not be used. Frequency is
relative to average over all codons for a
given amino acid.
:param frequency_cutoff: Codon frequency table to use.
:param weighted: Use codon table
:type weighted: bool
:param table: Codon frequency table to use. Table should be organized
by amino acid, then be a dict of codon: frequency.
Only relevant if weighted=True or frequency_cutoff > 0.
Tables available:
constants.molecular_bio.CODON_FREQ_BY_AA['sc'] (default)
:type table: dict
:returns: Randomized sequence of codons (DNA) that code for the input
peptide.
:rtype: coral.DNA
:raises: ValueError if frequency_cutoff is set so high that there are no
codons available for an amino acid in the input peptide.
'''
if table is None:
table = CODON_FREQ_BY_AA['sc']
# Process codon table using frequency_cutoff
new_table = _cutoff(table, frequency_cutoff)
# Select codons randomly or using weighted distribution
rna = ''
for amino_acid in str(peptide):
codons = new_table[amino_acid.upper()]
if not codons:
raise ValueError('No {} codons at freq cutoff'.format(amino_acid))
if weighted:
cumsum = []
running_sum = 0
for codon, frequency in codons.iteritems():
running_sum += frequency
cumsum.append(running_sum)
random_num = random.uniform(0, max(cumsum))
for codon, value in zip(codons, cumsum):
if value > random_num:
selection = codon
break
else:
selection = random.choice(codons.keys())
rna += selection
return coral.RNA(rna) | [
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:param peptide: Peptide sequence for which to generate randomized
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:type peptide: coral.Peptide
:param frequency_cutoff: Relative codon usage cutoff - codons that
are rarer will not be used. Frequency is
relative to average over all codons for a
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:param frequency_cutoff: Codon frequency table to use.
:param weighted: Use codon table
:type weighted: bool
:param table: Codon frequency table to use. Table should be organized
by amino acid, then be a dict of codon: frequency.
Only relevant if weighted=True or frequency_cutoff > 0.
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constants.molecular_bio.CODON_FREQ_BY_AA['sc'] (default)
:type table: dict
:returns: Randomized sequence of codons (DNA) that code for the input
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:rtype: coral.DNA
:raises: ValueError if frequency_cutoff is set so high that there are no
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/design/_sequence_generation/random_sequences.py#L19-L70 | train | Generates randomized codons given a peptide sequence. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b110 + 0o52) + '\157' + chr(52) + chr(153 - 105), ord("\x08")), nzTpIcepk0o8(chr(768 - 720) + chr(0b1000 + 0o147) + '\062' + '\x34' + chr(1824 - 1775), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b100000 + 0o117) + '\063' + '\x32' + '\063', 57950 - 57942), nzTpIcepk0o8(chr(1688 - 1640) + chr(111) + chr(1375 - 1325) + '\063' + chr(51), 0b1000), nzTpIcepk0o8(chr(1587 - 1539) + '\157' + chr(51) + '\065' + '\x31', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(11697 - 11586) + chr(0b110010 + 0o1) + chr(0b110000) + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1001100 + 0o43) + '\062' + chr(1508 - 1458) + '\063', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b11001 + 0o30) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(1868 - 1820) + '\x6f' + chr(0b10110 + 0o35) + '\062' + '\x34', 29355 - 29347), nzTpIcepk0o8(chr(0b11001 + 0o27) + '\157' + chr(50) + '\x36' + chr(561 - 508), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + '\062' + '\060' + chr(1336 - 1284), 0b1000), nzTpIcepk0o8(chr(0b11010 + 0o26) + chr(1653 - 1542) + '\x31' + '\060' + '\066', 0o10), nzTpIcepk0o8(chr(778 - 730) + chr(0b1101010 + 0o5) + chr(0b100 + 0o55) + chr(0b110110) + chr(53), 26676 - 26668), nzTpIcepk0o8(chr(0b110000) + chr(1161 - 1050) + chr(0b110011) + chr(0b110001) + '\x30', 64270 - 64262), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\061' + chr(0b101110 + 0o11) + chr(0b110111), 0o10), nzTpIcepk0o8(chr(974 - 926) + chr(0b1011010 + 0o25) + '\x31' + chr(50) + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(924 - 876) + chr(111) + chr(0b1101 + 0o44) + '\065' + chr(0b110010), 53066 - 53058), nzTpIcepk0o8('\x30' + chr(0b1100001 + 0o16) + chr(50) + chr(0b1000 + 0o57) + chr(52), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(0b10001 + 0o41) + chr(50) + chr(0b110010), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(2417 - 2366) + chr(0b100001 + 0o26) + '\064', ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110001) + chr(819 - 769) + chr(51), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1011110 + 0o21) + chr(2125 - 2074) + chr(0b100001 + 0o24) + chr(1672 - 1622), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b101101 + 0o102) + '\061' + '\x35' + chr(0b110101), 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(50) + chr(0b110001) + '\062', 64269 - 64261), nzTpIcepk0o8(chr(48) + chr(111) + '\065' + chr(1936 - 1882), 50198 - 50190), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(530 - 480) + chr(0b1 + 0o61) + chr(0b10011 + 0o44), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(4570 - 4459) + chr(0b110001) + '\x35' + chr(0b110011), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + '\x37' + '\x32', 4366 - 4358), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b1001 + 0o50) + '\061', 17264 - 17256), nzTpIcepk0o8(chr(2103 - 2055) + chr(0b1101111) + '\061' + chr(0b10101 + 0o37), 8), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b101110 + 0o3) + chr(0b110011), 0b1000), nzTpIcepk0o8('\060' + chr(111) + '\062' + chr(2019 - 1971) + chr(0b110001), 0b1000), nzTpIcepk0o8(chr(0b100101 + 0o13) + chr(0b110111 + 0o70) + chr(51) + chr(0b110000) + chr(2229 - 2174), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x31' + chr(0b110100 + 0o0) + chr(231 - 183), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(12033 - 11922) + '\063' + chr(50) + chr(0b101001 + 0o16), 0b1000), nzTpIcepk0o8('\060' + chr(0b111111 + 0o60) + chr(51) + chr(0b1011 + 0o45) + chr(0b110001), 0o10), nzTpIcepk0o8(chr(1146 - 1098) + chr(0b1010 + 0o145) + '\063', 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(1495 - 1441) + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(71 - 23) + chr(111) + '\062' + chr(2108 - 2058) + chr(51), 8), nzTpIcepk0o8(chr(233 - 185) + '\157' + '\061' + '\x37' + '\x35', ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b1010 + 0o46) + chr(0b1101111) + chr(53) + chr(0b110000), 59060 - 59052)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x0e'), chr(0b1001011 + 0o31) + chr(0b1100101) + chr(99) + chr(11501 - 11390) + '\144' + chr(0b10000 + 0o125))('\165' + chr(0b1110100) + '\146' + '\x2d' + chr(0b100101 + 0o23)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def Zy1AVbUmcSTi(ESHKoH8CAVdn, LE7P3Q9HLR5n=0.0, wM2Gw862wUkh=nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x30', 0o10), JlcDRbBtmPwV=None):
if JlcDRbBtmPwV is None:
JlcDRbBtmPwV = UrLTgUJjs1oL[roI3spqORKae(ES5oEprVxulp(b'S\xc2'), chr(0b1100100) + chr(101) + '\143' + chr(0b11010 + 0o125) + chr(2190 - 2090) + '\x65')(chr(0b1110101) + chr(0b1011110 + 0o26) + '\x66' + '\x2d' + chr(56))]
I4GbwGihgDWu = oJ_BFqJccpUU(JlcDRbBtmPwV, LE7P3Q9HLR5n)
PkxtrTYGw__U = roI3spqORKae(ES5oEprVxulp(b''), chr(0b1100100) + chr(0b1100101) + chr(672 - 573) + '\157' + chr(100) + '\x65')(chr(4538 - 4421) + '\164' + '\x66' + '\055' + '\x38')
for pDkutAMezzGv in N9zlRy29S1SS(ESHKoH8CAVdn):
P6NUCz3oWQOj = I4GbwGihgDWu[pDkutAMezzGv.iq1mNMefb1Zd()]
if not P6NUCz3oWQOj:
raise WbNHlDKpyPtQ(roI3spqORKae(roI3spqORKae(ES5oEprVxulp(b'n\xce\xf3\xe0\x94\xe3\xf0c\xb0\xda\xea5U\xa9\x0bu\x0c\xce\xf7\x8ds\x89\x18\xfeA\xf1\r'), chr(8442 - 8342) + chr(101) + chr(99) + '\x6f' + '\144' + chr(101))(chr(0b1110101) + '\164' + chr(3206 - 3104) + '\055' + chr(56)), roI3spqORKae(ES5oEprVxulp(b'Q\x92\xe0\xd0\xae\xf0\xf5c\x85\xea\xc7\x0c'), chr(100) + '\145' + '\143' + '\x6f' + '\x64' + chr(101))(chr(0b1001010 + 0o53) + '\164' + chr(102) + chr(263 - 218) + chr(0b111000)))(pDkutAMezzGv))
if wM2Gw862wUkh:
hThNUJrwvDVJ = []
QQkuWHNiec8i = nzTpIcepk0o8(chr(0b100010 + 0o16) + chr(0b1101111) + chr(48), 8)
for (kfLJMpd1iDsa, yRPgLQU6v3u6) in roI3spqORKae(P6NUCz3oWQOj, roI3spqORKae(ES5oEprVxulp(b'T\xc2\x80\xf0\x83\xa0\xe1@\xbf\xc6\xefw'), chr(0b1100011 + 0o1) + chr(9367 - 9266) + chr(0b0 + 0o143) + '\157' + chr(100) + chr(4560 - 4459))(chr(117) + '\164' + chr(102) + '\x2d' + chr(2064 - 2008)))():
QQkuWHNiec8i += yRPgLQU6v3u6
roI3spqORKae(hThNUJrwvDVJ, roI3spqORKae(ES5oEprVxulp(b'h\xf5\x80\xaf\x91\xa4\xd4c\xbe\xda\xd1s'), chr(0b1101 + 0o127) + chr(2958 - 2857) + chr(0b1100011) + '\x6f' + '\144' + chr(9660 - 9559))('\165' + '\164' + '\x66' + chr(0b101101) + chr(0b1110 + 0o52)))(QQkuWHNiec8i)
z7IbGMwTSeWr = PNI8nORkWcyJ.j1nUVhH0ryWy(nzTpIcepk0o8(chr(1213 - 1165) + chr(0b1101111) + '\060', 8), KV9ckIhroIia(hThNUJrwvDVJ))
for (kfLJMpd1iDsa, uV9iBiw0y_Mp) in TxMFWa_Xzviv(P6NUCz3oWQOj, hThNUJrwvDVJ):
if uV9iBiw0y_Mp > z7IbGMwTSeWr:
pB93jjau8BBL = kfLJMpd1iDsa
break
else:
pB93jjau8BBL = PNI8nORkWcyJ.choice(P6NUCz3oWQOj.keys())
PkxtrTYGw__U += pB93jjau8BBL
return roI3spqORKae(_bFWSozA7z0G, roI3spqORKae(ES5oEprVxulp(b'r\xef\x92'), '\x64' + '\145' + chr(0b100101 + 0o76) + chr(0b100110 + 0o111) + '\x64' + '\x65')(chr(0b11111 + 0o126) + '\164' + chr(102) + '\x2d' + chr(0b111000)))(PkxtrTYGw__U) |
klavinslab/coral | coral/design/_sequence_generation/random_sequences.py | _cutoff | def _cutoff(table, frequency_cutoff):
'''Generate new codon frequency table given a mean cutoff.
:param table: codon frequency table of form {amino acid: codon: frequency}
:type table: dict
:param frequency_cutoff: value between 0 and 1.0 for mean frequency cutoff
:type frequency_cutoff: float
:returns: A codon frequency table with some codons removed.
:rtype: dict
'''
new_table = {}
# IDEA: cutoff should be relative to most-frequent codon, not average?
for amino_acid, codons in table.iteritems():
average_cutoff = frequency_cutoff * sum(codons.values()) / len(codons)
new_table[amino_acid] = {}
for codon, frequency in codons.iteritems():
if frequency > average_cutoff:
new_table[amino_acid][codon] = frequency
return new_table | python | def _cutoff(table, frequency_cutoff):
'''Generate new codon frequency table given a mean cutoff.
:param table: codon frequency table of form {amino acid: codon: frequency}
:type table: dict
:param frequency_cutoff: value between 0 and 1.0 for mean frequency cutoff
:type frequency_cutoff: float
:returns: A codon frequency table with some codons removed.
:rtype: dict
'''
new_table = {}
# IDEA: cutoff should be relative to most-frequent codon, not average?
for amino_acid, codons in table.iteritems():
average_cutoff = frequency_cutoff * sum(codons.values()) / len(codons)
new_table[amino_acid] = {}
for codon, frequency in codons.iteritems():
if frequency > average_cutoff:
new_table[amino_acid][codon] = frequency
return new_table | [
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/design/_sequence_generation/random_sequences.py#L73-L92 | train | Generate a new codon frequency table given a mean cutoff. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(609 - 561) + chr(0b10001 + 0o136) + chr(0b110010) + chr(1648 - 1600), 0o10), nzTpIcepk0o8('\x30' + chr(0b111001 + 0o66) + chr(0b110101) + chr(49), 0o10), nzTpIcepk0o8(chr(0b10010 + 0o36) + '\x6f' + '\061' + '\x30', 2609 - 2601), nzTpIcepk0o8('\x30' + '\x6f' + '\x32' + chr(48) + chr(0b100010 + 0o22), ord("\x08")), nzTpIcepk0o8(chr(670 - 622) + chr(0b1101111) + chr(0b101110 + 0o5) + chr(48) + '\x37', ord("\x08")), nzTpIcepk0o8(chr(1575 - 1527) + chr(0b1101111) + chr(1377 - 1328) + chr(0b101100 + 0o4) + chr(49), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x32' + chr(0b1001 + 0o53) + chr(1492 - 1439), 0o10), nzTpIcepk0o8(chr(0b100000 + 0o20) + '\157' + chr(0b110011) + chr(0b110001) + chr(0b110001), 44417 - 44409), nzTpIcepk0o8(chr(0b110000) + '\157' + '\061' + '\x31' + chr(54), 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(0b11010 + 0o30) + '\064' + chr(419 - 367), 0o10), nzTpIcepk0o8(chr(2145 - 2097) + chr(10703 - 10592) + chr(0b110011) + chr(890 - 842) + '\067', 8), nzTpIcepk0o8(chr(2178 - 2130) + chr(0b111010 + 0o65) + '\063' + chr(0b10100 + 0o43) + chr(2586 - 2535), 0o10), nzTpIcepk0o8(chr(54 - 6) + chr(0b1101111) + '\061' + chr(2404 - 2353) + chr(49), 0o10), nzTpIcepk0o8('\060' + '\157' + '\x35' + '\064', 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(893 - 838) + '\062', 22709 - 22701), nzTpIcepk0o8('\060' + chr(0b11001 + 0o126) + chr(50) + '\065' + chr(599 - 544), 52533 - 52525), nzTpIcepk0o8('\x30' + chr(12284 - 12173) + chr(0b110011) + chr(0b110011) + chr(0b101 + 0o62), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + '\063' + '\x34' + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(903 - 849) + chr(49), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110011) + '\x34' + chr(0b10000 + 0o42), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x31' + chr(0b11111 + 0o24), 0b1000), nzTpIcepk0o8(chr(275 - 227) + chr(4113 - 4002) + chr(0b110001) + chr(52), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(49) + '\061' + chr(236 - 184), 0b1000), nzTpIcepk0o8('\x30' + chr(7764 - 7653) + chr(50) + '\065' + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(2116 - 2005) + '\x33' + '\064' + '\061', ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(281 - 230) + chr(0b10110 + 0o40) + chr(48), 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(1703 - 1652) + chr(48) + chr(1234 - 1185), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b101 + 0o152) + chr(0b101010 + 0o7) + chr(0b110111) + chr(88 - 35), 60304 - 60296), nzTpIcepk0o8('\x30' + chr(0b1100001 + 0o16) + chr(287 - 237) + '\064' + '\x36', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\063' + chr(0b100110 + 0o20) + '\x31', ord("\x08")), nzTpIcepk0o8('\x30' + chr(2930 - 2819) + chr(237 - 186) + '\061', 43870 - 43862), nzTpIcepk0o8(chr(48) + chr(111) + chr(52) + chr(49), 0o10), nzTpIcepk0o8(chr(578 - 530) + chr(0b1101001 + 0o6) + chr(0b110011) + chr(1234 - 1184) + chr(49), 0o10), nzTpIcepk0o8('\060' + '\x6f' + '\067' + chr(53), 0o10), nzTpIcepk0o8('\x30' + chr(0b100101 + 0o112) + chr(0b110011) + chr(0b110110) + chr(51), 0o10), nzTpIcepk0o8(chr(0b101 + 0o53) + chr(4680 - 4569) + '\066' + chr(1594 - 1543), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(652 - 599) + '\x32', ord("\x08")), nzTpIcepk0o8(chr(2241 - 2193) + '\x6f' + chr(271 - 217), 42669 - 42661), nzTpIcepk0o8(chr(0b11110 + 0o22) + chr(1607 - 1496) + chr(0b110110) + chr(0b101 + 0o54), 8), nzTpIcepk0o8('\060' + '\157' + chr(0b11011 + 0o30) + chr(0b100010 + 0o21) + chr(0b11111 + 0o21), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(430 - 382) + '\x6f' + chr(0b110101) + '\060', 18474 - 18466)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'>'), chr(100) + chr(9460 - 9359) + '\143' + chr(111) + '\x64' + '\145')(chr(0b10011 + 0o142) + chr(5945 - 5829) + chr(0b1010101 + 0o21) + chr(0b101101) + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def oJ_BFqJccpUU(JlcDRbBtmPwV, LE7P3Q9HLR5n):
I4GbwGihgDWu = {}
for (pDkutAMezzGv, P6NUCz3oWQOj) in roI3spqORKae(JlcDRbBtmPwV, roI3spqORKae(ES5oEprVxulp(b'dJ[\xef\xad"\xd7\x85%\xd7\xac\xca'), chr(100) + chr(10104 - 10003) + chr(8055 - 7956) + chr(0b1101111) + chr(0b1100100) + chr(0b1100101))(chr(0b1110011 + 0o2) + chr(1435 - 1319) + chr(0b1100110) + chr(0b101101) + chr(0b101100 + 0o14)))():
e0bndkWeZqWf = LE7P3Q9HLR5n * oclC8DLjA_lV(P6NUCz3oWQOj.CsodZJH6x9Tx()) / ftfygxgFas5X(P6NUCz3oWQOj)
I4GbwGihgDWu[pDkutAMezzGv] = {}
for (kfLJMpd1iDsa, yRPgLQU6v3u6) in roI3spqORKae(P6NUCz3oWQOj, roI3spqORKae(ES5oEprVxulp(b'dJ[\xef\xad"\xd7\x85%\xd7\xac\xca'), '\x64' + chr(0b1001000 + 0o35) + chr(99) + chr(111) + '\144' + chr(0b111011 + 0o52))(chr(117) + chr(116) + '\146' + chr(0b101101) + '\x38'))():
if yRPgLQU6v3u6 > e0bndkWeZqWf:
I4GbwGihgDWu[pDkutAMezzGv][kfLJMpd1iDsa] = yRPgLQU6v3u6
return I4GbwGihgDWu |
klavinslab/coral | coral/analysis/_structure/viennarna.py | ViennaRNA.cofold | def cofold(self, strand1, strand2, temp=37.0, dangles=2, nolp=False,
nogu=False, noclosinggu=False, constraints=None,
canonicalbponly=False, partition=-1, pfscale=None, gquad=False):
'''Run the RNAcofold command and retrieve the result in a dictionary.
:param strand1: Strand 1 for running RNAcofold.
:type strand1: coral.DNA or coral.RNA
:param strand1: Strand 2 for running RNAcofold.
:type strand2: coral.DNA or coral.RNA
:param temp: Temperature at which to run the calculations.
:type temp: float
:param dangles: How to treat dangling end energies. Set to 0 to ignore
dangling ends. Set to 1 to limit unpaired bases to
at most one dangling end (default for MFE calc). Set to
2 (the default) to remove the limit in 1. Set to 3 to
allow coaxial stacking of adjacent helices in
.multi-loops
:type dangles: int
:param nolp: Produce structures without lonely pairs (isolated single
base pairs).
:type nolp: bool
:param nogu: Do not allow GU pairs.
:type nogu: bool
:param noclosinggu: Do not allow GU pairs at the end of helices.
:type noclosinggu: bool
:param constraints: Any structural constraints to use. Format is
defined at
http://www.tbi.univie.ac.at/RNA/RNAfold.1.html
:type constraints: str
:param canonicalbponly: Remove non-canonical base pairs from the
structure constraint (if applicable).
:type canonicalbponly: bool
:param partition: Calculates the partition function for the sequence.
:type partition: int
:param pfscale: Scaling factor for the partition function.
:type pfScale: float
:param gquad: Incorporate G-Quadruplex formation into the structure
prediction.
:type gquad: bool
:returns: Dictionary of calculated values, defaulting to values of MFE
('mfe': float) and dotbracket structure ('dotbracket': str).
More keys are added depending on keyword arguments.
:rtype: dict
'''
cmd_args = []
cmd_kwargs = {'--temp=': str(temp)}
cmd_kwargs['--dangles='] = dangles
if nolp:
cmd_args.append('--noLP')
if nogu:
cmd_args.append('--noGU')
if noclosinggu:
cmd_args.append('--noClosingGU')
if constraints is not None:
cmd_args.append('--constraint')
if canonicalbponly:
cmd_args.append('--canonicalBPonly')
if partition:
cmd_args.append('--partfunc')
if pfscale is not None:
cmd_kwargs['pfScale'] = float(pfscale)
if gquad:
cmd_args.append('--gquad')
inputs = ['>strands\n{}&{}'.format(str(strand1), str(strand2))]
if constraints is not None:
inputs.append(constraints)
rnafold_output = self._run('RNAcofold', inputs, cmd_args, cmd_kwargs)
# Process the output
output = {}
lines = rnafold_output.splitlines()
# Line 1 is the name of the sequence input, line 2 is the sequence
lines.pop(0)
lines.pop(0)
# Line 3 is the dotbracket + mfe for strand1
line3 = lines.pop(0)
output['dotbracket'] = self._lparse(line3, '^(.*) \(')
output['mfe'] = float(self._lparse(line3, ' \((.*)\)$'))
# Optional outputs
if partition:
# Line 4 is 'a coarse representation of the pair probabilities' and
# the ensemble free energy
line4 = lines.pop(0)
output['coarse'] = self._lparse(line4, '^(.*) \[')
output['ensemble'] = float(self._lparse(line4, ' \[(.*)\]$'))
# Line 5 is the centroid structure, its free energy, and distance
# to the ensemble
line5 = lines.pop(0)
'ensemble (.*),'
output['frequency'] = float(self._lparse(line5, 'ensemble (.*),'))
output['deltaG'] = float(self._lparse(line5, 'binding=(.*)$'))
# Parse the postscript file (the only place the probability matrix
# is)
with open(os.path.join(self._tempdir, 'strands_dp.ps')) as f:
pattern = 'start of base pair probability data\n(.*)\nshowpage'
dotplot_file = f.read()
dotplot_data = re.search(pattern, dotplot_file,
flags=re.DOTALL).group(1).split('\n')
# Dimension of the dotplot - compares seq1, seq2 to self and
# to each other (concatenation of seq1 and seq2 = axis)
dim = len(strand1) + len(strand2)
ensemble_probs = np.zeros((dim, dim))
optimal_probs = np.zeros((dim, dim))
for point in dotplot_data:
point_split = point.split(' ')
# Use zero indexing
i = int(point_split[0]) - 1
j = int(point_split[1]) - 1
sqprob = float(point_split[2])
probtype = point_split[3]
if probtype == 'ubox':
ensemble_probs[i][j] = sqprob**2
else:
optimal_probs[i][j] = sqprob**2
output['ensemble_matrix'] = ensemble_probs
output['optimal_matrix'] = optimal_probs
return output | python | def cofold(self, strand1, strand2, temp=37.0, dangles=2, nolp=False,
nogu=False, noclosinggu=False, constraints=None,
canonicalbponly=False, partition=-1, pfscale=None, gquad=False):
'''Run the RNAcofold command and retrieve the result in a dictionary.
:param strand1: Strand 1 for running RNAcofold.
:type strand1: coral.DNA or coral.RNA
:param strand1: Strand 2 for running RNAcofold.
:type strand2: coral.DNA or coral.RNA
:param temp: Temperature at which to run the calculations.
:type temp: float
:param dangles: How to treat dangling end energies. Set to 0 to ignore
dangling ends. Set to 1 to limit unpaired bases to
at most one dangling end (default for MFE calc). Set to
2 (the default) to remove the limit in 1. Set to 3 to
allow coaxial stacking of adjacent helices in
.multi-loops
:type dangles: int
:param nolp: Produce structures without lonely pairs (isolated single
base pairs).
:type nolp: bool
:param nogu: Do not allow GU pairs.
:type nogu: bool
:param noclosinggu: Do not allow GU pairs at the end of helices.
:type noclosinggu: bool
:param constraints: Any structural constraints to use. Format is
defined at
http://www.tbi.univie.ac.at/RNA/RNAfold.1.html
:type constraints: str
:param canonicalbponly: Remove non-canonical base pairs from the
structure constraint (if applicable).
:type canonicalbponly: bool
:param partition: Calculates the partition function for the sequence.
:type partition: int
:param pfscale: Scaling factor for the partition function.
:type pfScale: float
:param gquad: Incorporate G-Quadruplex formation into the structure
prediction.
:type gquad: bool
:returns: Dictionary of calculated values, defaulting to values of MFE
('mfe': float) and dotbracket structure ('dotbracket': str).
More keys are added depending on keyword arguments.
:rtype: dict
'''
cmd_args = []
cmd_kwargs = {'--temp=': str(temp)}
cmd_kwargs['--dangles='] = dangles
if nolp:
cmd_args.append('--noLP')
if nogu:
cmd_args.append('--noGU')
if noclosinggu:
cmd_args.append('--noClosingGU')
if constraints is not None:
cmd_args.append('--constraint')
if canonicalbponly:
cmd_args.append('--canonicalBPonly')
if partition:
cmd_args.append('--partfunc')
if pfscale is not None:
cmd_kwargs['pfScale'] = float(pfscale)
if gquad:
cmd_args.append('--gquad')
inputs = ['>strands\n{}&{}'.format(str(strand1), str(strand2))]
if constraints is not None:
inputs.append(constraints)
rnafold_output = self._run('RNAcofold', inputs, cmd_args, cmd_kwargs)
# Process the output
output = {}
lines = rnafold_output.splitlines()
# Line 1 is the name of the sequence input, line 2 is the sequence
lines.pop(0)
lines.pop(0)
# Line 3 is the dotbracket + mfe for strand1
line3 = lines.pop(0)
output['dotbracket'] = self._lparse(line3, '^(.*) \(')
output['mfe'] = float(self._lparse(line3, ' \((.*)\)$'))
# Optional outputs
if partition:
# Line 4 is 'a coarse representation of the pair probabilities' and
# the ensemble free energy
line4 = lines.pop(0)
output['coarse'] = self._lparse(line4, '^(.*) \[')
output['ensemble'] = float(self._lparse(line4, ' \[(.*)\]$'))
# Line 5 is the centroid structure, its free energy, and distance
# to the ensemble
line5 = lines.pop(0)
'ensemble (.*),'
output['frequency'] = float(self._lparse(line5, 'ensemble (.*),'))
output['deltaG'] = float(self._lparse(line5, 'binding=(.*)$'))
# Parse the postscript file (the only place the probability matrix
# is)
with open(os.path.join(self._tempdir, 'strands_dp.ps')) as f:
pattern = 'start of base pair probability data\n(.*)\nshowpage'
dotplot_file = f.read()
dotplot_data = re.search(pattern, dotplot_file,
flags=re.DOTALL).group(1).split('\n')
# Dimension of the dotplot - compares seq1, seq2 to self and
# to each other (concatenation of seq1 and seq2 = axis)
dim = len(strand1) + len(strand2)
ensemble_probs = np.zeros((dim, dim))
optimal_probs = np.zeros((dim, dim))
for point in dotplot_data:
point_split = point.split(' ')
# Use zero indexing
i = int(point_split[0]) - 1
j = int(point_split[1]) - 1
sqprob = float(point_split[2])
probtype = point_split[3]
if probtype == 'ubox':
ensemble_probs[i][j] = sqprob**2
else:
optimal_probs[i][j] = sqprob**2
output['ensemble_matrix'] = ensemble_probs
output['optimal_matrix'] = optimal_probs
return output | [
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",",
"constraints",
"=",
"None",
",",
"canonical... | Run the RNAcofold command and retrieve the result in a dictionary.
:param strand1: Strand 1 for running RNAcofold.
:type strand1: coral.DNA or coral.RNA
:param strand1: Strand 2 for running RNAcofold.
:type strand2: coral.DNA or coral.RNA
:param temp: Temperature at which to run the calculations.
:type temp: float
:param dangles: How to treat dangling end energies. Set to 0 to ignore
dangling ends. Set to 1 to limit unpaired bases to
at most one dangling end (default for MFE calc). Set to
2 (the default) to remove the limit in 1. Set to 3 to
allow coaxial stacking of adjacent helices in
.multi-loops
:type dangles: int
:param nolp: Produce structures without lonely pairs (isolated single
base pairs).
:type nolp: bool
:param nogu: Do not allow GU pairs.
:type nogu: bool
:param noclosinggu: Do not allow GU pairs at the end of helices.
:type noclosinggu: bool
:param constraints: Any structural constraints to use. Format is
defined at
http://www.tbi.univie.ac.at/RNA/RNAfold.1.html
:type constraints: str
:param canonicalbponly: Remove non-canonical base pairs from the
structure constraint (if applicable).
:type canonicalbponly: bool
:param partition: Calculates the partition function for the sequence.
:type partition: int
:param pfscale: Scaling factor for the partition function.
:type pfScale: float
:param gquad: Incorporate G-Quadruplex formation into the structure
prediction.
:type gquad: bool
:returns: Dictionary of calculated values, defaulting to values of MFE
('mfe': float) and dotbracket structure ('dotbracket': str).
More keys are added depending on keyword arguments.
:rtype: dict | [
"Run",
"the",
"RNAcofold",
"command",
"and",
"retrieve",
"the",
"result",
"in",
"a",
"dictionary",
"."
] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/analysis/_structure/viennarna.py#L18-L140 | train | Run the RNAcofold command and retrieve the result in a dictionary. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b11000 + 0o30) + chr(0b1101111) + '\x33' + chr(1036 - 986) + '\066', 0o10), nzTpIcepk0o8('\x30' + chr(5016 - 4905) + chr(0b110001) + '\063' + chr(2303 - 2255), ord("\x08")), nzTpIcepk0o8(chr(1325 - 1277) + chr(111) + '\067' + chr(48), 0o10), nzTpIcepk0o8('\060' + '\157' + '\x36' + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(0b1110 + 0o42) + chr(0b11111 + 0o120) + chr(0b1110 + 0o43) + chr(1740 - 1688) + chr(0b100011 + 0o15), 0o10), nzTpIcepk0o8(chr(600 - 552) + chr(0b1101111) + chr(1127 - 1077) + chr(0b101111 + 0o4) + chr(0b11010 + 0o26), 58883 - 58875), nzTpIcepk0o8(chr(0b1 + 0o57) + chr(2204 - 2093) + chr(0b100011 + 0o21) + '\x33', 0o10), nzTpIcepk0o8(chr(0b100000 + 0o20) + chr(0b1101111) + chr(0b11111 + 0o22) + chr(0b11101 + 0o27), 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(1245 - 1195) + chr(50) + chr(0b110011), ord("\x08")), nzTpIcepk0o8(chr(1037 - 989) + '\x6f' + chr(0b101101 + 0o10) + chr(55), 2307 - 2299), nzTpIcepk0o8('\060' + chr(0b1011010 + 0o25) + chr(0b110010) + chr(0b1111 + 0o43) + chr(844 - 794), 0o10), nzTpIcepk0o8('\x30' + '\157' + '\062' + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(0b11111 + 0o21) + '\157' + '\x34' + chr(937 - 884), 15513 - 15505), nzTpIcepk0o8(chr(0b0 + 0o60) + '\157' + '\061' + chr(2053 - 1999) + '\066', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b10101 + 0o40) + '\062', 23021 - 23013), nzTpIcepk0o8(chr(0b101 + 0o53) + '\x6f' + chr(49) + chr(2330 - 2278) + '\067', 0b1000), nzTpIcepk0o8(chr(2050 - 2002) + chr(0b1101111) + chr(2362 - 2312) + '\x32' + chr(0b101110 + 0o7), ord("\x08")), nzTpIcepk0o8(chr(1303 - 1255) + '\157' + chr(2194 - 2145) + chr(2141 - 2090) + chr(2214 - 2161), 0b1000), nzTpIcepk0o8(chr(925 - 877) + '\157' + chr(2247 - 2198) + chr(0b101110 + 0o6) + chr(48), 8), nzTpIcepk0o8('\060' + '\157' + '\x31' + chr(55), 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(925 - 876) + '\060' + '\064', 42495 - 42487), nzTpIcepk0o8(chr(48) + chr(505 - 394) + chr(0b11111 + 0o23) + chr(0b110110) + '\066', 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110010) + '\x37' + '\060', 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(0b110011) + '\062' + '\x32', ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(0b1001 + 0o51) + chr(54) + '\x32', 0o10), nzTpIcepk0o8('\060' + chr(111) + '\x34' + chr(51), 8), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b101100 + 0o5) + chr(0b110001) + chr(0b110111), 0o10), nzTpIcepk0o8(chr(0b101110 + 0o2) + chr(4170 - 4059) + chr(0b11100 + 0o25) + chr(2421 - 2368) + '\x33', 39208 - 39200), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x31' + '\x30' + '\x35', 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x37' + '\x32', 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110001) + '\x37' + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110001) + '\x32' + chr(0b101 + 0o61), 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(0b110001) + '\062' + '\x31', ord("\x08")), nzTpIcepk0o8(chr(100 - 52) + '\x6f' + chr(0b11000 + 0o32) + '\067' + chr(0b101111 + 0o2), 59714 - 59706), nzTpIcepk0o8(chr(1365 - 1317) + chr(0b110101 + 0o72) + chr(0b100111 + 0o12) + chr(55) + '\x37', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\062' + '\065' + chr(0b110001), 0b1000), nzTpIcepk0o8(chr(48) + chr(5490 - 5379) + chr(0b110001) + chr(48) + chr(987 - 939), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\062' + chr(49) + chr(0b101010 + 0o7), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110011) + chr(52) + chr(0b110001), 0b1000), nzTpIcepk0o8(chr(215 - 167) + chr(0b110011 + 0o74) + '\x35', ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b101101 + 0o3) + chr(0b1000110 + 0o51) + chr(0b110101) + '\x30', ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xf8'), chr(100) + chr(9973 - 9872) + '\143' + chr(111) + chr(0b1010100 + 0o20) + chr(0b1100101))('\x75' + '\x74' + '\x66' + '\055' + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def ku4ja2vDxw62(hXMPsSrOQzbh, GlmwsQHQN3B1, gDjsZyDAOFaC, bhvcCFR07maA=37.0, dcIGdrKJIQqm=nzTpIcepk0o8('\060' + chr(111) + chr(0b110010), 42983 - 42975), mlhoP38jdudd=nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110000), 35996 - 35988), zCewwQUPbHLD=nzTpIcepk0o8(chr(0b110000) + chr(10419 - 10308) + chr(0b110000), 8), NugwvhZNCD5b=nzTpIcepk0o8(chr(1615 - 1567) + chr(0b11 + 0o154) + chr(0b110000), 8), WsRXUozGEySJ=None, HieMGlwzVBAU=nzTpIcepk0o8(chr(931 - 883) + chr(0b1100011 + 0o14) + chr(0b100110 + 0o12), 8), y6tm5LzgZc_E=-nzTpIcepk0o8(chr(0b10101 + 0o33) + chr(111) + chr(49), 31448 - 31440), yOoPgMu7dWsV=None, wCbMBpg1trXc=nzTpIcepk0o8(chr(1955 - 1907) + chr(0b11100 + 0o123) + chr(0b110000), 8)):
zF8oFOtHDCse = []
W6eknENeyhyW = {roI3spqORKae(ES5oEprVxulp(b'\xfbuLQ\r\xe8\x1e'), chr(0b1100100) + '\x65' + chr(0b1011101 + 0o6) + chr(111) + chr(100) + '\x65')(chr(117) + chr(116) + '\x66' + '\055' + chr(56)): N9zlRy29S1SS(bhvcCFR07maA)}
W6eknENeyhyW[roI3spqORKae(ES5oEprVxulp(b'\xfbu\\U\x0e\xffOi\xe0\x12'), '\x64' + '\x65' + chr(0b1100011) + chr(0b110 + 0o151) + chr(0b1100011 + 0o1) + chr(101))('\165' + '\x74' + '\x66' + chr(45) + chr(0b111000))] = dcIGdrKJIQqm
if mlhoP38jdudd:
roI3spqORKae(zF8oFOtHDCse, roI3spqORKae(ES5oEprVxulp(b'\x9e\x0ck\x00\x18\xffdc\xf9@\xc7%'), chr(100) + chr(101) + chr(99) + chr(0b100110 + 0o111) + '\144' + chr(124 - 23))('\165' + '\164' + '\x66' + '\055' + chr(0b100110 + 0o22)))(roI3spqORKae(ES5oEprVxulp(b'\xfbuV[,\xc8'), chr(100) + '\145' + '\143' + chr(0b1000101 + 0o52) + chr(0b1100100) + chr(101))(chr(13393 - 13276) + '\164' + chr(0b1100110) + chr(0b101101) + chr(56)))
if zCewwQUPbHLD:
roI3spqORKae(zF8oFOtHDCse, roI3spqORKae(ES5oEprVxulp(b'\x9e\x0ck\x00\x18\xffdc\xf9@\xc7%'), chr(0b101101 + 0o67) + chr(0b1100101) + chr(0b1010101 + 0o16) + '\x6f' + chr(8866 - 8766) + chr(0b111110 + 0o47))(chr(117) + chr(116) + chr(0b1100110) + '\055' + '\x38'))(roI3spqORKae(ES5oEprVxulp(b"\xfbuV['\xcd"), chr(9196 - 9096) + chr(0b11110 + 0o107) + '\x63' + chr(11401 - 11290) + chr(1703 - 1603) + '\145')(chr(0b1010110 + 0o37) + chr(0b1110 + 0o146) + chr(0b1100110) + '\x2d' + '\070'))
if NugwvhZNCD5b:
roI3spqORKae(zF8oFOtHDCse, roI3spqORKae(ES5oEprVxulp(b'\x9e\x0ck\x00\x18\xffdc\xf9@\xc7%'), chr(100) + '\x65' + chr(0b101110 + 0o65) + chr(0b111101 + 0o62) + chr(2256 - 2156) + chr(0b1000010 + 0o43))(chr(0b1001101 + 0o50) + '\x74' + chr(0b1100110) + chr(45) + chr(0b111000)))(roI3spqORKae(ES5oEprVxulp(b'\xfbuV[#\xf4L\x7f\xfaA\xf5Wp'), '\144' + '\145' + chr(0b1100011) + '\x6f' + chr(100) + '\x65')('\x75' + chr(116) + chr(630 - 528) + chr(0b0 + 0o55) + '\070'))
if WsRXUozGEySJ is not None:
roI3spqORKae(zF8oFOtHDCse, roI3spqORKae(ES5oEprVxulp(b'\x9e\x0ck\x00\x18\xffdc\xf9@\xc7%'), chr(0b1000010 + 0o42) + '\x65' + chr(1572 - 1473) + chr(0b1011100 + 0o23) + chr(0b1000100 + 0o40) + chr(9923 - 9822))(chr(11346 - 11229) + chr(0b1110100) + chr(0b1100110) + chr(0b100111 + 0o6) + '\x38'))(roI3spqORKae(ES5oEprVxulp(b'\xfbu[[\x0e\xebW~\xf2F\xfcd'), chr(0b1010010 + 0o22) + '\x65' + '\x63' + chr(0b1101111) + chr(0b1000001 + 0o43) + chr(0b1100011 + 0o2))('\165' + chr(4476 - 4360) + chr(0b110000 + 0o66) + '\055' + chr(56)))
if HieMGlwzVBAU:
roI3spqORKae(zF8oFOtHDCse, roI3spqORKae(ES5oEprVxulp(b'\x9e\x0ck\x00\x18\xffdc\xf9@\xc7%'), chr(2215 - 2115) + chr(9791 - 9690) + '\x63' + chr(0b1100101 + 0o12) + '\x64' + chr(0b1100101))(chr(12360 - 12243) + chr(0b1110100) + '\x66' + '\055' + chr(1020 - 964)))(roI3spqORKae(ES5oEprVxulp(b'\xfbu[U\x0e\xf7Me\xf0N\xfeRu\x19D\x0b\xec'), chr(0b10011 + 0o121) + chr(101) + chr(0b1100011) + chr(0b1000011 + 0o54) + chr(0b1001001 + 0o33) + '\145')(chr(117) + chr(13030 - 12914) + '\146' + chr(45) + chr(0b101001 + 0o17)))
if y6tm5LzgZc_E:
roI3spqORKae(zF8oFOtHDCse, roI3spqORKae(ES5oEprVxulp(b'\x9e\x0ck\x00\x18\xffdc\xf9@\xc7%'), chr(0b1100100) + '\x65' + '\143' + chr(0b1101111) + chr(100) + '\x65')(chr(0b101110 + 0o107) + chr(8598 - 8482) + chr(0b1100110) + chr(0b100 + 0o51) + '\x38'))(roI3spqORKae(ES5oEprVxulp(b'\xfbuHU\x12\xecEy\xfdL'), '\x64' + chr(6381 - 6280) + '\x63' + chr(111) + '\x64' + chr(1677 - 1576))('\165' + chr(8522 - 8406) + chr(9613 - 9511) + chr(0b11011 + 0o22) + chr(0b111000)))
if yOoPgMu7dWsV is not None:
W6eknENeyhyW[roI3spqORKae(ES5oEprVxulp(b'\xa6>kW\x01\xf4F'), chr(0b10110 + 0o116) + chr(0b1100101) + '\143' + chr(11925 - 11814) + chr(0b1100100) + chr(6443 - 6342))(chr(9166 - 9049) + chr(0b1110100) + chr(102) + chr(175 - 130) + chr(0b110011 + 0o5))] = jLW6pRf2DSRk(yOoPgMu7dWsV)
if wCbMBpg1trXc:
roI3spqORKae(zF8oFOtHDCse, roI3spqORKae(ES5oEprVxulp(b'\x9e\x0ck\x00\x18\xffdc\xf9@\xc7%'), chr(2887 - 2787) + '\x65' + chr(0b1010001 + 0o22) + chr(1718 - 1607) + '\144' + chr(0b1011001 + 0o14))(chr(0b1110101) + chr(116) + chr(102) + chr(0b101101) + chr(0b11100 + 0o34)))(roI3spqORKae(ES5oEprVxulp(b'\xfbu_E\x15\xf9G'), '\x64' + '\145' + chr(4872 - 4773) + chr(1483 - 1372) + chr(100) + '\x65')(chr(117) + chr(116) + chr(102) + chr(1575 - 1530) + '\x38'))
GKlPkmr7AqQT = [roI3spqORKae(ES5oEprVxulp(b'\xe8+LF\x01\xf6G\x7f\x99T\xef6^\x0b'), '\x64' + chr(4564 - 4463) + '\x63' + chr(0b101111 + 0o100) + chr(100) + chr(101))(chr(0b101100 + 0o111) + chr(0b1110100) + '\146' + '\055' + chr(0b100011 + 0o25)).q33KG3foQ_CJ(N9zlRy29S1SS(GlmwsQHQN3B1), N9zlRy29S1SS(gDjsZyDAOFaC))]
if WsRXUozGEySJ is not None:
roI3spqORKae(GKlPkmr7AqQT, roI3spqORKae(ES5oEprVxulp(b'\x9e\x0ck\x00\x18\xffdc\xf9@\xc7%'), chr(0b1100100) + chr(101) + chr(0b1010011 + 0o20) + '\157' + chr(5802 - 5702) + chr(4707 - 4606))(chr(5489 - 5372) + '\x74' + chr(102) + chr(0b11 + 0o52) + '\070'))(WsRXUozGEySJ)
bBOYBuR1kjY6 = hXMPsSrOQzbh.w878a10420A4(roI3spqORKae(ES5oEprVxulp(b'\x84\x16yW\x0f\xfeL`\xf7'), chr(8418 - 8318) + '\x65' + '\x63' + chr(0b110001 + 0o76) + chr(302 - 202) + chr(0b1001011 + 0o32))(chr(0b1110101) + chr(6575 - 6459) + chr(0b1100110) + chr(687 - 642) + chr(56)), GKlPkmr7AqQT, zF8oFOtHDCse, W6eknENeyhyW)
toKQXlEvBKaK = {}
vniSnlI09HNg = bBOYBuR1kjY6.splitlines()
roI3spqORKae(vniSnlI09HNg, roI3spqORKae(ES5oEprVxulp(b'\xa3\x1bgm\x0f\xe1At\xa4e\xa2Y'), chr(878 - 778) + '\145' + chr(8006 - 7907) + chr(0b101100 + 0o103) + chr(5680 - 5580) + chr(0b1100101))('\165' + chr(0b1110100) + chr(0b1100110) + '\x2d' + chr(56)))(nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110 + 0o52), 8))
roI3spqORKae(vniSnlI09HNg, roI3spqORKae(ES5oEprVxulp(b'\xa3\x1bgm\x0f\xe1At\xa4e\xa2Y'), '\144' + chr(101) + chr(9320 - 9221) + chr(111) + '\144' + '\x65')('\x75' + chr(0b1110100) + chr(0b1000111 + 0o37) + chr(0b11101 + 0o20) + '\x38'))(nzTpIcepk0o8('\x30' + chr(8606 - 8495) + chr(606 - 558), 8))
NrpWjFRKX4St = vniSnlI09HNg.uC_Yoybx7J0I(nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(1927 - 1879), 8))
toKQXlEvBKaK[roI3spqORKae(ES5oEprVxulp(b'\xb27LV\x12\xf9@g\xf6['), chr(8799 - 8699) + chr(101) + '\143' + '\x6f' + '\x64' + chr(0b10101 + 0o120))(chr(0b1011101 + 0o30) + chr(0b1001010 + 0o52) + chr(102) + chr(0b101101 + 0o0) + '\070')] = hXMPsSrOQzbh._lparse(NrpWjFRKX4St, roI3spqORKae(ES5oEprVxulp(b'\x88p\x16\x1eI\xb8\x7f$'), chr(4789 - 4689) + '\x65' + chr(0b1100011) + '\157' + chr(4021 - 3921) + '\x65')(chr(0b10110 + 0o137) + '\x74' + chr(6172 - 6070) + chr(801 - 756) + chr(0b110000 + 0o10)))
toKQXlEvBKaK[roI3spqORKae(ES5oEprVxulp(b'\xbb>]'), '\144' + '\145' + chr(99) + chr(0b1000101 + 0o52) + '\144' + '\145')('\x75' + '\x74' + '\x66' + '\055' + '\070')] = jLW6pRf2DSRk(hXMPsSrOQzbh._lparse(NrpWjFRKX4St, roI3spqORKae(ES5oEprVxulp(b'\xf6\x04\x10\x1cN\xb2\nP\xba\x0b'), '\144' + '\145' + chr(9439 - 9340) + chr(111) + '\144' + chr(0b101 + 0o140))(chr(117) + chr(116) + chr(0b10011 + 0o123) + chr(45) + chr(0b111000))))
if y6tm5LzgZc_E:
um9m0D6L7zLw = vniSnlI09HNg.uC_Yoybx7J0I(nzTpIcepk0o8('\060' + chr(0b1101111) + chr(48), 8))
toKQXlEvBKaK[roI3spqORKae(ES5oEprVxulp(b'\xb57YF\x13\xfd'), '\x64' + '\x65' + chr(99) + chr(4090 - 3979) + '\x64' + chr(0b1000 + 0o135))('\x75' + chr(8641 - 8525) + '\146' + '\x2d' + chr(0b111000))] = hXMPsSrOQzbh._lparse(um9m0D6L7zLw, roI3spqORKae(ES5oEprVxulp(b'\x88p\x16\x1eI\xb8\x7fW'), chr(100) + chr(0b10010 + 0o123) + chr(4833 - 4734) + '\157' + '\144' + chr(101))('\x75' + chr(5718 - 5602) + '\146' + chr(1544 - 1499) + '\x38'))
toKQXlEvBKaK[roI3spqORKae(ES5oEprVxulp(b'\xb36KQ\r\xfaOi'), '\x64' + chr(0b1100101) + '\143' + chr(0b110 + 0o151) + chr(0b1100100) + chr(9611 - 9510))(chr(117) + chr(6646 - 6530) + chr(1352 - 1250) + chr(768 - 723) + '\070')] = jLW6pRf2DSRk(hXMPsSrOQzbh._lparse(um9m0D6L7zLw, roI3spqORKae(ES5oEprVxulp(b'\xf6\x04c\x1cN\xb2\nP\xce\x0b'), '\x64' + '\145' + chr(1673 - 1574) + chr(689 - 578) + chr(0b10011 + 0o121) + '\x65')('\x75' + '\x74' + chr(0b1010010 + 0o24) + chr(45) + chr(0b11010 + 0o36))))
PU3Shar3ba2w = vniSnlI09HNg.uC_Yoybx7J0I(nzTpIcepk0o8('\x30' + '\x6f' + chr(48), 8))
roI3spqORKae(ES5oEprVxulp(b'\xb36KQ\r\xfaOi\xb3\x07\xbc:\x0cZ'), chr(100) + chr(0b1000101 + 0o40) + '\x63' + chr(0b1101111) + chr(0b1100100) + '\x65')('\x75' + chr(116) + chr(102) + chr(0b101101) + chr(56))
toKQXlEvBKaK[roI3spqORKae(ES5oEprVxulp(b'\xb0*]E\x15\xfdMo\xea'), chr(3835 - 3735) + chr(0b1100101) + chr(2782 - 2683) + '\157' + chr(100) + chr(0b1011010 + 0o13))(chr(0b110000 + 0o105) + chr(0b1110100) + chr(0b11000 + 0o116) + chr(1225 - 1180) + chr(56))] = jLW6pRf2DSRk(hXMPsSrOQzbh._lparse(PU3Shar3ba2w, roI3spqORKae(ES5oEprVxulp(b'\xb36KQ\r\xfaOi\xb3\x07\xbc:\x0cZ'), '\x64' + '\x65' + chr(99) + '\x6f' + '\144' + chr(5861 - 5760))(chr(12614 - 12497) + chr(0b111100 + 0o70) + '\146' + chr(45) + chr(0b10101 + 0o43))))
toKQXlEvBKaK[roI3spqORKae(ES5oEprVxulp(b'\xb2=T@\x01\xdf'), chr(4015 - 3915) + chr(0b1000000 + 0o45) + chr(725 - 626) + chr(0b1101 + 0o142) + chr(100) + chr(0b1100101))('\165' + '\x74' + '\x66' + chr(0b100001 + 0o14) + chr(2202 - 2146))] = jLW6pRf2DSRk(hXMPsSrOQzbh._lparse(PU3Shar3ba2w, roI3spqORKae(ES5oEprVxulp(b'\xb41VP\t\xf6D1\xbb\x01\xb89\x01'), chr(0b1100100) + chr(101) + chr(0b1100011) + chr(0b1000010 + 0o55) + '\144' + '\145')(chr(0b1110101) + chr(116) + '\146' + chr(0b101101) + chr(0b111000))))
with DnU3Rq9N5ala(roI3spqORKae(aHUqKstZLeS6.path, roI3spqORKae(ES5oEprVxulp(b'\x8flAyY\xda@j\xc7l\xdca'), chr(0b1100100) + chr(0b1001 + 0o134) + chr(99) + chr(0b1101111) + chr(0b110000 + 0o64) + chr(0b1101 + 0o130))(chr(4772 - 4655) + chr(0b101011 + 0o111) + chr(4445 - 4343) + chr(235 - 190) + chr(56)))(roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x89,]Y\x10\xfcJ~'), chr(0b1100100) + chr(4456 - 4355) + chr(99) + chr(2842 - 2731) + chr(0b1001110 + 0o26) + chr(101))(chr(5552 - 5435) + chr(10492 - 10376) + '\146' + chr(0b1100 + 0o41) + chr(0b11110 + 0o32))), roI3spqORKae(ES5oEprVxulp(b'\xa5,JU\x0e\xfcPS\xf7_\xbc`V'), chr(100) + '\145' + chr(99) + chr(0b100001 + 0o116) + chr(100) + chr(101))(chr(0b100101 + 0o120) + chr(0b1110100) + chr(0b1100110) + '\x2d' + '\x38'))) as _R8IKF5IwAfX:
UYtHA0XyNB9C = roI3spqORKae(ES5oEprVxulp(b'\xa5,YF\x14\xb8Lj\xb3M\xf3c@VZ\x06\xfc/@\x7f6\xd9\xda\xb3\xd0J#\x021C\\20\xcd\x1e\xa3h\xa7\xcb,\xdc+P[\x17\xe8Bk\xf6'), '\144' + '\x65' + chr(99) + '\157' + chr(100) + '\145')(chr(117) + chr(0b1110100) + chr(102) + chr(0b111 + 0o46) + '\x38')
VOTtt7P0sfBM = _R8IKF5IwAfX.eoXknH7XUn7m()
bIodCjQRdqc5 = aoTc4YA2bs2R.search(UYtHA0XyNB9C, VOTtt7P0sfBM, flags=aoTc4YA2bs2R.DOTALL).group(nzTpIcepk0o8(chr(0b101 + 0o53) + '\x6f' + '\x31', 8)).LfRrQOxuDvnC(roI3spqORKae(ES5oEprVxulp(b'\xdc'), chr(0b1100100) + chr(101) + chr(0b11111 + 0o104) + chr(0b1101111) + chr(0b1000101 + 0o37) + '\x65')('\165' + chr(0b1110100) + chr(0b1100110) + chr(45) + '\x38'))
L5CH4CVaTec6 = ftfygxgFas5X(GlmwsQHQN3B1) + ftfygxgFas5X(gDjsZyDAOFaC)
ZMOCKq9IH__h = nDF4gVNx0u9Q.UmwwEp7MzR6q((L5CH4CVaTec6, L5CH4CVaTec6))
UKIjitrAwDav = nDF4gVNx0u9Q.UmwwEp7MzR6q((L5CH4CVaTec6, L5CH4CVaTec6))
for l1u4whQWoPEl in bIodCjQRdqc5:
eg07YCrO4Omm = l1u4whQWoPEl.LfRrQOxuDvnC(roI3spqORKae(ES5oEprVxulp(b'\xf6'), chr(1245 - 1145) + chr(0b10011 + 0o122) + '\143' + chr(499 - 388) + '\x64' + chr(4833 - 4732))('\165' + '\x74' + chr(0b1100110) + '\x2d' + chr(262 - 206)))
ZlbFMSG8gCoF = nzTpIcepk0o8(eg07YCrO4Omm[nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(1562 - 1514), 8)]) - nzTpIcepk0o8('\060' + chr(0b1101111) + chr(2001 - 1952), 8)
sChW4gUsXrIC = nzTpIcepk0o8(eg07YCrO4Omm[nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110001), 8)]) - nzTpIcepk0o8(chr(48) + chr(2378 - 2267) + chr(0b1100 + 0o45), 8)
kRMcrmQh9wYY = jLW6pRf2DSRk(eg07YCrO4Omm[nzTpIcepk0o8(chr(0b110000) + chr(0b101110 + 0o101) + chr(0b110010), 8)])
YizPoFeWqT3N = eg07YCrO4Omm[nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110011), ord("\x08"))]
if YizPoFeWqT3N == roI3spqORKae(ES5oEprVxulp(b'\xa3:WL'), chr(0b1001 + 0o133) + chr(0b1100101) + '\143' + '\x6f' + chr(7525 - 7425) + '\145')(chr(4290 - 4173) + chr(0b110100 + 0o100) + chr(1912 - 1810) + chr(1638 - 1593) + chr(0b111000)):
ZMOCKq9IH__h[ZlbFMSG8gCoF][sChW4gUsXrIC] = kRMcrmQh9wYY ** nzTpIcepk0o8('\x30' + chr(0b101100 + 0o103) + chr(0b10001 + 0o41), 8)
else:
UKIjitrAwDav[ZlbFMSG8gCoF][sChW4gUsXrIC] = kRMcrmQh9wYY ** nzTpIcepk0o8(chr(2120 - 2072) + '\x6f' + chr(0b1000 + 0o52), 8)
toKQXlEvBKaK[roI3spqORKae(ES5oEprVxulp(b'\xb36KQ\r\xfaOi\xccB\xf3dW\x1fR'), chr(0b100100 + 0o100) + '\145' + chr(2869 - 2770) + '\x6f' + chr(0b111110 + 0o46) + '\145')(chr(117) + '\164' + '\146' + '\055' + '\070')] = ZMOCKq9IH__h
toKQXlEvBKaK[roI3spqORKae(ES5oEprVxulp(b'\xb9(L]\r\xf9OS\xfeN\xe6bL\x0e'), '\144' + '\x65' + chr(3203 - 3104) + '\157' + '\144' + '\x65')('\x75' + '\x74' + '\x66' + '\x2d' + chr(711 - 655))] = UKIjitrAwDav
return toKQXlEvBKaK |
klavinslab/coral | coral/analysis/_structure/viennarna.py | ViennaRNA.fold | def fold(self, strand, temp=37.0, dangles=2, nolp=False, nogu=False,
noclosinggu=False, constraints=None, canonicalbponly=False,
partition=False, pfscale=None, imfeelinglucky=False, gquad=False):
'''Run the RNAfold command and retrieve the result in a dictionary.
:param strand: The DNA or RNA sequence on which to run RNAfold.
:type strand: coral.DNA or coral.RNA
:param temp: Temperature at which to run the calculations.
:type temp: float
:param dangles: How to treat dangling end energies. Set to 0 to ignore
dangling ends. Set to 1 to limit unpaired bases to
at most one dangling end (default for MFE calc). Set to
2 (the default) to remove the limit in 1. Set to 3 to
allow coaxial stacking of adjacent helices in
.multi-loops
:type dangles: int
:param nolp: Produce structures without lonely pairs (isolated single
base pairs).
:type nolp: bool
:param nogu: Do not allow GU pairs.
:type nogu: bool
:param noclosinggu: Do not allow GU pairs at the end of helices.
:type noclosinggu: bool
:param constraints: Any structural constraints to use. Format is
defined at
http://www.tbi.univie.ac.at/RNA/RNAfold.1.html
:type constraints: str
:param canonicalbponly: Remove non-canonical base pairs from the
structure constraint (if applicable).
:type canonicalbponly: bool
:param partition: Generates the partition function, generating a coarse
grain structure ('coarse') in the format described at
http://www.itc.univie.ac.at/~ivo/RNA/RNAlib/PF-Fold.h
tml, the ensemble free energy ('ensemble'), the
centroid structure ('centroid'), the free energy of
the centroid structure ('centroid_fe'), and its
distance from the ensemble ('centroid_d').
:type partition: int
:param pfscale: Scaling factor for the partition function.
:type pfScale: float
:param imfeelinglucky: Returns the one secondary structure from the
Boltzmann equilibrium according to its
probability in the ensemble.
:type imfeelinglucky: bool
:param gquad: Incorporate G-Quadruplex formation into the structure
prediction.
:type gquad: bool
:returns: Dictionary of calculated values, defaulting to values of MFE
('mfe': float) and dotbracket structure ('dotbracket': str).
More keys are added depending on keyword arguments.
:rtype: dict
'''
cmd_args = []
cmd_kwargs = {'--temp=': str(temp)}
cmd_kwargs['--dangles='] = dangles
if nolp:
cmd_args.append('--noLP')
if nogu:
cmd_args.append('--noGU')
if noclosinggu:
cmd_args.append('--noClosingGU')
if constraints is not None:
cmd_args.append('--constraint')
if canonicalbponly:
cmd_args.append('--canonicalBPonly')
if partition:
cmd_args.append('--partfunc')
if pfscale is not None:
cmd_kwargs['pfScale'] = float(pfscale)
if gquad:
cmd_args.append('--gquad')
inputs = [str(strand)]
if constraints is not None:
inputs.append(constraints)
if strand.circular:
cmd_args.append('--circ')
rnafold_output = self._run('RNAfold', inputs, cmd_args, cmd_kwargs)
# Process the output
output = {}
lines = rnafold_output.splitlines()
# Line 1 is the sequence as RNA
lines.pop(0)
# Line 2 is the dotbracket + mfe
line2 = lines.pop(0)
output['dotbracket'] = self._lparse(line2, '^(.*) \(')
output['mfe'] = float(self._lparse(line2, ' \((.*)\)$'))
# Optional outputs
if partition:
# Line 3 is 'a coarse representation of the pair probabilities' and
# the ensemble free energy
line3 = lines.pop(0)
output['coarse'] = self._lparse(line3, '^(.*) \[')
output['ensemble'] = float(self._lparse(line3, ' \[(.*)\]$'))
# Line 4 is the centroid structure, its free energy, and distance
# to the ensemble
line4 = lines.pop(0)
output['centroid'] = self._lparse(line4, '^(.*) \{')
output['centroid_fe'] = float(self._lparse(line4, '^.*{(.*) d'))
output['centroid_d'] = float(self._lparse(line4, 'd=(.*)}$'))
return output | python | def fold(self, strand, temp=37.0, dangles=2, nolp=False, nogu=False,
noclosinggu=False, constraints=None, canonicalbponly=False,
partition=False, pfscale=None, imfeelinglucky=False, gquad=False):
'''Run the RNAfold command and retrieve the result in a dictionary.
:param strand: The DNA or RNA sequence on which to run RNAfold.
:type strand: coral.DNA or coral.RNA
:param temp: Temperature at which to run the calculations.
:type temp: float
:param dangles: How to treat dangling end energies. Set to 0 to ignore
dangling ends. Set to 1 to limit unpaired bases to
at most one dangling end (default for MFE calc). Set to
2 (the default) to remove the limit in 1. Set to 3 to
allow coaxial stacking of adjacent helices in
.multi-loops
:type dangles: int
:param nolp: Produce structures without lonely pairs (isolated single
base pairs).
:type nolp: bool
:param nogu: Do not allow GU pairs.
:type nogu: bool
:param noclosinggu: Do not allow GU pairs at the end of helices.
:type noclosinggu: bool
:param constraints: Any structural constraints to use. Format is
defined at
http://www.tbi.univie.ac.at/RNA/RNAfold.1.html
:type constraints: str
:param canonicalbponly: Remove non-canonical base pairs from the
structure constraint (if applicable).
:type canonicalbponly: bool
:param partition: Generates the partition function, generating a coarse
grain structure ('coarse') in the format described at
http://www.itc.univie.ac.at/~ivo/RNA/RNAlib/PF-Fold.h
tml, the ensemble free energy ('ensemble'), the
centroid structure ('centroid'), the free energy of
the centroid structure ('centroid_fe'), and its
distance from the ensemble ('centroid_d').
:type partition: int
:param pfscale: Scaling factor for the partition function.
:type pfScale: float
:param imfeelinglucky: Returns the one secondary structure from the
Boltzmann equilibrium according to its
probability in the ensemble.
:type imfeelinglucky: bool
:param gquad: Incorporate G-Quadruplex formation into the structure
prediction.
:type gquad: bool
:returns: Dictionary of calculated values, defaulting to values of MFE
('mfe': float) and dotbracket structure ('dotbracket': str).
More keys are added depending on keyword arguments.
:rtype: dict
'''
cmd_args = []
cmd_kwargs = {'--temp=': str(temp)}
cmd_kwargs['--dangles='] = dangles
if nolp:
cmd_args.append('--noLP')
if nogu:
cmd_args.append('--noGU')
if noclosinggu:
cmd_args.append('--noClosingGU')
if constraints is not None:
cmd_args.append('--constraint')
if canonicalbponly:
cmd_args.append('--canonicalBPonly')
if partition:
cmd_args.append('--partfunc')
if pfscale is not None:
cmd_kwargs['pfScale'] = float(pfscale)
if gquad:
cmd_args.append('--gquad')
inputs = [str(strand)]
if constraints is not None:
inputs.append(constraints)
if strand.circular:
cmd_args.append('--circ')
rnafold_output = self._run('RNAfold', inputs, cmd_args, cmd_kwargs)
# Process the output
output = {}
lines = rnafold_output.splitlines()
# Line 1 is the sequence as RNA
lines.pop(0)
# Line 2 is the dotbracket + mfe
line2 = lines.pop(0)
output['dotbracket'] = self._lparse(line2, '^(.*) \(')
output['mfe'] = float(self._lparse(line2, ' \((.*)\)$'))
# Optional outputs
if partition:
# Line 3 is 'a coarse representation of the pair probabilities' and
# the ensemble free energy
line3 = lines.pop(0)
output['coarse'] = self._lparse(line3, '^(.*) \[')
output['ensemble'] = float(self._lparse(line3, ' \[(.*)\]$'))
# Line 4 is the centroid structure, its free energy, and distance
# to the ensemble
line4 = lines.pop(0)
output['centroid'] = self._lparse(line4, '^(.*) \{')
output['centroid_fe'] = float(self._lparse(line4, '^.*{(.*) d'))
output['centroid_d'] = float(self._lparse(line4, 'd=(.*)}$'))
return output | [
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:param strand: The DNA or RNA sequence on which to run RNAfold.
:type strand: coral.DNA or coral.RNA
:param temp: Temperature at which to run the calculations.
:type temp: float
:param dangles: How to treat dangling end energies. Set to 0 to ignore
dangling ends. Set to 1 to limit unpaired bases to
at most one dangling end (default for MFE calc). Set to
2 (the default) to remove the limit in 1. Set to 3 to
allow coaxial stacking of adjacent helices in
.multi-loops
:type dangles: int
:param nolp: Produce structures without lonely pairs (isolated single
base pairs).
:type nolp: bool
:param nogu: Do not allow GU pairs.
:type nogu: bool
:param noclosinggu: Do not allow GU pairs at the end of helices.
:type noclosinggu: bool
:param constraints: Any structural constraints to use. Format is
defined at
http://www.tbi.univie.ac.at/RNA/RNAfold.1.html
:type constraints: str
:param canonicalbponly: Remove non-canonical base pairs from the
structure constraint (if applicable).
:type canonicalbponly: bool
:param partition: Generates the partition function, generating a coarse
grain structure ('coarse') in the format described at
http://www.itc.univie.ac.at/~ivo/RNA/RNAlib/PF-Fold.h
tml, the ensemble free energy ('ensemble'), the
centroid structure ('centroid'), the free energy of
the centroid structure ('centroid_fe'), and its
distance from the ensemble ('centroid_d').
:type partition: int
:param pfscale: Scaling factor for the partition function.
:type pfScale: float
:param imfeelinglucky: Returns the one secondary structure from the
Boltzmann equilibrium according to its
probability in the ensemble.
:type imfeelinglucky: bool
:param gquad: Incorporate G-Quadruplex formation into the structure
prediction.
:type gquad: bool
:returns: Dictionary of calculated values, defaulting to values of MFE
('mfe': float) and dotbracket structure ('dotbracket': str).
More keys are added depending on keyword arguments.
:rtype: dict | [
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"dictionary",
"."
] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/analysis/_structure/viennarna.py#L143-L248 | train | Run the RNAfold command and retrieve the result in a dictionary. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b101111 + 0o1) + chr(0b1101111) + '\x32' + chr(672 - 620) + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1000100 + 0o53) + '\063' + '\x36' + chr(49), 34761 - 34753), nzTpIcepk0o8(chr(48) + chr(0b1000010 + 0o55) + chr(49) + '\060' + chr(0b110110), 55672 - 55664), nzTpIcepk0o8(chr(48) + chr(3715 - 3604) + chr(51) + chr(0b110100) + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(0b10111 + 0o31) + '\157' + chr(0b110100) + chr(55), 56246 - 56238), nzTpIcepk0o8(chr(441 - 393) + chr(111) + '\062' + chr(49) + chr(48), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(6624 - 6513) + '\x32' + chr(50) + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\061' + '\060' + chr(0b110011), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1100110 + 0o11) + '\x33' + chr(0b110100) + '\062', 0b1000), nzTpIcepk0o8(chr(0b101011 + 0o5) + chr(0b1101111) + chr(0b111 + 0o52) + chr(2838 - 2783) + '\x32', 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(49) + chr(2517 - 2466) + chr(1167 - 1116), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + '\x33' + chr(0b110100) + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(948 - 900) + '\157' + '\x33' + '\x36' + chr(52), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\062' + chr(0b110001) + chr(49), 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x31' + '\x33' + chr(0b110110), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\063' + '\061' + chr(0b110011), 0o10), nzTpIcepk0o8(chr(48) + chr(8650 - 8539) + chr(2310 - 2259) + '\x36' + '\x31', 8), nzTpIcepk0o8('\x30' + '\157' + chr(0b10010 + 0o40) + chr(0b11000 + 0o30) + '\064', 0b1000), nzTpIcepk0o8('\060' + chr(0b1011111 + 0o20) + '\x33' + chr(0b11011 + 0o32) + chr(50), 0o10), nzTpIcepk0o8(chr(575 - 527) + chr(0b1101111) + chr(0b110011) + chr(0b11011 + 0o30) + chr(1851 - 1800), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b110100 + 0o73) + '\x32' + '\x31', 6884 - 6876), nzTpIcepk0o8('\060' + chr(0b1011101 + 0o22) + '\x36' + chr(51), 0b1000), nzTpIcepk0o8(chr(1847 - 1799) + '\157' + '\062' + chr(0b110000) + chr(51), 0o10), nzTpIcepk0o8('\060' + '\x6f' + '\061' + chr(0b100101 + 0o14) + chr(1544 - 1491), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1010100 + 0o33) + '\063' + chr(0b110110) + '\065', 0b1000), nzTpIcepk0o8(chr(1489 - 1441) + chr(0b1101111) + chr(814 - 764) + chr(0b110111) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(0b110000 + 0o0) + chr(0b1101111) + '\x32' + chr(55) + chr(53), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b11010 + 0o27) + '\064' + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(1308 - 1260) + chr(3569 - 3458) + '\062' + chr(0b100 + 0o57) + '\x36', 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x32' + '\066' + '\x36', 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(52) + '\x36', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1010010 + 0o35) + chr(53), 6935 - 6927), nzTpIcepk0o8(chr(0b10100 + 0o34) + chr(7525 - 7414) + '\062' + chr(1437 - 1388) + chr(0b1111 + 0o45), 0b1000), nzTpIcepk0o8('\060' + chr(111) + '\x35' + '\x36', 13610 - 13602), nzTpIcepk0o8(chr(0b110000) + chr(3179 - 3068) + chr(0b10100 + 0o36) + '\x34' + '\x31', 1719 - 1711), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110010) + chr(50) + chr(112 - 61), 0b1000), nzTpIcepk0o8('\060' + chr(0b1000110 + 0o51) + chr(614 - 564) + chr(993 - 940) + '\062', ord("\x08")), nzTpIcepk0o8(chr(0b101101 + 0o3) + chr(0b1101111) + '\x32' + chr(0b110011) + chr(51), 0o10), nzTpIcepk0o8(chr(1744 - 1696) + chr(0b1101111) + chr(55), 56637 - 56629), nzTpIcepk0o8(chr(48) + '\x6f' + chr(52) + chr(0b110001), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x35' + chr(2198 - 2150), ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x8d'), chr(0b1100100) + '\x65' + chr(0b1011 + 0o130) + chr(0b1101111) + '\x64' + chr(2448 - 2347))(chr(0b101 + 0o160) + '\x74' + chr(102) + chr(0b101101) + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def whwzl4LhvM_u(hXMPsSrOQzbh, sOvPdpw6JkD6, bhvcCFR07maA=37.0, dcIGdrKJIQqm=nzTpIcepk0o8('\060' + chr(0b100110 + 0o111) + chr(1012 - 962), 61633 - 61625), mlhoP38jdudd=nzTpIcepk0o8(chr(0b100000 + 0o20) + '\x6f' + chr(1189 - 1141), 0b1000), zCewwQUPbHLD=nzTpIcepk0o8('\x30' + chr(111) + '\060', 8), NugwvhZNCD5b=nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x30', 8), WsRXUozGEySJ=None, HieMGlwzVBAU=nzTpIcepk0o8(chr(0b10 + 0o56) + chr(0b1101111) + '\060', 8), y6tm5LzgZc_E=nzTpIcepk0o8(chr(0b101 + 0o53) + '\157' + chr(0b110000), 8), yOoPgMu7dWsV=None, gWFVAautSd_K=nzTpIcepk0o8(chr(48) + chr(111) + chr(48), 8), wCbMBpg1trXc=nzTpIcepk0o8('\060' + chr(10126 - 10015) + chr(1220 - 1172), 8)):
zF8oFOtHDCse = []
W6eknENeyhyW = {roI3spqORKae(ES5oEprVxulp(b'\x8e\xdc2\x81J\xf8\xaa'), '\x64' + chr(0b1100101) + '\x63' + '\x6f' + '\144' + chr(101))(chr(117) + chr(5935 - 5819) + chr(0b11001 + 0o115) + chr(1911 - 1866) + chr(0b111000)): N9zlRy29S1SS(bhvcCFR07maA)}
W6eknENeyhyW[roI3spqORKae(ES5oEprVxulp(b'\x8e\xdc"\x85I\xef\xfb&\x91G'), chr(100) + '\x65' + '\143' + '\157' + chr(0b1100100) + chr(0b110111 + 0o56))(chr(0b10110 + 0o137) + chr(0b1110100) + chr(0b1100000 + 0o6) + chr(1191 - 1146) + chr(908 - 852))] = dcIGdrKJIQqm
if mlhoP38jdudd:
roI3spqORKae(zF8oFOtHDCse, roI3spqORKae(ES5oEprVxulp(b'\xeb\xa5\x15\xd0_\xef\xd0,\x88\x15\x0e\xd0'), chr(0b1100100) + chr(4670 - 4569) + '\x63' + chr(111) + '\x64' + chr(0b0 + 0o145))('\165' + chr(0b1110100) + '\146' + chr(0b101101) + '\x38'))(roI3spqORKae(ES5oEprVxulp(b'\x8e\xdc(\x8bk\xd8'), chr(0b101 + 0o137) + chr(3673 - 3572) + chr(0b1100011) + '\157' + chr(0b101 + 0o137) + '\145')(chr(10032 - 9915) + chr(0b10100 + 0o140) + chr(9049 - 8947) + '\x2d' + chr(3069 - 3013)))
if zCewwQUPbHLD:
roI3spqORKae(zF8oFOtHDCse, roI3spqORKae(ES5oEprVxulp(b'\xeb\xa5\x15\xd0_\xef\xd0,\x88\x15\x0e\xd0'), '\144' + chr(101) + chr(99) + chr(0b1101111) + chr(100) + chr(101))(chr(117) + chr(3822 - 3706) + chr(0b1000001 + 0o45) + '\055' + '\070'))(roI3spqORKae(ES5oEprVxulp(b'\x8e\xdc(\x8b`\xdd'), chr(942 - 842) + chr(0b1100101) + chr(8127 - 8028) + '\x6f' + chr(100) + '\x65')(chr(13321 - 13204) + chr(11977 - 11861) + chr(0b1100110) + chr(0b101101) + chr(0b11110 + 0o32)))
if NugwvhZNCD5b:
roI3spqORKae(zF8oFOtHDCse, roI3spqORKae(ES5oEprVxulp(b'\xeb\xa5\x15\xd0_\xef\xd0,\x88\x15\x0e\xd0'), chr(6811 - 6711) + chr(0b1100101) + '\143' + chr(0b1101111) + chr(0b11110 + 0o106) + chr(6436 - 6335))(chr(0b1110101) + chr(0b1110100) + chr(2804 - 2702) + '\055' + chr(2377 - 2321)))(roI3spqORKae(ES5oEprVxulp(b'\x8e\xdc(\x8bd\xe4\xf80\x8b\x14<\xa2\xa1'), chr(989 - 889) + chr(101) + chr(0b11111 + 0o104) + chr(11997 - 11886) + chr(0b10 + 0o142) + '\145')('\x75' + chr(0b110111 + 0o75) + chr(9918 - 9816) + chr(45) + chr(0b101001 + 0o17)))
if WsRXUozGEySJ is not None:
roI3spqORKae(zF8oFOtHDCse, roI3spqORKae(ES5oEprVxulp(b'\xeb\xa5\x15\xd0_\xef\xd0,\x88\x15\x0e\xd0'), '\x64' + chr(0b110 + 0o137) + chr(99) + '\157' + chr(0b1100100) + chr(0b1100010 + 0o3))(chr(0b1110101) + chr(0b1110100) + chr(102) + chr(0b100100 + 0o11) + '\070'))(roI3spqORKae(ES5oEprVxulp(b'\x8e\xdc%\x8bI\xfb\xe31\x83\x135\x91'), '\x64' + '\x65' + chr(0b1100011) + chr(2992 - 2881) + '\144' + chr(0b1010111 + 0o16))(chr(11625 - 11508) + chr(0b1101001 + 0o13) + chr(0b111001 + 0o55) + chr(954 - 909) + '\070'))
if HieMGlwzVBAU:
roI3spqORKae(zF8oFOtHDCse, roI3spqORKae(ES5oEprVxulp(b'\xeb\xa5\x15\xd0_\xef\xd0,\x88\x15\x0e\xd0'), chr(5499 - 5399) + chr(0b1010101 + 0o20) + chr(0b1111 + 0o124) + chr(12295 - 12184) + chr(100) + chr(8894 - 8793))(chr(5455 - 5338) + '\x74' + chr(102) + '\055' + chr(0b11001 + 0o37)))(roI3spqORKae(ES5oEprVxulp(b'\x8e\xdc%\x85I\xe7\xf9*\x81\x1b7\xa7\xa4\xe60\xa7\x88'), chr(100) + chr(101) + '\143' + chr(111) + chr(100) + chr(0b1100101))(chr(0b1101 + 0o150) + chr(0b1110100) + chr(102) + chr(0b101101) + '\070'))
if y6tm5LzgZc_E:
roI3spqORKae(zF8oFOtHDCse, roI3spqORKae(ES5oEprVxulp(b'\xeb\xa5\x15\xd0_\xef\xd0,\x88\x15\x0e\xd0'), '\x64' + '\145' + chr(0b1100011) + chr(0b110110 + 0o71) + chr(0b1100100) + chr(7266 - 7165))(chr(0b100000 + 0o125) + '\x74' + chr(0b1100110) + '\x2d' + chr(56)))(roI3spqORKae(ES5oEprVxulp(b'\x8e\xdc6\x85U\xfc\xf16\x8c\x19'), chr(6749 - 6649) + chr(6042 - 5941) + chr(0b110011 + 0o60) + '\x6f' + chr(0b1100100) + chr(0b1100101))('\165' + chr(116) + chr(2494 - 2392) + chr(45) + chr(0b100 + 0o64)))
if yOoPgMu7dWsV is not None:
W6eknENeyhyW[roI3spqORKae(ES5oEprVxulp(b'\xd3\x97\x15\x87F\xe4\xf2'), '\x64' + chr(0b1100101) + chr(0b1100011) + chr(0b1101111) + '\x64' + chr(101))(chr(0b1000101 + 0o60) + chr(0b111100 + 0o70) + chr(0b1011101 + 0o11) + chr(0b11000 + 0o25) + chr(0b111000))] = jLW6pRf2DSRk(yOoPgMu7dWsV)
if wCbMBpg1trXc:
roI3spqORKae(zF8oFOtHDCse, roI3spqORKae(ES5oEprVxulp(b'\xeb\xa5\x15\xd0_\xef\xd0,\x88\x15\x0e\xd0'), chr(0b11001 + 0o113) + chr(101) + '\x63' + '\157' + chr(7284 - 7184) + '\x65')(chr(117) + chr(0b1110100) + chr(1279 - 1177) + '\055' + chr(0b111000)))(roI3spqORKae(ES5oEprVxulp(b'\x8e\xdc!\x95R\xe9\xf3'), chr(0b1100100) + chr(101) + chr(99) + chr(12139 - 12028) + chr(0b1100100) + '\145')(chr(117) + chr(116) + '\x66' + chr(386 - 341) + '\070'))
GKlPkmr7AqQT = [N9zlRy29S1SS(sOvPdpw6JkD6)]
if WsRXUozGEySJ is not None:
roI3spqORKae(GKlPkmr7AqQT, roI3spqORKae(ES5oEprVxulp(b'\xeb\xa5\x15\xd0_\xef\xd0,\x88\x15\x0e\xd0'), chr(0b1100100) + chr(0b1100101) + '\143' + chr(0b110111 + 0o70) + '\x64' + chr(7231 - 7130))(chr(13274 - 13157) + chr(2528 - 2412) + chr(0b1100110) + chr(0b100001 + 0o14) + chr(0b111000)))(WsRXUozGEySJ)
if roI3spqORKae(sOvPdpw6JkD6, roI3spqORKae(ES5oEprVxulp(b'\xc0\x984\x87R\xe4\xf61'), chr(0b111010 + 0o52) + '\x65' + '\x63' + chr(4450 - 4339) + '\x64' + chr(5830 - 5729))(chr(117) + '\x74' + chr(0b101111 + 0o67) + chr(0b101101) + '\x38')):
roI3spqORKae(zF8oFOtHDCse, roI3spqORKae(ES5oEprVxulp(b'\xeb\xa5\x15\xd0_\xef\xd0,\x88\x15\x0e\xd0'), chr(0b1010110 + 0o16) + chr(0b1100101) + '\x63' + '\157' + chr(3104 - 3004) + chr(101))('\x75' + chr(2922 - 2806) + chr(5944 - 5842) + chr(45) + '\070'))(roI3spqORKae(ES5oEprVxulp(b'\x8e\xdc%\x8dU\xeb'), chr(4642 - 4542) + '\x65' + chr(1608 - 1509) + '\157' + '\144' + chr(0b1100101))(chr(0b1110101) + chr(0b1110100) + chr(0b1111 + 0o127) + '\x2d' + chr(0b111000)))
bBOYBuR1kjY6 = hXMPsSrOQzbh.w878a10420A4(roI3spqORKae(ES5oEprVxulp(b'\xf1\xbf\x07\x82H\xe4\xf3'), chr(6038 - 5938) + chr(0b1100101) + '\143' + chr(111) + chr(5548 - 5448) + '\145')(chr(925 - 808) + chr(116) + chr(0b1100110) + '\055' + chr(2374 - 2318)), GKlPkmr7AqQT, zF8oFOtHDCse, W6eknENeyhyW)
toKQXlEvBKaK = {}
vniSnlI09HNg = bBOYBuR1kjY6.splitlines()
roI3spqORKae(vniSnlI09HNg, roI3spqORKae(ES5oEprVxulp(b'\xd6\xb2\x19\xbdH\xf1\xf5;\xd50k\xac'), chr(0b1110 + 0o126) + '\145' + '\143' + chr(6536 - 6425) + chr(100) + chr(1283 - 1182))('\165' + chr(116) + chr(0b101000 + 0o76) + '\055' + '\x38'))(nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(1227 - 1179), 8))
_LnPf57SSQAk = vniSnlI09HNg.uC_Yoybx7J0I(nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110000), 8))
toKQXlEvBKaK[roI3spqORKae(ES5oEprVxulp(b'\xc7\x9e2\x86U\xe9\xf4(\x87\x0e'), chr(100) + '\x65' + chr(0b1100011) + chr(4641 - 4530) + '\x64' + '\145')(chr(0b1110101) + chr(1647 - 1531) + chr(0b1100110) + '\055' + '\x38')] = hXMPsSrOQzbh._lparse(_LnPf57SSQAk, roI3spqORKae(ES5oEprVxulp(b'\xfd\xd9h\xce\x0e\xa8\xcbk'), chr(100) + '\x65' + chr(0b1100011) + '\x6f' + chr(7016 - 6916) + chr(0b1100101))(chr(0b1100111 + 0o16) + '\164' + '\x66' + chr(45) + chr(0b111000)))
toKQXlEvBKaK[roI3spqORKae(ES5oEprVxulp(b'\xce\x97#'), chr(0b111110 + 0o46) + chr(819 - 718) + '\143' + '\157' + chr(9500 - 9400) + '\145')(chr(0b10000 + 0o145) + chr(0b1110100) + '\x66' + '\x2d' + chr(1250 - 1194))] = jLW6pRf2DSRk(hXMPsSrOQzbh._lparse(_LnPf57SSQAk, roI3spqORKae(ES5oEprVxulp(b'\x83\xadn\xcc\t\xa2\xbe\x1f\xcb^'), chr(5013 - 4913) + '\145' + chr(0b1100011) + '\157' + chr(0b1000110 + 0o36) + chr(101))('\x75' + chr(12017 - 11901) + '\x66' + chr(0b101101) + chr(56))))
if y6tm5LzgZc_E:
NrpWjFRKX4St = vniSnlI09HNg.uC_Yoybx7J0I(nzTpIcepk0o8(chr(0b11 + 0o55) + chr(0b111100 + 0o63) + chr(48), 8))
toKQXlEvBKaK[roI3spqORKae(ES5oEprVxulp(b"\xc0\x9e'\x96T\xed"), chr(0b1100100) + chr(1017 - 916) + '\x63' + chr(8261 - 8150) + chr(0b111 + 0o135) + '\x65')(chr(117) + chr(116) + '\146' + chr(0b101101) + chr(0b111000))] = hXMPsSrOQzbh._lparse(NrpWjFRKX4St, roI3spqORKae(ES5oEprVxulp(b'\xfd\xd9h\xce\x0e\xa8\xcb\x18'), '\x64' + '\145' + chr(0b1100011) + chr(0b1101111) + chr(0b110011 + 0o61) + '\x65')(chr(0b1110101) + chr(116) + chr(102) + chr(45) + '\x38'))
toKQXlEvBKaK[roI3spqORKae(ES5oEprVxulp(b'\xc6\x9f5\x81J\xea\xfb&'), chr(100) + '\x65' + chr(6146 - 6047) + chr(0b1 + 0o156) + chr(0b1100100) + chr(0b1100101))('\165' + chr(0b1110100) + chr(0b1100110) + chr(0b1100 + 0o41) + '\x38')] = jLW6pRf2DSRk(hXMPsSrOQzbh._lparse(NrpWjFRKX4St, roI3spqORKae(ES5oEprVxulp(b'\x83\xad\x1d\xcc\t\xa2\xbe\x1f\xbf^'), chr(100) + chr(101) + chr(0b1100011) + '\157' + '\x64' + chr(101))(chr(0b1000011 + 0o62) + chr(0b1110100) + chr(0b100100 + 0o102) + '\x2d' + chr(0b111000))))
um9m0D6L7zLw = vniSnlI09HNg.uC_Yoybx7J0I(nzTpIcepk0o8(chr(48) + '\x6f' + chr(171 - 123), 8))
toKQXlEvBKaK[roI3spqORKae(ES5oEprVxulp(b"\xc0\x94(\x90U\xe7\xfe'"), chr(993 - 893) + chr(0b101001 + 0o74) + '\x63' + '\157' + chr(3148 - 3048) + chr(0b1100101))(chr(0b11110 + 0o127) + chr(0b110 + 0o156) + chr(7177 - 7075) + chr(45) + chr(1004 - 948))] = hXMPsSrOQzbh._lparse(um9m0D6L7zLw, roI3spqORKae(ES5oEprVxulp(b'\xfd\xd9h\xce\x0e\xa8\xcb8'), chr(0b1110 + 0o126) + '\145' + '\143' + chr(10959 - 10848) + '\x64' + '\145')(chr(117) + chr(116) + '\146' + chr(0b101101) + '\070'))
toKQXlEvBKaK[roI3spqORKae(ES5oEprVxulp(b"\xc0\x94(\x90U\xe7\xfe'\xbd\x1c>"), chr(100) + '\145' + chr(5609 - 5510) + '\157' + '\x64' + '\x65')(chr(12700 - 12583) + chr(0b1011100 + 0o30) + chr(1158 - 1056) + '\x2d' + chr(0b110101 + 0o3))] = jLW6pRf2DSRk(hXMPsSrOQzbh._lparse(um9m0D6L7zLw, roI3spqORKae(ES5oEprVxulp(b'\xfd\xdfl\x9f\x0f\xa6\xbdj\xc2\x1e'), chr(0b1100100) + chr(0b1100101) + '\143' + chr(9297 - 9186) + '\144' + '\145')('\x75' + chr(0b1011111 + 0o25) + '\x66' + chr(0b10000 + 0o35) + '\x38')))
toKQXlEvBKaK[roI3spqORKae(ES5oEprVxulp(b"\xc0\x94(\x90U\xe7\xfe'\xbd\x1e"), chr(100) + '\x65' + chr(0b1100011) + '\x6f' + chr(0b1100100) + chr(101))(chr(117) + '\x74' + chr(0b1010101 + 0o21) + chr(0b101101) + chr(0b111000))] = jLW6pRf2DSRk(hXMPsSrOQzbh._lparse(um9m0D6L7zLw, roI3spqORKae(ES5oEprVxulp(b'\xc7\xccn\xca\r\xa1\xeag'), '\x64' + '\145' + '\143' + chr(111) + '\x64' + '\x65')(chr(9587 - 9470) + chr(0b111 + 0o155) + '\x66' + '\055' + chr(0b100010 + 0o26))))
return toKQXlEvBKaK |
klavinslab/coral | coral/analysis/_structure/dimers.py | dimers | def dimers(primer1, primer2, concentrations=[5e-7, 3e-11]):
'''Calculate expected fraction of primer dimers.
:param primer1: Forward primer.
:type primer1: coral.DNA
:param primer2: Reverse primer.
:type primer2: coral.DNA
:param template: DNA template.
:type template: coral.DNA
:param concentrations: list of concentrations for primers and the
template. Defaults are those for PCR with 1kb
template.
:type concentrations: list
:returns: Fraction of dimers versus the total amount of primer added.
:rtype: float
'''
# It is not reasonable (yet) to use a long template for doing these
# computations directly, as NUPACK does an exhaustive calculation and
# would take too long without a cluster.
# Instead, this function compares primer-primer binding to
# primer-complement binding
# Simulate binding of template vs. primers
nupack = coral.analysis.NUPACK([primer1.primer(), primer2.primer(),
primer1.primer().reverse_complement(),
primer2.primer().reverse_complement()])
# Include reverse complement concentration
primer_concs = [concentrations[0]] * 2
template_concs = [concentrations[1]] * 2
concs = primer_concs + template_concs
nupack_concs = nupack.concentrations(2, conc=concs)
dimer_conc = nupack_concs['concentrations'][5]
#primer1_template = nupack_concs['concentrations'][6]
#primer2_template = nupack_concs['concentrations'][10]
return dimer_conc / concs[0] | python | def dimers(primer1, primer2, concentrations=[5e-7, 3e-11]):
'''Calculate expected fraction of primer dimers.
:param primer1: Forward primer.
:type primer1: coral.DNA
:param primer2: Reverse primer.
:type primer2: coral.DNA
:param template: DNA template.
:type template: coral.DNA
:param concentrations: list of concentrations for primers and the
template. Defaults are those for PCR with 1kb
template.
:type concentrations: list
:returns: Fraction of dimers versus the total amount of primer added.
:rtype: float
'''
# It is not reasonable (yet) to use a long template for doing these
# computations directly, as NUPACK does an exhaustive calculation and
# would take too long without a cluster.
# Instead, this function compares primer-primer binding to
# primer-complement binding
# Simulate binding of template vs. primers
nupack = coral.analysis.NUPACK([primer1.primer(), primer2.primer(),
primer1.primer().reverse_complement(),
primer2.primer().reverse_complement()])
# Include reverse complement concentration
primer_concs = [concentrations[0]] * 2
template_concs = [concentrations[1]] * 2
concs = primer_concs + template_concs
nupack_concs = nupack.concentrations(2, conc=concs)
dimer_conc = nupack_concs['concentrations'][5]
#primer1_template = nupack_concs['concentrations'][6]
#primer2_template = nupack_concs['concentrations'][10]
return dimer_conc / concs[0] | [
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:param primer1: Forward primer.
:type primer1: coral.DNA
:param primer2: Reverse primer.
:type primer2: coral.DNA
:param template: DNA template.
:type template: coral.DNA
:param concentrations: list of concentrations for primers and the
template. Defaults are those for PCR with 1kb
template.
:type concentrations: list
:returns: Fraction of dimers versus the total amount of primer added.
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/analysis/_structure/dimers.py#L5-L40 | train | Calculate expected fraction of primer dimers. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8('\x30' + '\157' + '\x31' + chr(50) + chr(0b110110), 30015 - 30007), nzTpIcepk0o8('\x30' + chr(11642 - 11531) + chr(49) + chr(0b110011 + 0o2) + '\x32', 55401 - 55393), nzTpIcepk0o8('\x30' + chr(5707 - 5596) + '\063' + chr(0b110111) + '\x37', 61928 - 61920), nzTpIcepk0o8(chr(0b110000 + 0o0) + '\157' + chr(51) + chr(51) + '\x36', 35025 - 35017), nzTpIcepk0o8('\x30' + chr(111) + chr(51) + '\x32' + '\063', 27996 - 27988), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x31' + chr(49) + '\x34', 0b1000), nzTpIcepk0o8(chr(0b110000 + 0o0) + '\157' + chr(50) + chr(0b110110) + chr(1286 - 1237), 63652 - 63644), nzTpIcepk0o8(chr(0b110000) + chr(0b110110 + 0o71) + '\x32' + '\067' + '\063', ord("\x08")), nzTpIcepk0o8(chr(0b11110 + 0o22) + chr(111) + chr(1561 - 1512) + chr(0b10111 + 0o33) + '\060', 0o10), nzTpIcepk0o8(chr(0b1101 + 0o43) + chr(111) + '\x32' + chr(2296 - 2248) + chr(2037 - 1983), 0o10), nzTpIcepk0o8(chr(48) + chr(10523 - 10412) + chr(0b110001) + '\x37' + '\x31', 0b1000), nzTpIcepk0o8(chr(1319 - 1271) + chr(0b1101111) + '\062' + chr(54), 9813 - 9805), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(1653 - 1603) + chr(0b1111 + 0o45) + chr(1355 - 1301), 0b1000), nzTpIcepk0o8(chr(0b100011 + 0o15) + chr(111) + chr(515 - 464) + chr(0b10110 + 0o36) + chr(55), ord("\x08")), nzTpIcepk0o8(chr(0b1001 + 0o47) + '\x6f' + chr(0b110010) + '\062' + '\063', 0b1000), nzTpIcepk0o8(chr(0b10010 + 0o36) + chr(0b1000010 + 0o55) + chr(51) + chr(0b101101 + 0o5) + '\x34', 0b1000), nzTpIcepk0o8('\060' + chr(0b111001 + 0o66) + '\x31' + chr(2198 - 2150) + chr(55), 0o10), nzTpIcepk0o8(chr(0b11011 + 0o25) + chr(0b1001111 + 0o40) + chr(1460 - 1410) + chr(0b111 + 0o53) + '\x30', 0b1000), nzTpIcepk0o8(chr(1250 - 1202) + '\x6f' + chr(0b110001) + '\066' + chr(53), 0o10), nzTpIcepk0o8(chr(48) + '\157' + '\x33' + '\x30' + chr(49), ord("\x08")), nzTpIcepk0o8(chr(1848 - 1800) + '\157' + chr(1046 - 995) + '\x31' + '\x36', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(1015 - 965) + '\x30' + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110010), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b11011 + 0o124) + '\x31' + chr(0b110100) + '\060', 0o10), nzTpIcepk0o8('\060' + chr(111) + '\062' + chr(0b110111) + chr(52), 0b1000), nzTpIcepk0o8(chr(159 - 111) + '\157' + '\063', 0b1000), nzTpIcepk0o8(chr(0b1101 + 0o43) + chr(10177 - 10066) + chr(1490 - 1437) + '\064', 0o10), nzTpIcepk0o8(chr(1718 - 1670) + '\x6f' + chr(0b100 + 0o56) + '\x34' + chr(0b0 + 0o64), 0b1000), nzTpIcepk0o8(chr(0b10001 + 0o37) + chr(0b1101111) + chr(2283 - 2232) + '\x34' + chr(329 - 278), 14222 - 14214), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(54), 0b1000), nzTpIcepk0o8(chr(0b1100 + 0o44) + chr(3545 - 3434) + '\063' + chr(0b110010) + chr(54), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x31' + chr(0b110111) + '\x32', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110001) + chr(1088 - 1038) + '\x30', 8), nzTpIcepk0o8(chr(0b10111 + 0o31) + '\157' + '\065', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\063' + chr(51) + chr(52), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b101 + 0o55) + chr(757 - 709) + chr(0b110001), 0o10), nzTpIcepk0o8(chr(820 - 772) + chr(5643 - 5532) + chr(50) + '\x36' + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b101001 + 0o106) + chr(51) + chr(749 - 697) + chr(0b110110), 338 - 330), nzTpIcepk0o8('\060' + chr(0b100011 + 0o114) + '\063' + chr(0b110110) + chr(1011 - 961), 57328 - 57320), nzTpIcepk0o8(chr(48) + chr(111) + '\062' + chr(0b110011) + chr(0b110000), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + '\x6f' + '\065' + chr(48), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'x'), '\144' + '\145' + chr(0b1100011) + chr(0b11001 + 0o126) + chr(3828 - 3728) + '\x65')(chr(0b1110101) + chr(0b1010100 + 0o40) + chr(0b1100110) + chr(0b11 + 0o52) + chr(782 - 726)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def e71JOCAoUe_P(QEHoVbpEj8nx, PG1U_Og1H3qR, folbSXYfYVv_=[5e-07, 3e-11]):
zPs0RBqzFue6 = _bFWSozA7z0G.analysis.NUPACK([QEHoVbpEj8nx.primer(), PG1U_Og1H3qR.primer(), QEHoVbpEj8nx.primer().reverse_complement(), PG1U_Og1H3qR.primer().reverse_complement()])
YHFxU5cSdvb8 = [folbSXYfYVv_[nzTpIcepk0o8(chr(567 - 519) + chr(0b1010110 + 0o31) + chr(0b110000), 0b1000)]] * nzTpIcepk0o8(chr(0b11110 + 0o22) + '\157' + chr(50), 8)
eJLhNhIH7f6a = [folbSXYfYVv_[nzTpIcepk0o8(chr(0b110000) + chr(0b101111 + 0o100) + chr(0b110001), ord("\x08"))]] * nzTpIcepk0o8(chr(0b110000) + chr(0b110011 + 0o74) + chr(547 - 497), 8)
lYJrZUKNh3zS = YHFxU5cSdvb8 + eJLhNhIH7f6a
RZkEUgzAIpb3 = zPs0RBqzFue6.concentrations(nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110010), 8), conc=lYJrZUKNh3zS)
TaQke7nGArmN = RZkEUgzAIpb3[roI3spqORKae(ES5oEprVxulp(b'5\x05\x91\xbd\xb6"\xc5\xc91\xf2\x10y\xc8\x94'), chr(0b1100100) + '\145' + '\143' + chr(0b1101111) + '\144' + '\145')('\x75' + '\164' + '\146' + chr(0b101101) + '\070')][nzTpIcepk0o8(chr(940 - 892) + chr(9484 - 9373) + chr(0b110101), 8)]
return TaQke7nGArmN / lYJrZUKNh3zS[nzTpIcepk0o8(chr(48) + chr(795 - 684) + chr(0b101111 + 0o1), 8)] |
klavinslab/coral | coral/seqio/_dna.py | read_dna | def read_dna(path):
'''Read DNA from file. Uses BioPython and coerces to coral format.
:param path: Full path to input file.
:type path: str
:returns: DNA sequence.
:rtype: coral.DNA
'''
filename, ext = os.path.splitext(os.path.split(path)[-1])
genbank_exts = ['.gb', '.ape']
fasta_exts = ['.fasta', '.fa', '.fsa', '.seq']
abi_exts = ['.abi', '.ab1']
if any([ext == extension for extension in genbank_exts]):
file_format = 'genbank'
elif any([ext == extension for extension in fasta_exts]):
file_format = 'fasta'
elif any([ext == extension for extension in abi_exts]):
file_format = 'abi'
else:
raise ValueError('File format not recognized.')
seq = SeqIO.read(path, file_format)
dna = coral.DNA(str(seq.seq))
if seq.name == '.':
dna.name = filename
else:
dna.name = seq.name
# Features
for feature in seq.features:
try:
dna.features.append(_seqfeature_to_coral(feature))
except FeatureNameError:
pass
dna.features = sorted(dna.features, key=lambda feature: feature.start)
# Used to use data_file_division, but it's inconsistent (not always the
# molecule type)
dna.circular = False
with open(path) as f:
first_line = f.read().split()
for word in first_line:
if word == 'circular':
dna.circular = True
return dna | python | def read_dna(path):
'''Read DNA from file. Uses BioPython and coerces to coral format.
:param path: Full path to input file.
:type path: str
:returns: DNA sequence.
:rtype: coral.DNA
'''
filename, ext = os.path.splitext(os.path.split(path)[-1])
genbank_exts = ['.gb', '.ape']
fasta_exts = ['.fasta', '.fa', '.fsa', '.seq']
abi_exts = ['.abi', '.ab1']
if any([ext == extension for extension in genbank_exts]):
file_format = 'genbank'
elif any([ext == extension for extension in fasta_exts]):
file_format = 'fasta'
elif any([ext == extension for extension in abi_exts]):
file_format = 'abi'
else:
raise ValueError('File format not recognized.')
seq = SeqIO.read(path, file_format)
dna = coral.DNA(str(seq.seq))
if seq.name == '.':
dna.name = filename
else:
dna.name = seq.name
# Features
for feature in seq.features:
try:
dna.features.append(_seqfeature_to_coral(feature))
except FeatureNameError:
pass
dna.features = sorted(dna.features, key=lambda feature: feature.start)
# Used to use data_file_division, but it's inconsistent (not always the
# molecule type)
dna.circular = False
with open(path) as f:
first_line = f.read().split()
for word in first_line:
if word == 'circular':
dna.circular = True
return dna | [
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:param path: Full path to input file.
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:rtype: coral.DNA | [
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/seqio/_dna.py#L22-L69 | train | Reads a DNA file and returns it as a sequence. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(1942 - 1894) + chr(0b1110 + 0o141) + '\x33' + chr(0b10100 + 0o35) + chr(49), 21282 - 21274), nzTpIcepk0o8(chr(48) + chr(0b111011 + 0o64) + '\x32' + '\061' + chr(0b10110 + 0o36), 0o10), nzTpIcepk0o8(chr(48) + chr(9912 - 9801) + chr(0b110101) + chr(0b1001 + 0o55), 1241 - 1233), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110111), 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(51) + chr(55), 5319 - 5311), nzTpIcepk0o8(chr(0b11 + 0o55) + chr(0b1101111) + chr(50) + '\x31' + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(0b1 + 0o57) + chr(111) + '\065' + chr(254 - 202), 2174 - 2166), nzTpIcepk0o8(chr(1248 - 1200) + chr(6471 - 6360) + chr(0b110111) + chr(0b11010 + 0o35), 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(0b11101 + 0o24) + chr(0b11011 + 0o27) + chr(0b100011 + 0o15), 64093 - 64085), nzTpIcepk0o8('\060' + chr(0b10110 + 0o131) + chr(0b110001) + chr(53) + '\066', 32515 - 32507), nzTpIcepk0o8(chr(0b110000) + chr(7327 - 7216) + chr(1326 - 1274) + '\064', 0b1000), nzTpIcepk0o8(chr(1752 - 1704) + '\157' + chr(0b110110) + chr(2554 - 2502), 10643 - 10635), nzTpIcepk0o8('\x30' + chr(11796 - 11685) + chr(130 - 80) + chr(0b110011) + '\x34', ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(0b100110 + 0o14) + chr(2224 - 2171) + '\060', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(6712 - 6601) + chr(0b110010 + 0o0) + '\x34' + chr(0b101101 + 0o6), ord("\x08")), nzTpIcepk0o8(chr(2285 - 2237) + chr(111) + '\x33' + chr(55) + '\x30', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110011) + chr(275 - 221) + '\061', 16594 - 16586), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(48), 29273 - 29265), nzTpIcepk0o8('\x30' + chr(0b1001 + 0o146) + chr(0b11000 + 0o33), 43696 - 43688), nzTpIcepk0o8(chr(48) + chr(8518 - 8407) + chr(53) + chr(48), 4649 - 4641), nzTpIcepk0o8(chr(48) + '\157' + '\065', 65111 - 65103), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110101) + '\061', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(775 - 726) + chr(54) + '\x37', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(4290 - 4179) + chr(0b1010 + 0o47) + chr(1177 - 1126) + chr(0b1111 + 0o42), 0o10), nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(6963 - 6852) + '\x31' + chr(1847 - 1797) + chr(53), 34892 - 34884), nzTpIcepk0o8(chr(0b100 + 0o54) + '\157' + chr(546 - 497) + chr(0b1 + 0o61) + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + '\063' + chr(1307 - 1252) + '\066', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(49) + '\x33' + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(1898 - 1849) + chr(52) + '\x36', 9321 - 9313), nzTpIcepk0o8('\060' + chr(0b11110 + 0o121) + '\x31' + '\064', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\063' + '\067' + chr(54), 8), nzTpIcepk0o8(chr(0b110000) + chr(3467 - 3356) + '\062' + chr(0b101100 + 0o11) + '\060', 8), nzTpIcepk0o8(chr(48) + '\157' + chr(52) + chr(0b100 + 0o61), 0o10), nzTpIcepk0o8(chr(1327 - 1279) + '\157' + '\062' + chr(0b10010 + 0o43) + chr(279 - 231), 8), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\061' + '\065' + chr(0b110101), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b11100 + 0o123) + chr(49) + chr(1755 - 1700) + chr(540 - 486), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(55) + chr(0b110111), 8), nzTpIcepk0o8(chr(400 - 352) + chr(0b110000 + 0o77) + chr(0b1000 + 0o51) + chr(52) + '\x35', 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110011) + '\x30' + chr(0b100110 + 0o13), ord("\x08")), nzTpIcepk0o8(chr(0b10111 + 0o31) + chr(0b1011100 + 0o23) + '\x33' + chr(0b110010) + chr(0b110011), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + chr(1575 - 1464) + '\065' + chr(463 - 415), 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xe7'), chr(0b1100100) + chr(0b1100101) + chr(5840 - 5741) + chr(111) + chr(0b1111 + 0o125) + chr(101))(chr(117) + chr(0b1110100) + chr(7397 - 7295) + '\x2d' + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def GjGcxrWNqqti(_pSYqrosNb95):
(FxZHtXEolYsL, MEyQziOWmxIx) = aHUqKstZLeS6.path.nKnjsA3UsXpY(aHUqKstZLeS6.path.LfRrQOxuDvnC(_pSYqrosNb95)[-nzTpIcepk0o8('\060' + chr(111) + '\x31', 0b1000)])
OKwTlMo2PNx2 = [roI3spqORKae(ES5oEprVxulp(b'\xe7\xebL'), '\x64' + chr(9790 - 9689) + '\x63' + '\x6f' + chr(100) + chr(0b101100 + 0o71))(chr(0b1010010 + 0o43) + chr(0b1110100) + '\x66' + chr(0b100100 + 0o11) + chr(56)), roI3spqORKae(ES5oEprVxulp(b'\xe7\xed^b'), chr(5061 - 4961) + '\145' + chr(99) + chr(0b1101111) + '\144' + '\145')(chr(0b1110101) + chr(116) + chr(677 - 575) + '\055' + chr(56))]
auVK_CjrsHAJ = [roI3spqORKae(ES5oEprVxulp(b'\xe7\xeaOtk\xee'), chr(100) + chr(1465 - 1364) + '\x63' + chr(7571 - 7460) + chr(0b1100100) + chr(5539 - 5438))(chr(0b1110101) + chr(0b1011001 + 0o33) + chr(102) + '\x2d' + chr(2774 - 2718)), roI3spqORKae(ES5oEprVxulp(b'\xe7\xeaO'), chr(0b101000 + 0o74) + chr(0b11100 + 0o111) + chr(0b1100011) + chr(11838 - 11727) + '\x64' + '\145')(chr(117) + '\164' + '\x66' + chr(0b110 + 0o47) + chr(0b111000)), roI3spqORKae(ES5oEprVxulp(b'\xe7\xea]f'), chr(0b1100100) + chr(0b1100101) + '\143' + '\x6f' + chr(0b111011 + 0o51) + chr(0b1100101))('\165' + chr(0b1110100) + '\x66' + chr(0b101101) + chr(0b111000)), roI3spqORKae(ES5oEprVxulp(b'\xe7\xffKv'), '\144' + '\x65' + chr(0b110111 + 0o54) + chr(2869 - 2758) + chr(100) + '\145')(chr(1276 - 1159) + '\164' + chr(0b1100110) + '\055' + chr(466 - 410))]
xhqzYwg0Wee0 = [roI3spqORKae(ES5oEprVxulp(b'\xe7\xedLn'), chr(0b1001100 + 0o30) + chr(0b10101 + 0o120) + chr(0b101010 + 0o71) + chr(0b1101111) + chr(0b1100010 + 0o2) + chr(1763 - 1662))(chr(0b1110101) + chr(116) + chr(0b1100110) + chr(1336 - 1291) + chr(0b1001 + 0o57)), roI3spqORKae(ES5oEprVxulp(b'\xe7\xedL6'), chr(3362 - 3262) + chr(3471 - 3370) + chr(0b1100011) + chr(111) + chr(3936 - 3836) + '\145')(chr(12118 - 12001) + chr(0b101100 + 0o110) + chr(0b1100110) + chr(0b101101) + chr(2987 - 2931))]
if VF4pKOObtlPc([MEyQziOWmxIx == hGd82gLxMaz9 for hGd82gLxMaz9 in OKwTlMo2PNx2]):
GjUZflgb7mHC = roI3spqORKae(ES5oEprVxulp(b'\xae\xe9@e~\xe1G'), chr(0b1100100) + chr(0b1011011 + 0o12) + chr(5767 - 5668) + '\157' + '\x64' + chr(6803 - 6702))(chr(117) + chr(0b1110100) + chr(8685 - 8583) + '\055' + chr(1306 - 1250))
elif VF4pKOObtlPc([MEyQziOWmxIx == hGd82gLxMaz9 for hGd82gLxMaz9 in auVK_CjrsHAJ]):
GjUZflgb7mHC = roI3spqORKae(ES5oEprVxulp(b'\xaf\xed]s~'), chr(7422 - 7322) + chr(0b1100101) + chr(3484 - 3385) + chr(9039 - 8928) + chr(100) + chr(101))(chr(117) + chr(12433 - 12317) + chr(102) + chr(0b101101) + chr(56))
elif VF4pKOObtlPc([MEyQziOWmxIx == hGd82gLxMaz9 for hGd82gLxMaz9 in xhqzYwg0Wee0]):
GjUZflgb7mHC = roI3spqORKae(ES5oEprVxulp(b'\xa8\xeeG'), '\x64' + chr(0b11001 + 0o114) + '\x63' + chr(7722 - 7611) + '\x64' + chr(0b1111 + 0o126))(chr(0b1110100 + 0o1) + chr(116) + '\x66' + chr(359 - 314) + chr(0b110010 + 0o6))
else:
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'\x8f\xe5Bb?\xe9CM=\x0fP\x14\xf2\xc7\xd7\xd8\x83e`GbG\x1e#03\xd0'), '\x64' + chr(0b1100101) + chr(0b1100011) + '\157' + '\144' + chr(0b1100101))(chr(0b110111 + 0o76) + chr(1302 - 1186) + '\x66' + chr(342 - 297) + chr(56)))
ftk9lc7G5FOo = rsFLJp8VAvTb.eoXknH7XUn7m(_pSYqrosNb95, GjUZflgb7mHC)
z3lWtzdILzgZ = _bFWSozA7z0G.DNA(N9zlRy29S1SS(ftk9lc7G5FOo.ftk9lc7G5FOo))
if roI3spqORKae(ftk9lc7G5FOo, roI3spqORKae(ES5oEprVxulp(b'\x9a\xc0xE-\xcd|~\x0f\x03mQ'), chr(0b1100100) + chr(0b1000001 + 0o44) + '\x63' + '\x6f' + chr(100) + chr(3668 - 3567))('\x75' + '\x74' + chr(0b1100110) + '\055' + '\x38')) == roI3spqORKae(ES5oEprVxulp(b'\xe7'), chr(1274 - 1174) + chr(101) + '\143' + chr(3537 - 3426) + '\x64' + chr(101))(chr(0b1110101) + chr(116) + '\146' + chr(1040 - 995) + '\070'):
z3lWtzdILzgZ.SLVB2BPA_mIe = FxZHtXEolYsL
else:
z3lWtzdILzgZ.SLVB2BPA_mIe = ftk9lc7G5FOo.SLVB2BPA_mIe
for gNPUvMsk9RKn in roI3spqORKae(ftk9lc7G5FOo, roI3spqORKae(ES5oEprVxulp(b'\xa8\xf6Vr\\\xc4\x7fg;X@B'), chr(0b1100100) + '\145' + chr(99) + '\x6f' + chr(100) + '\x65')('\165' + '\164' + '\146' + chr(45) + chr(0b110010 + 0o6))):
try:
roI3spqORKae(z3lWtzdILzgZ.features, roI3spqORKae(ES5oEprVxulp(b'\x81\xd8}3g\xe8kP:\x01q\x01'), '\144' + chr(0b1100101) + chr(99) + chr(0b1001101 + 0o42) + chr(7765 - 7665) + '\x65')(chr(117) + chr(2534 - 2418) + chr(102) + '\x2d' + chr(56)))(pcZxUIP73iPt(gNPUvMsk9RKn))
except AtlPdniGDq6Y:
pass
z3lWtzdILzgZ.azxuCKSXk6dv = V3OlOVg98A85(z3lWtzdILzgZ.azxuCKSXk6dv, key=lambda gNPUvMsk9RKn: gNPUvMsk9RKn.KQbHFTcl_LKy)
z3lWtzdILzgZ.z1jrZw1enaK_ = nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b1011 + 0o45), 8)
with DnU3Rq9N5ala(_pSYqrosNb95) as _R8IKF5IwAfX:
QZ2YskiDO0js = _R8IKF5IwAfX.read().LfRrQOxuDvnC()
for JXVFyF8k4nGR in QZ2YskiDO0js:
if JXVFyF8k4nGR == roI3spqORKae(ES5oEprVxulp(b'\xaa\xe5\\dj\xe3MM'), chr(0b10101 + 0o117) + chr(1411 - 1310) + chr(0b10011 + 0o120) + '\x6f' + chr(0b1100100) + chr(0b1010001 + 0o24))('\x75' + '\x74' + chr(102) + chr(45) + chr(0b10000 + 0o50)):
z3lWtzdILzgZ.z1jrZw1enaK_ = nzTpIcepk0o8(chr(845 - 797) + '\x6f' + '\061', 8)
return z3lWtzdILzgZ |
klavinslab/coral | coral/seqio/_dna.py | read_sequencing | def read_sequencing(directory):
'''Read .seq and .abi/.ab1 results files from a dir.
:param directory: Path to directory containing sequencing files.
:type directory: str
:returns: A list of DNA sequences.
:rtype: coral.DNA list
'''
dirfiles = os.listdir(directory)
seq_exts = ['.seq', '.abi', '.ab1']
# Exclude files that aren't sequencing results
seq_paths = [x for x in dirfiles if os.path.splitext(x)[1] in seq_exts]
paths = [os.path.join(directory, x) for x in seq_paths]
sequences = [read_dna(x) for x in paths]
return sequences | python | def read_sequencing(directory):
'''Read .seq and .abi/.ab1 results files from a dir.
:param directory: Path to directory containing sequencing files.
:type directory: str
:returns: A list of DNA sequences.
:rtype: coral.DNA list
'''
dirfiles = os.listdir(directory)
seq_exts = ['.seq', '.abi', '.ab1']
# Exclude files that aren't sequencing results
seq_paths = [x for x in dirfiles if os.path.splitext(x)[1] in seq_exts]
paths = [os.path.join(directory, x) for x in seq_paths]
sequences = [read_dna(x) for x in paths]
return sequences | [
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:param directory: Path to directory containing sequencing files.
:type directory: str
:returns: A list of DNA sequences.
:rtype: coral.DNA list | [
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/seqio/_dna.py#L72-L88 | train | Reads. seq and. ab1 results files from a directory. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8('\x30' + chr(10595 - 10484) + '\062' + chr(51) + chr(2336 - 2284), 0o10), nzTpIcepk0o8(chr(0b1000 + 0o50) + '\157' + chr(0b1001 + 0o52) + '\060' + chr(50), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(49) + chr(54) + '\x36', 48888 - 48880), nzTpIcepk0o8(chr(0b110000) + chr(6630 - 6519) + '\x31' + chr(0b110110) + chr(2154 - 2103), 42529 - 42521), nzTpIcepk0o8(chr(48) + chr(0b1 + 0o156) + chr(390 - 341) + chr(52) + '\064', 0b1000), nzTpIcepk0o8(chr(0b1110 + 0o42) + chr(111) + '\x32' + chr(0b101 + 0o55) + chr(0b111 + 0o53), 6626 - 6618), nzTpIcepk0o8('\x30' + chr(143 - 32) + chr(0b110011) + '\x35' + '\x37', 0b1000), nzTpIcepk0o8('\x30' + '\157' + '\063' + chr(1351 - 1301) + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(53) + chr(2365 - 2315), 11847 - 11839), nzTpIcepk0o8(chr(1766 - 1718) + '\x6f' + '\062' + chr(74 - 19) + '\063', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(3848 - 3737) + '\062' + '\062' + chr(226 - 174), ord("\x08")), nzTpIcepk0o8(chr(1742 - 1694) + chr(409 - 298) + '\061' + '\066' + '\061', 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(643 - 593) + chr(0b110010) + '\060', 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(1596 - 1546) + chr(0b110010) + chr(1592 - 1539), 0o10), nzTpIcepk0o8(chr(0b11001 + 0o27) + '\157' + chr(0b100000 + 0o22) + chr(0b110 + 0o54) + '\x32', 8), nzTpIcepk0o8(chr(48) + chr(111) + '\x31' + chr(2308 - 2255), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(0b100010 + 0o20) + chr(55) + '\x34', 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b10101 + 0o33), 0o10), nzTpIcepk0o8('\x30' + chr(8386 - 8275) + chr(1678 - 1627) + chr(0b1000 + 0o57) + '\060', 0b1000), nzTpIcepk0o8(chr(48) + '\157' + '\x31' + '\063' + chr(55), 0b1000), nzTpIcepk0o8(chr(1193 - 1145) + chr(111) + chr(50) + chr(48) + chr(1228 - 1177), 1761 - 1753), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x32' + '\x31' + '\065', 9214 - 9206), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b1011 + 0o46), 0o10), nzTpIcepk0o8(chr(145 - 97) + chr(7075 - 6964) + chr(0b101001 + 0o10) + '\x31' + '\064', 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(54) + chr(0b11000 + 0o30), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b101110 + 0o4) + '\064' + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(0b101111 + 0o1) + '\157' + chr(0b110001) + chr(0b10111 + 0o36) + chr(53), 7325 - 7317), nzTpIcepk0o8(chr(0b10100 + 0o34) + '\x6f' + '\x33' + chr(0b110001) + '\x32', 6888 - 6880), nzTpIcepk0o8(chr(0b10 + 0o56) + '\x6f' + '\x31' + chr(0b110 + 0o60) + chr(767 - 712), 12501 - 12493), nzTpIcepk0o8('\060' + chr(0b110010 + 0o75) + '\x31' + chr(2355 - 2303) + chr(0b10110 + 0o40), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110011) + '\x30' + '\062', 8), nzTpIcepk0o8('\060' + chr(111) + chr(0b110001) + '\x34' + '\x30', 0b1000), nzTpIcepk0o8(chr(0b111 + 0o51) + chr(11367 - 11256) + '\063' + '\061' + chr(0b110100), 0o10), nzTpIcepk0o8(chr(0b11 + 0o55) + chr(0b1101111) + chr(0b1011 + 0o46) + '\x30' + chr(0b110101), 64463 - 64455), nzTpIcepk0o8(chr(1467 - 1419) + chr(111) + chr(0b110010) + chr(0b110000), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(2392 - 2341) + chr(0b110100) + chr(51), 11216 - 11208), nzTpIcepk0o8(chr(0b1001 + 0o47) + chr(0b1101111) + chr(1913 - 1862) + chr(0b11001 + 0o30), ord("\x08")), nzTpIcepk0o8(chr(0b11010 + 0o26) + chr(111) + chr(0b1 + 0o65) + chr(1727 - 1674), ord("\x08")), nzTpIcepk0o8(chr(1931 - 1883) + '\x6f' + chr(0b110011) + chr(0b110101), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110010) + chr(0b110011) + chr(0b101011 + 0o5), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(0b1011010 + 0o25) + '\065' + '\060', 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xb2'), chr(2006 - 1906) + chr(0b100101 + 0o100) + '\x63' + chr(111) + '\144' + chr(0b1100101))(chr(0b1110101) + chr(116) + chr(3148 - 3046) + chr(0b101101) + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def nyZIiLOR2cwl(InVoWQwNBeGF):
OfnTFkJN06iL = aHUqKstZLeS6.listdir(InVoWQwNBeGF)
h6b3lGaIqtbu = [roI3spqORKae(ES5oEprVxulp(b'\xb2\xb1\x13\x02'), chr(100) + chr(0b1100101) + chr(3760 - 3661) + chr(0b1101111) + chr(0b1100000 + 0o4) + chr(0b1011 + 0o132))(chr(12980 - 12863) + chr(0b1110100) + '\146' + chr(1454 - 1409) + chr(0b111000)), roI3spqORKae(ES5oEprVxulp(b'\xb2\xa3\x14\x1a'), '\144' + chr(101) + '\x63' + '\x6f' + chr(100) + '\145')(chr(0b1110101) + chr(0b101011 + 0o111) + '\146' + '\055' + chr(0b1001 + 0o57)), roI3spqORKae(ES5oEprVxulp(b'\xb2\xa3\x14B'), '\x64' + '\x65' + '\143' + '\157' + '\x64' + chr(3454 - 3353))(chr(5876 - 5759) + '\x74' + chr(102) + chr(45) + chr(0b111000))]
iH1FY7UtHrMn = [bI5jsQ9OkQtj for bI5jsQ9OkQtj in OfnTFkJN06iL if aHUqKstZLeS6.path.nKnjsA3UsXpY(bI5jsQ9OkQtj)[nzTpIcepk0o8(chr(1770 - 1722) + '\x6f' + '\x31', 8)] in h6b3lGaIqtbu]
IQFTbBEt8buE = [aHUqKstZLeS6.path.Y4yM9BcfTCNq(InVoWQwNBeGF, bI5jsQ9OkQtj) for bI5jsQ9OkQtj in iH1FY7UtHrMn]
BBlgUX_QmYPa = [GjGcxrWNqqti(bI5jsQ9OkQtj) for bI5jsQ9OkQtj in IQFTbBEt8buE]
return BBlgUX_QmYPa |
klavinslab/coral | coral/seqio/_dna.py | write_dna | def write_dna(dna, path):
'''Write DNA to a file (genbank or fasta).
:param dna: DNA sequence to write to file
:type dna: coral.DNA
:param path: file path to write. Has to be genbank or fasta file.
:type path: str
'''
# Check if path filetype is valid, remember for later
ext = os.path.splitext(path)[1]
if ext == '.gb' or ext == '.ape':
filetype = 'genbank'
elif ext == '.fa' or ext == '.fasta':
filetype = 'fasta'
else:
raise ValueError('Only genbank or fasta files are supported.')
# Convert features to Biopython form
# Information lost on conversion:
# specificity of feature type
# strandedness
# topology
features = []
for feature in dna.features:
features.append(_coral_to_seqfeature(feature))
# Biopython doesn't like 'None' here
# FIXME: this is a legacy feature - remove?
bio_id = dna.id if hasattr(dna, 'id') else ''
# Maximum length of name is 16
seq = SeqRecord(Seq(str(dna), alphabet=ambiguous_dna), id=bio_id,
name=dna.name[0:16].replace(' ', '_'), features=features,
description=dna.name)
if dna.circular:
seq.annotations['data_file_division'] = 'circular'
else:
seq.annotations['data_file_division'] = 'linear'
if filetype == 'genbank':
SeqIO.write(seq, path, 'genbank')
elif filetype == 'fasta':
SeqIO.write(seq, path, 'fasta') | python | def write_dna(dna, path):
'''Write DNA to a file (genbank or fasta).
:param dna: DNA sequence to write to file
:type dna: coral.DNA
:param path: file path to write. Has to be genbank or fasta file.
:type path: str
'''
# Check if path filetype is valid, remember for later
ext = os.path.splitext(path)[1]
if ext == '.gb' or ext == '.ape':
filetype = 'genbank'
elif ext == '.fa' or ext == '.fasta':
filetype = 'fasta'
else:
raise ValueError('Only genbank or fasta files are supported.')
# Convert features to Biopython form
# Information lost on conversion:
# specificity of feature type
# strandedness
# topology
features = []
for feature in dna.features:
features.append(_coral_to_seqfeature(feature))
# Biopython doesn't like 'None' here
# FIXME: this is a legacy feature - remove?
bio_id = dna.id if hasattr(dna, 'id') else ''
# Maximum length of name is 16
seq = SeqRecord(Seq(str(dna), alphabet=ambiguous_dna), id=bio_id,
name=dna.name[0:16].replace(' ', '_'), features=features,
description=dna.name)
if dna.circular:
seq.annotations['data_file_division'] = 'circular'
else:
seq.annotations['data_file_division'] = 'linear'
if filetype == 'genbank':
SeqIO.write(seq, path, 'genbank')
elif filetype == 'fasta':
SeqIO.write(seq, path, 'fasta') | [
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:param dna: DNA sequence to write to file
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/seqio/_dna.py#L91-L132 | train | Write a DNA sequence to a file. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(1570 - 1522) + '\x6f' + chr(0b110001) + chr(0b110001) + '\x34', 0o10), nzTpIcepk0o8(chr(364 - 316) + chr(0b1101111) + chr(98 - 43) + chr(48), 33803 - 33795), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110010) + chr(0b110011) + chr(0b100100 + 0o14), 5697 - 5689), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b100101 + 0o16) + chr(52), 3240 - 3232), nzTpIcepk0o8('\x30' + chr(5793 - 5682) + '\x33' + chr(0b110110), ord("\x08")), nzTpIcepk0o8(chr(0b10110 + 0o32) + chr(0b1101111) + chr(0b101100 + 0o7) + '\x35' + chr(0b110010), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(53), ord("\x08")), nzTpIcepk0o8(chr(1719 - 1671) + chr(0b1101111) + chr(0b110010) + chr(55) + chr(157 - 103), 2525 - 2517), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110101) + chr(48), 24225 - 24217), nzTpIcepk0o8(chr(1588 - 1540) + chr(0b1101111) + chr(0b10110 + 0o34) + chr(53) + chr(0b110001), 58094 - 58086), nzTpIcepk0o8('\060' + chr(2036 - 1925) + chr(54) + '\065', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(52) + chr(2086 - 2034), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1010001 + 0o36) + chr(49) + chr(703 - 649) + chr(0b101 + 0o57), 7402 - 7394), nzTpIcepk0o8('\x30' + chr(0b10010 + 0o135) + chr(568 - 518) + '\x32' + '\063', 65246 - 65238), nzTpIcepk0o8(chr(2137 - 2089) + '\157' + '\x33' + '\x34' + chr(0b110110), 0b1000), nzTpIcepk0o8('\060' + chr(0b110001 + 0o76) + chr(410 - 361) + chr(53) + '\066', 48087 - 48079), nzTpIcepk0o8('\x30' + chr(111) + '\x33' + chr(48) + '\x30', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(1109 - 1058) + '\063' + chr(0b1100 + 0o47), 30178 - 30170), nzTpIcepk0o8(chr(0b100110 + 0o12) + chr(0b1101111) + chr(51) + chr(0b10000 + 0o43) + '\065', 11411 - 11403), nzTpIcepk0o8(chr(48) + '\157' + chr(0b100011 + 0o20) + '\x33' + chr(1254 - 1206), ord("\x08")), nzTpIcepk0o8(chr(0b0 + 0o60) + '\157' + '\066' + chr(0b100010 + 0o24), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(0b11010 + 0o27) + chr(0b110100) + '\x35', 11979 - 11971), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110011) + chr(300 - 247) + chr(48), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + '\062' + '\x31' + chr(49), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x32' + '\x35' + chr(0b101000 + 0o16), 0o10), nzTpIcepk0o8(chr(48) + '\157' + '\063', 36749 - 36741), nzTpIcepk0o8(chr(0b11010 + 0o26) + chr(111) + '\062' + chr(0b1000 + 0o51) + chr(52), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(49) + chr(1031 - 982) + chr(726 - 674), 8), nzTpIcepk0o8(chr(0b10000 + 0o40) + chr(0b10100 + 0o133) + chr(0b110011) + chr(0b1011 + 0o46) + '\065', 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(1800 - 1749) + chr(0b10 + 0o56) + chr(171 - 121), 31978 - 31970), nzTpIcepk0o8(chr(48) + chr(7381 - 7270) + chr(49) + chr(0b101 + 0o57) + chr(0b1 + 0o60), 0o10), nzTpIcepk0o8('\060' + chr(11979 - 11868) + '\x33' + '\x32' + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(0b11100 + 0o24) + '\x6f' + chr(51) + '\060' + chr(55), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110011) + chr(933 - 885) + '\x34', 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(1117 - 1068) + '\x34' + '\063', 17075 - 17067), nzTpIcepk0o8(chr(0b100010 + 0o16) + chr(0b1101111) + '\x31' + chr(51) + chr(50), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(7192 - 7081) + chr(0b110010) + '\x37' + '\060', 0o10), nzTpIcepk0o8(chr(294 - 246) + chr(111) + chr(0b11011 + 0o30) + chr(50) + '\x30', 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + '\x36' + chr(2682 - 2630), ord("\x08")), nzTpIcepk0o8(chr(1375 - 1327) + '\157' + chr(53) + '\x35', ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b100001 + 0o24) + chr(969 - 921), 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'b'), chr(0b1100100) + chr(9371 - 9270) + chr(0b1100011) + '\157' + '\x64' + chr(101))('\165' + chr(0b1110100) + chr(0b1010110 + 0o20) + '\055' + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def jRZUE7I22W7g(z3lWtzdILzgZ, _pSYqrosNb95):
MEyQziOWmxIx = aHUqKstZLeS6.path.nKnjsA3UsXpY(_pSYqrosNb95)[nzTpIcepk0o8('\x30' + chr(9792 - 9681) + '\x31', ord("\x08"))]
if MEyQziOWmxIx == roI3spqORKae(ES5oEprVxulp(b'b_\xfa'), '\144' + chr(0b1100101) + '\x63' + chr(0b1101111) + chr(100) + chr(0b1100101))(chr(9523 - 9406) + chr(0b1110100) + chr(102) + '\x2d' + chr(0b111000)) or MEyQziOWmxIx == roI3spqORKae(ES5oEprVxulp(b'bY\xe8y'), chr(7508 - 7408) + '\145' + chr(7480 - 7381) + chr(0b1000101 + 0o52) + '\x64' + chr(101))(chr(2868 - 2751) + chr(0b1110100) + '\146' + '\x2d' + chr(0b111000)):
H8nWYcuQKiIE = roI3spqORKae(ES5oEprVxulp(b'+]\xf6~\x7f\x84n'), chr(0b1100100) + chr(0b1000110 + 0o37) + '\x63' + chr(0b111000 + 0o67) + '\144' + chr(0b1100101))(chr(0b1110101) + chr(0b1110010 + 0o2) + chr(102) + chr(0b10110 + 0o27) + '\070')
elif MEyQziOWmxIx == roI3spqORKae(ES5oEprVxulp(b'b^\xf9'), chr(8545 - 8445) + '\145' + '\143' + chr(111) + chr(0b1011 + 0o131) + '\x65')(chr(0b1011111 + 0o26) + chr(0b1110100) + chr(102) + '\055' + chr(0b1110 + 0o52)) or MEyQziOWmxIx == roI3spqORKae(ES5oEprVxulp(b'b^\xf9oj\x8b'), '\144' + chr(101) + chr(8136 - 8037) + chr(111) + chr(0b111100 + 0o50) + chr(1031 - 930))('\165' + chr(6110 - 5994) + '\x66' + chr(0b101101) + chr(0b0 + 0o70)):
H8nWYcuQKiIE = roI3spqORKae(ES5oEprVxulp(b'*Y\xebh\x7f'), '\144' + '\x65' + '\143' + chr(0b1101111) + '\x64' + chr(0b1100101))(chr(4619 - 4502) + '\164' + '\x66' + '\055' + chr(56))
else:
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'\x03V\xf4e>\x8d`\xd0J\xc8[OT\xfc\x94N\xa6\xba\xae\xacWE\x8e\xe0\xc2f\xffl\xac\xb0\x04\xf7\xb4\xb1\x13*\xd7\xa2@H(\x16'), chr(100) + chr(0b1010111 + 0o16) + '\143' + '\x6f' + chr(0b1000011 + 0o41) + chr(9198 - 9097))(chr(0b1110101) + chr(393 - 277) + '\146' + chr(0b100111 + 0o6) + chr(0b101111 + 0o11)))
azxuCKSXk6dv = []
for gNPUvMsk9RKn in roI3spqORKae(z3lWtzdILzgZ, roI3spqORKae(ES5oEprVxulp(b'-B\xe0i]\xa1V\xe6C\x9fQR'), chr(0b1000011 + 0o41) + chr(9891 - 9790) + chr(99) + chr(0b1101111) + '\x64' + chr(0b110000 + 0o65))(chr(117) + chr(0b110110 + 0o76) + chr(7195 - 7093) + chr(45) + '\070')):
roI3spqORKae(azxuCKSXk6dv, roI3spqORKae(ES5oEprVxulp(b'\x04l\xcb(f\x8dB\xd1B\xc6`\x11'), chr(0b100101 + 0o77) + chr(8301 - 8200) + chr(4899 - 4800) + chr(0b1101 + 0o142) + chr(100) + '\x65')('\x75' + '\164' + '\146' + '\x2d' + chr(0b111000)))(nriuRuGxKSjY(gNPUvMsk9RKn))
gghOkBDeRcJV = z3lWtzdILzgZ.maLnLg8O5zPT if dRKdVnHPFq7C(z3lWtzdILzgZ, roI3spqORKae(ES5oEprVxulp(b'%\\'), '\144' + chr(0b101110 + 0o67) + chr(0b1100011) + chr(111) + '\x64' + chr(101))(chr(117) + chr(0b1110100) + '\x66' + '\055' + chr(1043 - 987))) else roI3spqORKae(ES5oEprVxulp(b''), '\x64' + '\145' + chr(99) + '\157' + chr(0b1100 + 0o130) + '\145')('\x75' + chr(116) + chr(2524 - 2422) + chr(0b100101 + 0o10) + chr(56))
ftk9lc7G5FOo = D9Fpf4AVz1sV(XJ082vRDvvgH(N9zlRy29S1SS(z3lWtzdILzgZ), alphabet=_ObRtTO8h_ED), id=gghOkBDeRcJV, name=z3lWtzdILzgZ.name[nzTpIcepk0o8(chr(966 - 918) + chr(0b1101111) + chr(2218 - 2170), ord("\x08")):nzTpIcepk0o8('\060' + chr(9891 - 9780) + chr(0b1011 + 0o47) + '\060', 0o10)].E91dbqOZXBpJ(roI3spqORKae(ES5oEprVxulp(b'l'), chr(900 - 800) + chr(0b1100001 + 0o4) + '\x63' + chr(0b111101 + 0o62) + '\x64' + chr(0b100011 + 0o102))(chr(0b101101 + 0o110) + '\x74' + '\146' + chr(1618 - 1573) + chr(0b110000 + 0o10)), roI3spqORKae(ES5oEprVxulp(b'\x13'), '\x64' + chr(0b1100101) + chr(99) + '\x6f' + chr(0b1100100) + '\x65')(chr(0b1110101) + chr(5766 - 5650) + '\x66' + chr(0b101101) + chr(0b11001 + 0o37))), features=azxuCKSXk6dv, description=z3lWtzdILzgZ.SLVB2BPA_mIe)
if roI3spqORKae(z3lWtzdILzgZ, roI3spqORKae(ES5oEprVxulp(b'6\t\xf2nD\x9d4\xdbF\xc8~{'), chr(100) + chr(101) + chr(0b1011001 + 0o12) + '\157' + chr(0b1100100) + chr(7493 - 7392))(chr(0b110 + 0o157) + chr(13129 - 13013) + chr(8179 - 8077) + chr(0b101101) + '\070')):
ftk9lc7G5FOo.jHRyQfcmt4BG[roI3spqORKae(ES5oEprVxulp(b'(Y\xec}A\x8cl\xd2M\xf6QM\x02\xfa\x95\x07\xaf\xb5'), chr(1194 - 1094) + '\x65' + '\x63' + chr(1454 - 1343) + chr(0b100100 + 0o100) + chr(0b1100101))(chr(117) + chr(527 - 411) + '\x66' + '\x2d' + chr(56))] = roI3spqORKae(ES5oEprVxulp(b'/Q\xea\x7fk\x86d\xcc'), '\144' + chr(0b101111 + 0o66) + '\143' + chr(5278 - 5167) + chr(100) + '\x65')('\165' + '\x74' + chr(102) + chr(0b1101 + 0o40) + chr(2507 - 2451))
else:
ftk9lc7G5FOo.jHRyQfcmt4BG[roI3spqORKae(ES5oEprVxulp(b'(Y\xec}A\x8cl\xd2M\xf6QM\x02\xfa\x95\x07\xaf\xb5'), chr(1433 - 1333) + chr(101) + chr(99) + chr(3348 - 3237) + chr(0b100101 + 0o77) + chr(0b1100101))(chr(0b1001001 + 0o54) + chr(0b1001011 + 0o51) + chr(102) + '\x2d' + chr(0b111000))] = roI3spqORKae(ES5oEprVxulp(b' Q\xf6y\x7f\x98'), chr(0b1100100) + chr(6573 - 6472) + '\x63' + chr(0b1101111) + chr(0b1011000 + 0o14) + chr(101))(chr(0b1110101) + chr(116) + '\x66' + chr(0b1110 + 0o37) + chr(0b111000))
if H8nWYcuQKiIE == roI3spqORKae(ES5oEprVxulp(b'+]\xf6~\x7f\x84n'), chr(0b11011 + 0o111) + chr(101) + chr(4015 - 3916) + '\x6f' + chr(0b1011010 + 0o12) + chr(0b1100101))(chr(0b1110101) + chr(4441 - 4325) + chr(0b1000100 + 0o42) + chr(0b101101) + chr(0b111000)):
roI3spqORKae(rsFLJp8VAvTb, roI3spqORKae(ES5oEprVxulp(b'!T\xa8tv\x9as\x8fd\xd9D\x16'), chr(7018 - 6918) + chr(0b1100101) + chr(0b111111 + 0o44) + chr(0b1101111) + chr(8171 - 8071) + chr(0b100000 + 0o105))(chr(6243 - 6126) + '\x74' + '\x66' + chr(45) + chr(0b10 + 0o66)))(ftk9lc7G5FOo, _pSYqrosNb95, roI3spqORKae(ES5oEprVxulp(b'+]\xf6~\x7f\x84n'), chr(0b1100100) + '\x65' + chr(0b11111 + 0o104) + '\x6f' + '\x64' + '\x65')(chr(0b1110010 + 0o3) + chr(0b1110100) + chr(102) + '\055' + chr(0b111000)))
elif H8nWYcuQKiIE == roI3spqORKae(ES5oEprVxulp(b'*Y\xebh\x7f'), chr(5373 - 5273) + '\145' + chr(0b10011 + 0o120) + chr(459 - 348) + chr(6174 - 6074) + chr(101))('\165' + '\164' + '\x66' + '\x2d' + chr(0b110100 + 0o4)):
roI3spqORKae(rsFLJp8VAvTb, roI3spqORKae(ES5oEprVxulp(b'!T\xa8tv\x9as\x8fd\xd9D\x16'), chr(0b1100100) + '\x65' + chr(3095 - 2996) + '\157' + chr(0b1100100) + chr(0b1011100 + 0o11))(chr(2953 - 2836) + '\164' + chr(102) + '\x2d' + '\070'))(ftk9lc7G5FOo, _pSYqrosNb95, roI3spqORKae(ES5oEprVxulp(b'*Y\xebh\x7f'), chr(100) + chr(101) + chr(178 - 79) + '\x6f' + chr(0b1100100) + '\145')(chr(3551 - 3434) + chr(116) + chr(102) + chr(0b100000 + 0o15) + '\070')) |
klavinslab/coral | coral/seqio/_dna.py | write_primers | def write_primers(primer_list, path, names=None, notes=None):
'''Write a list of primers out to a csv file. The first three columns are
compatible with the current IDT order form (name, sequence, notes). By
default there are no notes, which is an optional parameter.
:param primer_list: A list of primers.
:type primer_list: coral.Primer list
:param path: A path to the csv you want to write.
:type path: str
:param names: A list of strings to name each oligo. Must be the same length
as the primer_list.
:type names: str list
:param notes: A list of strings to provide a note for each oligo. Must be
the same length as the primer_list.
:type notes: str list
'''
# Check for notes and names having the right length, apply them to primers
if names is not None:
if len(names) != len(primer_list):
names_msg = 'Mismatch in number of notes and primers.'
raise PrimerAnnotationError(names_msg)
for i, name in enumerate(names):
primer_list[i].name = name
if notes is not None:
if len(notes) != len(primer_list):
notes_msg = 'Mismatch in number of notes and primers.'
raise PrimerAnnotationError(notes_msg)
for i, note in enumerate(notes):
primer_list[i].note = note
# Write to csv
with open(path, 'w') as csv_file:
writer = csv.writer(csv_file)
writer.writerow(['name', 'sequence', 'notes'])
for primer in primer_list:
string_rep = str(primer.overhang).lower() + str(primer.anneal)
writer.writerow([primer.name, string_rep, primer.note]) | python | def write_primers(primer_list, path, names=None, notes=None):
'''Write a list of primers out to a csv file. The first three columns are
compatible with the current IDT order form (name, sequence, notes). By
default there are no notes, which is an optional parameter.
:param primer_list: A list of primers.
:type primer_list: coral.Primer list
:param path: A path to the csv you want to write.
:type path: str
:param names: A list of strings to name each oligo. Must be the same length
as the primer_list.
:type names: str list
:param notes: A list of strings to provide a note for each oligo. Must be
the same length as the primer_list.
:type notes: str list
'''
# Check for notes and names having the right length, apply them to primers
if names is not None:
if len(names) != len(primer_list):
names_msg = 'Mismatch in number of notes and primers.'
raise PrimerAnnotationError(names_msg)
for i, name in enumerate(names):
primer_list[i].name = name
if notes is not None:
if len(notes) != len(primer_list):
notes_msg = 'Mismatch in number of notes and primers.'
raise PrimerAnnotationError(notes_msg)
for i, note in enumerate(notes):
primer_list[i].note = note
# Write to csv
with open(path, 'w') as csv_file:
writer = csv.writer(csv_file)
writer.writerow(['name', 'sequence', 'notes'])
for primer in primer_list:
string_rep = str(primer.overhang).lower() + str(primer.anneal)
writer.writerow([primer.name, string_rep, primer.note]) | [
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:param primer_list: A list of primers.
:type primer_list: coral.Primer list
:param path: A path to the csv you want to write.
:type path: str
:param names: A list of strings to name each oligo. Must be the same length
as the primer_list.
:type names: str list
:param notes: A list of strings to provide a note for each oligo. Must be
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... | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/seqio/_dna.py#L135-L172 | train | Write a list of primers out to a csv file. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110010) + '\066' + chr(2068 - 2018), 0o10), nzTpIcepk0o8(chr(396 - 348) + chr(0b1101011 + 0o4) + chr(0b110101) + chr(0b10 + 0o56), ord("\x08")), nzTpIcepk0o8(chr(593 - 545) + '\x6f' + '\063' + '\062' + chr(51), 43174 - 43166), nzTpIcepk0o8('\060' + '\157' + '\062' + '\060' + chr(0b110 + 0o52), 30611 - 30603), nzTpIcepk0o8(chr(1977 - 1929) + chr(5597 - 5486) + chr(0b0 + 0o64) + '\x31', 19789 - 19781), nzTpIcepk0o8(chr(1212 - 1164) + chr(111) + chr(0b110001) + '\x35' + chr(0b1110 + 0o50), 39017 - 39009), nzTpIcepk0o8('\x30' + '\x6f' + '\x33' + '\x37' + chr(1421 - 1369), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110111) + '\060', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(12063 - 11952) + chr(0b110001) + '\067', ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + '\062' + chr(0b11100 + 0o33) + '\064', 0b1000), nzTpIcepk0o8(chr(1578 - 1530) + '\x6f' + chr(49) + chr(0b110100), 0o10), nzTpIcepk0o8(chr(48) + chr(6577 - 6466) + '\x33' + '\x32' + chr(49), 0b1000), nzTpIcepk0o8(chr(513 - 465) + chr(0b10010 + 0o135) + '\063' + chr(0b110001) + '\061', 0b1000), nzTpIcepk0o8(chr(48) + '\157' + '\x33' + chr(55) + '\066', 0b1000), nzTpIcepk0o8(chr(1007 - 959) + chr(0b1101111) + chr(53), 45342 - 45334), nzTpIcepk0o8('\x30' + chr(4893 - 4782) + '\x32' + chr(1941 - 1890), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(0b100010 + 0o21) + chr(0b10011 + 0o40) + chr(0b110010), 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(0b100 + 0o56) + '\x36' + chr(49), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110001) + chr(53) + chr(0b1011 + 0o50), 0o10), nzTpIcepk0o8(chr(48) + chr(2393 - 2282) + chr(1337 - 1288) + chr(0b100000 + 0o20) + chr(2294 - 2243), 26770 - 26762), nzTpIcepk0o8(chr(0b10000 + 0o40) + '\157' + chr(84 - 33) + chr(0b100010 + 0o24) + chr(0b110001), 38319 - 38311), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(1185 - 1135) + chr(408 - 358) + chr(54), 0b1000), nzTpIcepk0o8(chr(0b1100 + 0o44) + chr(0b1011010 + 0o25) + chr(0b101001 + 0o12) + chr(1440 - 1390), 20507 - 20499), nzTpIcepk0o8(chr(0b100 + 0o54) + chr(3933 - 3822) + chr(1585 - 1531) + chr(0b110100), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(51) + '\064', 0o10), nzTpIcepk0o8('\x30' + chr(111) + '\063' + '\x34', 8), nzTpIcepk0o8(chr(48) + '\157' + '\x33' + '\062', 8), nzTpIcepk0o8('\060' + chr(2300 - 2189) + chr(50) + chr(0b101 + 0o56) + '\065', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(54) + chr(0b110111), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x34' + chr(0b10111 + 0o34), 0o10), nzTpIcepk0o8(chr(48) + '\157' + '\x31' + chr(50) + '\x30', 0o10), nzTpIcepk0o8(chr(1888 - 1840) + chr(111) + '\x33' + '\x36', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(1759 - 1709) + chr(1412 - 1360) + chr(53), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1100 + 0o143) + '\063' + '\065', 0o10), nzTpIcepk0o8(chr(48) + '\157' + '\x32' + chr(0b110110) + '\066', 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(1902 - 1853) + chr(50) + chr(0b110000), 8), nzTpIcepk0o8(chr(0b100 + 0o54) + chr(9295 - 9184) + chr(1199 - 1150) + chr(0b110000) + chr(0b1001 + 0o56), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\065' + chr(0b10 + 0o57), 0o10), nzTpIcepk0o8('\060' + '\157' + '\x31' + chr(616 - 568) + '\067', 8), nzTpIcepk0o8('\060' + '\157' + chr(0b110010), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + chr(111) + chr(2761 - 2708) + chr(1607 - 1559), 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x9c'), chr(8582 - 8482) + chr(9089 - 8988) + chr(5763 - 5664) + '\157' + chr(100) + chr(7488 - 7387))('\165' + chr(892 - 776) + chr(0b1100110) + '\055' + chr(2066 - 2010)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def UJJ1nJZbnLGE(aB0brEPgy33p, _pSYqrosNb95, TMMrjsiU6eED=None, oExJw5cc1At_=None):
if TMMrjsiU6eED is not None:
if ftfygxgFas5X(TMMrjsiU6eED) != ftfygxgFas5X(aB0brEPgy33p):
qkyIHHK1o6I7 = roI3spqORKae(ES5oEprVxulp(b'\xffA\xa0\xed@\x1a\x9fP/\xd5b\xf1\xa7\x8bhq\xbf\xc3K,\x97\xb6t[hyi\xbdVM4>\xd5o\xdf="[4,'), '\144' + '\x65' + '\x63' + chr(111) + chr(7148 - 7048) + chr(0b1100101))('\x75' + chr(0b1001101 + 0o47) + '\146' + '\x2d' + chr(0b111000))
raise dalHqZHW_Z2b(qkyIHHK1o6I7)
for (ZlbFMSG8gCoF, SLVB2BPA_mIe) in _kV_Bomx8PZ4(TMMrjsiU6eED):
aB0brEPgy33p[ZlbFMSG8gCoF].SLVB2BPA_mIe = SLVB2BPA_mIe
if oExJw5cc1At_ is not None:
if ftfygxgFas5X(oExJw5cc1At_) != ftfygxgFas5X(aB0brEPgy33p):
Tk4py5t_lCFI = roI3spqORKae(ES5oEprVxulp(b'\xffA\xa0\xed@\x1a\x9fP/\xd5b\xf1\xa7\x8bhq\xbf\xc3K,\x97\xb6t[hyi\xbdVM4>\xd5o\xdf="[4,'), chr(0b111000 + 0o54) + chr(101) + chr(99) + chr(1298 - 1187) + chr(0b1010011 + 0o21) + chr(101))(chr(0b1110101) + chr(116) + chr(0b11101 + 0o111) + chr(45) + chr(0b110000 + 0o10))
raise dalHqZHW_Z2b(Tk4py5t_lCFI)
for (ZlbFMSG8gCoF, dVamRRpm0eOX) in _kV_Bomx8PZ4(oExJw5cc1At_):
aB0brEPgy33p[ZlbFMSG8gCoF].dVamRRpm0eOX = dVamRRpm0eOX
with DnU3Rq9N5ala(_pSYqrosNb95, roI3spqORKae(ES5oEprVxulp(b'\xc5'), chr(0b111100 + 0o50) + chr(0b1000111 + 0o36) + chr(0b1100011) + chr(111) + chr(0b1100100) + '\145')(chr(0b111001 + 0o74) + chr(0b110111 + 0o75) + chr(0b1100110) + '\x2d' + '\070')) as uDVNh1KvXcj5:
OobcaiV2mshj = nwjlz70oVoys.OobcaiV2mshj(uDVNh1KvXcj5)
roI3spqORKae(OobcaiV2mshj, roI3spqORKae(ES5oEprVxulp(b'\xc5Z\xba\xf4D\x1c\x93O'), chr(100) + chr(101) + '\x63' + chr(5518 - 5407) + chr(0b1001000 + 0o34) + '\x65')(chr(0b1110000 + 0o5) + '\164' + chr(0b1000 + 0o136) + '\x2d' + chr(56)))([roI3spqORKae(ES5oEprVxulp(b'\xdcI\xbe\xe5'), chr(100) + chr(0b1100101) + '\x63' + chr(5848 - 5737) + '\x64' + chr(101))(chr(0b11100 + 0o131) + '\164' + chr(2204 - 2102) + chr(45) + chr(0b1000 + 0o60)), roI3spqORKae(ES5oEprVxulp(b'\xc1M\xa2\xf5D\x00\x9f]'), chr(0b1100100) + chr(0b1100101) + chr(0b1100011) + chr(0b1101111) + chr(100) + chr(5617 - 5516))('\x75' + '\164' + chr(0b11010 + 0o114) + '\x2d' + chr(56)), roI3spqORKae(ES5oEprVxulp(b'\xdcG\xa7\xe5R'), '\144' + '\145' + '\143' + chr(7313 - 7202) + chr(100) + chr(101))('\x75' + chr(12578 - 12462) + '\146' + chr(0b101000 + 0o5) + '\x38')])
for thHp9mlDSVMt in aB0brEPgy33p:
k1zEX1tvaod1 = N9zlRy29S1SS(thHp9mlDSVMt.overhang).Xn8ENWMZdIRt() + N9zlRy29S1SS(thHp9mlDSVMt.anneal)
roI3spqORKae(OobcaiV2mshj, roI3spqORKae(ES5oEprVxulp(b'\xc5Z\xba\xf4D\x1c\x93O'), chr(100) + '\145' + chr(0b1100011) + chr(0b101010 + 0o105) + chr(100) + '\x65')('\x75' + chr(0b1110100) + chr(0b100100 + 0o102) + '\055' + chr(821 - 765)))([roI3spqORKae(thHp9mlDSVMt, roI3spqORKae(ES5oEprVxulp(b'\xe1d\x85\xc2\x13,\xacyP\xd1E\xb4'), chr(1076 - 976) + '\x65' + chr(0b1100001 + 0o2) + chr(4469 - 4358) + chr(2198 - 2098) + chr(101))('\165' + chr(0b1110100) + '\146' + '\055' + '\070')), k1zEX1tvaod1, roI3spqORKae(thHp9mlDSVMt, roI3spqORKae(ES5oEprVxulp(b'\xd6~\xb2\xeds<\x8cU?\xd9C\x89'), '\144' + chr(0b1100101) + chr(0b100010 + 0o101) + '\157' + '\x64' + chr(5635 - 5534))('\165' + chr(0b1000000 + 0o64) + '\x66' + chr(0b101101 + 0o0) + chr(0b111000)))]) |
klavinslab/coral | coral/seqio/_dna.py | _process_feature_type | def _process_feature_type(feature_type, bio_to_coral=True):
'''Translate genbank feature types into usable ones (currently identical).
The feature table is derived from the official genbank spec (gbrel.txt)
available at http://www.insdc.org/documents/feature-table
:param feature_type: feature to convert
:type feature_type: str
:param bio_to_coral: from coral to Biopython (True) or the other direction
(False)
:param bio_to_coral: bool
:returns: coral version of genbank feature_type, or vice-versa.
:rtype: str
'''
err_msg = 'Unrecognized feature type: {}'.format(feature_type)
if bio_to_coral:
try:
name = coral.constants.genbank.TO_CORAL[feature_type]
except KeyError:
raise ValueError(err_msg)
else:
try:
name = coral.constants.genbank.TO_BIO[feature_type]
except KeyError:
raise ValueError(err_msg)
return name | python | def _process_feature_type(feature_type, bio_to_coral=True):
'''Translate genbank feature types into usable ones (currently identical).
The feature table is derived from the official genbank spec (gbrel.txt)
available at http://www.insdc.org/documents/feature-table
:param feature_type: feature to convert
:type feature_type: str
:param bio_to_coral: from coral to Biopython (True) or the other direction
(False)
:param bio_to_coral: bool
:returns: coral version of genbank feature_type, or vice-versa.
:rtype: str
'''
err_msg = 'Unrecognized feature type: {}'.format(feature_type)
if bio_to_coral:
try:
name = coral.constants.genbank.TO_CORAL[feature_type]
except KeyError:
raise ValueError(err_msg)
else:
try:
name = coral.constants.genbank.TO_BIO[feature_type]
except KeyError:
raise ValueError(err_msg)
return name | [
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"consta... | Translate genbank feature types into usable ones (currently identical).
The feature table is derived from the official genbank spec (gbrel.txt)
available at http://www.insdc.org/documents/feature-table
:param feature_type: feature to convert
:type feature_type: str
:param bio_to_coral: from coral to Biopython (True) or the other direction
(False)
:param bio_to_coral: bool
:returns: coral version of genbank feature_type, or vice-versa.
:rtype: str | [
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"http",... | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/seqio/_dna.py#L175-L201 | train | Translate genbank feature types into usable ones. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8('\x30' + chr(111) + chr(0b10000 + 0o43) + '\x37' + chr(0b10111 + 0o35), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(0b11 + 0o56) + '\x34' + chr(54), 36687 - 36679), nzTpIcepk0o8('\x30' + '\157' + chr(270 - 221) + chr(55) + '\x31', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + '\061' + chr(50) + chr(48), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(49) + '\066', 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(0b10001 + 0o42) + '\066' + chr(0b110010), 0o10), nzTpIcepk0o8('\060' + chr(0b101101 + 0o102) + chr(0b1110 + 0o45) + '\065' + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(999 - 947), ord("\x08")), nzTpIcepk0o8(chr(329 - 281) + '\157' + '\063' + chr(0b10010 + 0o42) + chr(50), 51504 - 51496), nzTpIcepk0o8(chr(0b101011 + 0o5) + chr(111) + '\x32' + chr(0b110011) + '\x37', 0b1000), nzTpIcepk0o8(chr(1053 - 1005) + chr(11526 - 11415) + chr(52) + chr(0b110100), ord("\x08")), nzTpIcepk0o8('\x30' + chr(7539 - 7428) + chr(0b110110) + chr(289 - 240), 55177 - 55169), nzTpIcepk0o8(chr(1263 - 1215) + chr(0b1101111) + chr(0b110100), 8), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b100011 + 0o16) + chr(53) + chr(55), 13878 - 13870), nzTpIcepk0o8(chr(0b110000 + 0o0) + chr(0b1101111) + '\x33' + chr(0b100110 + 0o13), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(1597 - 1546) + chr(0b100111 + 0o12), 8), nzTpIcepk0o8(chr(0b10011 + 0o35) + '\157' + '\063' + '\x35' + chr(1584 - 1530), 0o10), nzTpIcepk0o8('\060' + chr(111) + '\x31' + '\063' + chr(517 - 462), 0o10), nzTpIcepk0o8(chr(988 - 940) + chr(9140 - 9029) + chr(0b101101 + 0o11) + chr(0b110010), 1901 - 1893), nzTpIcepk0o8('\060' + chr(111) + chr(0b1111 + 0o42) + chr(0b110010) + chr(55), 0o10), nzTpIcepk0o8(chr(0b10100 + 0o34) + chr(0b100001 + 0o116) + '\061' + chr(2314 - 2264), 0b1000), nzTpIcepk0o8(chr(1172 - 1124) + '\x6f' + '\062' + chr(397 - 343) + chr(49), 27697 - 27689), nzTpIcepk0o8('\060' + chr(111) + chr(51) + '\x36' + '\060', 0b1000), nzTpIcepk0o8(chr(0b101111 + 0o1) + '\157' + chr(0b1101 + 0o45) + chr(2384 - 2332), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(1644 - 1594) + chr(52) + chr(1861 - 1807), 0b1000), nzTpIcepk0o8(chr(2008 - 1960) + '\157' + chr(0b110001) + chr(0b110101) + chr(0b110111), 8), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110010) + chr(0b110101) + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + '\061' + chr(0b100010 + 0o23), 16099 - 16091), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110011) + '\065' + chr(0b1100 + 0o53), 0b1000), nzTpIcepk0o8(chr(0b11 + 0o55) + chr(111) + chr(50) + chr(0b110011) + '\067', 8), nzTpIcepk0o8('\060' + '\157' + '\x32' + chr(51) + '\064', 0o10), nzTpIcepk0o8(chr(2130 - 2082) + '\157' + '\063' + chr(0b110100), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + '\x32' + chr(249 - 197), 8), nzTpIcepk0o8(chr(2181 - 2133) + chr(689 - 578) + chr(0b10000 + 0o42) + chr(0b1111 + 0o42) + chr(90 - 42), 0b1000), nzTpIcepk0o8(chr(1331 - 1283) + '\157' + '\061' + chr(1692 - 1644) + '\067', 0b1000), nzTpIcepk0o8(chr(48) + chr(270 - 159) + chr(1981 - 1930) + '\x30' + chr(0b10011 + 0o40), ord("\x08")), nzTpIcepk0o8(chr(0b11 + 0o55) + '\x6f' + chr(50) + chr(0b110000) + chr(2479 - 2424), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b101 + 0o56) + chr(783 - 733), 0b1000), nzTpIcepk0o8(chr(0b11000 + 0o30) + chr(0b1101111) + '\x33' + '\062' + '\x33', 0b1000), nzTpIcepk0o8(chr(2253 - 2205) + chr(0b1101111) + '\x31' + chr(0b110001) + chr(0b110110), 2362 - 2354)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + chr(0b1011011 + 0o24) + chr(2575 - 2522) + '\060', ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xd2'), chr(0b1011110 + 0o6) + chr(559 - 458) + chr(7674 - 7575) + '\157' + chr(0b1100100) + chr(0b1100101))(chr(11616 - 11499) + chr(116) + chr(102) + chr(45) + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def tektRgLlFYJo(kPnfwq1xBNHs, gTYEMrXFVGpc=nzTpIcepk0o8(chr(0b110000) + chr(2923 - 2812) + chr(0b1001 + 0o50), ord("\x08"))):
rz25atpOjIy0 = roI3spqORKae(ES5oEprVxulp(b'\xa9\x08\x0b5m\x9d\x8bj\x8b\xe5AU$\t|x\x9a*@2*\xc5\x89d\xc3U\x8fv\x92'), chr(0b1100100) + chr(101) + chr(5380 - 5281) + chr(0b1101111) + '\x64' + '\145')(chr(0b10101 + 0o140) + '\x74' + '\146' + chr(45) + '\070').q33KG3foQ_CJ(kPnfwq1xBNHs)
if gTYEMrXFVGpc:
try:
SLVB2BPA_mIe = _bFWSozA7z0G.constants.genbank.TO_CORAL[kPnfwq1xBNHs]
except knUxyjfq07F9:
raise WbNHlDKpyPtQ(rz25atpOjIy0)
else:
try:
SLVB2BPA_mIe = _bFWSozA7z0G.constants.genbank.TO_BIO[kPnfwq1xBNHs]
except knUxyjfq07F9:
raise WbNHlDKpyPtQ(rz25atpOjIy0)
return SLVB2BPA_mIe |
klavinslab/coral | coral/seqio/_dna.py | _seqfeature_to_coral | def _seqfeature_to_coral(feature):
'''Convert a Biopython SeqFeature to a coral.Feature.
:param feature: Biopython SeqFeature
:type feature: Bio.SeqFeature
'''
# Some genomic sequences don't have a label attribute
# TODO: handle genomic cases differently than others. Some features lack
# a label but should still be incorporated somehow.
qualifiers = feature.qualifiers
if 'label' in qualifiers:
feature_name = qualifiers['label'][0]
elif 'locus_tag' in qualifiers:
feature_name = qualifiers['locus_tag'][0]
else:
raise FeatureNameError('Unrecognized feature name')
# Features with gaps are special, require looking at subfeatures
# Assumption: subfeatures are never more than one level deep
if feature.location_operator == 'join':
# Feature has gaps. Have to figure out start/stop from subfeatures,
# calculate gap indices. A nested feature model may be required
# eventually.
# Reorder the sub_feature list by start location
# Assumption: none of the subfeatures overlap so the last entry in
# the reordered list also has the final stop point of the feature.
# FIXME: Getting a deprecation warning about using sub_features
# instead of feature.location being a CompoundFeatureLocation
reordered = sorted(feature.location.parts,
key=lambda location: location.start)
starts = [int(location.start) for location in reordered]
stops = [int(location.end) for location in reordered]
feature_start = starts.pop(0)
feature_stop = stops.pop(-1)
starts = [start - feature_start for start in starts]
stops = [stop - feature_start for stop in stops]
feature_gaps = list(zip(stops, starts))
else:
# Feature doesn't have gaps. Ignore subfeatures.
feature_start = int(feature.location.start)
feature_stop = int(feature.location.end)
feature_gaps = []
feature_type = _process_feature_type(feature.type)
if feature.location.strand == -1:
feature_strand = 1
else:
feature_strand = 0
if 'gene' in qualifiers:
gene = qualifiers['gene']
else:
gene = []
if 'locus_tag' in qualifiers:
locus_tag = qualifiers['locus_tag']
else:
locus_tag = []
coral_feature = coral.Feature(feature_name, feature_start,
feature_stop, feature_type,
gene=gene, locus_tag=locus_tag,
qualifiers=qualifiers,
strand=feature_strand,
gaps=feature_gaps)
return coral_feature | python | def _seqfeature_to_coral(feature):
'''Convert a Biopython SeqFeature to a coral.Feature.
:param feature: Biopython SeqFeature
:type feature: Bio.SeqFeature
'''
# Some genomic sequences don't have a label attribute
# TODO: handle genomic cases differently than others. Some features lack
# a label but should still be incorporated somehow.
qualifiers = feature.qualifiers
if 'label' in qualifiers:
feature_name = qualifiers['label'][0]
elif 'locus_tag' in qualifiers:
feature_name = qualifiers['locus_tag'][0]
else:
raise FeatureNameError('Unrecognized feature name')
# Features with gaps are special, require looking at subfeatures
# Assumption: subfeatures are never more than one level deep
if feature.location_operator == 'join':
# Feature has gaps. Have to figure out start/stop from subfeatures,
# calculate gap indices. A nested feature model may be required
# eventually.
# Reorder the sub_feature list by start location
# Assumption: none of the subfeatures overlap so the last entry in
# the reordered list also has the final stop point of the feature.
# FIXME: Getting a deprecation warning about using sub_features
# instead of feature.location being a CompoundFeatureLocation
reordered = sorted(feature.location.parts,
key=lambda location: location.start)
starts = [int(location.start) for location in reordered]
stops = [int(location.end) for location in reordered]
feature_start = starts.pop(0)
feature_stop = stops.pop(-1)
starts = [start - feature_start for start in starts]
stops = [stop - feature_start for stop in stops]
feature_gaps = list(zip(stops, starts))
else:
# Feature doesn't have gaps. Ignore subfeatures.
feature_start = int(feature.location.start)
feature_stop = int(feature.location.end)
feature_gaps = []
feature_type = _process_feature_type(feature.type)
if feature.location.strand == -1:
feature_strand = 1
else:
feature_strand = 0
if 'gene' in qualifiers:
gene = qualifiers['gene']
else:
gene = []
if 'locus_tag' in qualifiers:
locus_tag = qualifiers['locus_tag']
else:
locus_tag = []
coral_feature = coral.Feature(feature_name, feature_start,
feature_stop, feature_type,
gene=gene, locus_tag=locus_tag,
qualifiers=qualifiers,
strand=feature_strand,
gaps=feature_gaps)
return coral_feature | [
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"Feature",
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/seqio/_dna.py#L204-L265 | train | Convert a Biopython SeqFeature to a coral. Feature. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b11011 + 0o27) + '\x35' + chr(179 - 131), 0o10), nzTpIcepk0o8(chr(2069 - 2021) + '\x6f' + chr(0b110101) + '\x30', ord("\x08")), nzTpIcepk0o8(chr(1526 - 1478) + chr(0b1101111) + chr(49) + '\x36' + chr(1875 - 1824), 33806 - 33798), nzTpIcepk0o8(chr(0b110000) + chr(3391 - 3280) + chr(2327 - 2278) + chr(50) + chr(52), 1623 - 1615), nzTpIcepk0o8('\060' + chr(0b110010 + 0o75) + chr(1516 - 1463) + chr(0b10 + 0o56), 8), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b100111 + 0o14) + chr(2073 - 2020) + chr(0b101 + 0o54), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + '\061' + chr(2411 - 2361) + '\062', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(8848 - 8737) + chr(0b110001) + chr(0b101000 + 0o17) + chr(0b110110), 0o10), nzTpIcepk0o8(chr(2106 - 2058) + '\x6f' + chr(1282 - 1227) + chr(52), 0b1000), nzTpIcepk0o8(chr(0b100011 + 0o15) + '\157' + chr(0b110110) + chr(908 - 860), 40318 - 40310), nzTpIcepk0o8('\060' + chr(5289 - 5178) + '\064' + chr(51), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b100100 + 0o15) + '\067' + chr(55 - 4), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(2521 - 2470) + chr(235 - 186) + '\060', 57175 - 57167), nzTpIcepk0o8('\060' + chr(8856 - 8745) + chr(0b11001 + 0o30) + chr(0b10001 + 0o43), ord("\x08")), nzTpIcepk0o8(chr(0b111 + 0o51) + chr(0b1001 + 0o146) + chr(0b110011) + chr(0b10011 + 0o44), 0b1000), nzTpIcepk0o8(chr(0b100010 + 0o16) + chr(0b1101111) + chr(0b110011) + chr(0b110101) + '\064', 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + '\x33' + '\x31' + '\x33', 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(1377 - 1324) + chr(1803 - 1749), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1000000 + 0o57) + chr(0b110011) + '\x31' + chr(0b110100), 0b1000), nzTpIcepk0o8('\060' + chr(111) + '\062' + chr(0b110001) + chr(49), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(2192 - 2142) + '\061' + chr(52), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(1619 - 1570) + chr(0b0 + 0o65) + chr(1074 - 1026), 0b1000), nzTpIcepk0o8(chr(1716 - 1668) + chr(0b1101111) + '\x33' + chr(48), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b101 + 0o152) + chr(2027 - 1978) + '\066' + '\067', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110001) + chr(190 - 141) + chr(0b100101 + 0o21), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + '\x33' + '\x36' + '\x31', 57751 - 57743), nzTpIcepk0o8('\060' + chr(2699 - 2588) + chr(0b11010 + 0o27) + '\066' + '\067', 8), nzTpIcepk0o8('\x30' + chr(9268 - 9157) + '\x31' + chr(55) + chr(0b110001), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\063' + chr(0b110000), 8), nzTpIcepk0o8(chr(0b110000) + '\157' + '\063' + '\x30' + '\x30', 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(53) + chr(0b110001), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\061' + '\x33' + '\064', 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\061' + chr(967 - 913), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x31' + chr(52) + chr(0b100000 + 0o24), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(51) + '\066' + chr(0b110010), 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(0b101 + 0o55) + chr(0b110100) + chr(0b110110), 0b1000), nzTpIcepk0o8('\060' + '\157' + '\x31' + chr(0b11 + 0o63) + '\065', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110011) + chr(49) + chr(0b101101 + 0o10), 46920 - 46912), nzTpIcepk0o8(chr(2142 - 2094) + chr(111) + '\x31' + '\x30' + chr(386 - 334), 49546 - 49538), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(2018 - 1968) + '\x33' + '\062', 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(10176 - 10065) + chr(0b110101) + chr(48), 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x86'), '\144' + chr(2580 - 2479) + '\x63' + '\x6f' + '\x64' + '\x65')('\x75' + '\x74' + chr(0b110110 + 0o60) + chr(204 - 159) + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def pcZxUIP73iPt(gNPUvMsk9RKn):
Xju_rOGSSxAG = gNPUvMsk9RKn.Xju_rOGSSxAG
if roI3spqORKae(ES5oEprVxulp(b'\xc4I\x111D'), '\144' + chr(0b100001 + 0o104) + '\143' + chr(0b1101111) + chr(601 - 501) + '\145')(chr(3380 - 3263) + chr(8110 - 7994) + '\146' + chr(45) + chr(56)) in Xju_rOGSSxAG:
pfUYSUXLOw8A = Xju_rOGSSxAG[roI3spqORKae(ES5oEprVxulp(b'\xc4I\x111D'), chr(100) + chr(101) + '\143' + chr(1033 - 922) + '\x64' + '\x65')(chr(1541 - 1424) + '\x74' + chr(9040 - 8938) + chr(746 - 701) + chr(992 - 936))][nzTpIcepk0o8(chr(48) + chr(7998 - 7887) + chr(48), ord("\x08"))]
elif roI3spqORKae(ES5oEprVxulp(b'\xc4G\x10![\xb6&\x1f['), '\x64' + chr(101) + '\x63' + chr(6460 - 6349) + '\x64' + chr(3902 - 3801))('\x75' + '\x74' + '\146' + '\055' + chr(0b101111 + 0o11)) in Xju_rOGSSxAG:
pfUYSUXLOw8A = Xju_rOGSSxAG[roI3spqORKae(ES5oEprVxulp(b'\xc4G\x10![\xb6&\x1f['), chr(7532 - 7432) + '\145' + '\143' + chr(1769 - 1658) + '\x64' + chr(0b1100101))(chr(0b1101000 + 0o15) + chr(116) + '\x66' + '\055' + chr(56))][nzTpIcepk0o8(chr(0b101110 + 0o2) + '\157' + chr(48), 8)]
else:
raise AtlPdniGDq6Y(roI3spqORKae(ES5oEprVxulp(b'\xfdF\x011K\x865\x10UJF\x1f\xe8jz\x8d\xbf[\xbe\xec\xac\x06y\x1a+'), chr(0b1011001 + 0o13) + chr(0b1100101) + '\x63' + chr(111) + chr(100) + chr(0b1100101))('\165' + chr(0b111101 + 0o67) + chr(0b1100110) + chr(0b101101) + chr(0b111000)))
if roI3spqORKae(gNPUvMsk9RKn, roI3spqORKae(ES5oEprVxulp(b'\xc4G\x105\\\x80=\x10c_S\x1e\xbamk\x83\xb9'), chr(0b1100100) + '\x65' + '\x63' + '\157' + chr(0b1001110 + 0o26) + '\x65')('\165' + chr(0b1100100 + 0o20) + chr(102) + '\x2d' + chr(0b1100 + 0o54))) == roI3spqORKae(ES5oEprVxulp(b'\xc2G\x1a:'), chr(100) + chr(0b1100101) + '\143' + chr(0b1101111) + chr(100) + chr(101))(chr(0b1110101) + chr(0b101010 + 0o112) + '\146' + chr(45) + '\x38'):
qUfR6k9pMhvq = V3OlOVg98A85(gNPUvMsk9RKn.location.ws_9aXBYp0Zv, key=lambda y87dwGy_Qoj4: y87dwGy_Qoj4.KQbHFTcl_LKy)
g5iVgFwHFBy1 = [nzTpIcepk0o8(y87dwGy_Qoj4.KQbHFTcl_LKy) for y87dwGy_Qoj4 in qUfR6k9pMhvq]
I3_MCQBSPrV5 = [nzTpIcepk0o8(y87dwGy_Qoj4.NiWVjAWn0l6T) for y87dwGy_Qoj4 in qUfR6k9pMhvq]
jrSmtdrwpuIW = g5iVgFwHFBy1.uC_Yoybx7J0I(nzTpIcepk0o8('\x30' + chr(111) + chr(0b101 + 0o53), 8))
qEMbHb4ZKm6V = I3_MCQBSPrV5.uC_Yoybx7J0I(-nzTpIcepk0o8(chr(733 - 685) + '\157' + chr(49), 2489 - 2481))
g5iVgFwHFBy1 = [KQbHFTcl_LKy - jrSmtdrwpuIW for KQbHFTcl_LKy in g5iVgFwHFBy1]
I3_MCQBSPrV5 = [dYJbBiYO_nGE - jrSmtdrwpuIW for dYJbBiYO_nGE in I3_MCQBSPrV5]
AXjii_LF3nTo = H4NoA26ON7iG(TxMFWa_Xzviv(I3_MCQBSPrV5, g5iVgFwHFBy1))
else:
jrSmtdrwpuIW = nzTpIcepk0o8(gNPUvMsk9RKn.location.KQbHFTcl_LKy)
qEMbHb4ZKm6V = nzTpIcepk0o8(gNPUvMsk9RKn.location.NiWVjAWn0l6T)
AXjii_LF3nTo = []
kPnfwq1xBNHs = tektRgLlFYJo(gNPUvMsk9RKn.MJ07XsN5uFgW)
if roI3spqORKae(gNPUvMsk9RKn.location, roI3spqORKae(ES5oEprVxulp(b'\xdbg\x05\x04L\x99%Hv[gM'), '\x64' + '\145' + chr(0b1100011) + chr(0b111000 + 0o67) + chr(7718 - 7618) + chr(101))(chr(0b1110101) + chr(0b1110100) + chr(0b1100110) + chr(896 - 851) + chr(0b1011 + 0o55))) == -nzTpIcepk0o8(chr(48) + chr(111) + '\061', 8):
fw_VN9ry7DEP = nzTpIcepk0o8(chr(48) + '\x6f' + chr(2388 - 2339), 8)
else:
fw_VN9ry7DEP = nzTpIcepk0o8('\x30' + '\x6f' + chr(48), 8)
if roI3spqORKae(ES5oEprVxulp(b'\xcfM\x1d1'), chr(1872 - 1772) + chr(0b1100101 + 0o0) + chr(5138 - 5039) + chr(0b1101111) + '\144' + '\x65')('\165' + chr(0b1000010 + 0o62) + chr(102) + chr(804 - 759) + chr(0b110110 + 0o2)) in Xju_rOGSSxAG:
_Qb3Sp2ECG81 = Xju_rOGSSxAG[roI3spqORKae(ES5oEprVxulp(b'\xcfM\x1d1'), chr(100) + chr(6141 - 6040) + chr(0b1100011) + '\x6f' + chr(4157 - 4057) + '\145')(chr(0b11011 + 0o132) + chr(0b1110100) + chr(102) + chr(45) + chr(258 - 202))]
else:
_Qb3Sp2ECG81 = []
if roI3spqORKae(ES5oEprVxulp(b'\xc4G\x10![\xb6&\x1f['), chr(0b1100100) + chr(0b110 + 0o137) + chr(0b1100011) + chr(0b1101111) + '\x64' + '\145')(chr(0b1110101) + chr(116) + chr(560 - 458) + chr(0b101101) + chr(56)) in Xju_rOGSSxAG:
LA6cJY21WaTM = Xju_rOGSSxAG[roI3spqORKae(ES5oEprVxulp(b'\xc4G\x10![\xb6&\x1f['), chr(0b1100100) + '\x65' + chr(5292 - 5193) + chr(0b1101111) + '\144' + chr(8007 - 7906))('\x75' + chr(0b1110100) + chr(0b1100110) + chr(0b101101) + chr(0b111000))]
else:
LA6cJY21WaTM = []
D7aYEmJyBSM4 = _bFWSozA7z0G.Feature(pfUYSUXLOw8A, jrSmtdrwpuIW, qEMbHb4ZKm6V, kPnfwq1xBNHs, gene=_Qb3Sp2ECG81, locus_tag=LA6cJY21WaTM, qualifiers=Xju_rOGSSxAG, strand=fw_VN9ry7DEP, gaps=AXjii_LF3nTo)
return D7aYEmJyBSM4 |
klavinslab/coral | coral/seqio/_dna.py | _coral_to_seqfeature | def _coral_to_seqfeature(feature):
'''Convert a coral.Feature to a Biopython SeqFeature.
:param feature: coral Feature.
:type feature: coral.Feature
'''
bio_strand = 1 if feature.strand == 1 else -1
ftype = _process_feature_type(feature.feature_type, bio_to_coral=False)
sublocations = []
if feature.gaps:
# There are gaps. Have to define location_operator and add subfeatures
location_operator = 'join'
# Feature location means nothing for 'join' sequences?
# TODO: verify
location = FeatureLocation(ExactPosition(0), ExactPosition(1),
strand=bio_strand)
# Reconstruct start/stop indices for each subfeature
stops, starts = zip(*feature.gaps)
starts = [feature.start] + [start + feature.start for start in starts]
stops = [stop + feature.start for stop in stops] + [feature.stop]
# Build subfeatures
for start, stop in zip(starts, stops):
sublocation = FeatureLocation(ExactPosition(start),
ExactPosition(stop),
strand=bio_strand)
sublocations.append(sublocation)
location = CompoundLocation(sublocations, operator='join')
else:
# No gaps, feature is simple
location_operator = ''
location = FeatureLocation(ExactPosition(feature.start),
ExactPosition(feature.stop),
strand=bio_strand)
qualifiers = feature.qualifiers
qualifiers['label'] = [feature.name]
seqfeature = SeqFeature(location, type=ftype,
qualifiers=qualifiers,
location_operator=location_operator)
return seqfeature | python | def _coral_to_seqfeature(feature):
'''Convert a coral.Feature to a Biopython SeqFeature.
:param feature: coral Feature.
:type feature: coral.Feature
'''
bio_strand = 1 if feature.strand == 1 else -1
ftype = _process_feature_type(feature.feature_type, bio_to_coral=False)
sublocations = []
if feature.gaps:
# There are gaps. Have to define location_operator and add subfeatures
location_operator = 'join'
# Feature location means nothing for 'join' sequences?
# TODO: verify
location = FeatureLocation(ExactPosition(0), ExactPosition(1),
strand=bio_strand)
# Reconstruct start/stop indices for each subfeature
stops, starts = zip(*feature.gaps)
starts = [feature.start] + [start + feature.start for start in starts]
stops = [stop + feature.start for stop in stops] + [feature.stop]
# Build subfeatures
for start, stop in zip(starts, stops):
sublocation = FeatureLocation(ExactPosition(start),
ExactPosition(stop),
strand=bio_strand)
sublocations.append(sublocation)
location = CompoundLocation(sublocations, operator='join')
else:
# No gaps, feature is simple
location_operator = ''
location = FeatureLocation(ExactPosition(feature.start),
ExactPosition(feature.stop),
strand=bio_strand)
qualifiers = feature.qualifiers
qualifiers['label'] = [feature.name]
seqfeature = SeqFeature(location, type=ftype,
qualifiers=qualifiers,
location_operator=location_operator)
return seqfeature | [
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:param feature: coral Feature.
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/seqio/_dna.py#L268-L307 | train | Convert a coral. Feature to a Biopython SeqFeature. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(1116 - 1068) + chr(3360 - 3249) + '\x34' + chr(2580 - 2528), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(4678 - 4567) + chr(0b110001) + chr(0b110100) + chr(51), 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(2080 - 2031) + chr(53) + chr(1716 - 1668), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + '\x33' + '\x35' + '\063', 51842 - 51834), nzTpIcepk0o8('\060' + '\157' + chr(0b10111 + 0o34) + '\067' + chr(54), 0o10), nzTpIcepk0o8(chr(2276 - 2228) + chr(111) + '\x32' + chr(0b1100 + 0o52) + chr(49), 51034 - 51026), nzTpIcepk0o8(chr(0b101111 + 0o1) + chr(111) + chr(49) + chr(881 - 829) + '\061', ord("\x08")), nzTpIcepk0o8(chr(1196 - 1148) + chr(12257 - 12146) + chr(0b110001) + '\060' + chr(54), 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(0b1110 + 0o44) + '\x30' + '\x35', 37243 - 37235), nzTpIcepk0o8('\x30' + '\157' + '\064' + chr(50), 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(0b101000 + 0o12) + chr(1415 - 1367) + chr(55), 36348 - 36340), nzTpIcepk0o8(chr(874 - 826) + chr(0b1101111) + chr(0b110011) + chr(582 - 533) + chr(0b1111 + 0o50), 0o10), nzTpIcepk0o8(chr(48) + '\157' + '\x33' + chr(1266 - 1211) + chr(1799 - 1751), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(51) + '\064' + chr(0b1010 + 0o51), 0b1000), nzTpIcepk0o8('\x30' + chr(111) + '\061' + '\x36' + '\063', 0o10), nzTpIcepk0o8(chr(0b101111 + 0o1) + '\x6f' + chr(361 - 311) + '\067', ord("\x08")), nzTpIcepk0o8(chr(1594 - 1546) + '\157' + chr(0b11 + 0o60) + '\x36' + chr(419 - 366), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110010) + '\x34' + chr(0b110011 + 0o3), 6431 - 6423), nzTpIcepk0o8(chr(1081 - 1033) + '\x6f' + chr(50) + '\x31' + chr(0b110011), ord("\x08")), nzTpIcepk0o8('\x30' + chr(2615 - 2504) + chr(51) + '\063' + chr(49), ord("\x08")), nzTpIcepk0o8('\x30' + chr(7072 - 6961) + '\061' + chr(0b100000 + 0o22) + chr(0b110110), 0o10), nzTpIcepk0o8(chr(0b11101 + 0o23) + chr(0b1101111) + chr(50) + chr(0b110111) + chr(0b110 + 0o60), 0b1000), nzTpIcepk0o8('\x30' + chr(9321 - 9210) + chr(0b110010) + '\061' + '\066', ord("\x08")), nzTpIcepk0o8(chr(0b10000 + 0o40) + chr(0b101111 + 0o100) + chr(0b10001 + 0o43) + chr(51), ord("\x08")), nzTpIcepk0o8(chr(1824 - 1776) + '\157' + chr(596 - 547) + '\062' + '\x36', 8), nzTpIcepk0o8('\x30' + chr(0b111011 + 0o64) + '\x34' + '\064', 8), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110111), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b101101 + 0o5) + '\064', 0b1000), nzTpIcepk0o8(chr(0b10000 + 0o40) + chr(0b1101111) + chr(49) + chr(1558 - 1508) + chr(281 - 233), 0o10), nzTpIcepk0o8(chr(48) + chr(5520 - 5409) + chr(0b110110) + '\x31', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(1871 - 1820) + '\x37' + chr(0b10010 + 0o40), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(49) + chr(2560 - 2506) + chr(0b11 + 0o64), 12987 - 12979), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x32' + chr(1373 - 1322) + chr(0b110001), 0o10), nzTpIcepk0o8(chr(2099 - 2051) + '\157' + '\x31' + '\x31' + chr(720 - 671), 0b1000), nzTpIcepk0o8(chr(0b1011 + 0o45) + chr(2461 - 2350) + chr(0b100000 + 0o21) + chr(0b110110) + '\x32', 0o10), nzTpIcepk0o8(chr(2212 - 2164) + chr(0b1101111) + chr(1642 - 1593) + '\x33', 0o10), nzTpIcepk0o8(chr(796 - 748) + chr(111) + '\066' + chr(0b110100), 35439 - 35431), nzTpIcepk0o8(chr(0b110000) + chr(6508 - 6397) + '\x35' + '\x36', ord("\x08")), nzTpIcepk0o8(chr(1042 - 994) + chr(111) + chr(821 - 770) + chr(2095 - 2046) + '\063', 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + '\x32' + '\x35' + chr(0b110000), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + chr(3513 - 3402) + '\065' + chr(0b110000), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\n'), chr(0b1100100) + chr(101) + chr(0b1100011) + chr(0b1101111) + chr(0b1010010 + 0o22) + '\145')(chr(0b1110101) + chr(0b1110100) + '\146' + chr(0b101100 + 0o1) + chr(0b101101 + 0o13)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def nriuRuGxKSjY(gNPUvMsk9RKn):
Pnju7pNV32H2 = nzTpIcepk0o8(chr(0b10100 + 0o34) + chr(0b1101111) + chr(1937 - 1888), 0o10) if gNPUvMsk9RKn.sOvPdpw6JkD6 == nzTpIcepk0o8(chr(2295 - 2247) + chr(111) + chr(0b100 + 0o55), 8) else -nzTpIcepk0o8(chr(1646 - 1598) + chr(0b11101 + 0o122) + '\061', 8)
E_7xDwk9IR3s = tektRgLlFYJo(gNPUvMsk9RKn.feature_type, bio_to_coral=nzTpIcepk0o8('\060' + chr(0b1011101 + 0o22) + '\x30', ord("\x08")))
HVKcJ0Jg_9nk = []
if roI3spqORKae(gNPUvMsk9RKn, roI3spqORKae(ES5oEprVxulp(b'C\x02\x18\x98'), chr(3533 - 3433) + '\x65' + '\143' + chr(3274 - 3163) + '\x64' + chr(3693 - 3592))(chr(0b1110101) + chr(0b1001110 + 0o46) + chr(102) + '\x2d' + '\x38')):
OuIS_JPDWIvJ = roI3spqORKae(ES5oEprVxulp(b'N\x0c\x01\x85'), '\x64' + '\x65' + chr(2167 - 2068) + chr(0b1 + 0o156) + chr(0b1100100) + chr(0b1011111 + 0o6))(chr(0b1110101) + chr(0b1110100) + chr(0b10111 + 0o117) + chr(0b11000 + 0o25) + chr(0b10 + 0o66))
y87dwGy_Qoj4 = rS0ri3c9jcqD(NwmhEd2qeCUg(nzTpIcepk0o8(chr(958 - 910) + chr(0b1101111) + chr(0b110000), 8)), NwmhEd2qeCUg(nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\061', 8)), strand=Pnju7pNV32H2)
(I3_MCQBSPrV5, g5iVgFwHFBy1) = TxMFWa_Xzviv(*gNPUvMsk9RKn.gaps)
g5iVgFwHFBy1 = [gNPUvMsk9RKn.KQbHFTcl_LKy] + [KQbHFTcl_LKy + gNPUvMsk9RKn.KQbHFTcl_LKy for KQbHFTcl_LKy in g5iVgFwHFBy1]
I3_MCQBSPrV5 = [dYJbBiYO_nGE + gNPUvMsk9RKn.KQbHFTcl_LKy for dYJbBiYO_nGE in I3_MCQBSPrV5] + [gNPUvMsk9RKn.dYJbBiYO_nGE]
for (KQbHFTcl_LKy, dYJbBiYO_nGE) in TxMFWa_Xzviv(g5iVgFwHFBy1, I3_MCQBSPrV5):
Y9xkt94ul1QH = rS0ri3c9jcqD(NwmhEd2qeCUg(KQbHFTcl_LKy), NwmhEd2qeCUg(dYJbBiYO_nGE), strand=Pnju7pNV32H2)
roI3spqORKae(HVKcJ0Jg_9nk, roI3spqORKae(ES5oEprVxulp(b'l7;\xdf\x86\xd6&)\xefM\xd2\xfa'), '\x64' + chr(0b1100101) + chr(0b100010 + 0o101) + '\x6f' + '\144' + chr(0b1100101 + 0o0))('\x75' + '\x74' + chr(102) + chr(45) + '\070'))(Y9xkt94ul1QH)
y87dwGy_Qoj4 = GBvq3GrB3MTH(HVKcJ0Jg_9nk, operator=roI3spqORKae(ES5oEprVxulp(b'N\x0c\x01\x85'), chr(100) + chr(0b1100101) + '\143' + chr(0b1101111) + chr(9688 - 9588) + '\145')(chr(117) + '\x74' + '\x66' + chr(0b11100 + 0o21) + '\x38'))
else:
OuIS_JPDWIvJ = roI3spqORKae(ES5oEprVxulp(b''), '\144' + '\x65' + chr(9334 - 9235) + chr(0b1101111) + '\144' + chr(101))('\165' + chr(13048 - 12932) + '\x66' + chr(791 - 746) + '\x38')
y87dwGy_Qoj4 = rS0ri3c9jcqD(NwmhEd2qeCUg(gNPUvMsk9RKn.KQbHFTcl_LKy), NwmhEd2qeCUg(gNPUvMsk9RKn.dYJbBiYO_nGE), strand=Pnju7pNV32H2)
Xju_rOGSSxAG = gNPUvMsk9RKn.Xju_rOGSSxAG
Xju_rOGSSxAG[roI3spqORKae(ES5oEprVxulp(b'H\x02\n\x8e\x92'), chr(0b1100100) + '\145' + chr(0b1010000 + 0o23) + chr(10992 - 10881) + chr(100) + chr(0b1100101))('\x75' + '\x74' + chr(102) + chr(0b101101) + chr(1579 - 1523))] = [gNPUvMsk9RKn.SLVB2BPA_mIe]
XY7pUO_8aEl5 = fbAVIy6cW1Vf(y87dwGy_Qoj4, type=E_7xDwk9IR3s, qualifiers=Xju_rOGSSxAG, location_operator=OuIS_JPDWIvJ)
return XY7pUO_8aEl5 |
klavinslab/coral | coral/analysis/_sequencing/align.py | as_ord_matrix | def as_ord_matrix(matrix, alphabet):
'''Given the SubstitutionMatrix input, generate an equivalent matrix that
is indexed by the ASCII number of each residue (e.g. A -> 65).'''
ords = [ord(c) for c in alphabet]
ord_matrix = np.zeros((max(ords) + 1, max(ords) + 1), dtype=np.integer)
for i, row_ord in enumerate(ords):
for j, col_ord in enumerate(ords):
ord_matrix[row_ord, col_ord] = matrix[i, j]
return ord_matrix | python | def as_ord_matrix(matrix, alphabet):
'''Given the SubstitutionMatrix input, generate an equivalent matrix that
is indexed by the ASCII number of each residue (e.g. A -> 65).'''
ords = [ord(c) for c in alphabet]
ord_matrix = np.zeros((max(ords) + 1, max(ords) + 1), dtype=np.integer)
for i, row_ord in enumerate(ords):
for j, col_ord in enumerate(ords):
ord_matrix[row_ord, col_ord] = matrix[i, j]
return ord_matrix | [
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/analysis/_sequencing/align.py#L6-L15 | train | Given the SubstitutionMatrix input generate an equivalent matrix that contains the ASCII number of each residue. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b110000) + '\157' + chr(53) + chr(0b110000 + 0o1), 0o10), nzTpIcepk0o8('\x30' + chr(0b10011 + 0o134) + chr(1815 - 1766) + chr(2230 - 2181) + chr(1677 - 1624), ord("\x08")), nzTpIcepk0o8(chr(1637 - 1589) + '\157' + '\x37' + chr(1902 - 1847), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b11 + 0o57) + chr(1074 - 1020) + chr(0b101110 + 0o10), 57952 - 57944), nzTpIcepk0o8(chr(0b10110 + 0o32) + chr(0b10000 + 0o137) + '\063' + '\061' + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(51) + chr(0b110110) + chr(52), 17185 - 17177), nzTpIcepk0o8(chr(48) + '\157' + '\061' + chr(185 - 135) + '\064', 0o10), nzTpIcepk0o8('\060' + chr(796 - 685) + chr(0b1001 + 0o50) + chr(49) + chr(0b100111 + 0o15), 1927 - 1919), nzTpIcepk0o8(chr(48) + '\x6f' + chr(1609 - 1558) + '\063' + chr(54), 0o10), nzTpIcepk0o8('\060' + chr(0b1000101 + 0o52) + '\x34' + chr(0b110010), 11170 - 11162), nzTpIcepk0o8(chr(0b10101 + 0o33) + chr(111) + '\x32' + chr(50) + chr(678 - 624), 53481 - 53473), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(51) + '\x31' + '\x33', 32856 - 32848), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110001) + chr(1352 - 1302) + chr(0b11100 + 0o24), 6701 - 6693), nzTpIcepk0o8('\060' + '\x6f' + chr(53) + '\063', 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b1001 + 0o52) + chr(2139 - 2091) + chr(0b1101 + 0o43), 1587 - 1579), nzTpIcepk0o8('\060' + '\157' + '\x31' + chr(0b10000 + 0o42) + chr(0b110000), 8), nzTpIcepk0o8('\x30' + '\157' + '\x32' + '\x36' + chr(0b0 + 0o66), 8), nzTpIcepk0o8(chr(686 - 638) + '\x6f' + chr(1546 - 1496) + chr(51) + '\062', 38852 - 38844), nzTpIcepk0o8(chr(526 - 478) + chr(0b1101111) + chr(51) + chr(1690 - 1639) + chr(50), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(10370 - 10259) + chr(51) + '\064' + '\060', 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(50) + chr(49) + chr(0b110 + 0o56), 47897 - 47889), nzTpIcepk0o8(chr(0b100100 + 0o14) + chr(111) + chr(49) + '\x34' + chr(0b1010 + 0o54), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b10111 + 0o33) + chr(0b110100) + chr(1691 - 1639), 55976 - 55968), nzTpIcepk0o8(chr(612 - 564) + chr(0b1101111) + '\x33' + chr(700 - 646) + chr(0b110100 + 0o2), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110010) + chr(49) + '\065', 0b1000), nzTpIcepk0o8(chr(1790 - 1742) + chr(3646 - 3535) + chr(1913 - 1862) + chr(0b110110) + '\x34', 8), nzTpIcepk0o8(chr(110 - 62) + chr(7020 - 6909) + chr(51) + chr(1500 - 1447) + '\x34', 0o10), nzTpIcepk0o8(chr(0b11101 + 0o23) + chr(111) + chr(0b110010) + '\066', 0b1000), nzTpIcepk0o8(chr(48) + chr(5723 - 5612) + '\064' + '\062', 8), nzTpIcepk0o8(chr(48) + '\x6f' + chr(50) + '\x35' + '\x32', 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b101011 + 0o10) + chr(0b110100) + chr(0b100000 + 0o26), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + '\x33' + chr(0b110100) + '\x32', 0o10), nzTpIcepk0o8('\x30' + chr(111) + '\061' + '\x37' + '\x35', ord("\x08")), nzTpIcepk0o8(chr(0b101110 + 0o2) + chr(5248 - 5137) + chr(0b110011) + '\x31' + chr(53), 9414 - 9406), nzTpIcepk0o8('\060' + '\157' + chr(729 - 678) + '\x35' + chr(55), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(1329 - 1280) + chr(50) + chr(2628 - 2576), 8), nzTpIcepk0o8('\060' + chr(12284 - 12173) + '\062' + chr(0b11100 + 0o25) + chr(2405 - 2350), 0o10), nzTpIcepk0o8('\x30' + chr(0b110000 + 0o77) + '\062' + chr(50) + chr(0b110001), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(51) + '\060' + chr(0b110001), 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(50) + '\x37' + '\x31', 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b101110 + 0o2) + '\157' + chr(0b110101) + chr(0b110000), 12424 - 12416)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x07'), chr(0b1010 + 0o132) + chr(4802 - 4701) + chr(0b1100011) + chr(0b1101111) + chr(100) + chr(6470 - 6369))(chr(0b1110101) + chr(116) + chr(0b101111 + 0o67) + '\055' + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def YuiOQePEezm3(kcnyYx1RySWO, pX0zIwMxFkEl):
kPy8m2l94GLc = [RmKXV0QRcrJP(teUmM7cKWZUa) for teUmM7cKWZUa in pX0zIwMxFkEl]
IENl8LkzvDod = nDF4gVNx0u9Q.UmwwEp7MzR6q((KV9ckIhroIia(kPy8m2l94GLc) + nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x31', 60840 - 60832), KV9ckIhroIia(kPy8m2l94GLc) + nzTpIcepk0o8('\x30' + chr(3367 - 3256) + chr(474 - 425), 8)), dtype=nDF4gVNx0u9Q.integer)
for (ZlbFMSG8gCoF, RIyvcs7kOQ1h) in _kV_Bomx8PZ4(kPy8m2l94GLc):
for (sChW4gUsXrIC, ECNowB8QUsyw) in _kV_Bomx8PZ4(kPy8m2l94GLc):
IENl8LkzvDod[RIyvcs7kOQ1h, ECNowB8QUsyw] = kcnyYx1RySWO[ZlbFMSG8gCoF, sChW4gUsXrIC]
return IENl8LkzvDod |
klavinslab/coral | coral/analysis/_sequencing/align.py | aligner | def aligner(seqj, seqi, method='global', gap_open=-7, gap_extend=-7,
gap_double=-7, matrix=submat.DNA_SIMPLE.matrix,
alphabet=submat.DNA_SIMPLE.alphabet):
'''Calculates the alignment of two sequences. The global method uses
a global Needleman-Wunsh algorithm, local does a a local
Smith-Waterman alignment, global_cfe does a global alignment with
cost-free ends and glocal does an alignment which is global only with
respect to the shorter sequence, also known as a semi-global
alignment. Returns the aligned (sub)sequences as character arrays.
Gotoh, O. (1982). J. Mol. Biol. 162, 705-708.
Needleman, S. & Wunsch, C. (1970). J. Mol. Biol. 48(3), 443-53.
Smith, T.F. & Waterman M.S. (1981). J. Mol. Biol. 147, 195-197.
:param seqj: First sequence.
:type seqj: str
:param seqi: Second sequence.
:type seqi: str
:param method: Type of alignment: 'global', 'global_cfe', 'local', or
'glocal'.
:type method: str
:param gap_open: The cost of opening a gap (negative number).
:type gap_open: float
:param gap_extend: The cost of extending an open gap (negative number).
:type gap_extend: float
:param gap_double: The gap-opening cost if a gap is already open in the
other sequence (negative number).
:type gap_double: float
:param matrix: A score matrix dictionary name. Examples can be found in
the substitution_matrices module.
:type matrix: str
:param alphabet: The characters corresponding to matrix rows/columns.
:type alphabet: str
'''
amatrix = as_ord_matrix(matrix, alphabet)
NONE, LEFT, UP, DIAG = range(4) # NONE is 0
max_j = len(seqj)
max_i = len(seqi)
if max_j > max_i:
flip = 1
seqi, seqj = seqj, seqi
max_i, max_j = max_j, max_i
else:
flip = 0
F = np.zeros((max_i + 1, max_j + 1), dtype=np.float32)
I = np.ndarray((max_i + 1, max_j + 1), dtype=np.float32)
I.fill(-np.inf)
J = np.ndarray((max_i + 1, max_j + 1), dtype=np.float32)
J.fill(-np.inf)
pointer = np.zeros((max_i + 1, max_j + 1), dtype=np.uint) # NONE
if method == 'global':
pointer[0, 1:] = LEFT
pointer[1:, 0] = UP
F[0, 1:] = gap_open + gap_extend * np.arange(0, max_j,
dtype=np.float32)
F[1:, 0] = gap_open + gap_extend * np.arange(0, max_i,
dtype=np.float32)
elif method == 'global_cfe':
pointer[0, 1:] = LEFT
pointer[1:, 0] = UP
elif method == 'glocal':
pointer[0, 1:] = LEFT
F[0, 1:] = gap_open + gap_extend * np.arange(0, max_j,
dtype=np.float32)
seqi_ord = [ord(base) for base in seqi]
seqj_ord = [ord(base) for base in seqj]
for i in range(1, max_i + 1):
ci = seqi_ord[i - 1]
for j in range(1, max_j + 1):
cj = seqj_ord[j - 1]
# I
I[i, j] = max(F[i, j - 1] + gap_open,
I[i, j - 1] + gap_extend,
J[i, j - 1] + gap_double)
# J
J[i, j] = max(F[i - 1, j] + gap_open,
J[i - 1, j] + gap_extend,
I[i - 1, j] + gap_double)
# F
diag_score = F[i - 1, j - 1] + amatrix[ci, cj]
left_score = I[i, j]
up_score = J[i, j]
max_score = max(diag_score, up_score, left_score)
F[i, j] = max(0, max_score) if method == 'local' else max_score
if method == 'local':
if F[i, j] == 0:
pass # point[i,j] = NONE
elif max_score == diag_score:
pointer[i, j] = DIAG
elif max_score == up_score:
pointer[i, j] = UP
elif max_score == left_score:
pointer[i, j] = LEFT
elif method == 'glocal':
# In a semi-global alignment we want to consume as much as
# possible of the longer sequence.
if max_score == up_score:
pointer[i, j] = UP
elif max_score == diag_score:
pointer[i, j] = DIAG
elif max_score == left_score:
pointer[i, j] = LEFT
else:
# global
if max_score == up_score:
pointer[i, j] = UP
elif max_score == left_score:
pointer[i, j] = LEFT
else:
pointer[i, j] = DIAG
align_j = []
align_i = []
if method == 'local':
# max anywhere
i, j = max_index(F)
elif method == 'glocal':
# max in last col
i, j = (F[:, -1].argmax(), max_j)
elif method == 'global_cfe':
# from i,j to max(max(last row), max(last col)) for free
row_max, col_idx = F[-1].max(), F[-1].argmax()
col_max, row_idx = F[:, -1].max(), F[:, -1].argmax()
if row_max > col_max:
pointer[-1, col_idx + 1:] = LEFT
else:
pointer[row_idx + 1:, -1] = UP
p = pointer[i, j]
while p != NONE:
if p == DIAG:
i -= 1
j -= 1
align_j.append(seqj[j])
align_i.append(seqi[i])
elif p == LEFT:
j -= 1
align_j.append(seqj[j])
align_i.append('-')
elif p == UP:
i -= 1
align_j.append('-')
align_i.append(seqi[i])
else:
raise Exception('wtf!')
p = pointer[i, j]
align_i = ''.join(align_i[::-1])
align_j = ''.join(align_j[::-1])
# np.array(align_i.reverse())
return ((align_i, align_j) if flip else (align_j, align_i)) | python | def aligner(seqj, seqi, method='global', gap_open=-7, gap_extend=-7,
gap_double=-7, matrix=submat.DNA_SIMPLE.matrix,
alphabet=submat.DNA_SIMPLE.alphabet):
'''Calculates the alignment of two sequences. The global method uses
a global Needleman-Wunsh algorithm, local does a a local
Smith-Waterman alignment, global_cfe does a global alignment with
cost-free ends and glocal does an alignment which is global only with
respect to the shorter sequence, also known as a semi-global
alignment. Returns the aligned (sub)sequences as character arrays.
Gotoh, O. (1982). J. Mol. Biol. 162, 705-708.
Needleman, S. & Wunsch, C. (1970). J. Mol. Biol. 48(3), 443-53.
Smith, T.F. & Waterman M.S. (1981). J. Mol. Biol. 147, 195-197.
:param seqj: First sequence.
:type seqj: str
:param seqi: Second sequence.
:type seqi: str
:param method: Type of alignment: 'global', 'global_cfe', 'local', or
'glocal'.
:type method: str
:param gap_open: The cost of opening a gap (negative number).
:type gap_open: float
:param gap_extend: The cost of extending an open gap (negative number).
:type gap_extend: float
:param gap_double: The gap-opening cost if a gap is already open in the
other sequence (negative number).
:type gap_double: float
:param matrix: A score matrix dictionary name. Examples can be found in
the substitution_matrices module.
:type matrix: str
:param alphabet: The characters corresponding to matrix rows/columns.
:type alphabet: str
'''
amatrix = as_ord_matrix(matrix, alphabet)
NONE, LEFT, UP, DIAG = range(4) # NONE is 0
max_j = len(seqj)
max_i = len(seqi)
if max_j > max_i:
flip = 1
seqi, seqj = seqj, seqi
max_i, max_j = max_j, max_i
else:
flip = 0
F = np.zeros((max_i + 1, max_j + 1), dtype=np.float32)
I = np.ndarray((max_i + 1, max_j + 1), dtype=np.float32)
I.fill(-np.inf)
J = np.ndarray((max_i + 1, max_j + 1), dtype=np.float32)
J.fill(-np.inf)
pointer = np.zeros((max_i + 1, max_j + 1), dtype=np.uint) # NONE
if method == 'global':
pointer[0, 1:] = LEFT
pointer[1:, 0] = UP
F[0, 1:] = gap_open + gap_extend * np.arange(0, max_j,
dtype=np.float32)
F[1:, 0] = gap_open + gap_extend * np.arange(0, max_i,
dtype=np.float32)
elif method == 'global_cfe':
pointer[0, 1:] = LEFT
pointer[1:, 0] = UP
elif method == 'glocal':
pointer[0, 1:] = LEFT
F[0, 1:] = gap_open + gap_extend * np.arange(0, max_j,
dtype=np.float32)
seqi_ord = [ord(base) for base in seqi]
seqj_ord = [ord(base) for base in seqj]
for i in range(1, max_i + 1):
ci = seqi_ord[i - 1]
for j in range(1, max_j + 1):
cj = seqj_ord[j - 1]
# I
I[i, j] = max(F[i, j - 1] + gap_open,
I[i, j - 1] + gap_extend,
J[i, j - 1] + gap_double)
# J
J[i, j] = max(F[i - 1, j] + gap_open,
J[i - 1, j] + gap_extend,
I[i - 1, j] + gap_double)
# F
diag_score = F[i - 1, j - 1] + amatrix[ci, cj]
left_score = I[i, j]
up_score = J[i, j]
max_score = max(diag_score, up_score, left_score)
F[i, j] = max(0, max_score) if method == 'local' else max_score
if method == 'local':
if F[i, j] == 0:
pass # point[i,j] = NONE
elif max_score == diag_score:
pointer[i, j] = DIAG
elif max_score == up_score:
pointer[i, j] = UP
elif max_score == left_score:
pointer[i, j] = LEFT
elif method == 'glocal':
# In a semi-global alignment we want to consume as much as
# possible of the longer sequence.
if max_score == up_score:
pointer[i, j] = UP
elif max_score == diag_score:
pointer[i, j] = DIAG
elif max_score == left_score:
pointer[i, j] = LEFT
else:
# global
if max_score == up_score:
pointer[i, j] = UP
elif max_score == left_score:
pointer[i, j] = LEFT
else:
pointer[i, j] = DIAG
align_j = []
align_i = []
if method == 'local':
# max anywhere
i, j = max_index(F)
elif method == 'glocal':
# max in last col
i, j = (F[:, -1].argmax(), max_j)
elif method == 'global_cfe':
# from i,j to max(max(last row), max(last col)) for free
row_max, col_idx = F[-1].max(), F[-1].argmax()
col_max, row_idx = F[:, -1].max(), F[:, -1].argmax()
if row_max > col_max:
pointer[-1, col_idx + 1:] = LEFT
else:
pointer[row_idx + 1:, -1] = UP
p = pointer[i, j]
while p != NONE:
if p == DIAG:
i -= 1
j -= 1
align_j.append(seqj[j])
align_i.append(seqi[i])
elif p == LEFT:
j -= 1
align_j.append(seqj[j])
align_i.append('-')
elif p == UP:
i -= 1
align_j.append('-')
align_i.append(seqi[i])
else:
raise Exception('wtf!')
p = pointer[i, j]
align_i = ''.join(align_i[::-1])
align_j = ''.join(align_j[::-1])
# np.array(align_i.reverse())
return ((align_i, align_j) if flip else (align_j, align_i)) | [
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"al... | Calculates the alignment of two sequences. The global method uses
a global Needleman-Wunsh algorithm, local does a a local
Smith-Waterman alignment, global_cfe does a global alignment with
cost-free ends and glocal does an alignment which is global only with
respect to the shorter sequence, also known as a semi-global
alignment. Returns the aligned (sub)sequences as character arrays.
Gotoh, O. (1982). J. Mol. Biol. 162, 705-708.
Needleman, S. & Wunsch, C. (1970). J. Mol. Biol. 48(3), 443-53.
Smith, T.F. & Waterman M.S. (1981). J. Mol. Biol. 147, 195-197.
:param seqj: First sequence.
:type seqj: str
:param seqi: Second sequence.
:type seqi: str
:param method: Type of alignment: 'global', 'global_cfe', 'local', or
'glocal'.
:type method: str
:param gap_open: The cost of opening a gap (negative number).
:type gap_open: float
:param gap_extend: The cost of extending an open gap (negative number).
:type gap_extend: float
:param gap_double: The gap-opening cost if a gap is already open in the
other sequence (negative number).
:type gap_double: float
:param matrix: A score matrix dictionary name. Examples can be found in
the substitution_matrices module.
:type matrix: str
:param alphabet: The characters corresponding to matrix rows/columns.
:type alphabet: str | [
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"... | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/analysis/_sequencing/align.py#L29-L185 | train | Calculates the alignment of two sequences. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(1431 - 1382) + chr(0b110011) + chr(0b110110), 29946 - 29938), nzTpIcepk0o8(chr(0b100111 + 0o11) + chr(111) + chr(1620 - 1571) + '\x37' + '\066', 18034 - 18026), nzTpIcepk0o8(chr(48) + chr(9613 - 9502) + chr(485 - 436) + chr(0b110100) + chr(479 - 426), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1001111 + 0o40) + chr(54), 0o10), nzTpIcepk0o8(chr(433 - 385) + chr(0b1101111) + chr(0b110001) + '\x32' + chr(0b110111), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\063' + chr(995 - 943) + '\067', 0b1000), nzTpIcepk0o8(chr(1294 - 1246) + '\157' + chr(2251 - 2196) + chr(48), 28407 - 28399), nzTpIcepk0o8(chr(469 - 421) + chr(0b101111 + 0o100) + chr(49) + chr(2602 - 2549) + '\x32', 0b1000), nzTpIcepk0o8('\x30' + chr(432 - 321) + chr(0b110010) + '\066' + chr(0b10101 + 0o34), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b101010 + 0o10) + chr(0b110001) + chr(48), 0o10), nzTpIcepk0o8(chr(1252 - 1204) + chr(8632 - 8521) + chr(0b10110 + 0o33) + chr(52) + chr(0b10001 + 0o45), 0b1000), nzTpIcepk0o8(chr(0b1 + 0o57) + chr(111) + chr(0b11101 + 0o26) + '\062' + '\063', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(6336 - 6225) + chr(0b11110 + 0o23) + chr(0b110011), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(858 - 805) + chr(933 - 881), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + '\061' + '\x33', 8), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b100111 + 0o12) + chr(0b100010 + 0o16) + chr(0b10101 + 0o36), 32639 - 32631), nzTpIcepk0o8(chr(0b1001 + 0o47) + chr(111) + '\063' + chr(722 - 673), 0o10), nzTpIcepk0o8(chr(1557 - 1509) + chr(111) + '\x34' + '\x32', 41465 - 41457), nzTpIcepk0o8(chr(75 - 27) + chr(0b10000 + 0o137) + '\x35' + '\x37', ord("\x08")), nzTpIcepk0o8(chr(0b100111 + 0o11) + chr(111) + chr(0b100100 + 0o17) + chr(0b101101 + 0o11) + chr(0b1010 + 0o46), 0o10), nzTpIcepk0o8('\060' + chr(0b1100100 + 0o13) + chr(51) + chr(49) + chr(0b110010), 30482 - 30474), nzTpIcepk0o8(chr(1261 - 1213) + chr(0b1000110 + 0o51) + '\062' + '\x30' + chr(1160 - 1107), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(129 - 80) + '\x30' + chr(0b100001 + 0o24), 0b1000), nzTpIcepk0o8(chr(1330 - 1282) + chr(10836 - 10725) + chr(49) + '\x33' + chr(0b110000 + 0o3), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101 + 0o142) + chr(51) + chr(0b110101) + chr(0b110011), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + '\x32' + '\062' + '\061', 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(2102 - 2052) + chr(2411 - 2358) + '\x31', 0o10), nzTpIcepk0o8(chr(311 - 263) + '\x6f' + chr(0b10000 + 0o41) + chr(2582 - 2529) + chr(55), 0o10), nzTpIcepk0o8(chr(359 - 311) + chr(0b100001 + 0o116) + chr(0b101110 + 0o3) + '\067', 23914 - 23906), nzTpIcepk0o8(chr(48) + chr(0b10000 + 0o137) + '\x33' + chr(0b100111 + 0o16) + '\x37', ord("\x08")), nzTpIcepk0o8(chr(874 - 826) + chr(0b1000010 + 0o55) + chr(0b101100 + 0o5) + chr(0b110011) + chr(55), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(1010 - 959) + chr(50) + chr(49), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(53) + chr(936 - 884), 8), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110111) + chr(1616 - 1561), 13289 - 13281), nzTpIcepk0o8('\060' + chr(12236 - 12125) + '\065' + '\x36', 0o10), nzTpIcepk0o8(chr(0b11000 + 0o30) + chr(0b1101111) + chr(49) + chr(50) + chr(0b110110), 0b1000), nzTpIcepk0o8(chr(0b101111 + 0o1) + chr(0b1101110 + 0o1) + chr(0b110010) + chr(0b110100) + chr(2867 - 2813), 42036 - 42028), nzTpIcepk0o8('\x30' + chr(0b110101 + 0o72) + chr(0b110011) + chr(0b10010 + 0o45) + chr(0b110100), 0o10), nzTpIcepk0o8('\x30' + chr(0b1100100 + 0o13) + chr(1502 - 1451) + '\x31' + chr(51), 6649 - 6641), nzTpIcepk0o8(chr(1750 - 1702) + '\157' + '\062' + '\x33' + '\x32', ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b1010 + 0o46) + chr(0b11011 + 0o124) + chr(0b11010 + 0o33) + chr(0b110000), ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'p'), chr(4070 - 3970) + chr(0b1100101) + chr(0b1100011) + chr(0b1101111) + chr(100) + chr(101))('\x75' + chr(0b1110100) + '\x66' + chr(0b101101) + chr(2509 - 2453)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def Uoy_GvzhF4sl(wlNoVBLj8X4c, Lc5IsoUUe5Fv, e5rcHW8hR5dL=roI3spqORKae(ES5oEprVxulp(b'9\x12\nd6\x8b'), chr(0b1010100 + 0o20) + '\x65' + '\x63' + chr(111) + chr(0b1100100) + '\145')(chr(117) + chr(0b1110100) + '\146' + '\x2d' + chr(56)), uPHeZKKBo482=-nzTpIcepk0o8(chr(48) + '\x6f' + '\067', 12266 - 12258), rfmfuQvZ1V7R=-nzTpIcepk0o8(chr(48) + '\x6f' + chr(1683 - 1628), 8), xL4dVCKYDwtk=-nzTpIcepk0o8(chr(0b101010 + 0o6) + chr(0b1101111) + chr(1922 - 1867), 8), kcnyYx1RySWO=roI3spqORKae(lYtFBtIlVp5C.DNA_SIMPLE, roI3spqORKae(ES5oEprVxulp(b'5\x1d\x0b\x7f\x0e\x9f\t8\xc8\xdb1\x9c'), chr(100) + chr(0b10011 + 0o122) + '\143' + chr(0b1101111) + chr(0b1100100) + chr(101))(chr(117) + chr(4150 - 4034) + chr(102) + chr(0b10001 + 0o34) + chr(0b111000))), pX0zIwMxFkEl=roI3spqORKae(lYtFBtIlVp5C.DNA_SIMPLE, roI3spqORKae(ES5oEprVxulp(b'.&U|\x1e\x90u\x12\xf7\xe3#\xbf'), '\144' + '\145' + chr(0b1100011) + chr(111) + chr(0b1100100) + chr(0b1100101))('\x75' + '\x74' + chr(0b1 + 0o145) + chr(0b110 + 0o47) + chr(0b110111 + 0o1)))):
EkTKTKxFMozH = YuiOQePEezm3(kcnyYx1RySWO, pX0zIwMxFkEl)
(tuZoile_2cGG, tDOgRruOFN1z, ozwOPrTfONtH, vgH1B4QbBkCz) = bbT2xIe5pzk7(nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(1745 - 1693), 0o10))
sW5FYoPOo5CD = ftfygxgFas5X(wlNoVBLj8X4c)
kOPEgbQ9f_sI = ftfygxgFas5X(Lc5IsoUUe5Fv)
if sW5FYoPOo5CD > kOPEgbQ9f_sI:
LeuPzfhzM9U8 = nzTpIcepk0o8('\060' + '\157' + chr(49), 0o10)
(Lc5IsoUUe5Fv, wlNoVBLj8X4c) = (wlNoVBLj8X4c, Lc5IsoUUe5Fv)
(kOPEgbQ9f_sI, sW5FYoPOo5CD) = (sW5FYoPOo5CD, kOPEgbQ9f_sI)
else:
LeuPzfhzM9U8 = nzTpIcepk0o8(chr(48) + '\157' + chr(0b101 + 0o53), 0b1000)
GsKhodujj4DP = nDF4gVNx0u9Q.UmwwEp7MzR6q((kOPEgbQ9f_sI + nzTpIcepk0o8(chr(0b101011 + 0o5) + chr(0b1101010 + 0o5) + chr(0b101011 + 0o6), 8), sW5FYoPOo5CD + nzTpIcepk0o8(chr(1526 - 1478) + chr(111) + chr(1106 - 1057), 8)), dtype=nDF4gVNx0u9Q.float32)
J89Y4kGNG2Bs = nDF4gVNx0u9Q.ndarray((kOPEgbQ9f_sI + nzTpIcepk0o8(chr(0b110000) + chr(8679 - 8568) + '\061', 8), sW5FYoPOo5CD + nzTpIcepk0o8(chr(0b100101 + 0o13) + '\x6f' + '\x31', 8)), dtype=nDF4gVNx0u9Q.float32)
roI3spqORKae(J89Y4kGNG2Bs, roI3spqORKae(ES5oEprVxulp(b'..\x08m\x1b\xa4n+\x82\xba^\xb6'), chr(0b1100100) + chr(10084 - 9983) + chr(0b1100011) + chr(10322 - 10211) + chr(0b1111 + 0o125) + chr(2111 - 2010))(chr(0b1110101) + '\164' + '\x66' + chr(1492 - 1447) + chr(56)))(-roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'83+~\x0f\xde\\-\xd0\xbd.\xea'), '\144' + '\x65' + chr(6824 - 6725) + chr(1279 - 1168) + chr(100) + chr(101))(chr(117) + '\164' + chr(4952 - 4850) + '\x2d' + chr(0b111000))))
r3LBXuk8YXJl = nDF4gVNx0u9Q.ndarray((kOPEgbQ9f_sI + nzTpIcepk0o8(chr(0b1110 + 0o42) + '\x6f' + chr(1360 - 1311), 8), sW5FYoPOo5CD + nzTpIcepk0o8(chr(1243 - 1195) + chr(11126 - 11015) + chr(49), 8)), dtype=nDF4gVNx0u9Q.float32)
roI3spqORKae(r3LBXuk8YXJl, roI3spqORKae(ES5oEprVxulp(b'..\x08m\x1b\xa4n+\x82\xba^\xb6'), chr(100) + chr(0b10110 + 0o117) + '\x63' + chr(111) + chr(100) + chr(101))(chr(0b1000 + 0o155) + chr(3240 - 3124) + chr(9219 - 9117) + '\055' + chr(56)))(-roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'83+~\x0f\xde\\-\xd0\xbd.\xea'), chr(0b1100100) + chr(0b1000 + 0o135) + chr(8119 - 8020) + '\x6f' + chr(0b1000 + 0o134) + chr(0b11101 + 0o110))('\165' + '\x74' + chr(6526 - 6424) + chr(1754 - 1709) + chr(0b1100 + 0o54))))
VpexCJyQNp0O = nDF4gVNx0u9Q.UmwwEp7MzR6q((kOPEgbQ9f_sI + nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b11 + 0o56), 8), sW5FYoPOo5CD + nzTpIcepk0o8(chr(0b110000) + chr(0b100001 + 0o116) + '\061', 8)), dtype=nDF4gVNx0u9Q.uint)
if e5rcHW8hR5dL == roI3spqORKae(ES5oEprVxulp(b'9\x12\nd6\x8b'), '\x64' + '\x65' + '\x63' + chr(0b1101111) + chr(0b110001 + 0o63) + '\x65')(chr(0b1110011 + 0o2) + chr(1849 - 1733) + chr(8367 - 8265) + '\055' + chr(56)):
VpexCJyQNp0O[nzTpIcepk0o8('\060' + chr(0b1101111) + '\x30', 8), nzTpIcepk0o8(chr(0b101001 + 0o7) + chr(0b1101111) + chr(0b110001), 8):] = tDOgRruOFN1z
VpexCJyQNp0O[nzTpIcepk0o8('\x30' + chr(12256 - 12145) + '\x31', 8):, nzTpIcepk0o8(chr(1537 - 1489) + chr(111) + '\060', 8)] = ozwOPrTfONtH
GsKhodujj4DP[nzTpIcepk0o8(chr(1987 - 1939) + chr(11628 - 11517) + chr(0b110000), 8), nzTpIcepk0o8(chr(48) + '\157' + '\x31', 8):] = uPHeZKKBo482 + rfmfuQvZ1V7R * nDF4gVNx0u9Q.chmI_GMU_sEi(nzTpIcepk0o8(chr(0b101001 + 0o7) + chr(11105 - 10994) + '\x30', 8), sW5FYoPOo5CD, dtype=nDF4gVNx0u9Q.float32)
GsKhodujj4DP[nzTpIcepk0o8(chr(48) + '\157' + chr(0b10100 + 0o35), 8):, nzTpIcepk0o8('\x30' + '\x6f' + chr(1471 - 1423), 8)] = uPHeZKKBo482 + rfmfuQvZ1V7R * nDF4gVNx0u9Q.chmI_GMU_sEi(nzTpIcepk0o8('\x30' + chr(0b1011 + 0o144) + '\060', 8), kOPEgbQ9f_sI, dtype=nDF4gVNx0u9Q.float32)
elif e5rcHW8hR5dL == roI3spqORKae(ES5oEprVxulp(b'9\x12\nd6\x8bg\t\xd7\xed'), chr(0b1000100 + 0o40) + '\x65' + '\x63' + chr(9566 - 9455) + chr(0b1100100) + chr(8208 - 8107))(chr(0b100001 + 0o124) + chr(9511 - 9395) + chr(2495 - 2393) + chr(677 - 632) + '\x38'):
VpexCJyQNp0O[nzTpIcepk0o8('\x30' + chr(111) + chr(48), 8), nzTpIcepk0o8(chr(0b101101 + 0o3) + chr(0b1100 + 0o143) + chr(1973 - 1924), 8):] = tDOgRruOFN1z
VpexCJyQNp0O[nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(728 - 679), 8):, nzTpIcepk0o8(chr(0b0 + 0o60) + chr(111) + chr(48), 8)] = ozwOPrTfONtH
elif e5rcHW8hR5dL == roI3spqORKae(ES5oEprVxulp(b'9\x12\ne6\x8b'), chr(100) + '\145' + chr(99) + '\157' + chr(0b100001 + 0o103) + '\x65')(chr(0b1110101) + '\x74' + chr(102) + chr(0b10101 + 0o30) + chr(0b111000)):
VpexCJyQNp0O[nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b1100 + 0o44), 8), nzTpIcepk0o8(chr(48) + '\157' + '\061', 8):] = tDOgRruOFN1z
GsKhodujj4DP[nzTpIcepk0o8(chr(0b10100 + 0o34) + chr(0b1000001 + 0o56) + '\060', 8), nzTpIcepk0o8(chr(0b11 + 0o55) + '\157' + chr(49), 8):] = uPHeZKKBo482 + rfmfuQvZ1V7R * nDF4gVNx0u9Q.chmI_GMU_sEi(nzTpIcepk0o8(chr(284 - 236) + chr(0b1101110 + 0o1) + chr(1568 - 1520), 8), sW5FYoPOo5CD, dtype=nDF4gVNx0u9Q.float32)
WDk0gky_TBja = [RmKXV0QRcrJP(xvptlew7LsBo) for xvptlew7LsBo in Lc5IsoUUe5Fv]
PLPp2pj_57aQ = [RmKXV0QRcrJP(xvptlew7LsBo) for xvptlew7LsBo in wlNoVBLj8X4c]
for ZlbFMSG8gCoF in bbT2xIe5pzk7(nzTpIcepk0o8(chr(1595 - 1547) + '\x6f' + chr(0b100010 + 0o17), 8), kOPEgbQ9f_sI + nzTpIcepk0o8(chr(605 - 557) + chr(0b100101 + 0o112) + chr(49), 8)):
cjIqqAi052T8 = WDk0gky_TBja[ZlbFMSG8gCoF - nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b100101 + 0o14), 8)]
for sChW4gUsXrIC in bbT2xIe5pzk7(nzTpIcepk0o8('\060' + chr(2289 - 2178) + chr(49), 8), sW5FYoPOo5CD + nzTpIcepk0o8(chr(0b100000 + 0o20) + '\x6f' + chr(0b110 + 0o53), 8)):
FnDTpkEWgcm7 = PLPp2pj_57aQ[sChW4gUsXrIC - nzTpIcepk0o8(chr(0b10011 + 0o35) + chr(7808 - 7697) + '\061', 8)]
J89Y4kGNG2Bs[ZlbFMSG8gCoF, sChW4gUsXrIC] = KV9ckIhroIia(GsKhodujj4DP[ZlbFMSG8gCoF, sChW4gUsXrIC - nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x31', 8)] + uPHeZKKBo482, J89Y4kGNG2Bs[ZlbFMSG8gCoF, sChW4gUsXrIC - nzTpIcepk0o8('\x30' + chr(8135 - 8024) + '\x31', 8)] + rfmfuQvZ1V7R, r3LBXuk8YXJl[ZlbFMSG8gCoF, sChW4gUsXrIC - nzTpIcepk0o8(chr(1759 - 1711) + chr(0b1101111) + chr(298 - 249), 8)] + xL4dVCKYDwtk)
r3LBXuk8YXJl[ZlbFMSG8gCoF, sChW4gUsXrIC] = KV9ckIhroIia(GsKhodujj4DP[ZlbFMSG8gCoF - nzTpIcepk0o8(chr(0b10110 + 0o32) + chr(5421 - 5310) + chr(49), 8), sChW4gUsXrIC] + uPHeZKKBo482, r3LBXuk8YXJl[ZlbFMSG8gCoF - nzTpIcepk0o8(chr(1504 - 1456) + chr(111) + chr(0b110001), 8), sChW4gUsXrIC] + rfmfuQvZ1V7R, J89Y4kGNG2Bs[ZlbFMSG8gCoF - nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(1438 - 1389), 8), sChW4gUsXrIC] + xL4dVCKYDwtk)
PO8uGQpXv11P = GsKhodujj4DP[ZlbFMSG8gCoF - nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110001), 8), sChW4gUsXrIC - nzTpIcepk0o8('\060' + chr(4706 - 4595) + chr(0b110001), 8)] + EkTKTKxFMozH[cjIqqAi052T8, FnDTpkEWgcm7]
JU98hMInW9uR = J89Y4kGNG2Bs[ZlbFMSG8gCoF, sChW4gUsXrIC]
ei2slT7pQzPs = r3LBXuk8YXJl[ZlbFMSG8gCoF, sChW4gUsXrIC]
lZbxKPT1uYlN = KV9ckIhroIia(PO8uGQpXv11P, ei2slT7pQzPs, JU98hMInW9uR)
GsKhodujj4DP[ZlbFMSG8gCoF, sChW4gUsXrIC] = KV9ckIhroIia(nzTpIcepk0o8('\x30' + chr(0b1011001 + 0o26) + chr(2003 - 1955), 8), lZbxKPT1uYlN) if e5rcHW8hR5dL == roI3spqORKae(ES5oEprVxulp(b'2\x11\x06g;'), '\x64' + chr(0b1100101) + '\143' + chr(111) + chr(100) + '\x65')(chr(117) + '\164' + chr(102) + chr(0b10100 + 0o31) + chr(0b111000)) else lZbxKPT1uYlN
if e5rcHW8hR5dL == roI3spqORKae(ES5oEprVxulp(b'2\x11\x06g;'), '\x64' + chr(101) + '\x63' + chr(0b1101111) + chr(0b1100100) + chr(101))('\x75' + '\164' + chr(0b1100110) + chr(792 - 747) + chr(0b10011 + 0o45)):
if GsKhodujj4DP[ZlbFMSG8gCoF, sChW4gUsXrIC] == nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110000), 8):
pass
elif lZbxKPT1uYlN == PO8uGQpXv11P:
VpexCJyQNp0O[ZlbFMSG8gCoF, sChW4gUsXrIC] = vgH1B4QbBkCz
elif lZbxKPT1uYlN == ei2slT7pQzPs:
VpexCJyQNp0O[ZlbFMSG8gCoF, sChW4gUsXrIC] = ozwOPrTfONtH
elif lZbxKPT1uYlN == JU98hMInW9uR:
VpexCJyQNp0O[ZlbFMSG8gCoF, sChW4gUsXrIC] = tDOgRruOFN1z
elif e5rcHW8hR5dL == roI3spqORKae(ES5oEprVxulp(b'9\x12\ne6\x8b'), chr(0b1010010 + 0o22) + chr(7533 - 7432) + chr(99) + '\157' + chr(0b1010001 + 0o23) + '\x65')(chr(0b1110101) + chr(116) + '\x66' + '\055' + chr(56)):
if lZbxKPT1uYlN == ei2slT7pQzPs:
VpexCJyQNp0O[ZlbFMSG8gCoF, sChW4gUsXrIC] = ozwOPrTfONtH
elif lZbxKPT1uYlN == PO8uGQpXv11P:
VpexCJyQNp0O[ZlbFMSG8gCoF, sChW4gUsXrIC] = vgH1B4QbBkCz
elif lZbxKPT1uYlN == JU98hMInW9uR:
VpexCJyQNp0O[ZlbFMSG8gCoF, sChW4gUsXrIC] = tDOgRruOFN1z
elif lZbxKPT1uYlN == ei2slT7pQzPs:
VpexCJyQNp0O[ZlbFMSG8gCoF, sChW4gUsXrIC] = ozwOPrTfONtH
elif lZbxKPT1uYlN == JU98hMInW9uR:
VpexCJyQNp0O[ZlbFMSG8gCoF, sChW4gUsXrIC] = tDOgRruOFN1z
else:
VpexCJyQNp0O[ZlbFMSG8gCoF, sChW4gUsXrIC] = vgH1B4QbBkCz
KUIsAh6D2K2Z = []
qZgIQ9B1vos4 = []
if e5rcHW8hR5dL == roI3spqORKae(ES5oEprVxulp(b'2\x11\x06g;'), chr(100) + chr(0b100110 + 0o77) + chr(0b101100 + 0o67) + chr(6174 - 6063) + '\144' + chr(101))('\165' + '\164' + '\x66' + chr(45) + chr(0b101111 + 0o11)):
(ZlbFMSG8gCoF, sChW4gUsXrIC) = H706FT3kXp0G(GsKhodujj4DP)
elif e5rcHW8hR5dL == roI3spqORKae(ES5oEprVxulp(b'9\x12\ne6\x8b'), chr(100) + '\145' + '\x63' + chr(0b1011011 + 0o24) + '\x64' + chr(0b110110 + 0o57))('\x75' + chr(0b10010 + 0o142) + chr(9820 - 9718) + chr(946 - 901) + chr(0b111000)):
(ZlbFMSG8gCoF, sChW4gUsXrIC) = (GsKhodujj4DP[:, -nzTpIcepk0o8('\060' + '\157' + '\061', 8)].qWXgHopo6E5J(), sW5FYoPOo5CD)
elif e5rcHW8hR5dL == roI3spqORKae(ES5oEprVxulp(b'9\x12\nd6\x8bg\t\xd7\xed'), chr(100) + chr(8622 - 8521) + chr(0b101101 + 0o66) + chr(0b1101111) + chr(0b1011110 + 0o6) + chr(0b100000 + 0o105))('\165' + chr(0b1101101 + 0o7) + '\x66' + '\x2d' + chr(0b111000)):
(sToAopePGhv8, UxuRgdqMRXSu) = (GsKhodujj4DP[-nzTpIcepk0o8(chr(0b100 + 0o54) + chr(6360 - 6249) + chr(0b111 + 0o52), 8)].KV9ckIhroIia(), GsKhodujj4DP[-nzTpIcepk0o8(chr(938 - 890) + chr(111) + chr(0b100011 + 0o16), 8)].qWXgHopo6E5J())
(wqKxqDd9Y_Ju, hRM2U1ng6VGM) = (GsKhodujj4DP[:, -nzTpIcepk0o8('\060' + chr(0b1101111) + chr(509 - 460), 8)].KV9ckIhroIia(), GsKhodujj4DP[:, -nzTpIcepk0o8(chr(0b10111 + 0o31) + '\157' + '\x31', 8)].qWXgHopo6E5J())
if sToAopePGhv8 > wqKxqDd9Y_Ju:
VpexCJyQNp0O[-nzTpIcepk0o8(chr(0b110000) + chr(3389 - 3278) + chr(0b101000 + 0o11), 8), UxuRgdqMRXSu + nzTpIcepk0o8('\x30' + '\x6f' + chr(49), 8):] = tDOgRruOFN1z
else:
VpexCJyQNp0O[hRM2U1ng6VGM + nzTpIcepk0o8(chr(0b110000) + chr(8122 - 8011) + '\x31', 8):, -nzTpIcepk0o8(chr(0b101110 + 0o2) + '\x6f' + chr(49), 8)] = ozwOPrTfONtH
fSdw5wwLo9MO = VpexCJyQNp0O[ZlbFMSG8gCoF, sChW4gUsXrIC]
while fSdw5wwLo9MO != tuZoile_2cGG:
if fSdw5wwLo9MO == vgH1B4QbBkCz:
ZlbFMSG8gCoF -= nzTpIcepk0o8(chr(1072 - 1024) + '\x6f' + chr(49), 8)
sChW4gUsXrIC -= nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110001), 8)
roI3spqORKae(KUIsAh6D2K2Z, roI3spqORKae(ES5oEprVxulp(b'\x16*62/\x80\x7f\x05\xdb\xe73\xe6'), '\144' + '\145' + '\x63' + '\157' + chr(100) + chr(0b1100101))('\165' + chr(116) + chr(0b10101 + 0o121) + chr(45) + chr(56)))(wlNoVBLj8X4c[sChW4gUsXrIC])
roI3spqORKae(qZgIQ9B1vos4, roI3spqORKae(ES5oEprVxulp(b'\x16*62/\x80\x7f\x05\xdb\xe73\xe6'), chr(0b1100100) + '\x65' + '\143' + chr(0b1101111) + chr(0b1011010 + 0o12) + chr(0b1100101))(chr(0b1110101) + chr(10661 - 10545) + '\x66' + '\055' + '\070'))(Lc5IsoUUe5Fv[ZlbFMSG8gCoF])
elif fSdw5wwLo9MO == tDOgRruOFN1z:
sChW4gUsXrIC -= nzTpIcepk0o8(chr(542 - 494) + chr(111) + chr(0b110001), 8)
roI3spqORKae(KUIsAh6D2K2Z, roI3spqORKae(ES5oEprVxulp(b'\x16*62/\x80\x7f\x05\xdb\xe73\xe6'), chr(100) + chr(101) + '\143' + '\157' + chr(3666 - 3566) + '\x65')('\x75' + chr(116) + chr(102) + chr(0b10001 + 0o34) + chr(0b111000)))(wlNoVBLj8X4c[sChW4gUsXrIC])
roI3spqORKae(qZgIQ9B1vos4, roI3spqORKae(ES5oEprVxulp(b'\x16*62/\x80\x7f\x05\xdb\xe73\xe6'), '\x64' + chr(0b1100101) + chr(2779 - 2680) + '\157' + chr(100) + chr(6290 - 6189))(chr(13385 - 13268) + '\164' + chr(102) + chr(45) + '\070'))(roI3spqORKae(ES5oEprVxulp(b's'), '\144' + '\145' + chr(0b1100011) + '\x6f' + chr(0b1100100) + chr(2623 - 2522))(chr(0b1100010 + 0o23) + '\164' + '\x66' + '\055' + chr(56)))
elif fSdw5wwLo9MO == ozwOPrTfONtH:
ZlbFMSG8gCoF -= nzTpIcepk0o8(chr(0b10000 + 0o40) + chr(0b1101111) + '\x31', 8)
roI3spqORKae(KUIsAh6D2K2Z, roI3spqORKae(ES5oEprVxulp(b'\x16*62/\x80\x7f\x05\xdb\xe73\xe6'), chr(0b1000000 + 0o44) + chr(0b11010 + 0o113) + chr(0b1100011) + '\157' + chr(5313 - 5213) + chr(0b1100101))('\x75' + chr(0b1111 + 0o145) + '\x66' + '\x2d' + chr(2409 - 2353)))(roI3spqORKae(ES5oEprVxulp(b's'), chr(100) + chr(1069 - 968) + chr(0b1100011) + chr(0b1101111) + chr(4540 - 4440) + chr(3023 - 2922))('\x75' + chr(314 - 198) + chr(0b1011111 + 0o7) + chr(45) + chr(0b110100 + 0o4)))
roI3spqORKae(qZgIQ9B1vos4, roI3spqORKae(ES5oEprVxulp(b'\x16*62/\x80\x7f\x05\xdb\xe73\xe6'), '\144' + chr(101) + chr(0b1100011) + chr(0b100001 + 0o116) + chr(100) + chr(101))('\x75' + chr(903 - 787) + '\146' + '\055' + chr(0b111000)))(Lc5IsoUUe5Fv[ZlbFMSG8gCoF])
else:
raise zfo2Sgkz3IVJ(roI3spqORKae(ES5oEprVxulp(b")\n\x03'"), '\144' + chr(0b110110 + 0o57) + chr(99) + '\157' + '\x64' + '\145')(chr(9328 - 9211) + chr(116) + '\146' + chr(0b1 + 0o54) + chr(0b10011 + 0o45)))
fSdw5wwLo9MO = VpexCJyQNp0O[ZlbFMSG8gCoF, sChW4gUsXrIC]
qZgIQ9B1vos4 = roI3spqORKae(ES5oEprVxulp(b''), '\x64' + chr(0b1100101) + chr(3115 - 3016) + chr(111) + chr(3378 - 3278) + chr(0b1100101))(chr(0b1100110 + 0o17) + chr(0b1101000 + 0o14) + chr(0b1100110) + chr(45) + chr(573 - 517)).Y4yM9BcfTCNq(qZgIQ9B1vos4[::-nzTpIcepk0o8(chr(2268 - 2220) + '\157' + chr(0b1001 + 0o50), 8)])
KUIsAh6D2K2Z = roI3spqORKae(ES5oEprVxulp(b''), chr(0b1100100) + chr(0b1100101) + chr(0b1100011) + '\157' + chr(100) + chr(101))(chr(117) + chr(0b1110100) + chr(0b111101 + 0o51) + chr(301 - 256) + '\070').Y4yM9BcfTCNq(KUIsAh6D2K2Z[::-nzTpIcepk0o8('\x30' + '\x6f' + chr(82 - 33), 8)])
return (qZgIQ9B1vos4, KUIsAh6D2K2Z) if LeuPzfhzM9U8 else (KUIsAh6D2K2Z, qZgIQ9B1vos4) |
klavinslab/coral | coral/analysis/_sequencing/align.py | score_alignment | def score_alignment(a, b, gap_open, gap_extend, matrix):
'''Calculate the alignment score from two aligned sequences.
:param a: The first aligned sequence.
:type a: str
:param b: The second aligned sequence.
:type b: str
:param gap_open: The cost of opening a gap (negative number).
:type gap_open: int
:param gap_extend: The cost of extending an open gap (negative number).
:type gap_extend: int.
:param matrix: A score matrix dictionary name. Examples can be found in
the substitution_matrices module.
'''
al = a
bl = b
l = len(al)
score = 0
assert len(bl) == l, 'Alignment lengths must be the same'
mat = as_ord_matrix(matrix)
gap_started = 0
for i in range(l):
if al[i] == '-' or bl[i] == '-':
score += gap_extend if gap_started else gap_open
gap_started = 1
else:
score += mat[ord(al[i]), ord(bl[i])]
gap_started = 0
return score | python | def score_alignment(a, b, gap_open, gap_extend, matrix):
'''Calculate the alignment score from two aligned sequences.
:param a: The first aligned sequence.
:type a: str
:param b: The second aligned sequence.
:type b: str
:param gap_open: The cost of opening a gap (negative number).
:type gap_open: int
:param gap_extend: The cost of extending an open gap (negative number).
:type gap_extend: int.
:param matrix: A score matrix dictionary name. Examples can be found in
the substitution_matrices module.
'''
al = a
bl = b
l = len(al)
score = 0
assert len(bl) == l, 'Alignment lengths must be the same'
mat = as_ord_matrix(matrix)
gap_started = 0
for i in range(l):
if al[i] == '-' or bl[i] == '-':
score += gap_extend if gap_started else gap_open
gap_started = 1
else:
score += mat[ord(al[i]), ord(bl[i])]
gap_started = 0
return score | [
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"'... | Calculate the alignment score from two aligned sequences.
:param a: The first aligned sequence.
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:type b: str
:param gap_open: The cost of opening a gap (negative number).
:type gap_open: int
:param gap_extend: The cost of extending an open gap (negative number).
:type gap_extend: int.
:param matrix: A score matrix dictionary name. Examples can be found in
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/analysis/_sequencing/align.py#L188-L219 | train | Calculate the alignment score from two aligned sequences. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b100 + 0o54) + chr(0b111111 + 0o60) + '\065' + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(1902 - 1854) + chr(0b1101111) + chr(0b111 + 0o52) + '\066' + chr(48), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b10010 + 0o40) + '\061' + chr(0b101 + 0o54), 55885 - 55877), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b10011 + 0o40) + '\066' + chr(0b101 + 0o55), 52826 - 52818), nzTpIcepk0o8(chr(307 - 259) + chr(111) + chr(0b1110 + 0o47) + chr(49), 0o10), nzTpIcepk0o8(chr(0b111 + 0o51) + '\157' + '\x33' + '\066' + chr(578 - 527), 0b1000), nzTpIcepk0o8(chr(2236 - 2188) + chr(0b1101111) + '\061' + chr(53), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110010), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b111110 + 0o61) + chr(51) + chr(0b110011 + 0o4) + '\x31', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b1111 + 0o43) + chr(0b11101 + 0o26) + chr(0b110111), 22996 - 22988), nzTpIcepk0o8(chr(48) + chr(0b1101011 + 0o4) + chr(51) + chr(48) + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\063' + chr(49) + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(51) + chr(55) + chr(0b110000), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + '\x32' + '\065' + '\x32', 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(51) + chr(51) + chr(51), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(132 - 21) + chr(566 - 516) + '\067' + chr(55), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + '\x32' + chr(50) + '\066', 0b1000), nzTpIcepk0o8('\060' + chr(0b11110 + 0o121) + '\062' + chr(0b11010 + 0o35) + chr(0b100001 + 0o23), 57218 - 57210), nzTpIcepk0o8(chr(0b11010 + 0o26) + chr(0b1101111) + chr(0b110001) + '\061' + chr(51), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(2051 - 2002) + '\x30' + '\x34', 45790 - 45782), nzTpIcepk0o8(chr(0b11000 + 0o30) + chr(111) + chr(2426 - 2375) + chr(2982 - 2927) + chr(0b110000), 8), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b1 + 0o62) + chr(52) + chr(55), 61683 - 61675), nzTpIcepk0o8(chr(48) + chr(0b111111 + 0o60) + chr(0b100011 + 0o20) + chr(0b1001 + 0o52) + chr(48), 11667 - 11659), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x32' + chr(554 - 501) + chr(2516 - 2462), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + '\065' + chr(53), 8), nzTpIcepk0o8('\x30' + chr(9583 - 9472) + '\x33' + chr(55) + chr(0b100010 + 0o21), ord("\x08")), nzTpIcepk0o8(chr(0b11110 + 0o22) + chr(0b100001 + 0o116) + chr(0b110011) + '\x35' + chr(733 - 684), 37184 - 37176), nzTpIcepk0o8('\060' + '\157' + chr(0b101110 + 0o6) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110101) + chr(0b110000 + 0o4), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(4382 - 4271) + '\x32' + '\x33' + chr(55), 8), nzTpIcepk0o8(chr(48) + chr(111) + '\063' + '\064' + chr(2504 - 2453), 1416 - 1408), nzTpIcepk0o8('\x30' + chr(111) + chr(1732 - 1682), 8), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(429 - 379) + chr(52) + chr(0b0 + 0o66), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1100001 + 0o16) + '\062' + chr(0b10001 + 0o43) + chr(0b1000 + 0o50), 40129 - 40121), nzTpIcepk0o8(chr(0b110000) + chr(9347 - 9236) + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\062' + chr(0b110011), 8843 - 8835), nzTpIcepk0o8('\x30' + chr(0b101100 + 0o103) + '\063' + '\x34' + chr(49), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b11100 + 0o26) + chr(1545 - 1490) + chr(53), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x31' + chr(1214 - 1161) + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101100 + 0o3) + chr(2332 - 2281) + chr(496 - 448), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + '\157' + chr(0b100101 + 0o20) + chr(2212 - 2164), 39140 - 39132)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x03'), chr(0b1000110 + 0o36) + '\145' + chr(9710 - 9611) + chr(4757 - 4646) + chr(8237 - 8137) + chr(0b1100101))(chr(117) + '\164' + '\x66' + chr(45) + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def lzxcvk1bn41Z(AQ9ceR9AaoT1, xFDEVQn5qSdh, uPHeZKKBo482, rfmfuQvZ1V7R, kcnyYx1RySWO):
i6Oteg3Wiqr7 = AQ9ceR9AaoT1
UsIpVMDUDSVi = xFDEVQn5qSdh
fPrVrKACaFCC = ftfygxgFas5X(i6Oteg3Wiqr7)
CLmnnuotoMDU = nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\060', 0o10)
assert ftfygxgFas5X(UsIpVMDUDSVi) == fPrVrKACaFCC, roI3spqORKae(ES5oEprVxulp(b'l\x1c\xe0\x95G\x9ehl\x8d\xbf\xa9\xa9\x96\xcd\xaf\xd7\xe5\x9c&1\x8b\x93\xf8\xccH\xdb\x9dKI\xbf\x90c\xcb\xc5'), chr(6446 - 6346) + chr(0b1100101) + chr(4243 - 4144) + '\157' + chr(6526 - 6426) + chr(4910 - 4809))(chr(5227 - 5110) + chr(0b1110100) + chr(5795 - 5693) + chr(0b10100 + 0o31) + '\x38')
K_Ma2k2FCM8b = YuiOQePEezm3(kcnyYx1RySWO)
m8OQr54y0XQI = nzTpIcepk0o8(chr(48) + chr(111) + '\060', 8)
for ZlbFMSG8gCoF in bbT2xIe5pzk7(fPrVrKACaFCC):
if i6Oteg3Wiqr7[ZlbFMSG8gCoF] == roI3spqORKae(ES5oEprVxulp(b'\x00'), chr(7809 - 7709) + chr(101) + chr(819 - 720) + chr(0b10011 + 0o134) + '\x64' + '\145')('\165' + chr(1242 - 1126) + '\146' + '\055' + '\070') or UsIpVMDUDSVi[ZlbFMSG8gCoF] == roI3spqORKae(ES5oEprVxulp(b'\x00'), chr(100) + chr(5787 - 5686) + '\143' + chr(5838 - 5727) + chr(0b101000 + 0o74) + chr(101))('\165' + chr(11005 - 10889) + chr(3328 - 3226) + chr(0b101101) + chr(56)):
CLmnnuotoMDU += rfmfuQvZ1V7R if m8OQr54y0XQI else uPHeZKKBo482
m8OQr54y0XQI = nzTpIcepk0o8('\060' + '\x6f' + chr(49), 0b1000)
else:
CLmnnuotoMDU += K_Ma2k2FCM8b[RmKXV0QRcrJP(i6Oteg3Wiqr7[ZlbFMSG8gCoF]), RmKXV0QRcrJP(UsIpVMDUDSVi[ZlbFMSG8gCoF])]
m8OQr54y0XQI = nzTpIcepk0o8(chr(0b1111 + 0o41) + '\157' + chr(48), 8)
return CLmnnuotoMDU |
klavinslab/coral | bin/build_sphinx_docs.py | build_docs | def build_docs(directory):
"""Builds sphinx docs from a given directory."""
os.chdir(directory)
process = subprocess.Popen(["make", "html"], cwd=directory)
process.communicate() | python | def build_docs(directory):
"""Builds sphinx docs from a given directory."""
os.chdir(directory)
process = subprocess.Popen(["make", "html"], cwd=directory)
process.communicate() | [
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"."
] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/bin/build_sphinx_docs.py#L11-L15 | train | Builds sphinx docs from a given directory. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8('\060' + '\157' + chr(49) + chr(2403 - 2351) + chr(0b100001 + 0o17), ord("\x08")), nzTpIcepk0o8(chr(1277 - 1229) + chr(11692 - 11581) + chr(50) + chr(699 - 648) + chr(2027 - 1976), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111 + 0o0) + chr(50) + '\065' + '\061', ord("\x08")), nzTpIcepk0o8('\x30' + chr(10729 - 10618) + chr(53) + chr(51), 39362 - 39354), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110011) + chr(0b110111) + chr(0b10100 + 0o43), ord("\x08")), nzTpIcepk0o8(chr(0b110000 + 0o0) + chr(3448 - 3337) + '\063' + chr(0b100111 + 0o11) + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(0b1000 + 0o50) + chr(0b10001 + 0o136) + chr(0b110010) + chr(0b0 + 0o64) + '\x32', 0b1000), nzTpIcepk0o8(chr(478 - 430) + '\157' + chr(0b110010) + chr(0b110110) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(0b100011 + 0o15) + chr(0b1101111) + chr(49) + chr(55) + chr(0b110001), 0o10), nzTpIcepk0o8(chr(1497 - 1449) + chr(0b1101001 + 0o6) + chr(0b1101 + 0o47), ord("\x08")), nzTpIcepk0o8(chr(0b110000 + 0o0) + '\157' + '\x31' + chr(547 - 497) + chr(51), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + '\x37' + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x37' + chr(48), 8), nzTpIcepk0o8('\060' + chr(0b1000110 + 0o51) + chr(0b101111 + 0o7), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111 + 0o0) + chr(0b100101 + 0o16) + chr(660 - 609) + '\065', 8055 - 8047), nzTpIcepk0o8('\x30' + chr(111) + chr(0b100000 + 0o21) + '\067' + '\065', 47057 - 47049), nzTpIcepk0o8(chr(1010 - 962) + chr(0b1100010 + 0o15) + chr(0b1000 + 0o54), 8), nzTpIcepk0o8('\x30' + chr(4321 - 4210) + '\061' + chr(51) + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b11101 + 0o25) + '\060' + '\066', 0b1000), nzTpIcepk0o8(chr(619 - 571) + chr(4580 - 4469) + chr(1955 - 1906) + chr(0b1110 + 0o51) + '\061', 8), nzTpIcepk0o8(chr(58 - 10) + '\157' + chr(0b110100) + chr(0b110111), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b101110 + 0o5) + chr(51) + chr(1698 - 1650), 57499 - 57491), nzTpIcepk0o8(chr(0b11000 + 0o30) + chr(0b11010 + 0o125) + chr(0b110011) + chr(55) + chr(0b110110), 49760 - 49752), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b100100 + 0o17) + '\067' + chr(49), 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(0b100111 + 0o13) + '\x33' + chr(0b100100 + 0o15), 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(0b100110 + 0o13) + chr(256 - 208), 0o10), nzTpIcepk0o8(chr(0b11101 + 0o23) + chr(0b1010101 + 0o32) + chr(50) + '\065' + '\x36', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110011) + chr(1567 - 1515) + chr(0b101010 + 0o10), 0o10), nzTpIcepk0o8(chr(0b101110 + 0o2) + '\157' + chr(2115 - 2066) + '\065' + chr(54 - 2), 0b1000), nzTpIcepk0o8('\060' + '\157' + '\x31' + chr(0b110100) + '\062', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b11001 + 0o126) + chr(0b100001 + 0o24) + '\060', 0o10), nzTpIcepk0o8(chr(992 - 944) + '\x6f' + chr(50) + chr(0b110111), 16187 - 16179), nzTpIcepk0o8(chr(48) + chr(9051 - 8940) + chr(0b110110) + chr(284 - 230), 0o10), nzTpIcepk0o8('\x30' + chr(2781 - 2670) + chr(1621 - 1571) + '\x34' + '\x33', ord("\x08")), nzTpIcepk0o8(chr(0b1100 + 0o44) + chr(111) + chr(0b100010 + 0o17) + '\067' + chr(51), 0o10), nzTpIcepk0o8(chr(824 - 776) + chr(0b1101111) + chr(0b110011) + chr(0b110110) + chr(486 - 433), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + '\063' + chr(2170 - 2116) + chr(0b110011), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(1668 - 1616) + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(0b100100 + 0o14) + chr(0b110111 + 0o70) + chr(813 - 762) + chr(50) + chr(0b10111 + 0o40), ord("\x08")), nzTpIcepk0o8(chr(1761 - 1713) + '\x6f' + chr(0b110001) + chr(52) + '\067', ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + '\x6f' + '\x35' + chr(0b110000), 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'N'), chr(7856 - 7756) + chr(0b1000011 + 0o42) + '\x63' + '\x6f' + '\144' + chr(101))(chr(117) + chr(0b1110100) + '\x66' + '\x2d' + chr(0b1 + 0o67)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def YxFQOCqTP2jI(InVoWQwNBeGF):
roI3spqORKae(aHUqKstZLeS6, roI3spqORKae(ES5oEprVxulp(b'\x03\xf3\xcdB\x8d'), '\x64' + chr(0b1100101) + chr(0b1100011) + chr(0b1101111) + '\x64' + '\145')(chr(0b10010 + 0o143) + '\164' + chr(0b1110 + 0o130) + '\x2d' + chr(797 - 741)))(InVoWQwNBeGF)
conU5pBPX9i7 = eT8Y087E_kfd.Popen([roI3spqORKae(ES5oEprVxulp(b'\r\xfa\xc2N'), '\x64' + '\x65' + chr(6415 - 6316) + chr(0b1101111) + '\144' + '\145')('\165' + '\x74' + '\146' + chr(0b10001 + 0o34) + chr(0b111000)), roI3spqORKae(ES5oEprVxulp(b'\x08\xef\xc4G'), chr(0b10100 + 0o120) + chr(0b100010 + 0o103) + '\143' + '\157' + chr(0b1100100) + '\x65')('\165' + chr(116) + '\146' + chr(0b101101) + '\x38')], cwd=InVoWQwNBeGF)
roI3spqORKae(conU5pBPX9i7, roI3spqORKae(ES5oEprVxulp(b'\x04\xf4\x9fA\xce\x93\xf3\xde\x12R!a'), chr(1583 - 1483) + chr(0b10101 + 0o120) + chr(99) + chr(10456 - 10345) + '\144' + chr(0b1001010 + 0o33))('\165' + '\x74' + chr(0b1100110) + chr(0b101101) + '\x38'))() |
klavinslab/coral | coral/design/_gibson.py | gibson_primers | def gibson_primers(dna1, dna2, overlap='mixed', maxlen=80, overlap_tm=65.0,
insert=None, primer_kwargs=None):
'''Design Gibson primers given two DNA sequences (connect left to right)
:param dna1: First piece of DNA for which to design primers. Once Gibsoned,
would be connected at its right side to dna2.
:type dna1: coral.DNA
:param dna2: First piece of DNA for which to design primers. Once Gibsoned,
would be connected at its right side to dna2.
:type dna2: coral.DNA
:param overlap: Specifies location of overlap. 'left' puts it on the 'dna1'
side (i.e. the primer to amplify dna2). 'right' puts it on
the dna2 side, and 'mixed' does a ~50:50 split
:type overlap: str
:param maxlen: Maximum length of each primer.
:type maxlen: int
:param overlap_tm: Minimum Tm of overlap
:type overlap_tm: float
:param insert: A DNA insert to add with primers and use as assembly
homology. This overrides the 'split' argument.
:type insert: coral.DNA
:param primer_kwargs: keyword arguments to pass to design_primer()
:type primer_kwargs: dict
:returns: Reverse, then forward primer for bridging the two sequences.
Note that the forward primer binds dna2, reverse dna1.
:rtype: A sequence.Primer tuple
:raises: ValueError if split parameter is an invalid string.
'''
if primer_kwargs is None:
primer_kwargs = {}
# Annealing sequences
# DNA 2 primer is a forward primer
fwd_anneal = coral.design.primer(dna2, **primer_kwargs)
# DNA 1 primer is a reverse primer
rev_anneal = coral.design.primer(dna1.flip(), **primer_kwargs)
# Overhangs
if insert is None:
# No insert, so follow split argument
if overlap == 'left':
# If splitting left, put overhang on forward primer
overlap_revcomp = coral.design.primer(dna1.flip(), tm=overlap_tm,
tm_undershoot=0)
fwd_overhang = overlap_revcomp.primer().reverse_complement()
rev_overhang = None
elif overlap == 'right':
# If splitting right, put overhang on reverse primer
overlap = coral.design.primer(dna2, tm=overlap_tm, tm_undershoot=0)
fwd_overhang = None
rev_overhang = overlap.primer().reverse_complement()
elif overlap == 'mixed':
# If mixed, grow size of both until overlap Tm is reached
overlap_l = dna1[0:0] # Empty sequence.DNA
overlap_r = dna2[0] # First base
overlap_melt = overlap_r.tm()
while overlap_melt < overlap_tm:
rlen = len(overlap_r)
llen = len(overlap_l)
if rlen > llen:
# Increase left side of overlap
overlap_l = dna1[-(rlen + 1):]
else:
# Increase right side of overlap
overlap_r = dna2[:(llen + 1)]
overlap = overlap_l + overlap_r
overlap_melt = overlap.tm()
fwd_overhang = overlap_l
rev_overhang = overlap_r.reverse_complement()
else:
raise ValueError('split argument must be left, right, or mixed')
# Generate primers using anneal, overhang, and tm data
fwd = coral.Primer(fwd_anneal.primer(), tm=fwd_anneal.tm,
overhang=fwd_overhang)
rev = coral.Primer(rev_anneal.primer(), tm=rev_anneal.tm,
overhang=rev_overhang)
else:
# There's an insert to use as the overhang
overlap = insert
fwd_overhang = insert.primer()
rev_overhang = insert.reverse_complement().primer()
# Generate primers using anneal, overhang, and tm data
fwd = coral.Primer(fwd_anneal.primer(), tm=fwd_anneal.tm,
overhang=fwd_overhang)
rev = coral.Primer(rev_anneal.primer(), tm=rev_anneal.tm,
overhang=rev_overhang)
left_trim = 0
# If either primer is too long, try trimming the overhang
while len(fwd) > maxlen:
# Generate new overlap
overlap = insert[left_trim:]
# Tm must be above overlap_tm
if coral.analysis.tm(overlap) < overlap_tm:
raise TmError('Right primer is too long with this Tm setting.')
# Regenerate forward overhang
fwd_overhang = overlap.primer()
# Regenerate primer with new overhang
fwd = coral.Primer(fwd_anneal.primer(), tm=fwd_anneal.tm,
overhang=fwd_overhang)
# Increase 'trimming' index
left_trim += 1
right_trim = 0
while len(rev) > maxlen:
# Generate new overlap
overlap = insert[:len(insert) - right_trim]
# Tm must be above overlap_tm
if coral.analysis.tm(overlap) < overlap_tm:
raise TmError('Left primer is too long with this Tm setting.')
# Regenerate reverse overhang
rev_overhang = overlap.reverse_complement().to_ss()
rev = coral.Primer(rev_anneal.to_ss(), tm=rev_anneal.tm,
overhang=rev_overhang)
# Increase 'trimming' index
right_trim += 1
# Check primer lengths
if any([len(primer) > maxlen for primer in (fwd, rev)]):
raise LengthError('At least one of the primers is longer than maxlen.')
return rev, fwd | python | def gibson_primers(dna1, dna2, overlap='mixed', maxlen=80, overlap_tm=65.0,
insert=None, primer_kwargs=None):
'''Design Gibson primers given two DNA sequences (connect left to right)
:param dna1: First piece of DNA for which to design primers. Once Gibsoned,
would be connected at its right side to dna2.
:type dna1: coral.DNA
:param dna2: First piece of DNA for which to design primers. Once Gibsoned,
would be connected at its right side to dna2.
:type dna2: coral.DNA
:param overlap: Specifies location of overlap. 'left' puts it on the 'dna1'
side (i.e. the primer to amplify dna2). 'right' puts it on
the dna2 side, and 'mixed' does a ~50:50 split
:type overlap: str
:param maxlen: Maximum length of each primer.
:type maxlen: int
:param overlap_tm: Minimum Tm of overlap
:type overlap_tm: float
:param insert: A DNA insert to add with primers and use as assembly
homology. This overrides the 'split' argument.
:type insert: coral.DNA
:param primer_kwargs: keyword arguments to pass to design_primer()
:type primer_kwargs: dict
:returns: Reverse, then forward primer for bridging the two sequences.
Note that the forward primer binds dna2, reverse dna1.
:rtype: A sequence.Primer tuple
:raises: ValueError if split parameter is an invalid string.
'''
if primer_kwargs is None:
primer_kwargs = {}
# Annealing sequences
# DNA 2 primer is a forward primer
fwd_anneal = coral.design.primer(dna2, **primer_kwargs)
# DNA 1 primer is a reverse primer
rev_anneal = coral.design.primer(dna1.flip(), **primer_kwargs)
# Overhangs
if insert is None:
# No insert, so follow split argument
if overlap == 'left':
# If splitting left, put overhang on forward primer
overlap_revcomp = coral.design.primer(dna1.flip(), tm=overlap_tm,
tm_undershoot=0)
fwd_overhang = overlap_revcomp.primer().reverse_complement()
rev_overhang = None
elif overlap == 'right':
# If splitting right, put overhang on reverse primer
overlap = coral.design.primer(dna2, tm=overlap_tm, tm_undershoot=0)
fwd_overhang = None
rev_overhang = overlap.primer().reverse_complement()
elif overlap == 'mixed':
# If mixed, grow size of both until overlap Tm is reached
overlap_l = dna1[0:0] # Empty sequence.DNA
overlap_r = dna2[0] # First base
overlap_melt = overlap_r.tm()
while overlap_melt < overlap_tm:
rlen = len(overlap_r)
llen = len(overlap_l)
if rlen > llen:
# Increase left side of overlap
overlap_l = dna1[-(rlen + 1):]
else:
# Increase right side of overlap
overlap_r = dna2[:(llen + 1)]
overlap = overlap_l + overlap_r
overlap_melt = overlap.tm()
fwd_overhang = overlap_l
rev_overhang = overlap_r.reverse_complement()
else:
raise ValueError('split argument must be left, right, or mixed')
# Generate primers using anneal, overhang, and tm data
fwd = coral.Primer(fwd_anneal.primer(), tm=fwd_anneal.tm,
overhang=fwd_overhang)
rev = coral.Primer(rev_anneal.primer(), tm=rev_anneal.tm,
overhang=rev_overhang)
else:
# There's an insert to use as the overhang
overlap = insert
fwd_overhang = insert.primer()
rev_overhang = insert.reverse_complement().primer()
# Generate primers using anneal, overhang, and tm data
fwd = coral.Primer(fwd_anneal.primer(), tm=fwd_anneal.tm,
overhang=fwd_overhang)
rev = coral.Primer(rev_anneal.primer(), tm=rev_anneal.tm,
overhang=rev_overhang)
left_trim = 0
# If either primer is too long, try trimming the overhang
while len(fwd) > maxlen:
# Generate new overlap
overlap = insert[left_trim:]
# Tm must be above overlap_tm
if coral.analysis.tm(overlap) < overlap_tm:
raise TmError('Right primer is too long with this Tm setting.')
# Regenerate forward overhang
fwd_overhang = overlap.primer()
# Regenerate primer with new overhang
fwd = coral.Primer(fwd_anneal.primer(), tm=fwd_anneal.tm,
overhang=fwd_overhang)
# Increase 'trimming' index
left_trim += 1
right_trim = 0
while len(rev) > maxlen:
# Generate new overlap
overlap = insert[:len(insert) - right_trim]
# Tm must be above overlap_tm
if coral.analysis.tm(overlap) < overlap_tm:
raise TmError('Left primer is too long with this Tm setting.')
# Regenerate reverse overhang
rev_overhang = overlap.reverse_complement().to_ss()
rev = coral.Primer(rev_anneal.to_ss(), tm=rev_anneal.tm,
overhang=rev_overhang)
# Increase 'trimming' index
right_trim += 1
# Check primer lengths
if any([len(primer) > maxlen for primer in (fwd, rev)]):
raise LengthError('At least one of the primers is longer than maxlen.')
return rev, fwd | [
"def",
"gibson_primers",
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"dna2",
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"'mixed'",
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",",
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"=",
"65.0",
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"... | Design Gibson primers given two DNA sequences (connect left to right)
:param dna1: First piece of DNA for which to design primers. Once Gibsoned,
would be connected at its right side to dna2.
:type dna1: coral.DNA
:param dna2: First piece of DNA for which to design primers. Once Gibsoned,
would be connected at its right side to dna2.
:type dna2: coral.DNA
:param overlap: Specifies location of overlap. 'left' puts it on the 'dna1'
side (i.e. the primer to amplify dna2). 'right' puts it on
the dna2 side, and 'mixed' does a ~50:50 split
:type overlap: str
:param maxlen: Maximum length of each primer.
:type maxlen: int
:param overlap_tm: Minimum Tm of overlap
:type overlap_tm: float
:param insert: A DNA insert to add with primers and use as assembly
homology. This overrides the 'split' argument.
:type insert: coral.DNA
:param primer_kwargs: keyword arguments to pass to design_primer()
:type primer_kwargs: dict
:returns: Reverse, then forward primer for bridging the two sequences.
Note that the forward primer binds dna2, reverse dna1.
:rtype: A sequence.Primer tuple
:raises: ValueError if split parameter is an invalid string. | [
"Design",
"Gibson",
"primers",
"given",
"two",
"DNA",
"sequences",
"(",
"connect",
"left",
"to",
"right",
")"
] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/design/_gibson.py#L15-L133 | train | Design Gibson primers given two DNA sequences. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(48) + chr(9810 - 9699) + chr(0b110011) + chr(2151 - 2098), 0o10), nzTpIcepk0o8(chr(0b11101 + 0o23) + chr(0b100000 + 0o117) + '\x33' + chr(0b101011 + 0o6) + '\x34', 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + '\x31' + chr(0b110101) + chr(0b110100), 0o10), nzTpIcepk0o8(chr(48) + chr(0b101111 + 0o100) + '\063' + '\x37' + '\066', ord("\x08")), nzTpIcepk0o8(chr(2010 - 1962) + chr(0b111000 + 0o67) + chr(49) + chr(49) + chr(0b110101), 40816 - 40808), nzTpIcepk0o8(chr(48) + '\x6f' + '\x31' + chr(53) + chr(0b110011), 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110011) + '\062' + '\061', 0o10), nzTpIcepk0o8(chr(48) + chr(7955 - 7844) + chr(49) + '\065' + chr(0b110010 + 0o1), 8), nzTpIcepk0o8('\060' + chr(111) + '\061' + '\x31' + '\x34', ord("\x08")), nzTpIcepk0o8('\060' + '\157' + '\062' + chr(0b110000 + 0o7) + '\x36', 0o10), nzTpIcepk0o8('\060' + chr(6703 - 6592) + chr(0b111 + 0o52) + chr(0b11000 + 0o32) + chr(0b101010 + 0o12), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b110110 + 0o71) + chr(0b110010) + chr(0b110100) + chr(0b110011), 0o10), nzTpIcepk0o8('\x30' + chr(111) + '\061' + '\x36' + chr(0b101000 + 0o16), 0o10), nzTpIcepk0o8('\x30' + chr(0b101 + 0o152) + chr(50) + '\x34' + '\060', ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(0b1101 + 0o45) + '\062' + '\061', 0b1000), nzTpIcepk0o8(chr(0b1110 + 0o42) + chr(3585 - 3474) + chr(0b110001 + 0o1) + chr(0b100100 + 0o15) + '\062', 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x33' + chr(2104 - 2054) + chr(0b110000), 0b1000), nzTpIcepk0o8('\060' + chr(6214 - 6103) + '\x32' + chr(416 - 367) + chr(0b110000), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1001 + 0o146) + '\061' + '\x34' + chr(48), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(9144 - 9033) + chr(1368 - 1319) + chr(209 - 160) + chr(0b110000), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(851 - 800) + chr(48) + chr(371 - 316), 0o10), nzTpIcepk0o8('\060' + chr(2315 - 2204) + chr(0b101100 + 0o5) + chr(0b110110) + chr(0b10100 + 0o34), 42121 - 42113), nzTpIcepk0o8(chr(0b110000) + chr(7301 - 7190) + '\062' + '\066' + chr(53), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(6271 - 6160) + chr(51) + '\x33' + chr(0b1111 + 0o46), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(4433 - 4322) + chr(0b110011) + chr(51) + chr(2276 - 2226), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(2526 - 2415) + chr(0b110010) + '\066' + chr(0b110111), 10475 - 10467), nzTpIcepk0o8(chr(246 - 198) + chr(0b100110 + 0o111) + chr(2214 - 2162), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110010) + chr(50), 18994 - 18986), nzTpIcepk0o8(chr(2049 - 2001) + chr(0b1011 + 0o144) + '\x33' + chr(54) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(2041 - 1993) + chr(6152 - 6041) + chr(0b110100) + chr(53), 6048 - 6040), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110010) + chr(0b100001 + 0o22) + '\065', 0o10), nzTpIcepk0o8('\x30' + chr(2997 - 2886) + '\067' + chr(1698 - 1644), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x32' + '\060' + '\061', 43751 - 43743), nzTpIcepk0o8('\x30' + '\x6f' + chr(334 - 283) + '\x34' + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110010) + chr(0b110001 + 0o3) + '\060', 8), nzTpIcepk0o8('\060' + chr(4892 - 4781) + chr(49) + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(49) + '\067' + chr(52), ord("\x08")), nzTpIcepk0o8(chr(2166 - 2118) + chr(111) + chr(0b110011) + chr(0b11011 + 0o26) + '\x32', 43643 - 43635), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(972 - 923) + '\x33' + chr(0b110111), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110111) + chr(0b0 + 0o62), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + '\157' + chr(53) + '\060', 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'3'), chr(0b1100100) + chr(0b1001011 + 0o32) + '\143' + '\x6f' + chr(0b110100 + 0o60) + chr(5406 - 5305))('\165' + chr(0b1110100) + chr(0b111 + 0o137) + chr(1816 - 1771) + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def jqT3uQnH4ZeC(OeMNWHY0H6WC, bRsJ3WtCQnRh, ld_y4NQrCDaG=roI3spqORKae(ES5oEprVxulp(b'p\xa5\x14\x9b)'), chr(100) + chr(101) + '\x63' + chr(0b101100 + 0o103) + chr(0b110010 + 0o62) + chr(4381 - 4280))(chr(117) + chr(116) + chr(5773 - 5671) + '\x2d' + chr(0b1000 + 0o60)), bkEe14a1B30s=nzTpIcepk0o8(chr(48) + chr(1797 - 1686) + '\x31' + chr(909 - 859) + chr(0b110000), ord("\x08")), iQ3fevH6TJA9=65.0, Pv_O0UBzNUCL=None, BvmDTzQ9_6tg=None):
if BvmDTzQ9_6tg is None:
BvmDTzQ9_6tg = {}
s4IHm3XQ0oTc = _bFWSozA7z0G.design.primer(bRsJ3WtCQnRh, **BvmDTzQ9_6tg)
B2CCvKlHvjuo = _bFWSozA7z0G.design.primer(OeMNWHY0H6WC.flip(), **BvmDTzQ9_6tg)
if Pv_O0UBzNUCL is None:
if ld_y4NQrCDaG == roI3spqORKae(ES5oEprVxulp(b'q\xa9\n\x8a'), chr(100) + chr(0b11101 + 0o110) + chr(4993 - 4894) + chr(0b1001000 + 0o47) + chr(0b111011 + 0o51) + '\145')(chr(117) + '\x74' + chr(102) + chr(0b101101) + chr(0b101000 + 0o20)):
oUVu5EsQVJW2 = _bFWSozA7z0G.design.primer(OeMNWHY0H6WC.flip(), tm=iQ3fevH6TJA9, tm_undershoot=nzTpIcepk0o8('\060' + chr(9066 - 8955) + chr(0b111 + 0o51), 23768 - 23760))
mlwSKwkTxZBP = oUVu5EsQVJW2.primer().reverse_complement()
VU2zc5rCdloJ = None
elif ld_y4NQrCDaG == roI3spqORKae(ES5oEprVxulp(b'o\xa5\x0b\x969'), chr(0b1100100) + chr(101) + '\143' + chr(0b1111 + 0o140) + '\x64' + chr(0b101001 + 0o74))(chr(0b1110101) + chr(0b1010110 + 0o36) + chr(102) + chr(0b1100 + 0o41) + chr(0b1101 + 0o53)):
ld_y4NQrCDaG = _bFWSozA7z0G.design.primer(bRsJ3WtCQnRh, tm=iQ3fevH6TJA9, tm_undershoot=nzTpIcepk0o8('\x30' + chr(6184 - 6073) + chr(0b100000 + 0o20), 8))
mlwSKwkTxZBP = None
VU2zc5rCdloJ = ld_y4NQrCDaG.primer().reverse_complement()
elif ld_y4NQrCDaG == roI3spqORKae(ES5oEprVxulp(b'p\xa5\x14\x9b)'), '\144' + '\x65' + chr(0b1000011 + 0o40) + chr(1400 - 1289) + chr(0b1100011 + 0o1) + chr(101))(chr(2652 - 2535) + '\164' + chr(0b1100110) + chr(0b101101) + chr(452 - 396)):
bIy6jTJwd9un = OeMNWHY0H6WC[nzTpIcepk0o8('\060' + chr(6393 - 6282) + chr(0b100010 + 0o16), 8):nzTpIcepk0o8(chr(48) + '\x6f' + '\060', 8)]
j_b9EKdRL8q0 = bRsJ3WtCQnRh[nzTpIcepk0o8('\x30' + chr(111) + '\x30', 8)]
ZEALPJW4wN9U = j_b9EKdRL8q0.VH5NUDuH5Da3()
while ZEALPJW4wN9U < iQ3fevH6TJA9:
xtxVNkUAzXlF = ftfygxgFas5X(j_b9EKdRL8q0)
w1nNjaiR_Mzn = ftfygxgFas5X(bIy6jTJwd9un)
if xtxVNkUAzXlF > w1nNjaiR_Mzn:
bIy6jTJwd9un = OeMNWHY0H6WC[-(xtxVNkUAzXlF + nzTpIcepk0o8('\060' + chr(0b1101111) + chr(1087 - 1038), 10408 - 10400)):]
else:
j_b9EKdRL8q0 = bRsJ3WtCQnRh[:w1nNjaiR_Mzn + nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110001), 8)]
ld_y4NQrCDaG = bIy6jTJwd9un + j_b9EKdRL8q0
ZEALPJW4wN9U = ld_y4NQrCDaG.VH5NUDuH5Da3()
mlwSKwkTxZBP = bIy6jTJwd9un
VU2zc5rCdloJ = j_b9EKdRL8q0.reverse_complement()
else:
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'n\xbc\x00\x979K\xb0\x19+\xcb9\xc6\x18\xd4\xb1\xe7\xa5\xfb\x14h\xa5\x15\x95\xb1\xbf\xd1p>\xd3W\xf4Y\xe9\x90\x8c/\x13\xb8\x7fWt\xb4\t\x9a'), chr(0b1100100) + chr(0b1100101) + chr(0b101 + 0o136) + chr(111) + '\x64' + chr(101))(chr(0b1110101) + chr(0b1110100) + '\146' + chr(389 - 344) + '\070'))
f6ucHbZL4GdI = _bFWSozA7z0G.Primer(s4IHm3XQ0oTc.primer(), tm=s4IHm3XQ0oTc.VH5NUDuH5Da3, overhang=mlwSKwkTxZBP)
dizdA8h9BTE_ = _bFWSozA7z0G.Primer(B2CCvKlHvjuo.primer(), tm=B2CCvKlHvjuo.VH5NUDuH5Da3, overhang=VU2zc5rCdloJ)
else:
ld_y4NQrCDaG = Pv_O0UBzNUCL
mlwSKwkTxZBP = Pv_O0UBzNUCL.primer()
VU2zc5rCdloJ = Pv_O0UBzNUCL.reverse_complement().primer()
f6ucHbZL4GdI = _bFWSozA7z0G.Primer(s4IHm3XQ0oTc.primer(), tm=s4IHm3XQ0oTc.VH5NUDuH5Da3, overhang=mlwSKwkTxZBP)
dizdA8h9BTE_ = _bFWSozA7z0G.Primer(B2CCvKlHvjuo.primer(), tm=B2CCvKlHvjuo.VH5NUDuH5Da3, overhang=VU2zc5rCdloJ)
ipWoTTVUSkS_ = nzTpIcepk0o8(chr(0b10010 + 0o36) + '\x6f' + chr(0b110000 + 0o0), 8)
while ftfygxgFas5X(f6ucHbZL4GdI) > bkEe14a1B30s:
ld_y4NQrCDaG = Pv_O0UBzNUCL[ipWoTTVUSkS_:]
if roI3spqORKae(_bFWSozA7z0G.analysis, roI3spqORKae(ES5oEprVxulp(b'K\x84Y\xb0\x18/\xa4#y\xfa5\x90'), chr(0b1100100) + '\145' + chr(0b1100011) + chr(111) + chr(0b1100100) + '\145')(chr(13667 - 13550) + chr(116) + chr(8202 - 8100) + '\x2d' + chr(56)))(ld_y4NQrCDaG) < iQ3fevH6TJA9:
raise fcQOG4ggCT8R(roI3spqORKae(ES5oEprVxulp(b'O\xa5\x0b\x969K\xa1\x19%\xd31\xd1V\xc9\xe2\xaa\xa4\xe7\x0fh\xab\x1f\xdb\xba\xfa\xc0mf\x9b\x05\xe9V\xe8\x97\x80[\x11\xea,_i\xb8\x05\x90*E'), '\144' + chr(6031 - 5930) + '\143' + chr(0b0 + 0o157) + chr(100) + chr(0b10100 + 0o121))('\x75' + '\x74' + '\x66' + chr(45) + chr(411 - 355)))
mlwSKwkTxZBP = ld_y4NQrCDaG.primer()
f6ucHbZL4GdI = _bFWSozA7z0G.Primer(s4IHm3XQ0oTc.primer(), tm=s4IHm3XQ0oTc.VH5NUDuH5Da3, overhang=mlwSKwkTxZBP)
ipWoTTVUSkS_ += nzTpIcepk0o8('\x30' + chr(6294 - 6183) + '\x31', 8)
Y6bbKAvaNg9D = nzTpIcepk0o8('\x30' + '\157' + chr(0b110000), 8)
while ftfygxgFas5X(dizdA8h9BTE_) > bkEe14a1B30s:
ld_y4NQrCDaG = Pv_O0UBzNUCL[:ftfygxgFas5X(Pv_O0UBzNUCL) - Y6bbKAvaNg9D]
if roI3spqORKae(_bFWSozA7z0G.analysis, roI3spqORKae(ES5oEprVxulp(b'K\x84Y\xb0\x18/\xa4#y\xfa5\x90'), '\144' + chr(0b1100101) + '\x63' + chr(0b1101111) + '\x64' + chr(0b1100101))('\165' + '\x74' + '\x66' + chr(0b1001 + 0o44) + '\x38'))(ld_y4NQrCDaG) < iQ3fevH6TJA9:
raise fcQOG4ggCT8R(roI3spqORKae(ES5oEprVxulp(b'Q\xa9\n\x8am\x1b\xa3\x02!\xdb&\x83\x1f\xd3\xb1\xfe\xbf\xe7@$\xa8\x1e\xd2\xfd\xad\xdepz\xd3Q\xf5W\xf2\xc4\xf4b\\\xb9:Ni\xa5\x02\x99c'), chr(0b1100010 + 0o2) + chr(101) + chr(0b1100011) + '\x6f' + '\x64' + chr(5400 - 5299))(chr(0b1101001 + 0o14) + chr(0b1110100) + chr(102) + '\055' + '\070'))
VU2zc5rCdloJ = ld_y4NQrCDaG.reverse_complement().to_ss()
dizdA8h9BTE_ = _bFWSozA7z0G.Primer(B2CCvKlHvjuo.to_ss(), tm=B2CCvKlHvjuo.VH5NUDuH5Da3, overhang=VU2zc5rCdloJ)
Y6bbKAvaNg9D += nzTpIcepk0o8(chr(0b110000) + '\157' + '\x31', 8)
if VF4pKOObtlPc([ftfygxgFas5X(thHp9mlDSVMt) > bkEe14a1B30s for thHp9mlDSVMt in (f6ucHbZL4GdI, dizdA8h9BTE_)]):
raise XEvzRXVpdVSB(roI3spqORKae(ES5oEprVxulp(b'\\\xb8L\x92(\n\xa2\x1fl\xd1:\xc6V\xcf\xf7\xaa\xa4\xe0\x05h\xb7\x02\xdc\xb0\xbf\xc5w2\x9aV\xbdR\xee\x8a\xc7j\x0e\xea+R|\xa2L\x93,\x13\xbd\x0e"\x90'), chr(0b1010101 + 0o17) + chr(5956 - 5855) + chr(511 - 412) + chr(0b101101 + 0o102) + chr(100) + '\145')('\165' + chr(0b1110100) + '\x66' + chr(1093 - 1048) + chr(56)))
return (dizdA8h9BTE_, f6ucHbZL4GdI) |
klavinslab/coral | coral/design/_gibson.py | gibson | def gibson(seq_list, circular=True, overlaps='mixed', overlap_tm=65,
maxlen=80, terminal_primers=True, primer_kwargs=None):
'''Design Gibson primers given a set of sequences
:param seq_list: List of DNA sequences to stitch together
:type seq_list: list containing coral.DNA
:param circular: If true, designs primers for making a circular construct.
If false, designs primers for a linear construct.
:type circular: bool
:param splits: Specifies locations of overlap. Must be either a single
entry of the same type as the 'split' parameter in
gibson_primers or a list of those types of the appropriate
length (for circular construct, len(seq_list), for
linear construct, len(seq_list) - 1)
:type splits: str or list of str
:param overlap_tm: Minimum Tm of overlap
:type overlap_tm: float
:param maxlen: Maximum length of each primer.
:type maxlen: int
:param terminal_primers: If the output is not circular, will design
non-Gibson primers for amplifying the first and
last fragments sans homology. If False, there will
be one less set of primers returned.
:type terminal_primers: bool
:param primer_kwargs: keyword arguments to pass to design.primer
:type primer_kwargs: dict
:returns: Forward and reverse primers for amplifying every fragment.
:rtype: a list of sequence.Primer tuples
:raises: ValueError if split parameter is an invalid string or wrong size.
'''
# Input checking
if circular:
n_overlaps = len(seq_list)
else:
n_overlaps = len(seq_list) - 1
if type(overlaps) is str:
overlaps = [overlaps] * n_overlaps
else:
if len(overlaps) != n_overlaps:
raise ValueError('Incorrect number of \'overlaps\' entries.')
else:
for overlap in overlaps:
if overlap not in ['left', 'right', 'mixed']:
raise ValueError('Invalid \'overlaps\' setting.')
if primer_kwargs is None:
primer_kwargs = {}
# If here, inputs were good
# Design primers for linear constructs:
primers_list = []
for i, (left, right) in enumerate(zip(seq_list[:-1], seq_list[1:])):
primers_list.append(gibson_primers(left, right, overlaps[i],
overlap_tm=overlap_tm,
primer_kwargs=primer_kwargs))
if circular:
primers_list.append(gibson_primers(seq_list[-1], seq_list[0],
overlaps[-1],
overlap_tm=overlap_tm,
primer_kwargs=primer_kwargs))
else:
if terminal_primers:
primer_f = coral.design.primer(seq_list[0], **primer_kwargs)
primer_r = coral.design.primer(seq_list[-1].reverse_complement(),
**primer_kwargs)
primers_list.append((primer_r, primer_f))
# Primers are now in order of 'reverse for seq1, forward for seq2' config
# Should be in 'forward and reverse primers for seq1, then seq2', etc
# Just need to rotate one to the right
flat = [y for x in primers_list for y in x]
flat = [flat[-1]] + flat[:-1]
grouped_primers = [(flat[2 * i], flat[2 * i + 1]) for i in
range(len(flat) / 2)]
return grouped_primers | python | def gibson(seq_list, circular=True, overlaps='mixed', overlap_tm=65,
maxlen=80, terminal_primers=True, primer_kwargs=None):
'''Design Gibson primers given a set of sequences
:param seq_list: List of DNA sequences to stitch together
:type seq_list: list containing coral.DNA
:param circular: If true, designs primers for making a circular construct.
If false, designs primers for a linear construct.
:type circular: bool
:param splits: Specifies locations of overlap. Must be either a single
entry of the same type as the 'split' parameter in
gibson_primers or a list of those types of the appropriate
length (for circular construct, len(seq_list), for
linear construct, len(seq_list) - 1)
:type splits: str or list of str
:param overlap_tm: Minimum Tm of overlap
:type overlap_tm: float
:param maxlen: Maximum length of each primer.
:type maxlen: int
:param terminal_primers: If the output is not circular, will design
non-Gibson primers for amplifying the first and
last fragments sans homology. If False, there will
be one less set of primers returned.
:type terminal_primers: bool
:param primer_kwargs: keyword arguments to pass to design.primer
:type primer_kwargs: dict
:returns: Forward and reverse primers for amplifying every fragment.
:rtype: a list of sequence.Primer tuples
:raises: ValueError if split parameter is an invalid string or wrong size.
'''
# Input checking
if circular:
n_overlaps = len(seq_list)
else:
n_overlaps = len(seq_list) - 1
if type(overlaps) is str:
overlaps = [overlaps] * n_overlaps
else:
if len(overlaps) != n_overlaps:
raise ValueError('Incorrect number of \'overlaps\' entries.')
else:
for overlap in overlaps:
if overlap not in ['left', 'right', 'mixed']:
raise ValueError('Invalid \'overlaps\' setting.')
if primer_kwargs is None:
primer_kwargs = {}
# If here, inputs were good
# Design primers for linear constructs:
primers_list = []
for i, (left, right) in enumerate(zip(seq_list[:-1], seq_list[1:])):
primers_list.append(gibson_primers(left, right, overlaps[i],
overlap_tm=overlap_tm,
primer_kwargs=primer_kwargs))
if circular:
primers_list.append(gibson_primers(seq_list[-1], seq_list[0],
overlaps[-1],
overlap_tm=overlap_tm,
primer_kwargs=primer_kwargs))
else:
if terminal_primers:
primer_f = coral.design.primer(seq_list[0], **primer_kwargs)
primer_r = coral.design.primer(seq_list[-1].reverse_complement(),
**primer_kwargs)
primers_list.append((primer_r, primer_f))
# Primers are now in order of 'reverse for seq1, forward for seq2' config
# Should be in 'forward and reverse primers for seq1, then seq2', etc
# Just need to rotate one to the right
flat = [y for x in primers_list for y in x]
flat = [flat[-1]] + flat[:-1]
grouped_primers = [(flat[2 * i], flat[2 * i + 1]) for i in
range(len(flat) / 2)]
return grouped_primers | [
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... | Design Gibson primers given a set of sequences
:param seq_list: List of DNA sequences to stitch together
:type seq_list: list containing coral.DNA
:param circular: If true, designs primers for making a circular construct.
If false, designs primers for a linear construct.
:type circular: bool
:param splits: Specifies locations of overlap. Must be either a single
entry of the same type as the 'split' parameter in
gibson_primers or a list of those types of the appropriate
length (for circular construct, len(seq_list), for
linear construct, len(seq_list) - 1)
:type splits: str or list of str
:param overlap_tm: Minimum Tm of overlap
:type overlap_tm: float
:param maxlen: Maximum length of each primer.
:type maxlen: int
:param terminal_primers: If the output is not circular, will design
non-Gibson primers for amplifying the first and
last fragments sans homology. If False, there will
be one less set of primers returned.
:type terminal_primers: bool
:param primer_kwargs: keyword arguments to pass to design.primer
:type primer_kwargs: dict
:returns: Forward and reverse primers for amplifying every fragment.
:rtype: a list of sequence.Primer tuples
:raises: ValueError if split parameter is an invalid string or wrong size. | [
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/design/_gibson.py#L136-L214 | train | Design Gibson primers given a set of DNA sequences. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8('\060' + chr(8952 - 8841) + chr(0b110011) + '\x33' + chr(2034 - 1981), 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(50) + chr(208 - 155) + chr(0b110001), 20318 - 20310), nzTpIcepk0o8(chr(1818 - 1770) + chr(3950 - 3839) + '\063' + '\066' + chr(53), ord("\x08")), nzTpIcepk0o8(chr(2256 - 2208) + chr(9403 - 9292) + '\062' + '\x35' + chr(55), 5007 - 4999), nzTpIcepk0o8('\x30' + chr(0b1010001 + 0o36) + '\062' + '\066' + '\067', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x34' + chr(50), ord("\x08")), nzTpIcepk0o8(chr(2157 - 2109) + '\x6f' + chr(49) + chr(306 - 258) + chr(55), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110001) + chr(50) + chr(0b100110 + 0o12), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + '\061' + '\065', 60405 - 60397), nzTpIcepk0o8(chr(48) + chr(1349 - 1238) + '\x31' + chr(0b0 + 0o63) + chr(0b10110 + 0o34), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110011) + chr(0b1111 + 0o44) + chr(0b110110), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x31' + chr(54) + chr(2268 - 2217), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(51) + '\x30' + chr(0b101100 + 0o6), 0o10), nzTpIcepk0o8(chr(1349 - 1301) + chr(0b1101111) + '\062' + chr(0b1011 + 0o45) + '\065', 0o10), nzTpIcepk0o8(chr(0b11100 + 0o24) + chr(111) + chr(50) + chr(0b100100 + 0o14) + chr(0b100110 + 0o21), 0o10), nzTpIcepk0o8(chr(48) + chr(0b101100 + 0o103) + '\x31' + '\066' + chr(870 - 822), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(0b110011) + '\x34' + chr(0b110100), 0o10), nzTpIcepk0o8(chr(2073 - 2025) + chr(0b1101111) + chr(0b110010) + chr(1239 - 1188), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101 + 0o142) + '\063' + '\x37' + '\064', 0o10), nzTpIcepk0o8(chr(0b10101 + 0o33) + chr(0b110111 + 0o70) + chr(0b10 + 0o65), 0o10), nzTpIcepk0o8(chr(0b1001 + 0o47) + '\x6f' + chr(50) + chr(0b110001) + chr(52), 5333 - 5325), nzTpIcepk0o8('\x30' + '\157' + '\061' + '\061' + chr(0b110010), 11893 - 11885), nzTpIcepk0o8(chr(0b110000) + chr(0b1010011 + 0o34) + chr(1113 - 1060) + '\064', 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b10010 + 0o37) + chr(2489 - 2438) + '\x32', 8), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b101000 + 0o12) + chr(2563 - 2508) + '\x30', 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(51) + '\x37', 0b1000), nzTpIcepk0o8(chr(0b1011 + 0o45) + '\x6f' + chr(1410 - 1361) + '\x33' + chr(0b110000), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + chr(0b110110) + '\x35', 36127 - 36119), nzTpIcepk0o8('\x30' + chr(0b1000101 + 0o52) + chr(699 - 647) + '\x34', ord("\x08")), nzTpIcepk0o8(chr(0b11111 + 0o21) + '\x6f' + chr(51) + chr(480 - 432) + chr(0b11 + 0o62), 0o10), nzTpIcepk0o8(chr(1771 - 1723) + chr(111) + chr(0b110010) + chr(0b110000 + 0o6) + chr(53), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b11100 + 0o26) + chr(0b100011 + 0o16) + chr(1317 - 1264), ord("\x08")), nzTpIcepk0o8(chr(1645 - 1597) + chr(0b1101111) + chr(49) + chr(0b101111 + 0o10) + '\x30', 0o10), nzTpIcepk0o8('\060' + '\x6f' + '\x32' + chr(51) + chr(1256 - 1205), ord("\x08")), nzTpIcepk0o8(chr(1250 - 1202) + chr(111) + chr(0b110100) + '\066', 59269 - 59261), nzTpIcepk0o8(chr(996 - 948) + chr(0b1010001 + 0o36) + chr(0b110010) + chr(1078 - 1024), ord("\x08")), nzTpIcepk0o8(chr(0b101110 + 0o2) + chr(0b1101111) + chr(51) + chr(50) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110110) + chr(0b11 + 0o60), 0b1000), nzTpIcepk0o8('\060' + chr(0b110 + 0o151) + chr(117 - 67) + chr(1145 - 1091) + '\x37', 8), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x33' + '\x37' + chr(0b110010 + 0o0), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + chr(111) + chr(53) + '\x30', 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xf3'), chr(0b1011011 + 0o11) + '\145' + '\x63' + '\x6f' + '\144' + '\x65')(chr(0b101001 + 0o114) + chr(116) + chr(0b1100110) + '\055' + chr(1583 - 1527)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def p7rOrY_RTdUz(X9MwysUNJZ2p, z1jrZw1enaK_=nzTpIcepk0o8('\060' + chr(111) + '\061', 0o10), Iw_BtKwnYu5G=roI3spqORKae(ES5oEprVxulp(b'\xb0\xc0\x8d\xca\xd3'), chr(100) + '\x65' + '\143' + chr(111) + '\144' + chr(0b1011111 + 0o6))(chr(117) + '\x74' + '\x66' + chr(0b101101) + chr(0b111000)), iQ3fevH6TJA9=nzTpIcepk0o8(chr(48) + '\x6f' + chr(49) + chr(0b110000) + '\x31', 0b1000), bkEe14a1B30s=nzTpIcepk0o8(chr(1152 - 1104) + chr(6631 - 6520) + chr(0b110001) + chr(50) + '\x30', 8), y7Jg5lObR_sM=nzTpIcepk0o8(chr(0b101010 + 0o6) + chr(111) + '\x31', 8), BvmDTzQ9_6tg=None):
if z1jrZw1enaK_:
uGEo4IUsZBOx = ftfygxgFas5X(X9MwysUNJZ2p)
else:
uGEo4IUsZBOx = ftfygxgFas5X(X9MwysUNJZ2p) - nzTpIcepk0o8('\x30' + chr(111) + chr(0b10110 + 0o33), 8)
if suIjIS24Zkqw(Iw_BtKwnYu5G, N9zlRy29S1SS):
Iw_BtKwnYu5G = [Iw_BtKwnYu5G] * uGEo4IUsZBOx
elif ftfygxgFas5X(Iw_BtKwnYu5G) != uGEo4IUsZBOx:
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'\x94\xc7\x96\xc0\xc5P"3yz\xb0\x06\xaf\xe7\xe2\x02\xc4|\x9a\'\xab%Z?\xcas9EW\xe2\x95\xe8\x16\xefT\x7f\xb6@\x99'), '\x64' + '\x65' + '\x63' + chr(0b1101111) + chr(0b1100100) + '\x65')('\x75' + chr(0b1100000 + 0o24) + chr(9728 - 9626) + chr(45) + chr(1273 - 1217)))
else:
for ld_y4NQrCDaG in Iw_BtKwnYu5G:
if ld_y4NQrCDaG not in [roI3spqORKae(ES5oEprVxulp(b'\xb1\xcc\x93\xdb'), chr(9595 - 9495) + chr(0b1100101) + chr(0b1111 + 0o124) + chr(5540 - 5429) + chr(0b1000010 + 0o42) + chr(101))(chr(6829 - 6712) + chr(12758 - 12642) + chr(0b1100110) + '\055' + '\x38'), roI3spqORKae(ES5oEprVxulp(b'\xaf\xc0\x92\xc7\xc3'), chr(0b1100100) + chr(0b1100101) + chr(99) + chr(111) + chr(100) + '\145')('\165' + chr(8568 - 8452) + '\146' + chr(45) + chr(0b1110 + 0o52)), roI3spqORKae(ES5oEprVxulp(b'\xb0\xc0\x8d\xca\xd3'), chr(5958 - 5858) + '\x65' + chr(4978 - 4879) + chr(0b1011000 + 0o27) + chr(100) + '\x65')(chr(117) + '\x74' + '\146' + chr(0b101101) + chr(0b111000))]:
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'\x94\xc7\x83\xce\xdbK#p*5\xa8\x16\xb0\xe9\xe6\x00\x974\xdct\xe9>X3\xd6xv'), '\144' + chr(101) + '\143' + chr(0b1011011 + 0o24) + chr(0b1100100) + '\x65')(chr(0b111010 + 0o73) + chr(116) + chr(102) + chr(45) + chr(564 - 508)))
if BvmDTzQ9_6tg is None:
BvmDTzQ9_6tg = {}
MbZo4QGPFldP = []
for (ZlbFMSG8gCoF, (ZJRgJr1hTjIz, HDutv6NlG_yf)) in _kV_Bomx8PZ4(TxMFWa_Xzviv(X9MwysUNJZ2p[:-nzTpIcepk0o8(chr(1183 - 1135) + chr(111) + '\x31', 8)], X9MwysUNJZ2p[nzTpIcepk0o8(chr(1938 - 1890) + chr(111) + '\061', 8):])):
roI3spqORKae(MbZo4QGPFldP, roI3spqORKae(ES5oEprVxulp(b'\x95\xfd\xa6\x9b\xcfE\x00?g5\x8bF'), chr(100) + chr(0b1100101) + '\x63' + '\157' + '\144' + '\x65')('\x75' + chr(0b111110 + 0o66) + chr(4351 - 4249) + '\x2d' + chr(279 - 223)))(jqT3uQnH4ZeC(ZJRgJr1hTjIz, HDutv6NlG_yf, Iw_BtKwnYu5G[ZlbFMSG8gCoF], overlap_tm=iQ3fevH6TJA9, primer_kwargs=BvmDTzQ9_6tg))
if z1jrZw1enaK_:
roI3spqORKae(MbZo4QGPFldP, roI3spqORKae(ES5oEprVxulp(b'\x95\xfd\xa6\x9b\xcfE\x00?g5\x8bF'), chr(100) + chr(0b1100101) + chr(0b1100011) + chr(0b111011 + 0o64) + '\x64' + chr(787 - 686))(chr(6235 - 6118) + chr(0b1001 + 0o153) + chr(7339 - 7237) + '\055' + chr(1320 - 1264)))(jqT3uQnH4ZeC(X9MwysUNJZ2p[-nzTpIcepk0o8('\060' + chr(2472 - 2361) + '\061', 8)], X9MwysUNJZ2p[nzTpIcepk0o8(chr(48) + '\157' + '\060', 0b1000)], Iw_BtKwnYu5G[-nzTpIcepk0o8('\x30' + chr(0b1101111) + '\061', 8)], overlap_tm=iQ3fevH6TJA9, primer_kwargs=BvmDTzQ9_6tg))
elif y7Jg5lObR_sM:
GEluRd_yd1Fl = _bFWSozA7z0G.design.primer(X9MwysUNJZ2p[nzTpIcepk0o8(chr(48) + chr(111) + '\060', 8)], **BvmDTzQ9_6tg)
aMc8zP98Ng__ = _bFWSozA7z0G.design.primer(X9MwysUNJZ2p[-nzTpIcepk0o8(chr(1993 - 1945) + chr(0b1101111) + '\061', 8)].reverse_complement(), **BvmDTzQ9_6tg)
roI3spqORKae(MbZo4QGPFldP, roI3spqORKae(ES5oEprVxulp(b'\x95\xfd\xa6\x9b\xcfE\x00?g5\x8bF'), chr(0b1100100) + chr(2269 - 2168) + '\143' + '\x6f' + chr(0b10010 + 0o122) + '\x65')(chr(5009 - 4892) + chr(0b1000101 + 0o57) + '\146' + '\x2d' + '\070'))((aMc8zP98Ng__, GEluRd_yd1Fl))
clpVTJH7YcoX = [Fi3yzxctM1zW for bI5jsQ9OkQtj in MbZo4QGPFldP for Fi3yzxctM1zW in bI5jsQ9OkQtj]
clpVTJH7YcoX = [clpVTJH7YcoX[-nzTpIcepk0o8('\060' + '\x6f' + chr(1812 - 1763), 8)]] + clpVTJH7YcoX[:-nzTpIcepk0o8('\x30' + '\157' + chr(2031 - 1982), 8)]
ZTqPP0MA0DTL = [(clpVTJH7YcoX[nzTpIcepk0o8(chr(0b1011 + 0o45) + chr(0b1011000 + 0o27) + '\x32', ord("\x08")) * ZlbFMSG8gCoF], clpVTJH7YcoX[nzTpIcepk0o8(chr(48) + chr(0b111111 + 0o60) + chr(0b110010), 8) * ZlbFMSG8gCoF + nzTpIcepk0o8(chr(0b11111 + 0o21) + chr(0b1101111) + chr(0b110001), 8)]) for ZlbFMSG8gCoF in bbT2xIe5pzk7(ftfygxgFas5X(clpVTJH7YcoX) / nzTpIcepk0o8('\060' + chr(0b1101111) + chr(50), 8))]
return ZTqPP0MA0DTL |
klavinslab/coral | coral/sequence/_sequence.py | _decompose | def _decompose(string, n):
'''Given string and multiplier n, find m**2 decomposition.
:param string: input string
:type string: str
:param n: multiplier
:type n: int
:returns: generator that produces m**2 * string if m**2 is a factor of n
:rtype: generator of 0 or 1
'''
binary = [int(x) for x in bin(n)[2:]]
new_string = string
counter = 1
while counter <= len(binary):
if binary[-counter]:
yield new_string
new_string += new_string
counter += 1 | python | def _decompose(string, n):
'''Given string and multiplier n, find m**2 decomposition.
:param string: input string
:type string: str
:param n: multiplier
:type n: int
:returns: generator that produces m**2 * string if m**2 is a factor of n
:rtype: generator of 0 or 1
'''
binary = [int(x) for x in bin(n)[2:]]
new_string = string
counter = 1
while counter <= len(binary):
if binary[-counter]:
yield new_string
new_string += new_string
counter += 1 | [
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ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(48) + '\157' + '\x33' + chr(0b11001 + 0o35) + chr(0b110110), 7343 - 7335), nzTpIcepk0o8(chr(0b110000) + chr(2457 - 2346) + chr(0b110011) + '\064' + '\x35', 0o10), nzTpIcepk0o8(chr(0b10 + 0o56) + chr(0b10101 + 0o132) + '\063' + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(0b1111 + 0o41) + chr(3097 - 2986) + chr(0b110001) + '\066' + chr(0b110001), 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(1164 - 1113) + '\x31' + chr(0b1 + 0o61), 46094 - 46086), nzTpIcepk0o8(chr(464 - 416) + chr(111) + chr(0b110101) + chr(127 - 72), 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(0b111 + 0o53) + chr(0b100011 + 0o16) + '\x36', 0b1000), nzTpIcepk0o8(chr(0b101011 + 0o5) + chr(0b1101111) + chr(0b110010) + chr(48) + chr(0b110000 + 0o7), 18644 - 18636), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b101010 + 0o10) + chr(1084 - 1029) + '\x37', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b110111 + 0o70) + chr(50) + chr(0b1000 + 0o55) + chr(1167 - 1113), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(1047 - 998) + chr(0b10001 + 0o45) + '\067', 0b1000), nzTpIcepk0o8(chr(48) + chr(1657 - 1546) + chr(1360 - 1309) + chr(0b11101 + 0o25) + chr(85 - 34), 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(0b101110 + 0o6) + chr(2901 - 2847), 44525 - 44517), nzTpIcepk0o8(chr(48) + '\157' + chr(0b10 + 0o60) + chr(0b110111) + chr(0b110000), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b100 + 0o153) + chr(1533 - 1483) + chr(0b110111) + '\067', 8), nzTpIcepk0o8('\060' + chr(111) + chr(0b101100 + 0o5) + chr(0b110000) + chr(55), 32552 - 32544), nzTpIcepk0o8(chr(212 - 164) + chr(111) + '\x32' + '\067' + chr(0b0 + 0o65), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b11111 + 0o120) + '\x31' + chr(51) + '\064', ord("\x08")), nzTpIcepk0o8(chr(2134 - 2086) + chr(0b1101111) + '\x35' + chr(1037 - 985), 27863 - 27855), nzTpIcepk0o8(chr(48) + '\157' + chr(0b111 + 0o60) + chr(0b11010 + 0o34), 0b1000), nzTpIcepk0o8(chr(996 - 948) + '\157' + chr(0b110010) + '\064' + chr(1791 - 1737), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(1265 - 1216) + chr(0b100111 + 0o16), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b111001 + 0o66) + chr(51) + '\067' + chr(48), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1100011 + 0o14) + chr(49) + '\x34' + '\064', 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(51) + chr(0b11111 + 0o22) + chr(0b110111), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(50) + chr(1200 - 1152) + '\x37', 8), nzTpIcepk0o8(chr(0b11101 + 0o23) + chr(11180 - 11069) + '\x36' + '\x33', 0b1000), nzTpIcepk0o8('\x30' + chr(111) + '\063' + chr(0b10000 + 0o46) + chr(0b1001 + 0o50), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(9043 - 8932) + '\x31' + chr(0b110101) + chr(126 - 72), 0o10), nzTpIcepk0o8('\060' + '\157' + '\061' + chr(180 - 132) + chr(53), 30515 - 30507), nzTpIcepk0o8(chr(0b11110 + 0o22) + chr(6099 - 5988) + chr(0b110010) + '\x31' + '\x36', 8), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110010) + chr(0b110000) + '\063', 0b1000), nzTpIcepk0o8('\060' + '\157' + '\x32' + chr(0b110000) + chr(1460 - 1405), 8), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110001) + chr(2094 - 2042) + chr(50), 15506 - 15498), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(1987 - 1937) + chr(0b110000) + chr(399 - 347), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110010) + chr(1709 - 1658) + chr(54), 39199 - 39191), nzTpIcepk0o8(chr(0b100 + 0o54) + '\157' + chr(0b10000 + 0o42) + '\065' + chr(0b110101), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(0b110011) + chr(53), 0b1000), nzTpIcepk0o8(chr(1094 - 1046) + chr(0b1101111) + chr(0b110011) + '\x36' + chr(0b100000 + 0o20), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(9892 - 9781) + '\x37' + '\x30', 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b100001 + 0o24) + chr(0b110000), 51128 - 51120)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xd8'), chr(0b1100100) + chr(6552 - 6451) + '\x63' + '\157' + chr(0b1010 + 0o132) + '\x65')(chr(0b1110101) + chr(0b1110100) + chr(7129 - 7027) + chr(45) + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def ELTaXu4FX2L_(aji3jF4_nqWL, NoZxuO7wjArS):
V2Ih8wqmyzJG = [nzTpIcepk0o8(bI5jsQ9OkQtj) for bI5jsQ9OkQtj in fBqfYi7uj_uC(NoZxuO7wjArS)[nzTpIcepk0o8(chr(0b100110 + 0o12) + '\x6f' + '\062', 0b1000):]]
B5NXbXVpfw7z = aji3jF4_nqWL
AISxp6RQlnj5 = nzTpIcepk0o8(chr(880 - 832) + chr(0b1101111) + chr(0b10 + 0o57), 14487 - 14479)
while AISxp6RQlnj5 <= ftfygxgFas5X(V2Ih8wqmyzJG):
if V2Ih8wqmyzJG[-AISxp6RQlnj5]:
yield B5NXbXVpfw7z
B5NXbXVpfw7z += B5NXbXVpfw7z
AISxp6RQlnj5 += nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110001), 8) |
klavinslab/coral | coral/sequence/_sequence.py | reverse_complement | def reverse_complement(sequence, material):
'''Reverse complement a sequence.
:param sequence: Sequence to reverse complement
:type sequence: str
:param material: dna, rna, or peptide.
:type material: str
'''
code = dict(COMPLEMENTS[material])
reverse_sequence = sequence[::-1]
return ''.join([code[str(base)] for base in reverse_sequence]) | python | def reverse_complement(sequence, material):
'''Reverse complement a sequence.
:param sequence: Sequence to reverse complement
:type sequence: str
:param material: dna, rna, or peptide.
:type material: str
'''
code = dict(COMPLEMENTS[material])
reverse_sequence = sequence[::-1]
return ''.join([code[str(base)] for base in reverse_sequence]) | [
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ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b100 + 0o54) + chr(0b1010010 + 0o35) + chr(0b110111) + '\x30', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\061' + chr(51) + '\x34', 0o10), nzTpIcepk0o8(chr(0b1110 + 0o42) + chr(8727 - 8616) + '\x33' + chr(0b110000) + chr(0b110111), 52984 - 52976), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110011) + chr(0b110111) + '\x33', 21367 - 21359), nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(1032 - 921) + chr(0b10110 + 0o35) + '\x33' + chr(675 - 623), 52900 - 52892), nzTpIcepk0o8(chr(1938 - 1890) + '\157' + chr(54) + chr(966 - 911), 0b1000), nzTpIcepk0o8(chr(2134 - 2086) + chr(0b1101111) + chr(629 - 575) + chr(0b1011 + 0o46), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(11490 - 11379) + chr(0b1010 + 0o51) + chr(0b1010 + 0o46) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(0b0 + 0o60) + chr(6553 - 6442) + chr(2430 - 2379), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1000001 + 0o56) + chr(0b101 + 0o55) + chr(55) + chr(0b110101), 12952 - 12944), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(49) + chr(2201 - 2150) + chr(0b10 + 0o61), 35020 - 35012), nzTpIcepk0o8('\x30' + '\157' + chr(0b10 + 0o57) + '\063', 8243 - 8235), nzTpIcepk0o8(chr(0b10 + 0o56) + chr(0b1101111) + chr(51) + chr(0b110100) + chr(2008 - 1959), 0b1000), nzTpIcepk0o8('\060' + chr(0b111110 + 0o61) + chr(0b110001 + 0o1) + chr(0b10111 + 0o32) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b110000 + 0o77) + chr(1134 - 1084) + chr(506 - 455) + '\x34', ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(1184 - 1135) + chr(49) + '\x31', 0b1000), nzTpIcepk0o8(chr(0b1011 + 0o45) + '\x6f' + chr(427 - 377) + chr(51) + chr(2188 - 2139), 0b1000), nzTpIcepk0o8(chr(926 - 878) + chr(0b1101111) + chr(981 - 928) + chr(50), 7312 - 7304), nzTpIcepk0o8(chr(48) + chr(5449 - 5338) + chr(50) + chr(0b101101 + 0o6) + '\062', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b10110 + 0o35) + chr(0b110010) + chr(49), 37272 - 37264), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\061' + chr(48) + '\067', ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110010) + '\x32' + '\066', 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(49) + chr(0b11101 + 0o30) + '\066', 30645 - 30637), nzTpIcepk0o8('\x30' + chr(0b1000001 + 0o56) + chr(0b110101) + '\x35', 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(49) + chr(50) + '\x31', ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b1001 + 0o51) + chr(0b100111 + 0o11), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(51) + chr(0b10110 + 0o37) + chr(52), ord("\x08")), nzTpIcepk0o8('\x30' + chr(9979 - 9868) + chr(0b1001 + 0o51) + chr(0b10100 + 0o36) + chr(0b100011 + 0o21), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x32' + '\x30' + chr(0b100100 + 0o15), 0o10), nzTpIcepk0o8('\x30' + chr(12101 - 11990) + chr(1172 - 1123) + chr(0b110111) + chr(0b101101 + 0o7), 0o10), nzTpIcepk0o8('\060' + chr(0b1101000 + 0o7) + chr(880 - 829) + chr(0b10100 + 0o43) + chr(1096 - 1046), ord("\x08")), nzTpIcepk0o8(chr(0b11111 + 0o21) + chr(0b100001 + 0o116) + '\061' + chr(1392 - 1340) + chr(0b110100), 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(0b101101 + 0o4) + chr(53) + '\063', 0b1000), nzTpIcepk0o8(chr(0b101 + 0o53) + chr(0b1101111) + '\064' + '\x31', 38330 - 38322), nzTpIcepk0o8(chr(0b101000 + 0o10) + chr(0b1100001 + 0o16) + '\061' + '\067', 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110001) + chr(50) + chr(49), 8), nzTpIcepk0o8(chr(0b100101 + 0o13) + chr(0b1101111) + chr(0b1001 + 0o50) + chr(0b101010 + 0o15) + chr(0b110001), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110000 + 0o3) + '\x34' + '\061', 8), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110000 + 0o3) + '\x35' + '\060', 21649 - 21641), nzTpIcepk0o8('\x30' + '\157' + '\x32' + '\x36' + chr(0b110000), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\065' + chr(0b101000 + 0o10), 18881 - 18873)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x16'), chr(100) + '\x65' + '\143' + chr(111) + chr(100) + chr(2899 - 2798))(chr(0b1000101 + 0o60) + chr(3440 - 3324) + chr(0b110000 + 0o66) + chr(45) + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def YkW9XOryYN8M(AaFeo0lw34C3, P6MCancmTVIW):
MJEGgvK3nnE9 = znjnJWK64FDT(N0rIPC6EBFud[P6MCancmTVIW])
jT1IYWcheoW5 = AaFeo0lw34C3[::-nzTpIcepk0o8(chr(48) + chr(5422 - 5311) + chr(237 - 188), ord("\x08"))]
return roI3spqORKae(roI3spqORKae(ES5oEprVxulp(b''), '\x64' + '\x65' + chr(99) + chr(0b1101 + 0o142) + chr(100) + chr(0b111000 + 0o55))(chr(117) + chr(0b10111 + 0o135) + chr(6269 - 6167) + chr(45) + '\070'), roI3spqORKae(ES5oEprVxulp(b'ah\xbe\xb6\xe5uR\xa2W\xfe\x15z'), chr(0b1100100) + chr(5952 - 5851) + chr(0b1100010 + 0o1) + '\x6f' + '\144' + chr(0b1010101 + 0o20))(chr(5244 - 5127) + '\164' + '\x66' + chr(45) + chr(1387 - 1331)))([MJEGgvK3nnE9[N9zlRy29S1SS(xvptlew7LsBo)] for xvptlew7LsBo in jT1IYWcheoW5]) |
klavinslab/coral | coral/sequence/_sequence.py | check_alphabet | def check_alphabet(seq, material):
'''Verify that a given string is valid DNA, RNA, or peptide characters.
:param seq: DNA, RNA, or peptide sequence.
:type seq: str
:param material: Input material - 'dna', 'rna', or 'pepide'.
:type sequence: str
:returns: Whether the `seq` is a valid string of `material`.
:rtype: bool
:raises: ValueError if `material` isn't \'dna\', \'rna\', or \'peptide\'.
ValueError if `seq` contains invalid characters for its
material type.
'''
errs = {'dna': 'DNA', 'rna': 'RNA', 'peptide': 'peptide'}
if material == 'dna' or material == 'rna' or material == 'peptide':
alphabet = ALPHABETS[material]
err_msg = errs[material]
else:
msg = 'Input material must be \'dna\', \'rna\', or \'peptide\'.'
raise ValueError(msg)
# This is a bottleneck when modifying sequence - hence the run_checks
# optional parameter in sequence objects..
# First attempt with cython was slower. Could also try pypy.
if re.search('[^' + alphabet + ']', seq):
raise ValueError('Encountered a non-%s character' % err_msg) | python | def check_alphabet(seq, material):
'''Verify that a given string is valid DNA, RNA, or peptide characters.
:param seq: DNA, RNA, or peptide sequence.
:type seq: str
:param material: Input material - 'dna', 'rna', or 'pepide'.
:type sequence: str
:returns: Whether the `seq` is a valid string of `material`.
:rtype: bool
:raises: ValueError if `material` isn't \'dna\', \'rna\', or \'peptide\'.
ValueError if `seq` contains invalid characters for its
material type.
'''
errs = {'dna': 'DNA', 'rna': 'RNA', 'peptide': 'peptide'}
if material == 'dna' or material == 'rna' or material == 'peptide':
alphabet = ALPHABETS[material]
err_msg = errs[material]
else:
msg = 'Input material must be \'dna\', \'rna\', or \'peptide\'.'
raise ValueError(msg)
# This is a bottleneck when modifying sequence - hence the run_checks
# optional parameter in sequence objects..
# First attempt with cython was slower. Could also try pypy.
if re.search('[^' + alphabet + ']', seq):
raise ValueError('Encountered a non-%s character' % err_msg) | [
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/sequence/_sequence.py#L399-L424 | train | Verify that a given string is a valid DNA RNA or peptide character sequence. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(1027 - 978) + chr(1042 - 993) + chr(55), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(1654 - 1605) + chr(48) + '\x30', ord("\x08")), nzTpIcepk0o8(chr(477 - 429) + chr(0b1101111) + '\x32' + chr(0b11000 + 0o32) + '\x30', 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(0b1101 + 0o52) + chr(1693 - 1644), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110010 + 0o1) + chr(1462 - 1408) + chr(53), 0b1000), nzTpIcepk0o8(chr(1843 - 1795) + '\157' + chr(0b11010 + 0o32) + chr(0b10010 + 0o41), 9130 - 9122), nzTpIcepk0o8('\x30' + '\157' + chr(131 - 81) + '\061' + '\062', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b100 + 0o57) + '\065' + chr(0b10000 + 0o43), ord("\x08")), nzTpIcepk0o8(chr(0b0 + 0o60) + '\157' + '\x32' + chr(2251 - 2199) + chr(619 - 568), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(1223 - 1173) + chr(49) + chr(0b10011 + 0o36), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(4847 - 4736) + '\x32' + '\x31' + chr(1699 - 1651), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(1036 - 925) + chr(0b1100 + 0o47) + '\064' + '\067', 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(1207 - 1158) + chr(0b10010 + 0o40) + chr(0b110111), 62490 - 62482), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b101000 + 0o15) + '\064', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b1111 + 0o42) + chr(48) + '\x33', 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(0b110010) + chr(1349 - 1301) + '\x37', 37642 - 37634), nzTpIcepk0o8(chr(0b100101 + 0o13) + chr(111) + '\062' + '\x32' + '\060', 8), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110011) + chr(52), ord("\x08")), nzTpIcepk0o8(chr(0b11101 + 0o23) + chr(1265 - 1154) + chr(732 - 683) + chr(0b101001 + 0o7) + chr(0b10100 + 0o36), 0o10), nzTpIcepk0o8('\060' + chr(0b1100001 + 0o16) + '\x32' + chr(718 - 666) + '\x30', 0b1000), nzTpIcepk0o8('\x30' + chr(4769 - 4658) + chr(50) + chr(0b100011 + 0o23) + chr(55), 0o10), nzTpIcepk0o8('\060' + chr(7496 - 7385) + chr(0b110001 + 0o3), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(49) + chr(54) + '\x31', 0o10), nzTpIcepk0o8(chr(0b1010 + 0o46) + chr(0b1101111) + chr(51) + chr(223 - 175), 0o10), nzTpIcepk0o8(chr(48) + chr(0b101011 + 0o104) + chr(1876 - 1821) + '\066', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x32' + chr(51) + '\x30', 0b1000), nzTpIcepk0o8(chr(0b101010 + 0o6) + chr(111) + chr(0b110011) + '\067' + '\065', 0o10), nzTpIcepk0o8('\x30' + chr(9895 - 9784) + chr(49) + chr(2377 - 2327) + '\x32', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\061' + chr(0b110001) + '\x35', ord("\x08")), nzTpIcepk0o8(chr(0b100101 + 0o13) + '\157' + chr(52) + chr(2313 - 2259), 0o10), nzTpIcepk0o8('\060' + chr(0b111001 + 0o66) + '\061' + chr(0b11000 + 0o36) + chr(54), ord("\x08")), nzTpIcepk0o8('\x30' + chr(3039 - 2928) + chr(50) + chr(0b110010) + chr(1399 - 1348), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110010) + chr(0b10101 + 0o35) + chr(0b100101 + 0o16), 8), nzTpIcepk0o8(chr(0b110000) + chr(0b100 + 0o153) + chr(0b1011 + 0o50) + chr(0b11 + 0o60), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b1 + 0o63) + chr(48), 20708 - 20700), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x33' + '\066', 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(1459 - 1408) + '\x33' + '\063', 0o10), nzTpIcepk0o8(chr(0b11100 + 0o24) + chr(0b10 + 0o155) + chr(245 - 190) + '\066', 8), nzTpIcepk0o8(chr(0b110000) + chr(11626 - 11515) + '\062' + chr(54) + chr(48), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(180 - 131) + chr(724 - 676) + '\x32', 8)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + chr(111) + chr(53) + chr(0b10001 + 0o37), ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'a'), '\x64' + chr(2566 - 2465) + '\143' + chr(111) + chr(0b1100100) + chr(0b110011 + 0o62))('\x75' + chr(0b1110100) + '\146' + chr(0b100000 + 0o15) + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def Vt6wT_XWhfrB(ftk9lc7G5FOo, P6MCancmTVIW):
DI1hIB0rgA8W = {roI3spqORKae(ES5oEprVxulp(b'+.\xf1'), chr(100) + chr(6502 - 6401) + chr(0b1100011) + chr(111) + '\x64' + '\x65')('\x75' + '\164' + chr(102) + chr(1133 - 1088) + chr(2748 - 2692)): roI3spqORKae(ES5oEprVxulp(b'\x0b\x0e\xd1'), chr(3088 - 2988) + chr(101) + '\143' + chr(111) + chr(100) + chr(0b1100101))(chr(117) + chr(0b1110100) + '\x66' + '\x2d' + chr(56)), roI3spqORKae(ES5oEprVxulp(b'=.\xf1'), chr(100) + chr(8728 - 8627) + chr(0b1100011) + chr(0b1000100 + 0o53) + chr(2331 - 2231) + '\145')(chr(0b1110101) + chr(0b1110100) + chr(102) + chr(0b101101) + chr(56)): roI3spqORKae(ES5oEprVxulp(b'\x1d\x0e\xd1'), chr(0b110 + 0o136) + chr(101) + chr(0b1011 + 0o130) + '\x6f' + chr(0b1100100) + chr(0b1010001 + 0o24))(chr(0b1110100 + 0o1) + chr(0b1110100) + chr(3864 - 3762) + chr(1356 - 1311) + '\070'), roI3spqORKae(ES5oEprVxulp(b'?%\xe0M\x9cG\xef'), chr(0b1100100) + chr(8070 - 7969) + chr(8623 - 8524) + '\x6f' + '\144' + chr(0b1100101))(chr(0b1110101) + chr(0b1110100) + chr(102) + chr(45) + chr(0b111000)): roI3spqORKae(ES5oEprVxulp(b'?%\xe0M\x9cG\xef'), chr(100) + '\x65' + chr(99) + chr(0b1101111) + '\144' + '\x65')(chr(1567 - 1450) + chr(8978 - 8862) + chr(102) + chr(0b10110 + 0o27) + chr(0b111000))}
if P6MCancmTVIW == roI3spqORKae(ES5oEprVxulp(b'+.\xf1'), '\144' + '\145' + chr(0b1100011) + '\x6f' + chr(100) + chr(101))(chr(0b1110101) + '\164' + chr(10065 - 9963) + '\x2d' + chr(56)) or P6MCancmTVIW == roI3spqORKae(ES5oEprVxulp(b'=.\xf1'), '\144' + '\x65' + chr(0b1100011) + chr(0b1001000 + 0o47) + chr(0b1100100) + '\x65')(chr(0b1110101) + chr(0b1110100) + chr(1619 - 1517) + '\x2d' + '\070') or P6MCancmTVIW == roI3spqORKae(ES5oEprVxulp(b'?%\xe0M\x9cG\xef'), chr(0b110110 + 0o56) + '\145' + '\x63' + chr(3258 - 3147) + chr(100) + '\x65')(chr(117) + '\164' + '\x66' + chr(0b10011 + 0o32) + chr(2586 - 2530)):
pX0zIwMxFkEl = xHEBINT7ZIQQ[P6MCancmTVIW]
rz25atpOjIy0 = DI1hIB0rgA8W[P6MCancmTVIW]
else:
sldzbHve8G1S = roI3spqORKae(ES5oEprVxulp(b'\x06.\xe0L\x81\x03\xe7\x8a\xd7\xec\xfa\x8e6@c\xea\xe5o6\x80\xd5aQ?Z\xf6\x9cua\x06Q\xe1\xfdz\x072\xfbQ\xc2bh0\xf5I\x81J\xee\x8e\x84\xa7'), chr(7161 - 7061) + chr(0b110 + 0o137) + '\x63' + chr(0b1101111) + '\x64' + chr(7307 - 7206))(chr(117) + '\164' + chr(0b1100110) + chr(45) + '\x38')
raise WbNHlDKpyPtQ(sldzbHve8G1S)
if roI3spqORKae(aoTc4YA2bs2R, roI3spqORKae(ES5oEprVxulp(b'\x0b!\xca\x01\xbcM\xf0\xba\xc4\xcf\xc2\x91'), chr(0b1100 + 0o130) + chr(0b100100 + 0o101) + chr(0b1011111 + 0o4) + '\x6f' + chr(0b1100100) + chr(726 - 625))(chr(117) + '\x74' + chr(102) + chr(45) + chr(0b111000)))(roI3spqORKae(ES5oEprVxulp(b'\x14\x1e'), chr(0b1100010 + 0o2) + chr(0b1010011 + 0o22) + '\x63' + chr(8013 - 7902) + chr(2676 - 2576) + '\x65')('\165' + chr(0b1000111 + 0o55) + chr(102) + '\x2d' + '\070') + pX0zIwMxFkEl + roI3spqORKae(ES5oEprVxulp(b'\x12'), chr(0b1100100) + chr(0b1010 + 0o133) + '\143' + chr(7732 - 7621) + '\144' + chr(0b111101 + 0o50))(chr(117) + chr(116) + '\146' + chr(0b101101) + chr(0b100101 + 0o23)), ftk9lc7G5FOo):
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'\n.\xf3V\x80M\xfe\x8e\xd1\xec\xec\xc76\x0c-\xe8\xfe1g\xd3\x97g\x19yL\xf9\x9e&(T'), '\x64' + chr(0b1101 + 0o130) + chr(99) + '\x6f' + '\x64' + '\x65')(chr(8265 - 8148) + chr(11260 - 11144) + chr(102) + chr(0b101101) + chr(0b111000)) % rz25atpOjIy0) |
klavinslab/coral | coral/sequence/_sequence.py | process_seq | def process_seq(seq, material):
'''Validate and process sequence inputs.
:param seq: input sequence
:type seq: str
:param material: DNA, RNA, or peptide
:type: str
:returns: Uppercase version of `seq` with the alphabet checked by
check_alphabet().
:rtype: str
'''
check_alphabet(seq, material)
seq = seq.upper()
return seq | python | def process_seq(seq, material):
'''Validate and process sequence inputs.
:param seq: input sequence
:type seq: str
:param material: DNA, RNA, or peptide
:type: str
:returns: Uppercase version of `seq` with the alphabet checked by
check_alphabet().
:rtype: str
'''
check_alphabet(seq, material)
seq = seq.upper()
return seq | [
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:param material: DNA, RNA, or peptide
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/sequence/_sequence.py#L427-L441 | train | Validate and process sequence inputs. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(1386 - 1338) + chr(0b1101111) + chr(0b110011) + '\x30' + chr(1101 - 1048), 0b1000), nzTpIcepk0o8(chr(900 - 852) + chr(7800 - 7689) + '\x32' + '\062' + '\x35', ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + '\x33' + chr(0b110010) + chr(0b110011), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110001) + chr(0b110101) + chr(53), ord("\x08")), nzTpIcepk0o8('\060' + chr(4334 - 4223) + chr(0b110001) + chr(0b110100) + chr(51), 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110010) + chr(48) + chr(52), 8107 - 8099), nzTpIcepk0o8(chr(1592 - 1544) + chr(10644 - 10533) + chr(0b110001) + chr(53) + '\066', ord("\x08")), nzTpIcepk0o8(chr(0b100001 + 0o17) + chr(111) + chr(0b110011) + chr(55) + '\061', 62746 - 62738), nzTpIcepk0o8(chr(0b10100 + 0o34) + chr(0b10011 + 0o134) + chr(1446 - 1394) + chr(0b11110 + 0o24), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b111101 + 0o62) + '\063' + chr(2306 - 2251) + chr(0b1111 + 0o44), 9242 - 9234), nzTpIcepk0o8(chr(0b10110 + 0o32) + chr(0b10011 + 0o134) + chr(50) + chr(0b110110 + 0o1) + chr(0b11100 + 0o33), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(49) + '\064' + chr(0b10011 + 0o42), 59294 - 59286), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(49) + chr(860 - 806) + chr(1190 - 1136), 64094 - 64086), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110001) + chr(0b1011 + 0o45) + chr(52), 0o10), nzTpIcepk0o8(chr(0b101111 + 0o1) + chr(0b1101111) + '\x31' + chr(52), 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(0b101011 + 0o6) + '\x33' + chr(0b110101), 61738 - 61730), nzTpIcepk0o8(chr(0b10101 + 0o33) + '\x6f' + '\x32' + '\x30' + chr(55), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(0b10 + 0o60) + chr(2325 - 2274) + chr(0b11100 + 0o30), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110010) + chr(0b110100) + chr(55), ord("\x08")), nzTpIcepk0o8(chr(1185 - 1137) + chr(0b1000000 + 0o57) + chr(0b110 + 0o55) + '\061' + chr(2068 - 2016), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b10100 + 0o133) + chr(49) + '\x37' + '\065', 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b100110 + 0o14) + '\x30' + chr(0b101010 + 0o11), 40145 - 40137), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x32' + '\x32' + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(51) + '\065', 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(0b110001) + chr(403 - 351) + chr(53), 8), nzTpIcepk0o8(chr(0b1 + 0o57) + chr(6691 - 6580) + chr(0b110101) + '\x32', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\061' + chr(0b100110 + 0o14) + chr(0b11001 + 0o33), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(49) + chr(0b110010) + chr(0b11 + 0o61), 8), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b1111 + 0o44) + '\x35' + chr(0b110110), 48805 - 48797), nzTpIcepk0o8(chr(0b101000 + 0o10) + chr(0b1101111) + '\063' + chr(0b110110) + chr(53), 0b1000), nzTpIcepk0o8(chr(48) + chr(5032 - 4921) + chr(0b100 + 0o63) + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(54) + '\061', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b100000 + 0o23) + '\x37', 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(51) + chr(0b110100) + chr(0b1001 + 0o47), 0o10), nzTpIcepk0o8(chr(0b10101 + 0o33) + chr(0b10100 + 0o133) + chr(0b101000 + 0o10), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x33' + '\062' + '\064', 0b1000), nzTpIcepk0o8(chr(1677 - 1629) + chr(0b1010 + 0o145) + '\x32' + chr(0b10011 + 0o37) + chr(52), 0o10), nzTpIcepk0o8(chr(48) + chr(10796 - 10685) + chr(1913 - 1864) + chr(1342 - 1291) + '\063', ord("\x08")), nzTpIcepk0o8(chr(0b11111 + 0o21) + '\157' + chr(50) + '\x35' + '\x37', 10382 - 10374), nzTpIcepk0o8(chr(0b110000) + chr(10507 - 10396) + '\x33' + chr(975 - 924) + chr(52), 24239 - 24231)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(0b1101111 + 0o0) + '\065' + chr(0b110 + 0o52), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xeb'), chr(100) + chr(0b1100101) + chr(99) + chr(111) + '\144' + chr(101))(chr(117) + '\164' + '\x66' + chr(1577 - 1532) + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def EpNp_NdhuJS8(ftk9lc7G5FOo, P6MCancmTVIW):
Vt6wT_XWhfrB(ftk9lc7G5FOo, P6MCancmTVIW)
ftk9lc7G5FOo = ftk9lc7G5FOo.iq1mNMefb1Zd()
return ftk9lc7G5FOo |
klavinslab/coral | coral/sequence/_sequence.py | palindrome | def palindrome(seq):
'''Test whether a sequence is palindrome.
:param seq: Sequence to analyze (DNA or RNA).
:type seq: coral.DNA or coral.RNA
:returns: Whether a sequence is a palindrome.
:rtype: bool
'''
seq_len = len(seq)
if seq_len % 2 == 0:
# Sequence has even number of bases, can test non-overlapping seqs
wing = seq_len / 2
l_wing = seq[0: wing]
r_wing = seq[wing:]
if l_wing == r_wing.reverse_complement():
return True
else:
return False
else:
# Sequence has odd number of bases and cannot be a palindrome
return False | python | def palindrome(seq):
'''Test whether a sequence is palindrome.
:param seq: Sequence to analyze (DNA or RNA).
:type seq: coral.DNA or coral.RNA
:returns: Whether a sequence is a palindrome.
:rtype: bool
'''
seq_len = len(seq)
if seq_len % 2 == 0:
# Sequence has even number of bases, can test non-overlapping seqs
wing = seq_len / 2
l_wing = seq[0: wing]
r_wing = seq[wing:]
if l_wing == r_wing.reverse_complement():
return True
else:
return False
else:
# Sequence has odd number of bases and cannot be a palindrome
return False | [
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:param seq: Sequence to analyze (DNA or RNA).
:type seq: coral.DNA or coral.RNA
:returns: Whether a sequence is a palindrome.
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/sequence/_sequence.py#L444-L465 | train | Test whether a sequence is a palindrome. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(48) + chr(0b1100 + 0o143) + chr(0b110001) + chr(0b110101) + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + '\065' + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b0 + 0o157) + chr(0b110111) + chr(0b110011), 0o10), nzTpIcepk0o8('\060' + chr(6233 - 6122) + chr(925 - 875) + '\063' + chr(55), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110010) + chr(882 - 827) + chr(0b1000 + 0o52), 0o10), nzTpIcepk0o8('\060' + '\157' + '\x31' + chr(0b10 + 0o62) + chr(54), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(49) + '\x34' + chr(50), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x33' + chr(948 - 896) + chr(0b110000), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(1315 - 1266) + chr(0b110001), 59286 - 59278), nzTpIcepk0o8(chr(0b101010 + 0o6) + '\157' + chr(0b110011) + '\067' + '\x30', 64717 - 64709), nzTpIcepk0o8('\060' + chr(6502 - 6391) + chr(1723 - 1672) + '\x36' + '\x36', 44859 - 44851), nzTpIcepk0o8(chr(0b101000 + 0o10) + chr(111) + chr(2584 - 2533) + '\x34' + chr(0b110001 + 0o5), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b100110 + 0o13) + chr(609 - 554), 11192 - 11184), nzTpIcepk0o8('\060' + '\157' + '\062' + chr(54) + chr(0b1010 + 0o51), 0b1000), nzTpIcepk0o8(chr(1384 - 1336) + chr(813 - 702) + chr(0b110011) + chr(0b1111 + 0o43) + '\x33', 0o10), nzTpIcepk0o8(chr(1718 - 1670) + '\157' + chr(49) + chr(1710 - 1661) + chr(934 - 886), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\066' + chr(51), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1010101 + 0o32) + '\x33' + chr(0b110110) + '\065', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\062' + '\060' + chr(0b110000), 3853 - 3845), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\061' + chr(54) + chr(0b110010), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + '\x33' + chr(52) + chr(0b110111), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b110000 + 0o77) + '\062' + chr(414 - 361) + chr(0b110110), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b11001 + 0o31) + chr(49) + chr(0b110010), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b0 + 0o62) + chr(0b110001) + chr(0b110010), 8), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(49), 5438 - 5430), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x32' + chr(0b11 + 0o55) + chr(2671 - 2619), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110011) + '\065' + '\065', ord("\x08")), nzTpIcepk0o8('\060' + chr(7157 - 7046) + chr(0b100011 + 0o17) + chr(49) + '\063', 16211 - 16203), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110010) + '\067' + chr(50), 8), nzTpIcepk0o8(chr(971 - 923) + '\157' + chr(0b110011) + '\067' + chr(0b110110), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(6771 - 6660) + chr(2522 - 2471) + '\x37' + chr(2809 - 2755), 8), nzTpIcepk0o8(chr(48) + chr(411 - 300) + chr(0b10011 + 0o36) + '\x30' + chr(0b1110 + 0o47), 0b1000), nzTpIcepk0o8('\060' + chr(0b101 + 0o152) + '\062' + chr(0b110111) + '\060', 42858 - 42850), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110011) + chr(54) + chr(1206 - 1151), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b101001 + 0o106) + chr(0b110011) + chr(607 - 555) + '\x36', 8), nzTpIcepk0o8('\060' + '\157' + '\x35' + chr(0b10000 + 0o47), 23395 - 23387), nzTpIcepk0o8('\060' + '\x6f' + chr(49) + chr(55) + '\x30', 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110000 + 0o2) + '\062' + '\063', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x31' + chr(0b101001 + 0o7) + chr(0b110010), 0b1000), nzTpIcepk0o8(chr(1362 - 1314) + chr(12050 - 11939) + '\x33' + chr(49) + chr(1293 - 1241), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b101110 + 0o2) + '\x6f' + '\065' + chr(0b101100 + 0o4), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'A'), chr(0b1100100) + '\x65' + chr(7716 - 7617) + '\157' + chr(100) + '\x65')(chr(0b1001101 + 0o50) + '\x74' + chr(6053 - 5951) + '\055' + chr(0b11010 + 0o36)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def sLnRmvAxuYi9(ftk9lc7G5FOo):
ZLuOM9Oj71hE = ftfygxgFas5X(ftk9lc7G5FOo)
if ZLuOM9Oj71hE % nzTpIcepk0o8(chr(0b110000) + chr(1987 - 1876) + '\x32', 15017 - 15009) == nzTpIcepk0o8('\060' + '\x6f' + '\x30', ord("\x08")):
NFm8y4e1N6N0 = ZLuOM9Oj71hE / nzTpIcepk0o8('\060' + '\157' + chr(0b1100 + 0o46), 8)
FSeaupSp9clH = ftk9lc7G5FOo[nzTpIcepk0o8(chr(1987 - 1939) + chr(0b1101111) + chr(0b110000), 8):NFm8y4e1N6N0]
awXia8ZwxaPk = ftk9lc7G5FOo[NFm8y4e1N6N0:]
if FSeaupSp9clH == roI3spqORKae(awXia8ZwxaPk, roI3spqORKae(ES5oEprVxulp(b'\x1dHM\xfa\xc8\x15\x07\xbfj\x97\x9b\x96c\xd6\xbe-]\x81'), chr(100) + '\145' + '\x63' + chr(111) + '\x64' + chr(0b11011 + 0o112))(chr(0b11001 + 0o134) + chr(4802 - 4686) + chr(102) + chr(1666 - 1621) + chr(1334 - 1278)))():
return nzTpIcepk0o8('\060' + chr(0b1101111) + chr(49), 8)
else:
return nzTpIcepk0o8(chr(1248 - 1200) + chr(1670 - 1559) + chr(48), 8)
else:
return nzTpIcepk0o8(chr(48) + chr(111) + chr(0b10110 + 0o32), 8) |
klavinslab/coral | coral/sequence/_sequence.py | Sequence.copy | def copy(self):
'''Create a copy of the current instance.
:returns: A safely editable copy of the current sequence.
'''
# Significant performance improvements by skipping alphabet check
return type(self)(self.seq, self.material, run_checks=False) | python | def copy(self):
'''Create a copy of the current instance.
:returns: A safely editable copy of the current sequence.
'''
# Significant performance improvements by skipping alphabet check
return type(self)(self.seq, self.material, run_checks=False) | [
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/sequence/_sequence.py#L40-L47 | train | Create a safely editable copy of the current instance. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x31' + chr(48) + '\063', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\066' + chr(886 - 836), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b10011 + 0o37) + chr(0b110001 + 0o1) + chr(1743 - 1695), ord("\x08")), nzTpIcepk0o8(chr(0b10 + 0o56) + '\157' + '\x32' + '\064' + chr(0b101101 + 0o3), 54166 - 54158), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110111) + chr(53), 0o10), nzTpIcepk0o8(chr(0b0 + 0o60) + chr(4410 - 4299) + chr(0b110010) + '\x31' + '\x31', ord("\x08")), nzTpIcepk0o8(chr(1432 - 1384) + chr(111) + chr(0b100101 + 0o16) + chr(437 - 387) + '\065', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b110000 + 0o77) + '\062' + chr(1800 - 1751) + '\x31', 8), nzTpIcepk0o8('\060' + chr(0b1100100 + 0o13) + chr(49) + chr(53) + '\064', ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110011) + '\x32' + '\063', 53893 - 53885), nzTpIcepk0o8('\060' + chr(111) + '\x31' + chr(372 - 317) + chr(50), 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(0b11010 + 0o27) + chr(209 - 154) + chr(0b100000 + 0o23), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + '\066', 0o10), nzTpIcepk0o8(chr(48) + chr(111) + '\x31' + chr(2456 - 2405) + chr(51), 0b1000), nzTpIcepk0o8(chr(0b11111 + 0o21) + chr(0b1101111) + chr(50) + '\067' + chr(49), 0o10), nzTpIcepk0o8('\x30' + '\157' + '\x31' + chr(0b110001) + chr(1396 - 1348), 1384 - 1376), nzTpIcepk0o8(chr(1816 - 1768) + '\x6f' + chr(0b110101) + chr(0b110010 + 0o3), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b101000 + 0o107) + '\x31' + chr(308 - 260) + chr(51), 8), nzTpIcepk0o8(chr(0b11101 + 0o23) + chr(0b1101 + 0o142) + chr(51) + chr(0b110111) + '\x32', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(2618 - 2563) + chr(0b10011 + 0o36), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(2310 - 2261) + '\063' + chr(55), 7154 - 7146), nzTpIcepk0o8(chr(450 - 402) + '\x6f' + chr(51) + chr(54) + chr(0b110000), 0o10), nzTpIcepk0o8('\060' + chr(0b1011111 + 0o20) + '\061' + '\x30' + chr(1095 - 1041), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(10329 - 10218) + chr(0b100101 + 0o14) + '\065' + chr(2688 - 2633), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + '\x31' + chr(0b1110 + 0o42) + chr(49), 0o10), nzTpIcepk0o8(chr(0b100001 + 0o17) + chr(0b101101 + 0o102) + chr(0b110010) + chr(0b11001 + 0o32) + chr(1185 - 1135), 22415 - 22407), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110101) + '\x34', 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + '\062' + chr(53) + chr(1602 - 1549), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(2136 - 2085) + '\065' + chr(2250 - 2200), 0b1000), nzTpIcepk0o8('\x30' + chr(10811 - 10700) + chr(0b0 + 0o63) + chr(0b101100 + 0o7) + chr(0b10110 + 0o40), 48738 - 48730), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(901 - 852) + '\x31' + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1000011 + 0o54) + chr(921 - 871) + chr(55) + chr(484 - 429), 0b1000), nzTpIcepk0o8('\x30' + chr(0b111110 + 0o61) + chr(1329 - 1278) + chr(1116 - 1065) + '\067', 9077 - 9069), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x33' + chr(105 - 50) + chr(48), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(51) + chr(0b110111) + chr(0b110010 + 0o4), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b111000 + 0o67) + '\061' + chr(53) + '\061', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1010100 + 0o33) + '\061' + chr(0b101010 + 0o14), 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(0b10101 + 0o36) + chr(0b100100 + 0o17) + chr(2886 - 2831), 8), nzTpIcepk0o8(chr(48) + chr(11590 - 11479) + chr(0b100111 + 0o14) + chr(0b110011) + chr(0b110101), 47790 - 47782), nzTpIcepk0o8(chr(0b1001 + 0o47) + chr(0b1101111) + '\x33' + '\062' + chr(53), 8)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + chr(12159 - 12048) + chr(0b11101 + 0o30) + chr(0b1101 + 0o43), 27860 - 27852)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'm'), chr(8737 - 8637) + '\x65' + chr(7589 - 7490) + '\157' + chr(8383 - 8283) + '\x65')(chr(9162 - 9045) + chr(0b1001000 + 0o54) + chr(0b10101 + 0o121) + chr(0b101101) + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def aZTCj4v5QdfO(hXMPsSrOQzbh):
return MJ07XsN5uFgW(hXMPsSrOQzbh)(roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'%F\xfb\x99Q\xea\xe2\xceY\x955\x14'), '\144' + '\145' + '\143' + chr(0b1101111) + chr(0b1011010 + 0o12) + chr(3590 - 3489))(chr(2391 - 2274) + '\164' + chr(0b100 + 0o142) + '\055' + '\x38')), roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'.S\xe4\xc5O\xe0\xb4\xe5'), chr(0b1100100) + chr(0b1100101) + chr(99) + '\x6f' + '\x64' + '\145')('\x75' + chr(116) + '\146' + chr(45) + chr(0b111000))), run_checks=nzTpIcepk0o8(chr(0b110000) + chr(0b111100 + 0o63) + '\060', 0b1000)) |
klavinslab/coral | coral/sequence/_sequence.py | Sequence.locate | def locate(self, pattern):
'''Find sequences matching a pattern.
:param pattern: Sequence for which to find matches.
:type pattern: str
:returns: Indices of pattern matches.
:rtype: list of ints
'''
if len(pattern) > len(self):
raise ValueError('Search pattern longer than searchable ' +
'sequence.')
seq = self.seq
pattern = str(pattern).upper()
re_pattern = '(?=' + pattern + ')'
matches = [index.start() % len(self) for index in
re.finditer(re_pattern, seq)]
return matches | python | def locate(self, pattern):
'''Find sequences matching a pattern.
:param pattern: Sequence for which to find matches.
:type pattern: str
:returns: Indices of pattern matches.
:rtype: list of ints
'''
if len(pattern) > len(self):
raise ValueError('Search pattern longer than searchable ' +
'sequence.')
seq = self.seq
pattern = str(pattern).upper()
re_pattern = '(?=' + pattern + ')'
matches = [index.start() % len(self) for index in
re.finditer(re_pattern, seq)]
return matches | [
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/sequence/_sequence.py#L49-L68 | train | Find sequences matching a pattern. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(48) + chr(8085 - 7974) + chr(724 - 675) + '\061', 62583 - 62575), nzTpIcepk0o8(chr(0b110000) + chr(8644 - 8533) + chr(0b110010) + chr(2442 - 2388), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(4118 - 4007) + chr(50) + '\x35' + chr(0b110000 + 0o0), 52928 - 52920), nzTpIcepk0o8('\060' + chr(0b11000 + 0o127) + '\063' + chr(50) + chr(0b101 + 0o56), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(49) + chr(0b110101 + 0o2) + chr(0b110010 + 0o5), ord("\x08")), nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(0b1100000 + 0o17) + chr(50) + chr(567 - 518) + chr(0b110100), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + '\062' + chr(2377 - 2323) + chr(340 - 286), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(711 - 661) + chr(970 - 915) + chr(1044 - 991), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\062' + chr(0b101111 + 0o2) + chr(54), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b1110 + 0o45) + chr(0b110110) + '\x34', ord("\x08")), nzTpIcepk0o8(chr(0b11110 + 0o22) + chr(0b1101111) + chr(49) + chr(0b101111 + 0o6) + chr(48), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(11737 - 11626) + chr(0b1 + 0o62) + chr(54) + chr(1329 - 1278), 0o10), nzTpIcepk0o8(chr(0b10011 + 0o35) + '\x6f' + '\061' + chr(50) + chr(0b110001), 40549 - 40541), nzTpIcepk0o8(chr(48) + chr(111) + chr(54), 29926 - 29918), nzTpIcepk0o8(chr(0b11111 + 0o21) + chr(0b10001 + 0o136) + '\062' + chr(50) + chr(1728 - 1674), 9649 - 9641), nzTpIcepk0o8(chr(0b1100 + 0o44) + chr(0b1101111) + '\063' + '\x35' + '\x32', 0o10), nzTpIcepk0o8('\x30' + chr(5625 - 5514) + chr(0b101 + 0o54) + chr(53) + chr(51), 0b1000), nzTpIcepk0o8(chr(1990 - 1942) + '\157' + chr(2430 - 2379) + chr(0b110001), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(1195 - 1084) + '\061' + chr(1302 - 1248) + chr(55), 63057 - 63049), nzTpIcepk0o8('\x30' + chr(111) + '\063' + chr(54) + chr(0b101010 + 0o12), 8), nzTpIcepk0o8(chr(0b11001 + 0o27) + '\157' + chr(386 - 337) + chr(50) + chr(2201 - 2152), 8), nzTpIcepk0o8(chr(2138 - 2090) + chr(111) + chr(1560 - 1511) + '\x34' + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(163 - 115) + chr(111) + chr(0b110010) + chr(54) + chr(108 - 60), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b100000 + 0o117) + chr(50) + chr(2633 - 2581) + '\065', 662 - 654), nzTpIcepk0o8(chr(0b11011 + 0o25) + chr(6567 - 6456) + '\063' + '\x30', 0b1000), nzTpIcepk0o8(chr(0b100101 + 0o13) + '\157' + chr(49) + chr(48) + '\x31', 0o10), nzTpIcepk0o8('\x30' + chr(2583 - 2472) + chr(49) + '\x37' + '\x32', 17336 - 17328), nzTpIcepk0o8(chr(0b1110 + 0o42) + chr(0b1101111) + '\062' + '\060' + chr(1102 - 1048), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + '\062' + chr(48) + '\062', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(9714 - 9603) + chr(1377 - 1328) + chr(547 - 494) + '\x37', 31341 - 31333), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(50) + chr(0b110110) + '\063', 46485 - 46477), nzTpIcepk0o8('\060' + chr(111) + '\063' + chr(49) + '\x33', 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b100111 + 0o13) + chr(1451 - 1402) + '\067', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b11101 + 0o122) + chr(501 - 452) + '\062' + '\x33', 8499 - 8491), nzTpIcepk0o8(chr(440 - 392) + '\x6f' + chr(0b11001 + 0o36) + '\060', 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(0b100000 + 0o23) + '\x35' + '\063', 0b1000), nzTpIcepk0o8(chr(2162 - 2114) + chr(3045 - 2934) + chr(0b110011) + '\x37' + chr(2062 - 2014), 38214 - 38206), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(495 - 444) + '\x32' + chr(55), 59529 - 59521), nzTpIcepk0o8(chr(1884 - 1836) + chr(111) + chr(1620 - 1571) + chr(0b11 + 0o55) + chr(0b101110 + 0o11), 41267 - 41259), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\063' + chr(50) + chr(0b110011), 8)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110 + 0o52) + chr(2110 - 1999) + chr(2038 - 1985) + '\060', 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b"'"), chr(1174 - 1074) + chr(0b10011 + 0o122) + chr(0b110101 + 0o56) + '\x6f' + '\144' + chr(0b1010101 + 0o20))('\x75' + chr(116) + chr(0b1100110) + chr(1300 - 1255) + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def ujxQhc4_HiKA(hXMPsSrOQzbh, UYtHA0XyNB9C):
if ftfygxgFas5X(UYtHA0XyNB9C) > ftfygxgFas5X(hXMPsSrOQzbh):
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'Zs\xc9\xa1\x1c\xe4\x96\xcd\xef\x80\x1c\x96#h\xb6\x86\x04w\x10\x91#E\xc4\xcdy/Z\xf5\xe7\x0e\xc1\xa8\xe72Z\x87\x9d\xf7'), '\144' + '\145' + '\143' + '\157' + chr(0b10100 + 0o120) + chr(0b1100101))(chr(0b1110101) + chr(10323 - 10207) + chr(2634 - 2532) + '\055' + chr(2684 - 2628)) + roI3spqORKae(ES5oEprVxulp(b'zs\xd9\xa6\x1a\xe2\xd5\xd8\xa0'), chr(5318 - 5218) + chr(101) + chr(0b1100011) + chr(0b0 + 0o157) + chr(250 - 150) + chr(0b1100101))('\x75' + chr(0b1101100 + 0o10) + '\146' + '\055' + '\070'))
ftk9lc7G5FOo = hXMPsSrOQzbh.ftk9lc7G5FOo
UYtHA0XyNB9C = N9zlRy29S1SS(UYtHA0XyNB9C).iq1mNMefb1Zd()
WoD6YFngKS8l = roI3spqORKae(ES5oEprVxulp(b'!)\x95'), '\144' + chr(0b100010 + 0o103) + '\x63' + chr(111) + '\x64' + chr(0b1100101))('\x75' + chr(0b1110100) + chr(7124 - 7022) + chr(0b10000 + 0o35) + chr(0b111000)) + UYtHA0XyNB9C + roI3spqORKae(ES5oEprVxulp(b' '), '\x64' + chr(0b1100101) + chr(7126 - 7027) + '\157' + chr(0b1001000 + 0o34) + chr(2733 - 2632))(chr(0b1100110 + 0o17) + '\164' + '\x66' + '\055' + '\x38')
ONopK8INb53O = [ZpfN5tSLaZze.KQbHFTcl_LKy() % ftfygxgFas5X(hXMPsSrOQzbh) for ZpfN5tSLaZze in aoTc4YA2bs2R.finditer(WoD6YFngKS8l, ftk9lc7G5FOo)]
return ONopK8INb53O |
klavinslab/coral | coral/sequence/_sequence.py | Feature.copy | def copy(self):
'''Return a copy of the Feature.
:returns: A safely editable copy of the current feature.
:rtype: coral.Feature
'''
return type(self)(self.name, self.start, self.stop, self.feature_type,
gene=self.gene, locus_tag=self.locus_tag,
qualifiers=self.qualifiers, strand=self.strand) | python | def copy(self):
'''Return a copy of the Feature.
:returns: A safely editable copy of the current feature.
:rtype: coral.Feature
'''
return type(self)(self.name, self.start, self.stop, self.feature_type,
gene=self.gene, locus_tag=self.locus_tag,
qualifiers=self.qualifiers, strand=self.strand) | [
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/sequence/_sequence.py#L334-L343 | train | Return a safely editable copy of the current feature. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110010) + '\066' + chr(629 - 574), 0b1000), nzTpIcepk0o8(chr(1495 - 1447) + chr(0b1101111) + chr(0b10001 + 0o41) + chr(50) + '\067', 0o10), nzTpIcepk0o8(chr(0b10000 + 0o40) + chr(0b111 + 0o150) + chr(54) + chr(172 - 124), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110010 + 0o1) + chr(0b110010), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + '\x32' + chr(0b110101) + '\x34', 0b1000), nzTpIcepk0o8(chr(1838 - 1790) + chr(12206 - 12095) + chr(0b10001 + 0o43) + chr(1318 - 1266), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110011) + '\065', 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(50) + '\064' + '\x37', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(51) + '\x37' + chr(0b11001 + 0o31), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1001011 + 0o44) + chr(50) + '\066' + chr(0b1100 + 0o46), 0b1000), nzTpIcepk0o8(chr(789 - 741) + chr(0b100111 + 0o110) + chr(0b10110 + 0o36) + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(0b110000 + 0o0) + chr(111) + chr(2079 - 2029) + chr(1928 - 1874) + chr(0b10101 + 0o41), ord("\x08")), nzTpIcepk0o8(chr(844 - 796) + '\157' + chr(426 - 377) + chr(52) + '\063', 20314 - 20306), nzTpIcepk0o8('\060' + chr(7878 - 7767) + '\061' + chr(2115 - 2065) + chr(52), ord("\x08")), nzTpIcepk0o8(chr(1134 - 1086) + chr(0b1101111) + '\x33' + chr(55) + chr(0b110010), 8), nzTpIcepk0o8('\060' + chr(0b110 + 0o151) + chr(0b1111 + 0o44) + chr(52) + '\x34', ord("\x08")), nzTpIcepk0o8(chr(611 - 563) + chr(10533 - 10422) + chr(0b110001) + '\x37' + chr(0b110010), 56030 - 56022), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(1362 - 1311) + chr(0b110111) + chr(0b111 + 0o52), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110001) + '\x33' + chr(128 - 76), 26725 - 26717), nzTpIcepk0o8(chr(2297 - 2249) + chr(0b1101111) + '\063' + chr(163 - 115) + chr(55), 9292 - 9284), nzTpIcepk0o8('\x30' + chr(0b1000001 + 0o56) + '\062' + '\x33' + chr(49), 40706 - 40698), nzTpIcepk0o8(chr(0b110000) + chr(11638 - 11527) + '\x31' + chr(49) + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(1802 - 1754) + chr(0b1101111) + '\x37' + chr(0b1011 + 0o51), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + '\066' + chr(54), 38472 - 38464), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110001) + '\060' + '\067', 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(1658 - 1607) + chr(0b110000 + 0o4) + chr(0b10101 + 0o36), 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110010) + chr(52) + chr(51), ord("\x08")), nzTpIcepk0o8(chr(0b1000 + 0o50) + '\x6f' + '\x33' + chr(54) + chr(51), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + chr(134 - 84) + chr(1361 - 1307) + chr(0b1001 + 0o53), 14346 - 14338), nzTpIcepk0o8(chr(48) + '\x6f' + '\061' + '\x37' + chr(770 - 721), 0b1000), nzTpIcepk0o8(chr(0b100001 + 0o17) + chr(564 - 453) + '\063' + chr(0b11101 + 0o30) + '\064', 0o10), nzTpIcepk0o8(chr(0b1000 + 0o50) + chr(0b1000 + 0o147) + '\x31' + chr(0b110000) + chr(855 - 800), 8), nzTpIcepk0o8(chr(438 - 390) + chr(5636 - 5525) + '\x32' + '\066' + chr(0b110100), 8), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b11011 + 0o27) + chr(2842 - 2787) + chr(50), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(1361 - 1250) + '\062' + chr(67 - 16) + chr(49), 8), nzTpIcepk0o8(chr(248 - 200) + chr(8332 - 8221) + chr(50) + chr(53) + '\061', 28413 - 28405), nzTpIcepk0o8(chr(2254 - 2206) + chr(0b1101111) + chr(0b110000 + 0o3) + chr(0b100011 + 0o17) + chr(53), 0b1000), nzTpIcepk0o8('\060' + chr(2196 - 2085) + chr(0b100111 + 0o12) + chr(0b100100 + 0o20) + '\061', ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(50) + '\066' + chr(0b100110 + 0o15), 0b1000), nzTpIcepk0o8(chr(172 - 124) + chr(0b1101111) + chr(50) + '\067' + chr(0b110001 + 0o6), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + '\x6f' + chr(1327 - 1274) + chr(0b11 + 0o55), 51012 - 51004)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x99'), '\x64' + chr(0b1100101) + chr(99) + chr(8612 - 8501) + chr(5459 - 5359) + chr(0b1100101))('\x75' + '\164' + chr(0b1001001 + 0o35) + chr(45) + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def aZTCj4v5QdfO(hXMPsSrOQzbh):
return MJ07XsN5uFgW(hXMPsSrOQzbh)(roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xe4\xdbfX\x9efM\xe6\xa5\xdfn\xd3'), chr(0b11100 + 0o110) + chr(101) + '\x63' + '\x6f' + '\144' + chr(101))(chr(117) + '\164' + chr(0b100111 + 0o77) + chr(0b101101) + '\x38')), roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xfc\xc6RR\xeap~\xcb\xa5\xfel\xcf'), '\144' + '\x65' + chr(99) + chr(11713 - 11602) + chr(0b10100 + 0o120) + chr(2489 - 2388))(chr(7138 - 7021) + chr(0b11100 + 0o130) + '\x66' + chr(0b1 + 0o54) + chr(0b101110 + 0o12))), roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xd3\xcezx\xeeMD\xe8\xa5\xdc`\xf3'), chr(0b100101 + 0o77) + '\x65' + '\x63' + chr(111) + chr(3459 - 3359) + chr(0b100011 + 0o102))('\x75' + chr(0b1110100) + chr(102) + '\x2d' + chr(0b11 + 0o65))), roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xd1\xf2Qn\xd9Vx\xf8\x8e\xcbW\xd3'), '\x64' + '\145' + chr(0b111010 + 0o51) + chr(0b1 + 0o156) + '\x64' + chr(0b1011111 + 0o6))(chr(117) + '\164' + '\146' + '\x2d' + chr(0b101111 + 0o11))), gene=roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xd0\xf2^\x7f'), '\x64' + chr(0b1100101) + chr(8505 - 8406) + chr(111) + '\x64' + chr(101))('\x75' + '\x74' + '\x66' + '\055' + chr(56))), locus_tag=roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xdb\xf8So\xdf{i\xc6\x9d'), '\144' + '\x65' + chr(4545 - 4446) + '\157' + '\144' + chr(101))(chr(117) + chr(0b1110100) + chr(102) + chr(45) + chr(0b101001 + 0o17))), qualifiers=roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xef\xfdEE\xdekZ\xf4\xa9\xcaf\xf1'), chr(6495 - 6395) + '\x65' + '\x63' + chr(0b1101111) + chr(0b11010 + 0o112) + chr(745 - 644))(chr(0b1110101) + chr(116) + chr(102) + chr(1645 - 1600) + '\070')), strand=roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xc4\xd8FJ\xc8Tj\x91\xb0\xd9c\x80'), chr(2512 - 2412) + chr(0b1100101) + chr(4856 - 4757) + chr(0b101110 + 0o101) + chr(3125 - 3025) + chr(0b1100101))(chr(9333 - 9216) + chr(0b1110100) + chr(0b1100110) + chr(0b101101) + chr(0b111000)))) |
klavinslab/coral | coral/analysis/_structure/nupack.py | run_nupack | def run_nupack(kwargs):
'''Run picklable Nupack command.
:param kwargs: keyword arguments to pass to Nupack as well as 'cmd'.
:returns: Variable - whatever `cmd` returns.
'''
run = NUPACK(kwargs['seq'])
output = getattr(run, kwargs['cmd'])(**kwargs['arguments'])
return output | python | def run_nupack(kwargs):
'''Run picklable Nupack command.
:param kwargs: keyword arguments to pass to Nupack as well as 'cmd'.
:returns: Variable - whatever `cmd` returns.
'''
run = NUPACK(kwargs['seq'])
output = getattr(run, kwargs['cmd'])(**kwargs['arguments'])
return output | [
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/analysis/_structure/nupack.py#L1536-L1545 | train | Run picklable Nupack command. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b10110 + 0o32) + '\157' + chr(49) + chr(51) + chr(0b10110 + 0o34), 0o10), nzTpIcepk0o8(chr(0b100101 + 0o13) + chr(0b1101111) + chr(0b110001) + chr(548 - 497) + '\x30', 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(1054 - 1004) + chr(318 - 263) + chr(0b100011 + 0o21), 0b1000), nzTpIcepk0o8('\x30' + chr(0b11000 + 0o127) + '\x31' + '\x36' + chr(0b10011 + 0o35), 2307 - 2299), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(55) + chr(0b11110 + 0o30), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(1147 - 1098) + '\x37' + '\x32', 12301 - 12293), nzTpIcepk0o8(chr(0b0 + 0o60) + chr(111) + '\063' + '\x37' + chr(1941 - 1893), 11748 - 11740), nzTpIcepk0o8('\x30' + '\157' + chr(2130 - 2081) + '\x36' + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(813 - 765) + chr(111) + chr(1492 - 1443) + chr(2046 - 1994) + '\064', ord("\x08")), nzTpIcepk0o8(chr(1494 - 1446) + '\x6f' + chr(0b110011) + '\x34' + '\x34', 0b1000), nzTpIcepk0o8(chr(0b1011 + 0o45) + '\157' + chr(2502 - 2451) + chr(54) + chr(323 - 270), 0o10), nzTpIcepk0o8(chr(48) + chr(1919 - 1808) + chr(0b110001) + '\x34' + '\060', ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(50) + chr(0b110000) + '\x31', 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(1367 - 1317) + '\064' + chr(986 - 938), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(49) + '\x35' + chr(51), 0b1000), nzTpIcepk0o8('\060' + chr(10604 - 10493) + chr(0b110010) + chr(0b110000) + '\067', 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(51) + chr(78 - 24) + chr(53), 8), nzTpIcepk0o8(chr(2259 - 2211) + '\x6f' + chr(0b110010) + chr(0b100010 + 0o22), ord("\x08")), nzTpIcepk0o8(chr(0b10 + 0o56) + chr(0b1101111) + chr(0b10111 + 0o32) + chr(0b1011 + 0o51) + chr(48), 8), nzTpIcepk0o8('\060' + '\x6f' + '\063' + chr(0b110111) + chr(0b10100 + 0o43), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x31' + '\x36' + chr(0b110100), 8), nzTpIcepk0o8('\060' + '\x6f' + '\x33' + chr(0b1 + 0o60) + chr(0b11100 + 0o27), 50237 - 50229), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(49) + chr(1994 - 1941) + '\062', 0o10), nzTpIcepk0o8(chr(0b10000 + 0o40) + chr(111) + chr(0b110001) + '\064' + chr(53), ord("\x08")), nzTpIcepk0o8('\x30' + chr(11109 - 10998) + chr(933 - 881) + '\x35', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1001011 + 0o44) + chr(0b110001) + chr(55) + chr(49), 8250 - 8242), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(55) + chr(0b110110), 8), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\063' + chr(0b110000 + 0o7) + chr(0b110001 + 0o1), 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110001) + '\065', 35619 - 35611), nzTpIcepk0o8(chr(59 - 11) + chr(0b1101111) + chr(49) + chr(49) + '\x34', 0o10), nzTpIcepk0o8(chr(0b101111 + 0o1) + chr(111) + chr(49) + '\x31', ord("\x08")), nzTpIcepk0o8(chr(0b10010 + 0o36) + chr(0b1101111) + chr(0b1101 + 0o45) + '\064' + chr(52), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + chr(0b110010) + '\060' + '\061', 8), nzTpIcepk0o8(chr(48) + chr(1127 - 1016) + chr(50) + chr(2587 - 2533), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110001) + chr(2378 - 2325) + chr(0b110100), 55726 - 55718), nzTpIcepk0o8('\060' + '\x6f' + chr(0b11111 + 0o23) + '\065' + '\x36', 62734 - 62726), nzTpIcepk0o8('\060' + chr(111) + chr(0b100010 + 0o24) + chr(1296 - 1241), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(52) + chr(0b110011), ord("\x08")), nzTpIcepk0o8(chr(1104 - 1056) + chr(0b1101111 + 0o0) + chr(0b111 + 0o54) + chr(0b110011 + 0o2) + chr(1737 - 1688), 0b1000), nzTpIcepk0o8(chr(0b1100 + 0o44) + chr(7412 - 7301) + '\x32' + chr(0b100 + 0o61) + chr(0b110001), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\065' + chr(0b110000), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b't'), chr(0b111000 + 0o54) + chr(8105 - 8004) + chr(0b111010 + 0o51) + '\x6f' + chr(0b1000 + 0o134) + chr(101))(chr(0b1110101) + chr(116) + '\146' + '\055' + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def fKia2X5K7e22(q5n0sHDDTy90):
qnPOIdBQJdzY = KyaYFILOkp3C(q5n0sHDDTy90[roI3spqORKae(ES5oEprVxulp(b')=\xcd'), '\x64' + chr(8632 - 8531) + '\x63' + chr(0b1101111) + chr(9646 - 9546) + chr(101))('\165' + '\x74' + chr(0b1100110) + '\055' + '\x38')])
toKQXlEvBKaK = roI3spqORKae(qnPOIdBQJdzY, q5n0sHDDTy90[roI3spqORKae(ES5oEprVxulp(b'95\xd8'), chr(100) + chr(0b1011101 + 0o10) + chr(0b1000 + 0o133) + '\x6f' + chr(0b101010 + 0o72) + '\145')('\165' + chr(0b1000 + 0o154) + '\146' + chr(0b101101) + chr(2442 - 2386))])(**q5n0sHDDTy90[roI3spqORKae(ES5oEprVxulp(b';*\xdb\x05S\x1f\x96\x00\x17'), chr(0b1100000 + 0o4) + chr(0b101010 + 0o73) + chr(0b100101 + 0o76) + chr(2027 - 1916) + chr(0b1100100) + chr(3317 - 3216))(chr(0b1110101) + chr(116) + chr(0b1100000 + 0o6) + chr(0b101101) + chr(0b10111 + 0o41))])
return toKQXlEvBKaK |
klavinslab/coral | coral/analysis/_structure/nupack.py | NUPACK.pfunc_multi | def pfunc_multi(self, strands, permutation=None, temp=37.0, pseudo=False,
material=None, dangles='some', sodium=1.0, magnesium=0.0):
'''Compute the partition function for an ordered complex of strands.
Runs the \'pfunc\' command.
:param strands: List of strands to use as inputs to pfunc -multi.
:type strands: list
:param permutation: The circular permutation of strands to test in
complex. e.g. to test in the order that was input
for 4 strands, the permutation would be [1,2,3,4].
If set to None, defaults to the order of the
input strands.
:type permutation: list
:param temp: Temperature setting for the computation. Negative values
are not allowed.
:type temp: float
:param pseudo: Enable pseudoknots.
:type pseudo: bool
:param material: The material setting to use in the computation. If set
to None (the default), the material type is inferred
from the strands. Other settings available: 'dna' for
DNA parameters, 'rna' for RNA (1995) parameters, and
'rna1999' for the RNA 1999 parameters.
:type material: str
:param dangles: How to treat dangles in the computation. From the
user guide: For \'none\': Dangle energies are ignored.
For \'some\': \'A dangle energy is incorporated for
each unpaired base flanking a duplex\'. For 'all': all
dangle energy is considered.
:type dangles: str
:param sodium: Sodium concentration in solution (molar), only applies
to DNA.
:type sodium: float
:param magnesium: Magnesium concentration in solution (molar), only
applies to DNA>
:type magnesium: float
:returns: A 2-tuple of the free energy of the ordered complex
(float) and the partition function (float).
:rtype: tuple
'''
# Set the material (will be used to set command material flag)
material = self._set_material(strands, material, multi=True)
# Set up command flags
cmd_args = self._prep_cmd_args(temp, dangles, material, pseudo, sodium,
magnesium, multi=True)
# Set up the input file and run the command
if permutation is None:
permutation = range(1, len(strands) + 1)
lines = self._multi_lines(strands, permutation)
stdout = self._run('pfunc', cmd_args, lines).split('\n')
return (float(stdout[-3]), float(stdout[-2])) | python | def pfunc_multi(self, strands, permutation=None, temp=37.0, pseudo=False,
material=None, dangles='some', sodium=1.0, magnesium=0.0):
'''Compute the partition function for an ordered complex of strands.
Runs the \'pfunc\' command.
:param strands: List of strands to use as inputs to pfunc -multi.
:type strands: list
:param permutation: The circular permutation of strands to test in
complex. e.g. to test in the order that was input
for 4 strands, the permutation would be [1,2,3,4].
If set to None, defaults to the order of the
input strands.
:type permutation: list
:param temp: Temperature setting for the computation. Negative values
are not allowed.
:type temp: float
:param pseudo: Enable pseudoknots.
:type pseudo: bool
:param material: The material setting to use in the computation. If set
to None (the default), the material type is inferred
from the strands. Other settings available: 'dna' for
DNA parameters, 'rna' for RNA (1995) parameters, and
'rna1999' for the RNA 1999 parameters.
:type material: str
:param dangles: How to treat dangles in the computation. From the
user guide: For \'none\': Dangle energies are ignored.
For \'some\': \'A dangle energy is incorporated for
each unpaired base flanking a duplex\'. For 'all': all
dangle energy is considered.
:type dangles: str
:param sodium: Sodium concentration in solution (molar), only applies
to DNA.
:type sodium: float
:param magnesium: Magnesium concentration in solution (molar), only
applies to DNA>
:type magnesium: float
:returns: A 2-tuple of the free energy of the ordered complex
(float) and the partition function (float).
:rtype: tuple
'''
# Set the material (will be used to set command material flag)
material = self._set_material(strands, material, multi=True)
# Set up command flags
cmd_args = self._prep_cmd_args(temp, dangles, material, pseudo, sodium,
magnesium, multi=True)
# Set up the input file and run the command
if permutation is None:
permutation = range(1, len(strands) + 1)
lines = self._multi_lines(strands, permutation)
stdout = self._run('pfunc', cmd_args, lines).split('\n')
return (float(stdout[-3]), float(stdout[-2])) | [
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:param strands: List of strands to use as inputs to pfunc -multi.
:type strands: list
:param permutation: The circular permutation of strands to test in
complex. e.g. to test in the order that was input
for 4 strands, the permutation would be [1,2,3,4].
If set to None, defaults to the order of the
input strands.
:type permutation: list
:param temp: Temperature setting for the computation. Negative values
are not allowed.
:type temp: float
:param pseudo: Enable pseudoknots.
:type pseudo: bool
:param material: The material setting to use in the computation. If set
to None (the default), the material type is inferred
from the strands. Other settings available: 'dna' for
DNA parameters, 'rna' for RNA (1995) parameters, and
'rna1999' for the RNA 1999 parameters.
:type material: str
:param dangles: How to treat dangles in the computation. From the
user guide: For \'none\': Dangle energies are ignored.
For \'some\': \'A dangle energy is incorporated for
each unpaired base flanking a duplex\'. For 'all': all
dangle energy is considered.
:type dangles: str
:param sodium: Sodium concentration in solution (molar), only applies
to DNA.
:type sodium: float
:param magnesium: Magnesium concentration in solution (molar), only
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:type magnesium: float
:returns: A 2-tuple of the free energy of the ordered complex
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/analysis/_structure/nupack.py#L97-L150 | train | Compute the partition function for an ordered complex of strands. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b101001 + 0o7) + chr(111) + '\x36' + chr(0b110001), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x31' + chr(0b110000) + chr(387 - 334), 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110001) + chr(0b110001) + chr(55), 0b1000), nzTpIcepk0o8(chr(0b100110 + 0o12) + chr(0b1001110 + 0o41) + '\062' + chr(49) + '\x35', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(379 - 330) + chr(0b101010 + 0o6) + '\064', 0o10), nzTpIcepk0o8('\060' + chr(0b1011001 + 0o26) + '\061' + chr(55) + '\063', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1010001 + 0o36) + chr(0b11101 + 0o25) + '\064' + chr(269 - 220), 60213 - 60205), nzTpIcepk0o8(chr(1651 - 1603) + '\x6f' + chr(1530 - 1480) + chr(0b110001) + chr(0b10110 + 0o37), 8), nzTpIcepk0o8('\x30' + '\x6f' + '\x31' + chr(785 - 737), 0b1000), nzTpIcepk0o8(chr(1036 - 988) + chr(0b1010111 + 0o30) + chr(0b110011 + 0o1) + chr(1673 - 1619), 28785 - 28777), nzTpIcepk0o8(chr(1238 - 1190) + '\x6f' + chr(0b110001) + chr(50), 0b1000), nzTpIcepk0o8(chr(1601 - 1553) + '\157' + chr(49) + chr(49) + '\x37', 8), nzTpIcepk0o8('\x30' + chr(111) + '\x31' + chr(478 - 423) + chr(0b110010), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b1000 + 0o53) + chr(50), ord("\x08")), nzTpIcepk0o8(chr(0b1011 + 0o45) + chr(8969 - 8858) + chr(1915 - 1866) + chr(0b110000 + 0o0) + '\061', 20185 - 20177), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b101010 + 0o7) + chr(2677 - 2625) + '\x34', 0b1000), nzTpIcepk0o8('\060' + chr(5308 - 5197) + chr(972 - 919) + chr(0b110011), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b100001 + 0o116) + chr(0b110001) + chr(2079 - 2029) + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(0b11 + 0o55) + '\157' + chr(0b110101) + '\067', 0b1000), nzTpIcepk0o8('\060' + '\157' + '\063' + chr(682 - 628) + '\x37', 0b1000), nzTpIcepk0o8('\x30' + chr(7420 - 7309) + chr(51) + chr(0b110010) + chr(1047 - 997), 52173 - 52165), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(51) + chr(0b110010) + '\064', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b110000 + 0o77) + '\x31', 58939 - 58931), nzTpIcepk0o8('\x30' + chr(111) + chr(50) + chr(0b110111) + chr(2017 - 1966), 17973 - 17965), nzTpIcepk0o8(chr(48) + chr(0b1101111 + 0o0) + '\x32' + chr(53) + '\065', ord("\x08")), nzTpIcepk0o8(chr(1529 - 1481) + '\157' + chr(51) + chr(0b110001) + chr(52), 0o10), nzTpIcepk0o8(chr(2041 - 1993) + chr(0b1101001 + 0o6) + chr(0b101100 + 0o7) + chr(0b110001) + '\062', 41718 - 41710), nzTpIcepk0o8(chr(1224 - 1176) + '\157' + chr(50) + '\x33' + '\x37', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(4154 - 4043) + chr(1506 - 1455) + chr(0b10110 + 0o36), 3948 - 3940), nzTpIcepk0o8('\x30' + chr(12243 - 12132) + chr(0b110010) + chr(0b10110 + 0o33) + chr(0b11000 + 0o36), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110011) + chr(1697 - 1646) + chr(0b1010 + 0o51), 0o10), nzTpIcepk0o8(chr(811 - 763) + '\157' + chr(0b11101 + 0o23), 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(49) + chr(0b100100 + 0o22) + chr(0b110100), 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(0b11100 + 0o25) + '\060' + chr(0b110000), 50051 - 50043), nzTpIcepk0o8(chr(533 - 485) + chr(0b1101111) + '\063' + chr(1969 - 1921) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(0b1001 + 0o47) + chr(111) + chr(51) + chr(54) + chr(0b10010 + 0o40), 2567 - 2559), nzTpIcepk0o8(chr(290 - 242) + chr(0b1101111) + '\061' + '\065' + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\062' + '\062' + chr(0b1 + 0o63), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b10 + 0o155) + chr(0b100010 + 0o24), 0o10), nzTpIcepk0o8('\x30' + '\157' + '\061' + chr(2271 - 2217), 62276 - 62268)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(2379 - 2326) + '\060', 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x1f'), chr(0b1111 + 0o125) + '\145' + '\x63' + '\x6f' + '\144' + chr(5772 - 5671))(chr(117) + chr(116) + chr(0b1100110) + chr(0b10011 + 0o32) + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def uQ5VF4GlAMec(hXMPsSrOQzbh, r_D0HyqK4grO, bmmTXKdBuMbO=None, bhvcCFR07maA=37.0, jif2BXBXDWe0=nzTpIcepk0o8(chr(0b11010 + 0o26) + chr(0b1101111) + chr(1540 - 1492), 8), P6MCancmTVIW=None, dcIGdrKJIQqm=roI3spqORKae(ES5oEprVxulp(b'B*"\xe8'), '\x64' + chr(0b1100101) + chr(99) + chr(0b1011101 + 0o22) + '\144' + chr(4915 - 4814))(chr(10976 - 10859) + chr(0b1110100) + '\x66' + chr(0b10010 + 0o33) + chr(1154 - 1098)), N53N20X2V9t8=1.0, _fwxLQ0Lh__w=0.0):
P6MCancmTVIW = hXMPsSrOQzbh._set_material(r_D0HyqK4grO, P6MCancmTVIW, multi=nzTpIcepk0o8('\x30' + '\157' + '\061', 8))
zF8oFOtHDCse = hXMPsSrOQzbh._prep_cmd_args(bhvcCFR07maA, dcIGdrKJIQqm, P6MCancmTVIW, jif2BXBXDWe0, N53N20X2V9t8, _fwxLQ0Lh__w, multi=nzTpIcepk0o8(chr(2162 - 2114) + chr(10340 - 10229) + '\061', 8))
if bmmTXKdBuMbO is None:
bmmTXKdBuMbO = bbT2xIe5pzk7(nzTpIcepk0o8('\060' + chr(0b101110 + 0o101) + '\x31', 8), ftfygxgFas5X(r_D0HyqK4grO) + nzTpIcepk0o8(chr(0b110000) + chr(111) + '\061', 8))
vniSnlI09HNg = hXMPsSrOQzbh._multi_lines(r_D0HyqK4grO, bmmTXKdBuMbO)
E4teKT3YJIcH = hXMPsSrOQzbh._run(roI3spqORKae(ES5oEprVxulp(b"A#:\xe3'"), '\x64' + '\x65' + chr(99) + chr(0b1101111) + '\x64' + '\x65')('\x75' + chr(1888 - 1772) + '\x66' + chr(45) + chr(0b111000)), zF8oFOtHDCse, vniSnlI09HNg).LfRrQOxuDvnC(roI3spqORKae(ES5oEprVxulp(b';'), chr(0b1100100) + '\x65' + chr(0b1100011) + chr(111) + chr(0b1100100) + '\x65')(chr(0b1110101) + chr(116) + chr(102) + chr(1527 - 1482) + chr(56)))
return (jLW6pRf2DSRk(E4teKT3YJIcH[-nzTpIcepk0o8(chr(48) + '\157' + chr(1072 - 1021), 0o10)]), jLW6pRf2DSRk(E4teKT3YJIcH[-nzTpIcepk0o8('\060' + chr(111) + '\062', 49519 - 49511)])) |
klavinslab/coral | coral/analysis/_structure/nupack.py | NUPACK.pairs | def pairs(self, strand, cutoff=0.001, temp=37.0, pseudo=False,
material=None, dangles='some', sodium=1.0, magnesium=0.0):
'''Compute the pair probabilities for an ordered complex of strands.
Runs the \'pairs\' command.
:param strand: Strand on which to run pairs. Strands must be either
coral.DNA or coral.RNA).
:type strand: list
:param cutoff: Only probabilities above this cutoff appear in the
output.
:type cutoff: float
:param temp: Temperature setting for the computation. Negative values
are not allowed.
:type temp: float
:param pseudo: Enable pseudoknots.
:type pseudo: bool
:param material: The material setting to use in the computation. If set
to None (the default), the material type is inferred
from the strands. Other settings available: 'dna' for
DNA parameters, 'rna' for RNA (1995) parameters, and
'rna1999' for the RNA 1999 parameters.
:type material: str
:param dangles: How to treat dangles in the computation. From the
user guide: For \'none\': Dangle energies are ignored.
For \'some\': \'A dangle energy is incorporated for
each unpaired base flanking a duplex\'. For 'all': all
dangle energy is considered.
:type dangles: str
:param sodium: Sodium concentration in solution (molar), only applies
to DNA.
:type sodium: float
:param magnesium: Magnesium concentration in solution (molar), only
applies to DNA>
:type magnesium: float
:returns: The probability matrix, where the (i, j)th entry
is the probability that base i is bound to base j. The matrix
is augmented (it's N+1 by N+1, where N is the number of bases
in the sequence) with an (N+1)th column containing the
probability that each base is unpaired.
:rtype: numpy.array
'''
# Set the material (will be used to set command material flag)
material = self._set_material(strand, material)
# Set up command flags
cmd_args = self._prep_cmd_args(temp, dangles, material, pseudo, sodium,
magnesium, multi=False)
# Set up the input file and run the command. Note: no STDOUT
lines = [str(strand)]
self._run('pairs', cmd_args, lines)
# Read the output from file
ppairs = self._read_tempfile('pairs.ppairs')
data = re.search('\n\n\d*\n(.*)', ppairs, flags=re.DOTALL).group(1)
N = len(strand)
data_lines = [line.split('\t') for line in data.split('\n') if line]
prob_matrix = self._pairs_to_np(data_lines, N)
return prob_matrix | python | def pairs(self, strand, cutoff=0.001, temp=37.0, pseudo=False,
material=None, dangles='some', sodium=1.0, magnesium=0.0):
'''Compute the pair probabilities for an ordered complex of strands.
Runs the \'pairs\' command.
:param strand: Strand on which to run pairs. Strands must be either
coral.DNA or coral.RNA).
:type strand: list
:param cutoff: Only probabilities above this cutoff appear in the
output.
:type cutoff: float
:param temp: Temperature setting for the computation. Negative values
are not allowed.
:type temp: float
:param pseudo: Enable pseudoknots.
:type pseudo: bool
:param material: The material setting to use in the computation. If set
to None (the default), the material type is inferred
from the strands. Other settings available: 'dna' for
DNA parameters, 'rna' for RNA (1995) parameters, and
'rna1999' for the RNA 1999 parameters.
:type material: str
:param dangles: How to treat dangles in the computation. From the
user guide: For \'none\': Dangle energies are ignored.
For \'some\': \'A dangle energy is incorporated for
each unpaired base flanking a duplex\'. For 'all': all
dangle energy is considered.
:type dangles: str
:param sodium: Sodium concentration in solution (molar), only applies
to DNA.
:type sodium: float
:param magnesium: Magnesium concentration in solution (molar), only
applies to DNA>
:type magnesium: float
:returns: The probability matrix, where the (i, j)th entry
is the probability that base i is bound to base j. The matrix
is augmented (it's N+1 by N+1, where N is the number of bases
in the sequence) with an (N+1)th column containing the
probability that each base is unpaired.
:rtype: numpy.array
'''
# Set the material (will be used to set command material flag)
material = self._set_material(strand, material)
# Set up command flags
cmd_args = self._prep_cmd_args(temp, dangles, material, pseudo, sodium,
magnesium, multi=False)
# Set up the input file and run the command. Note: no STDOUT
lines = [str(strand)]
self._run('pairs', cmd_args, lines)
# Read the output from file
ppairs = self._read_tempfile('pairs.ppairs')
data = re.search('\n\n\d*\n(.*)', ppairs, flags=re.DOTALL).group(1)
N = len(strand)
data_lines = [line.split('\t') for line in data.split('\n') if line]
prob_matrix = self._pairs_to_np(data_lines, N)
return prob_matrix | [
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Runs the \'pairs\' command.
:param strand: Strand on which to run pairs. Strands must be either
coral.DNA or coral.RNA).
:type strand: list
:param cutoff: Only probabilities above this cutoff appear in the
output.
:type cutoff: float
:param temp: Temperature setting for the computation. Negative values
are not allowed.
:type temp: float
:param pseudo: Enable pseudoknots.
:type pseudo: bool
:param material: The material setting to use in the computation. If set
to None (the default), the material type is inferred
from the strands. Other settings available: 'dna' for
DNA parameters, 'rna' for RNA (1995) parameters, and
'rna1999' for the RNA 1999 parameters.
:type material: str
:param dangles: How to treat dangles in the computation. From the
user guide: For \'none\': Dangle energies are ignored.
For \'some\': \'A dangle energy is incorporated for
each unpaired base flanking a duplex\'. For 'all': all
dangle energy is considered.
:type dangles: str
:param sodium: Sodium concentration in solution (molar), only applies
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:type sodium: float
:param magnesium: Magnesium concentration in solution (molar), only
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:type magnesium: float
:returns: The probability matrix, where the (i, j)th entry
is the probability that base i is bound to base j. The matrix
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in the sequence) with an (N+1)th column containing the
probability that each base is unpaired.
:rtype: numpy.array | [
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/analysis/_structure/nupack.py#L153-L213 | train | Compute the pair probabilities for an ordered complex of strands. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(216 - 168) + chr(0b1101111) + '\x33' + chr(0b110001 + 0o1) + chr(53), 45759 - 45751), nzTpIcepk0o8(chr(0b1 + 0o57) + chr(1252 - 1141) + '\062' + chr(52), ord("\x08")), nzTpIcepk0o8(chr(0b101 + 0o53) + chr(0b1101111) + chr(0b110001) + '\x34', ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + '\x32' + chr(51) + '\067', 0o10), nzTpIcepk0o8(chr(48) + chr(10939 - 10828) + chr(0b100 + 0o56) + chr(49) + chr(0b110111), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + '\x31' + '\x35' + chr(0b110100), 22894 - 22886), nzTpIcepk0o8(chr(48) + chr(295 - 184) + '\063' + chr(0b11011 + 0o30) + chr(2313 - 2263), 0o10), nzTpIcepk0o8('\x30' + chr(111) + '\061' + chr(0b110011) + chr(51), 0o10), nzTpIcepk0o8('\060' + chr(0b1010110 + 0o31) + chr(0b110001) + chr(0b111 + 0o53) + chr(0b110111 + 0o0), 55612 - 55604), nzTpIcepk0o8('\060' + '\157' + '\062' + chr(0b101100 + 0o10) + '\060', 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(0b101 + 0o55) + chr(774 - 721) + chr(0b110000), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b101010 + 0o105) + chr(0b110010) + chr(52), 8), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110011) + chr(0b110110) + chr(1481 - 1427), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1000011 + 0o54) + chr(50) + '\x35' + '\060', 8), nzTpIcepk0o8(chr(0b11000 + 0o30) + '\157' + chr(50) + chr(50) + chr(0b101001 + 0o13), ord("\x08")), nzTpIcepk0o8(chr(679 - 631) + chr(5910 - 5799) + '\061' + chr(55) + '\064', 0o10), nzTpIcepk0o8('\x30' + chr(10963 - 10852) + chr(0b110100) + chr(0b10001 + 0o37), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b1011 + 0o50) + '\x34' + '\x31', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b101 + 0o62) + chr(0b11101 + 0o25), 0b1000), nzTpIcepk0o8('\060' + chr(111) + '\x32' + '\x31' + '\064', 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(0b0 + 0o67), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + '\x32' + chr(267 - 216) + '\060', 0b1000), nzTpIcepk0o8(chr(1762 - 1714) + chr(1432 - 1321) + '\061' + chr(49), 0b1000), nzTpIcepk0o8('\060' + '\157' + '\x31' + chr(51) + chr(0b101101 + 0o3), 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(50) + chr(54) + chr(0b100001 + 0o23), 0b1000), nzTpIcepk0o8(chr(1159 - 1111) + chr(0b111100 + 0o63) + chr(51) + chr(1125 - 1070) + chr(0b110001), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110000 + 0o2) + chr(49) + '\x35', 32133 - 32125), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110010) + chr(54) + chr(0b10001 + 0o44), 6161 - 6153), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(50) + chr(54), ord("\x08")), nzTpIcepk0o8(chr(0b11110 + 0o22) + chr(111) + chr(49) + chr(53) + chr(883 - 831), 8), nzTpIcepk0o8('\x30' + chr(3643 - 3532) + chr(1332 - 1282) + '\061' + '\062', ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + '\x31', 32893 - 32885), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x33' + chr(48) + chr(0b110001), ord("\x08")), nzTpIcepk0o8(chr(0b110000 + 0o0) + '\157' + chr(0b110011), 7985 - 7977), nzTpIcepk0o8(chr(48) + chr(8659 - 8548) + chr(0b110110) + chr(48), ord("\x08")), nzTpIcepk0o8(chr(931 - 883) + chr(0b110011 + 0o74) + chr(0b1111 + 0o43) + '\067' + chr(2455 - 2403), 0b1000), nzTpIcepk0o8('\x30' + chr(10426 - 10315) + '\x34' + chr(0b11010 + 0o30), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110011) + '\062' + '\x32', 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(51) + '\x36' + chr(0b100010 + 0o23), 0o10), nzTpIcepk0o8(chr(0b1110 + 0o42) + '\x6f' + chr(0b110001) + chr(553 - 500) + '\x31', ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(1036 - 988) + chr(5901 - 5790) + chr(0b101010 + 0o13) + chr(0b100110 + 0o12), 15390 - 15382)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xfb'), chr(5342 - 5242) + chr(0b1100101) + '\x63' + '\x6f' + chr(0b1001111 + 0o25) + '\x65')(chr(2258 - 2141) + chr(0b1010000 + 0o44) + chr(0b1100110) + '\x2d' + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def VxbmnfX6T_2s(hXMPsSrOQzbh, sOvPdpw6JkD6, y_m39_E8rwSf=0.001, bhvcCFR07maA=37.0, jif2BXBXDWe0=nzTpIcepk0o8(chr(0b110000) + chr(0b11 + 0o154) + chr(0b10001 + 0o37), 0o10), P6MCancmTVIW=None, dcIGdrKJIQqm=roI3spqORKae(ES5oEprVxulp(b'\xa6{a\xfa'), '\144' + chr(0b1100101) + chr(0b1100011) + chr(2580 - 2469) + '\144' + '\145')('\165' + chr(9055 - 8939) + chr(102) + chr(0b10110 + 0o27) + chr(0b11001 + 0o37)), N53N20X2V9t8=1.0, _fwxLQ0Lh__w=0.0):
P6MCancmTVIW = hXMPsSrOQzbh._set_material(sOvPdpw6JkD6, P6MCancmTVIW)
zF8oFOtHDCse = hXMPsSrOQzbh._prep_cmd_args(bhvcCFR07maA, dcIGdrKJIQqm, P6MCancmTVIW, jif2BXBXDWe0, N53N20X2V9t8, _fwxLQ0Lh__w, multi=nzTpIcepk0o8(chr(447 - 399) + '\157' + chr(0b1 + 0o57), 8))
vniSnlI09HNg = [N9zlRy29S1SS(sOvPdpw6JkD6)]
roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xa2,;\xa7\xee]\xeaoe\x90\xe9 '), chr(7053 - 6953) + chr(7404 - 7303) + chr(99) + chr(643 - 532) + chr(100) + chr(0b1000111 + 0o36))(chr(4518 - 4401) + '\164' + chr(0b1001100 + 0o32) + chr(45) + chr(1997 - 1941)))(roI3spqORKae(ES5oEprVxulp(b'\xa5ue\xed\xfc'), chr(0b1100100) + '\145' + chr(99) + chr(0b1101111) + chr(0b1000010 + 0o42) + chr(0b10010 + 0o123))(chr(117) + '\164' + chr(1272 - 1170) + chr(0b101101) + chr(0b111000)), zF8oFOtHDCse, vniSnlI09HNg)
Z7f7JRko6mZg = hXMPsSrOQzbh._read_tempfile(roI3spqORKae(ES5oEprVxulp(b'\xa5ue\xed\xfcB\xaa+6\xc9\xdag'), '\x64' + chr(0b1100101) + chr(0b1100011) + '\157' + chr(0b1100100) + chr(0b1100101))(chr(0b11010 + 0o133) + chr(9461 - 9345) + chr(102) + '\x2d' + '\070'))
FfKOThdpoDTb = aoTc4YA2bs2R.search(roI3spqORKae(ES5oEprVxulp(b'\xdf\x1eP\xfb\xa5f\xf2u}\x89'), chr(5229 - 5129) + '\145' + chr(0b100100 + 0o77) + '\x6f' + chr(0b1011110 + 0o6) + '\x65')(chr(117) + chr(0b11101 + 0o127) + '\x66' + '\x2d' + chr(1775 - 1719)), Z7f7JRko6mZg, flags=aoTc4YA2bs2R.DOTALL).F9lJ8RbIonqb(nzTpIcepk0o8(chr(0b110000) + '\157' + chr(49), 8))
UtB2m8Xmgf5k = ftfygxgFas5X(sOvPdpw6JkD6)
zWrFex2hcHaX = [ffiOpFBWGmZU.LfRrQOxuDvnC(roI3spqORKae(ES5oEprVxulp(b'\xdc'), '\144' + '\x65' + chr(0b1100010 + 0o1) + chr(111) + '\144' + chr(101))(chr(117) + chr(0b1100110 + 0o16) + chr(102) + chr(0b10010 + 0o33) + chr(0b100011 + 0o25))) for ffiOpFBWGmZU in FfKOThdpoDTb.LfRrQOxuDvnC(roI3spqORKae(ES5oEprVxulp(b'\xdf'), chr(0b101111 + 0o65) + chr(3135 - 3034) + chr(0b1100011) + '\x6f' + chr(0b101010 + 0o72) + '\145')(chr(117) + chr(116) + '\x66' + chr(0b101101) + chr(0b110001 + 0o7))) if ffiOpFBWGmZU]
yIIfGh3vzoHp = hXMPsSrOQzbh._pairs_to_np(zWrFex2hcHaX, UtB2m8Xmgf5k)
return yIIfGh3vzoHp |
klavinslab/coral | coral/analysis/_structure/nupack.py | NUPACK.pairs_multi | def pairs_multi(self, strands, cutoff=0.001, permutation=None, temp=37.0,
pseudo=False, material=None, dangles='some', sodium=1.0,
magnesium=0.0):
'''Compute the pair probabilities for an ordered complex of strands.
Runs the \'pairs\' command.
:param strands: List of strands to use as inputs to pairs -multi.
:type strands: list
:param permutation: The circular permutation of strands to test in
complex. e.g. to test in the order that was input
for 4 strands, the permutation would be [1,2,3,4].
If set to None, defaults to the order of the
input strands.
:type permutation: list
:param temp: Temperature setting for the computation. Negative values
are not allowed.
:type temp: float
:param pseudo: Enable pseudoknots.
:type pseudo: bool
:param material: The material setting to use in the computation. If set
to None (the default), the material type is inferred
from the strands. Other settings available: 'dna' for
DNA parameters, 'rna' for RNA (1995) parameters, and
'rna1999' for the RNA 1999 parameters.
:type material: str
:param dangles: How to treat dangles in the computation. From the
user guide: For \'none\': Dangle energies are ignored.
For \'some\': \'A dangle energy is incorporated for
each unpaired base flanking a duplex\'. For 'all': all
dangle energy is considered.
:type dangles: str
:param sodium: Sodium concentration in solution (molar), only applies
to DNA.
:type sodium: float
:param magnesium: Magnesium concentration in solution (molar), only
applies to DNA>
:type magnesium: float
:param cutoff: Only probabilities above this cutoff appear in the
output.
:type cutoff: float
:returns: Two probability matrices: The probability matrix as in the
pairs method (but with a dimension equal to the sum of the
lengths of the sequences in the permutation), and a similar
probability matrix where multiple strands of the same species
are considered to be indistinguishable.
:rtype: list
'''
# Set the material (will be used to set command material flag)
material = self._set_material(strands, material, multi=True)
# Set up command flags
cmd_args = self._prep_cmd_args(temp, dangles, material, pseudo, sodium,
magnesium, multi=True)
# Set up the input file and run the command. Note: no STDOUT
if permutation is None:
permutation = range(1, len(strands) + 1)
lines = self._multi_lines(strands, permutation)
self._run('pairs', cmd_args, lines)
# Read the output from file
N = sum([len(s) for s in strands])
matrices = []
for mat_type in ['ppairs', 'epairs']:
data = self._read_tempfile('pairs.' + mat_type)
probs = re.search('\n\n\d*\n(.*)', data, flags=re.DOTALL).group(1)
lines = probs.split('\n')
# Remove the last line (empty)
lines.pop()
pairlist = [line.split('\t') for line in lines]
prob_matrix = self._pairs_to_np(pairlist, N)
matrices.append(prob_matrix)
return matrices | python | def pairs_multi(self, strands, cutoff=0.001, permutation=None, temp=37.0,
pseudo=False, material=None, dangles='some', sodium=1.0,
magnesium=0.0):
'''Compute the pair probabilities for an ordered complex of strands.
Runs the \'pairs\' command.
:param strands: List of strands to use as inputs to pairs -multi.
:type strands: list
:param permutation: The circular permutation of strands to test in
complex. e.g. to test in the order that was input
for 4 strands, the permutation would be [1,2,3,4].
If set to None, defaults to the order of the
input strands.
:type permutation: list
:param temp: Temperature setting for the computation. Negative values
are not allowed.
:type temp: float
:param pseudo: Enable pseudoknots.
:type pseudo: bool
:param material: The material setting to use in the computation. If set
to None (the default), the material type is inferred
from the strands. Other settings available: 'dna' for
DNA parameters, 'rna' for RNA (1995) parameters, and
'rna1999' for the RNA 1999 parameters.
:type material: str
:param dangles: How to treat dangles in the computation. From the
user guide: For \'none\': Dangle energies are ignored.
For \'some\': \'A dangle energy is incorporated for
each unpaired base flanking a duplex\'. For 'all': all
dangle energy is considered.
:type dangles: str
:param sodium: Sodium concentration in solution (molar), only applies
to DNA.
:type sodium: float
:param magnesium: Magnesium concentration in solution (molar), only
applies to DNA>
:type magnesium: float
:param cutoff: Only probabilities above this cutoff appear in the
output.
:type cutoff: float
:returns: Two probability matrices: The probability matrix as in the
pairs method (but with a dimension equal to the sum of the
lengths of the sequences in the permutation), and a similar
probability matrix where multiple strands of the same species
are considered to be indistinguishable.
:rtype: list
'''
# Set the material (will be used to set command material flag)
material = self._set_material(strands, material, multi=True)
# Set up command flags
cmd_args = self._prep_cmd_args(temp, dangles, material, pseudo, sodium,
magnesium, multi=True)
# Set up the input file and run the command. Note: no STDOUT
if permutation is None:
permutation = range(1, len(strands) + 1)
lines = self._multi_lines(strands, permutation)
self._run('pairs', cmd_args, lines)
# Read the output from file
N = sum([len(s) for s in strands])
matrices = []
for mat_type in ['ppairs', 'epairs']:
data = self._read_tempfile('pairs.' + mat_type)
probs = re.search('\n\n\d*\n(.*)', data, flags=re.DOTALL).group(1)
lines = probs.split('\n')
# Remove the last line (empty)
lines.pop()
pairlist = [line.split('\t') for line in lines]
prob_matrix = self._pairs_to_np(pairlist, N)
matrices.append(prob_matrix)
return matrices | [
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Runs the \'pairs\' command.
:param strands: List of strands to use as inputs to pairs -multi.
:type strands: list
:param permutation: The circular permutation of strands to test in
complex. e.g. to test in the order that was input
for 4 strands, the permutation would be [1,2,3,4].
If set to None, defaults to the order of the
input strands.
:type permutation: list
:param temp: Temperature setting for the computation. Negative values
are not allowed.
:type temp: float
:param pseudo: Enable pseudoknots.
:type pseudo: bool
:param material: The material setting to use in the computation. If set
to None (the default), the material type is inferred
from the strands. Other settings available: 'dna' for
DNA parameters, 'rna' for RNA (1995) parameters, and
'rna1999' for the RNA 1999 parameters.
:type material: str
:param dangles: How to treat dangles in the computation. From the
user guide: For \'none\': Dangle energies are ignored.
For \'some\': \'A dangle energy is incorporated for
each unpaired base flanking a duplex\'. For 'all': all
dangle energy is considered.
:type dangles: str
:param sodium: Sodium concentration in solution (molar), only applies
to DNA.
:type sodium: float
:param magnesium: Magnesium concentration in solution (molar), only
applies to DNA>
:type magnesium: float
:param cutoff: Only probabilities above this cutoff appear in the
output.
:type cutoff: float
:returns: Two probability matrices: The probability matrix as in the
pairs method (but with a dimension equal to the sum of the
lengths of the sequences in the permutation), and a similar
probability matrix where multiple strands of the same species
are considered to be indistinguishable.
:rtype: list | [
"Compute",
"the",
"pair",
"probabilities",
"for",
"an",
"ordered",
"complex",
"of",
"strands",
".",
"Runs",
"the",
"\\",
"pairs",
"\\",
"command",
"."
] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/analysis/_structure/nupack.py#L216-L290 | train | Compute the pair probabilities for a set of strands in a single base. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(48) + chr(111) + chr(51) + '\060' + '\063', ord("\x08")), nzTpIcepk0o8(chr(427 - 379) + '\157' + '\061' + '\x35' + '\065', 0b1000), nzTpIcepk0o8('\060' + chr(5755 - 5644) + chr(0b110001 + 0o1) + chr(51) + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(1820 - 1772) + '\157' + chr(2401 - 2352) + chr(0b10 + 0o63) + chr(0b110101), 8), nzTpIcepk0o8(chr(0b10110 + 0o32) + chr(3864 - 3753) + chr(0b110010) + '\x33' + '\060', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b1010 + 0o47) + chr(216 - 165) + chr(51), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(1100 - 1049) + chr(2531 - 2480) + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110001) + chr(0b10 + 0o63) + '\x34', ord("\x08")), nzTpIcepk0o8(chr(0b100101 + 0o13) + '\x6f' + chr(597 - 547) + chr(0b1110 + 0o42), 0b1000), nzTpIcepk0o8('\060' + chr(7172 - 7061) + chr(0b110001) + chr(53) + chr(0b1100 + 0o45), 43280 - 43272), nzTpIcepk0o8(chr(956 - 908) + '\x6f' + chr(1547 - 1492) + chr(0b101111 + 0o2), 0o10), nzTpIcepk0o8(chr(0b100001 + 0o17) + chr(0b1101111) + chr(49) + chr(0b110110) + chr(0b110110), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(49) + chr(0b10110 + 0o41) + chr(0b110000), 0o10), nzTpIcepk0o8(chr(1300 - 1252) + chr(6962 - 6851) + chr(51) + chr(1140 - 1086) + chr(1891 - 1843), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\061' + chr(51) + chr(1538 - 1486), 25931 - 25923), nzTpIcepk0o8('\060' + '\x6f' + chr(51), 0o10), nzTpIcepk0o8(chr(48) + chr(0b10100 + 0o133) + '\061' + chr(0b110011) + chr(2190 - 2136), 19779 - 19771), nzTpIcepk0o8('\x30' + '\157' + chr(266 - 217) + '\063', 0o10), nzTpIcepk0o8('\060' + chr(4186 - 4075) + '\x33' + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110010) + chr(0b101010 + 0o13) + chr(0b110011), 0o10), nzTpIcepk0o8('\060' + chr(0b10001 + 0o136) + '\062' + chr(304 - 252), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(50) + chr(1079 - 1026) + '\x36', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110010) + chr(1651 - 1603) + chr(0b1001 + 0o55), 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(0b1110 + 0o44) + chr(0b10110 + 0o37) + chr(0b110010), 0o10), nzTpIcepk0o8(chr(0b11010 + 0o26) + '\157' + '\x32' + chr(1859 - 1810) + chr(0b100000 + 0o20), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1111 + 0o140) + '\x32' + '\x35' + chr(0b1110 + 0o43), 0o10), nzTpIcepk0o8(chr(1260 - 1212) + '\x6f' + '\x31' + chr(0b110 + 0o54) + chr(49), 0b1000), nzTpIcepk0o8('\060' + chr(0b1000000 + 0o57) + '\063' + chr(727 - 677), ord("\x08")), nzTpIcepk0o8(chr(0b11 + 0o55) + chr(7766 - 7655) + '\x33' + '\066' + '\064', 42823 - 42815), nzTpIcepk0o8(chr(0b110000) + chr(3491 - 3380) + '\061' + chr(398 - 350) + '\x32', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b11011 + 0o124) + chr(0b110010) + '\x36' + chr(0b110000), 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b0 + 0o63) + '\066' + '\x30', 8), nzTpIcepk0o8(chr(1592 - 1544) + chr(3186 - 3075) + chr(0b110010) + '\067' + chr(0b110100), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(51) + chr(0b110110), ord("\x08")), nzTpIcepk0o8(chr(0b101011 + 0o5) + chr(9153 - 9042) + chr(49) + chr(259 - 209) + chr(0b101111 + 0o10), 0b1000), nzTpIcepk0o8(chr(0b1100 + 0o44) + chr(111) + chr(262 - 213) + '\064' + '\x37', 0b1000), nzTpIcepk0o8(chr(0b11111 + 0o21) + chr(2120 - 2009) + chr(51) + '\x31' + '\x37', 28594 - 28586), nzTpIcepk0o8('\x30' + chr(0b111010 + 0o65) + chr(1787 - 1737) + chr(48) + chr(1972 - 1923), 32817 - 32809), nzTpIcepk0o8(chr(48) + chr(111) + '\x32' + chr(48) + '\x32', 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(51) + '\x33', 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + chr(0b100100 + 0o113) + chr(53) + '\060', 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xed'), '\144' + chr(0b101111 + 0o66) + '\x63' + chr(0b1101111) + chr(1736 - 1636) + chr(7510 - 7409))(chr(12521 - 12404) + chr(0b110010 + 0o102) + chr(5363 - 5261) + chr(0b101101) + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def JmhEn8gE7x5q(hXMPsSrOQzbh, r_D0HyqK4grO, y_m39_E8rwSf=0.001, bmmTXKdBuMbO=None, bhvcCFR07maA=37.0, jif2BXBXDWe0=nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b11110 + 0o22), 0o10), P6MCancmTVIW=None, dcIGdrKJIQqm=roI3spqORKae(ES5oEprVxulp(b'\xb0\x02\xf7\x08'), chr(778 - 678) + '\x65' + chr(0b1001101 + 0o26) + chr(3449 - 3338) + '\x64' + chr(4138 - 4037))('\x75' + chr(9636 - 9520) + '\x66' + chr(1935 - 1890) + '\070'), N53N20X2V9t8=1.0, _fwxLQ0Lh__w=0.0):
P6MCancmTVIW = hXMPsSrOQzbh._set_material(r_D0HyqK4grO, P6MCancmTVIW, multi=nzTpIcepk0o8(chr(0b10000 + 0o40) + chr(111) + '\x31', ord("\x08")))
zF8oFOtHDCse = hXMPsSrOQzbh._prep_cmd_args(bhvcCFR07maA, dcIGdrKJIQqm, P6MCancmTVIW, jif2BXBXDWe0, N53N20X2V9t8, _fwxLQ0Lh__w, multi=nzTpIcepk0o8(chr(0b110000) + chr(0b1001001 + 0o46) + chr(1534 - 1485), 8))
if bmmTXKdBuMbO is None:
bmmTXKdBuMbO = bbT2xIe5pzk7(nzTpIcepk0o8('\060' + '\x6f' + chr(49), 8), ftfygxgFas5X(r_D0HyqK4grO) + nzTpIcepk0o8(chr(0b11111 + 0o21) + chr(0b100110 + 0o111) + '\061', 8))
vniSnlI09HNg = hXMPsSrOQzbh._multi_lines(r_D0HyqK4grO, bmmTXKdBuMbO)
roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xb4U\xadU\xf9j\xebX"YxB'), chr(8589 - 8489) + chr(0b111000 + 0o55) + '\143' + chr(0b1101111) + chr(0b1010111 + 0o15) + chr(101))(chr(10979 - 10862) + chr(0b1110100) + '\x66' + chr(48 - 3) + chr(0b111000)))(roI3spqORKae(ES5oEprVxulp(b'\xb3\x0c\xf3\x1f\xeb'), '\144' + chr(809 - 708) + chr(0b1100011) + '\157' + '\x64' + chr(0b1100101))(chr(117) + '\x74' + chr(1217 - 1115) + chr(0b1 + 0o54) + chr(0b11110 + 0o32)), zF8oFOtHDCse, vniSnlI09HNg)
UtB2m8Xmgf5k = oclC8DLjA_lV([ftfygxgFas5X(PmE5_h409JAA) for PmE5_h409JAA in r_D0HyqK4grO])
EUyOnoRME2Rr = []
for iuZtnh73PosL in [roI3spqORKae(ES5oEprVxulp(b'\xb3\x1d\xfb\x04\xea('), chr(100) + '\x65' + chr(5949 - 5850) + chr(7453 - 7342) + chr(0b110011 + 0o61) + '\x65')(chr(5677 - 5560) + chr(0b1110 + 0o146) + '\146' + '\055' + chr(0b111000)), roI3spqORKae(ES5oEprVxulp(b'\xa6\x1d\xfb\x04\xea('), chr(0b1010 + 0o132) + chr(101) + '\143' + chr(1206 - 1095) + '\x64' + chr(0b1100101))(chr(0b10111 + 0o136) + '\x74' + '\146' + chr(977 - 932) + chr(0b111000))]:
FfKOThdpoDTb = hXMPsSrOQzbh._read_tempfile(roI3spqORKae(ES5oEprVxulp(b'\xb3\x0c\xf3\x1f\xebu'), chr(0b1010110 + 0o16) + chr(4752 - 4651) + chr(99) + '\157' + chr(0b100010 + 0o102) + '\x65')(chr(0b1110101) + '\164' + '\146' + chr(453 - 408) + chr(56)) + iuZtnh73PosL)
gf4DaxRbq5cX = aoTc4YA2bs2R.search(roI3spqORKae(ES5oEprVxulp(b'\xc9g\xc6\t\xb2Q\xf3B:@'), chr(0b1100100) + '\145' + chr(7631 - 7532) + chr(111) + '\144' + chr(0b11110 + 0o107))(chr(10741 - 10624) + chr(0b1110100) + chr(102) + '\x2d' + chr(1925 - 1869)), FfKOThdpoDTb, flags=aoTc4YA2bs2R.DOTALL).F9lJ8RbIonqb(nzTpIcepk0o8(chr(0b10000 + 0o40) + chr(0b1101111) + '\061', 8))
vniSnlI09HNg = gf4DaxRbq5cX.LfRrQOxuDvnC(roI3spqORKae(ES5oEprVxulp(b'\xc9'), '\144' + '\145' + '\143' + '\x6f' + '\x64' + chr(101))(chr(0b1100110 + 0o17) + '\164' + chr(102) + chr(1474 - 1429) + '\x38'))
roI3spqORKae(vniSnlI09HNg, roI3spqORKae(ES5oEprVxulp(b'\xb6.\xc54\xf7"\xb9\x14\'#\t?'), '\144' + chr(0b10 + 0o143) + chr(99) + '\x6f' + chr(0b11 + 0o141) + '\145')('\165' + chr(0b1110100) + chr(927 - 825) + '\055' + chr(56)))()
DS9tX9Lj5VA7 = [ffiOpFBWGmZU.LfRrQOxuDvnC(roI3spqORKae(ES5oEprVxulp(b'\xca'), '\x64' + '\x65' + '\x63' + chr(0b1101101 + 0o2) + '\x64' + chr(101))(chr(117) + chr(0b1101110 + 0o6) + chr(0b1100110) + chr(1635 - 1590) + '\x38')) for ffiOpFBWGmZU in vniSnlI09HNg]
yIIfGh3vzoHp = hXMPsSrOQzbh._pairs_to_np(DS9tX9Lj5VA7, UtB2m8Xmgf5k)
roI3spqORKae(EUyOnoRME2Rr, roI3spqORKae(ES5oEprVxulp(b'\x8b9\xc9Y\xe0<\x9c\x03z\x06lC'), chr(100) + '\x65' + chr(99) + chr(0b1101111) + chr(0b1100100) + chr(0b1100101))(chr(1368 - 1251) + '\164' + '\146' + '\055' + '\x38'))(yIIfGh3vzoHp)
return EUyOnoRME2Rr |
klavinslab/coral | coral/analysis/_structure/nupack.py | NUPACK.mfe | def mfe(self, strand, degenerate=False, temp=37.0, pseudo=False,
material=None, dangles='some', sodium=1.0, magnesium=0.0):
'''Compute the MFE for an ordered complex of strands. Runs the \'mfe\'
command.
:param strand: Strand on which to run mfe. Strands must be either
coral.DNA or coral.RNA).
:type strand: coral.DNA or coral.RNA
:param degenerate: Setting to True will result in returning a list of
dictionaries associated with structures having the
same, minimal MFE value.
:type degenerate: bool
:param temp: Temperature setting for the computation. Negative values
are not allowed.
:type temp: float
:param pseudo: Enable pseudoknots.
:type pseudo: bool
:param material: The material setting to use in the computation. If set
to None (the default), the material type is inferred
from the strands. Other settings available: 'dna' for
DNA parameters, 'rna' for RNA (1995) parameters, and
'rna1999' for the RNA 1999 parameters.
:type material: str
:param dangles: How to treat dangles in the computation. From the
user guide: For \'none\': Dangle energies are ignored.
For \'some\': \'A dangle energy is incorporated for
each unpaired base flanking a duplex\'. For 'all': all
dangle energy is considered.
:type dangles: str
:param sodium: Sodium concentration in solution (molar), only applies
to DNA.
:type sodium: float
:param magnesium: Magnesium concentration in solution (molar), only
applies to DNA>
:type magnesium: float
:returns: A dictionary with keys for 'mfe' (a float), 'dotparens'
(dot-parens notation of the MFE structure), and 'pairlist'
(a pair list notation of the MFE structure). Note that the
pair list will be an empty list if the MFE is unstructured.
:rtype: dict
'''
# Set the material (will be used to set command material flag)
material = self._set_material(strand, material)
# Set up command flags
cmd_args = self._prep_cmd_args(temp, dangles, material, pseudo, sodium,
magnesium, multi=False)
if degenerate:
cmd_args.append('-degenerate')
# Set up the input file and run the command. Note: no STDOUT
lines = [str(strand)]
self._run('mfe', cmd_args, lines)
# Read the output from file
structures = self._process_mfe(self._read_tempfile('mfe.mfe'))
if degenerate:
return structures
else:
return structures[0] | python | def mfe(self, strand, degenerate=False, temp=37.0, pseudo=False,
material=None, dangles='some', sodium=1.0, magnesium=0.0):
'''Compute the MFE for an ordered complex of strands. Runs the \'mfe\'
command.
:param strand: Strand on which to run mfe. Strands must be either
coral.DNA or coral.RNA).
:type strand: coral.DNA or coral.RNA
:param degenerate: Setting to True will result in returning a list of
dictionaries associated with structures having the
same, minimal MFE value.
:type degenerate: bool
:param temp: Temperature setting for the computation. Negative values
are not allowed.
:type temp: float
:param pseudo: Enable pseudoknots.
:type pseudo: bool
:param material: The material setting to use in the computation. If set
to None (the default), the material type is inferred
from the strands. Other settings available: 'dna' for
DNA parameters, 'rna' for RNA (1995) parameters, and
'rna1999' for the RNA 1999 parameters.
:type material: str
:param dangles: How to treat dangles in the computation. From the
user guide: For \'none\': Dangle energies are ignored.
For \'some\': \'A dangle energy is incorporated for
each unpaired base flanking a duplex\'. For 'all': all
dangle energy is considered.
:type dangles: str
:param sodium: Sodium concentration in solution (molar), only applies
to DNA.
:type sodium: float
:param magnesium: Magnesium concentration in solution (molar), only
applies to DNA>
:type magnesium: float
:returns: A dictionary with keys for 'mfe' (a float), 'dotparens'
(dot-parens notation of the MFE structure), and 'pairlist'
(a pair list notation of the MFE structure). Note that the
pair list will be an empty list if the MFE is unstructured.
:rtype: dict
'''
# Set the material (will be used to set command material flag)
material = self._set_material(strand, material)
# Set up command flags
cmd_args = self._prep_cmd_args(temp, dangles, material, pseudo, sodium,
magnesium, multi=False)
if degenerate:
cmd_args.append('-degenerate')
# Set up the input file and run the command. Note: no STDOUT
lines = [str(strand)]
self._run('mfe', cmd_args, lines)
# Read the output from file
structures = self._process_mfe(self._read_tempfile('mfe.mfe'))
if degenerate:
return structures
else:
return structures[0] | [
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... | Compute the MFE for an ordered complex of strands. Runs the \'mfe\'
command.
:param strand: Strand on which to run mfe. Strands must be either
coral.DNA or coral.RNA).
:type strand: coral.DNA or coral.RNA
:param degenerate: Setting to True will result in returning a list of
dictionaries associated with structures having the
same, minimal MFE value.
:type degenerate: bool
:param temp: Temperature setting for the computation. Negative values
are not allowed.
:type temp: float
:param pseudo: Enable pseudoknots.
:type pseudo: bool
:param material: The material setting to use in the computation. If set
to None (the default), the material type is inferred
from the strands. Other settings available: 'dna' for
DNA parameters, 'rna' for RNA (1995) parameters, and
'rna1999' for the RNA 1999 parameters.
:type material: str
:param dangles: How to treat dangles in the computation. From the
user guide: For \'none\': Dangle energies are ignored.
For \'some\': \'A dangle energy is incorporated for
each unpaired base flanking a duplex\'. For 'all': all
dangle energy is considered.
:type dangles: str
:param sodium: Sodium concentration in solution (molar), only applies
to DNA.
:type sodium: float
:param magnesium: Magnesium concentration in solution (molar), only
applies to DNA>
:type magnesium: float
:returns: A dictionary with keys for 'mfe' (a float), 'dotparens'
(dot-parens notation of the MFE structure), and 'pairlist'
(a pair list notation of the MFE structure). Note that the
pair list will be an empty list if the MFE is unstructured.
:rtype: dict | [
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ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8('\060' + '\x6f' + chr(0b101111 + 0o4) + chr(0b110111 + 0o0) + chr(55), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(1680 - 1629) + '\x30' + '\x34', 45638 - 45630), nzTpIcepk0o8(chr(0b110000) + chr(6641 - 6530) + chr(49) + chr(52) + chr(0b100111 + 0o15), 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(49) + chr(49) + chr(55), 4570 - 4562), nzTpIcepk0o8(chr(2216 - 2168) + chr(111) + chr(825 - 774) + chr(0b110011) + chr(0b110111), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x31' + '\x31' + chr(0b110101), 42262 - 42254), nzTpIcepk0o8(chr(48) + '\157' + '\062' + chr(2138 - 2087) + chr(52), ord("\x08")), nzTpIcepk0o8(chr(0b1100 + 0o44) + chr(0b1101111) + '\061' + '\x36' + chr(0b101001 + 0o12), 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(1869 - 1818) + chr(0b1000 + 0o54) + chr(1345 - 1297), 0b1000), nzTpIcepk0o8('\060' + chr(0b11011 + 0o124) + '\063' + '\x30' + chr(2724 - 2671), 5568 - 5560), nzTpIcepk0o8(chr(48) + chr(11502 - 11391) + chr(50) + chr(51) + chr(51), 2388 - 2380), nzTpIcepk0o8(chr(48) + chr(8022 - 7911) + chr(50) + chr(49) + chr(0b110111), 28743 - 28735), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(849 - 799) + chr(0b110110) + chr(848 - 795), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(7169 - 7058) + chr(49) + '\065' + '\061', 0b1000), nzTpIcepk0o8(chr(0b101100 + 0o4) + '\157' + '\x32' + '\064' + chr(0b110001), ord("\x08")), nzTpIcepk0o8(chr(274 - 226) + '\x6f' + chr(50) + chr(0b110010) + '\060', 0b1000), nzTpIcepk0o8(chr(415 - 367) + chr(111) + chr(49) + '\x33' + '\060', 48504 - 48496), nzTpIcepk0o8('\060' + chr(9620 - 9509) + '\061' + chr(0b110011) + '\062', 16082 - 16074), nzTpIcepk0o8(chr(0b1000 + 0o50) + chr(0b1101111) + '\x31' + chr(0b110101) + chr(50), 0o10), nzTpIcepk0o8(chr(0b11001 + 0o27) + chr(111) + chr(0b110101) + chr(0b110101), 33639 - 33631), nzTpIcepk0o8(chr(0b100011 + 0o15) + chr(111) + chr(0b101001 + 0o11) + chr(0b110001 + 0o5) + '\064', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1010110 + 0o31) + '\x32' + chr(0b1000 + 0o55) + chr(1886 - 1836), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + '\063' + '\065' + chr(0b11100 + 0o25), ord("\x08")), nzTpIcepk0o8(chr(0b1101 + 0o43) + '\x6f' + chr(50) + chr(54), 0o10), nzTpIcepk0o8(chr(0b101010 + 0o6) + '\x6f' + chr(0b110010) + '\063' + chr(51), 8), nzTpIcepk0o8('\x30' + '\157' + chr(0b110001) + chr(550 - 502) + '\064', 0b1000), nzTpIcepk0o8(chr(795 - 747) + '\x6f' + '\x36' + chr(49), 36999 - 36991), nzTpIcepk0o8(chr(237 - 189) + chr(0b10100 + 0o133) + chr(0b110011) + chr(2486 - 2434) + '\064', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1001010 + 0o45) + '\x31' + chr(1006 - 955) + '\x34', 0b1000), nzTpIcepk0o8('\060' + chr(0b110001 + 0o76) + chr(0b11010 + 0o27) + '\x32' + '\x37', 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(0b1011 + 0o46) + chr(319 - 265) + chr(0b110001), 0b1000), nzTpIcepk0o8(chr(1835 - 1787) + '\x6f' + chr(330 - 276) + chr(628 - 576), 0b1000), nzTpIcepk0o8(chr(1335 - 1287) + '\x6f' + '\061' + '\065' + '\066', ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + '\062' + chr(49) + chr(1610 - 1556), 0o10), nzTpIcepk0o8(chr(0b1110 + 0o42) + chr(0b110010 + 0o75) + chr(0b110010) + '\x33' + '\061', 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(49) + '\064' + chr(0b110110), 0o10), nzTpIcepk0o8('\x30' + '\157' + '\061' + '\060' + chr(0b100001 + 0o25), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1000001 + 0o56) + chr(51) + chr(55) + chr(734 - 681), ord("\x08")), nzTpIcepk0o8(chr(205 - 157) + chr(111) + chr(49) + chr(53) + '\x35', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + '\063' + '\064' + '\067', 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b1111 + 0o41) + '\157' + chr(0b1010 + 0o53) + chr(0b101000 + 0o10), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xd1'), chr(100) + chr(101) + '\x63' + '\157' + chr(0b1100100) + '\145')(chr(117) + chr(116) + chr(1011 - 909) + chr(45) + chr(0b100011 + 0o25)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def jszsUWiIS498(hXMPsSrOQzbh, sOvPdpw6JkD6, SUcYaF9gAJAW=nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x30', 0b1000), bhvcCFR07maA=37.0, jif2BXBXDWe0=nzTpIcepk0o8(chr(0b110000) + chr(0b10100 + 0o133) + '\x30', 8), P6MCancmTVIW=None, dcIGdrKJIQqm=roI3spqORKae(ES5oEprVxulp(b'\x8c\xab\t*'), '\x64' + chr(0b1100101) + chr(0b110010 + 0o61) + chr(139 - 28) + chr(100) + '\145')(chr(12511 - 12394) + '\164' + '\x66' + '\x2d' + chr(56)), N53N20X2V9t8=1.0, _fwxLQ0Lh__w=0.0):
P6MCancmTVIW = hXMPsSrOQzbh._set_material(sOvPdpw6JkD6, P6MCancmTVIW)
zF8oFOtHDCse = hXMPsSrOQzbh._prep_cmd_args(bhvcCFR07maA, dcIGdrKJIQqm, P6MCancmTVIW, jif2BXBXDWe0, N53N20X2V9t8, _fwxLQ0Lh__w, multi=nzTpIcepk0o8(chr(48) + chr(111) + '\x30', 8))
if SUcYaF9gAJAW:
roI3spqORKae(zF8oFOtHDCse, roI3spqORKae(ES5oEprVxulp(b'\xb7\x907{\xa7*\xdb\x1c\x8a\xaa\xce\xba'), '\x64' + chr(0b1010 + 0o133) + chr(2966 - 2867) + '\x6f' + chr(0b111100 + 0o50) + chr(0b1100101))('\x75' + chr(116) + chr(8971 - 8869) + chr(0b101101) + chr(673 - 617)))(roI3spqORKae(ES5oEprVxulp(b'\xd2\xa0\x01(\xba#\xf9\x01\x81\xb1\xfe'), chr(0b1100100) + chr(2221 - 2120) + chr(0b111101 + 0o46) + chr(111) + chr(1379 - 1279) + chr(0b1100101))(chr(0b1011011 + 0o32) + chr(116) + chr(102) + chr(0b1010 + 0o43) + chr(56)))
vniSnlI09HNg = [N9zlRy29S1SS(sOvPdpw6JkD6)]
roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x88\xfcSw\xbe|\xacG\xd2\xf5\xda\xbb'), chr(9389 - 9289) + '\x65' + chr(99) + chr(1643 - 1532) + chr(0b1100100) + chr(0b1100101))(chr(1411 - 1294) + chr(0b100110 + 0o116) + '\x66' + chr(0b1111 + 0o36) + '\x38'))(roI3spqORKae(ES5oEprVxulp(b'\x92\xa2\x01'), chr(1752 - 1652) + chr(0b101 + 0o140) + chr(99) + chr(8040 - 7929) + '\144' + '\145')(chr(0b1110101) + chr(6333 - 6217) + chr(2672 - 2570) + chr(0b101101) + chr(3082 - 3026)), zF8oFOtHDCse, vniSnlI09HNg)
pDD0JFrFHFd1 = hXMPsSrOQzbh._process_mfe(hXMPsSrOQzbh._read_tempfile(roI3spqORKae(ES5oEprVxulp(b'\x92\xa2\x01a\xb2+\xf9'), '\144' + chr(101) + '\143' + chr(2085 - 1974) + chr(0b111011 + 0o51) + chr(2361 - 2260))('\x75' + '\164' + '\x66' + chr(0b10000 + 0o35) + '\x38')))
if SUcYaF9gAJAW:
return pDD0JFrFHFd1
else:
return pDD0JFrFHFd1[nzTpIcepk0o8(chr(0b11000 + 0o30) + '\x6f' + chr(105 - 57), 8)] |
klavinslab/coral | coral/analysis/_structure/nupack.py | NUPACK.mfe_multi | def mfe_multi(self, strands, permutation=None, degenerate=False, temp=37.0,
pseudo=False, material=None, dangles='some', sodium=1.0,
magnesium=0.0):
'''Compute the MFE for an ordered complex of strands. Runs the \'mfe\'
command.
:param strands: Strands on which to run mfe. Strands must be either
coral.DNA or coral.RNA).
:type strands: list
:param permutation: The circular permutation of strands to test in
complex. e.g. to test in the order that was input
for 4 strands, the permutation would be [1,2,3,4].
If set to None, defaults to the order of the
input strands.
:type permutation: list
:param temp: Temperature setting for the computation. Negative values
are not allowed.
:type temp: float
:param pseudo: Enable pseudoknots.
:type pseudo: bool
:param material: The material setting to use in the computation. If set
to None (the default), the material type is inferred
from the strands. Other settings available: 'dna' for
DNA parameters, 'rna' for RNA (1995) parameters, and
'rna1999' for the RNA 1999 parameters.
:type material: str
:param dangles: How to treat dangles in the computation. From the
user guide: For \'none\': Dangle energies are ignored.
For \'some\': \'A dangle energy is incorporated for
each unpaired base flanking a duplex\'. For 'all': all
dangle energy is considered.
:type dangles: str
:param sodium: Sodium concentration in solution (molar), only applies
to DNA.
:type sodium: float
:param magnesium: Magnesium concentration in solution (molar), only
applies to DNA>
:type magnesium: float
:param degenerate: Setting to True will result in returning a list of
dictionaries associated with structures having the
same, minimal MFE value.
:type degenerate: bool
:returns: A dictionary with keys for 'mfe' (a float), 'dotparens'
(dot-parens notation of the MFE structure), and 'pairlist'
(a pair list notation of the MFE structure). Note that the
pair list will be an empty list if the MFE is unstructured.
:rtype: dict
'''
# Set the material (will be used to set command material flag)
material = self._set_material(strands, material, multi=True)
# Set up command flags
cmd_args = self._prep_cmd_args(temp, dangles, material, pseudo, sodium,
magnesium, multi=True)
if degenerate:
cmd_args.append('-degenerate')
# Set up the input file and run the command. Note: no STDOUT
if permutation is None:
permutation = range(1, len(strands) + 1)
lines = self._multi_lines(strands, permutation)
self._run('mfe', cmd_args, lines)
# Read the output from file
structures = self._process_mfe(self._read_tempfile('mfe.mfe'))
if degenerate:
return structures
else:
return structures[0] | python | def mfe_multi(self, strands, permutation=None, degenerate=False, temp=37.0,
pseudo=False, material=None, dangles='some', sodium=1.0,
magnesium=0.0):
'''Compute the MFE for an ordered complex of strands. Runs the \'mfe\'
command.
:param strands: Strands on which to run mfe. Strands must be either
coral.DNA or coral.RNA).
:type strands: list
:param permutation: The circular permutation of strands to test in
complex. e.g. to test in the order that was input
for 4 strands, the permutation would be [1,2,3,4].
If set to None, defaults to the order of the
input strands.
:type permutation: list
:param temp: Temperature setting for the computation. Negative values
are not allowed.
:type temp: float
:param pseudo: Enable pseudoknots.
:type pseudo: bool
:param material: The material setting to use in the computation. If set
to None (the default), the material type is inferred
from the strands. Other settings available: 'dna' for
DNA parameters, 'rna' for RNA (1995) parameters, and
'rna1999' for the RNA 1999 parameters.
:type material: str
:param dangles: How to treat dangles in the computation. From the
user guide: For \'none\': Dangle energies are ignored.
For \'some\': \'A dangle energy is incorporated for
each unpaired base flanking a duplex\'. For 'all': all
dangle energy is considered.
:type dangles: str
:param sodium: Sodium concentration in solution (molar), only applies
to DNA.
:type sodium: float
:param magnesium: Magnesium concentration in solution (molar), only
applies to DNA>
:type magnesium: float
:param degenerate: Setting to True will result in returning a list of
dictionaries associated with structures having the
same, minimal MFE value.
:type degenerate: bool
:returns: A dictionary with keys for 'mfe' (a float), 'dotparens'
(dot-parens notation of the MFE structure), and 'pairlist'
(a pair list notation of the MFE structure). Note that the
pair list will be an empty list if the MFE is unstructured.
:rtype: dict
'''
# Set the material (will be used to set command material flag)
material = self._set_material(strands, material, multi=True)
# Set up command flags
cmd_args = self._prep_cmd_args(temp, dangles, material, pseudo, sodium,
magnesium, multi=True)
if degenerate:
cmd_args.append('-degenerate')
# Set up the input file and run the command. Note: no STDOUT
if permutation is None:
permutation = range(1, len(strands) + 1)
lines = self._multi_lines(strands, permutation)
self._run('mfe', cmd_args, lines)
# Read the output from file
structures = self._process_mfe(self._read_tempfile('mfe.mfe'))
if degenerate:
return structures
else:
return structures[0] | [
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... | Compute the MFE for an ordered complex of strands. Runs the \'mfe\'
command.
:param strands: Strands on which to run mfe. Strands must be either
coral.DNA or coral.RNA).
:type strands: list
:param permutation: The circular permutation of strands to test in
complex. e.g. to test in the order that was input
for 4 strands, the permutation would be [1,2,3,4].
If set to None, defaults to the order of the
input strands.
:type permutation: list
:param temp: Temperature setting for the computation. Negative values
are not allowed.
:type temp: float
:param pseudo: Enable pseudoknots.
:type pseudo: bool
:param material: The material setting to use in the computation. If set
to None (the default), the material type is inferred
from the strands. Other settings available: 'dna' for
DNA parameters, 'rna' for RNA (1995) parameters, and
'rna1999' for the RNA 1999 parameters.
:type material: str
:param dangles: How to treat dangles in the computation. From the
user guide: For \'none\': Dangle energies are ignored.
For \'some\': \'A dangle energy is incorporated for
each unpaired base flanking a duplex\'. For 'all': all
dangle energy is considered.
:type dangles: str
:param sodium: Sodium concentration in solution (molar), only applies
to DNA.
:type sodium: float
:param magnesium: Magnesium concentration in solution (molar), only
applies to DNA>
:type magnesium: float
:param degenerate: Setting to True will result in returning a list of
dictionaries associated with structures having the
same, minimal MFE value.
:type degenerate: bool
:returns: A dictionary with keys for 'mfe' (a float), 'dotparens'
(dot-parens notation of the MFE structure), and 'pairlist'
(a pair list notation of the MFE structure). Note that the
pair list will be an empty list if the MFE is unstructured.
:rtype: dict | [
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/analysis/_structure/nupack.py#L357-L427 | train | Compute the MFE for an ordered complex of strands. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(736 - 687) + '\060' + chr(0b110111), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1010010 + 0o35) + '\x32' + chr(1092 - 1044) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(187 - 137) + chr(0b110000) + '\067', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b100011 + 0o114) + chr(0b110011) + chr(0b110000 + 0o1) + '\061', 27147 - 27139), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b100 + 0o56) + chr(0b110000) + chr(0b1101 + 0o52), 8), nzTpIcepk0o8(chr(1630 - 1582) + '\x6f' + '\066' + chr(0b11100 + 0o25), 34553 - 34545), nzTpIcepk0o8(chr(0b101111 + 0o1) + chr(111) + chr(1922 - 1872) + chr(0b110001 + 0o5) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(978 - 930) + '\x6f' + chr(49) + chr(2307 - 2254) + chr(0b110111), 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + '\061' + chr(2421 - 2369) + '\x35', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(2284 - 2173) + '\066' + chr(55), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x31' + chr(0b110101) + '\x31', ord("\x08")), nzTpIcepk0o8(chr(0b110000 + 0o0) + '\x6f' + chr(51) + '\066' + chr(1710 - 1658), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(0b110001) + chr(0b110001) + '\067', 0b1000), nzTpIcepk0o8(chr(0b100100 + 0o14) + chr(111) + '\063' + '\x30' + chr(0b101010 + 0o7), ord("\x08")), nzTpIcepk0o8(chr(0b1011 + 0o45) + chr(0b1100000 + 0o17) + '\066' + '\x36', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b100000 + 0o117) + chr(0b110010) + '\063' + chr(0b110000), 2667 - 2659), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(433 - 382) + chr(0b110001) + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(674 - 626) + chr(0b1101111) + '\062' + chr(0b11111 + 0o25) + chr(1658 - 1604), 61668 - 61660), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b101101 + 0o11) + chr(52), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(1340 - 1290) + chr(1172 - 1119) + chr(53), 0b1000), nzTpIcepk0o8('\060' + chr(10616 - 10505) + chr(51) + chr(0b110110) + chr(0b100010 + 0o23), ord("\x08")), nzTpIcepk0o8(chr(0b101000 + 0o10) + chr(111) + chr(0b110010) + chr(0b110111) + chr(0b1101 + 0o44), ord("\x08")), nzTpIcepk0o8(chr(60 - 12) + chr(111) + chr(0b110010) + '\064' + '\065', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x33' + chr(0b110 + 0o55) + chr(49), 0o10), nzTpIcepk0o8(chr(0b10001 + 0o37) + '\x6f' + '\062' + '\x31' + '\x37', 14741 - 14733), nzTpIcepk0o8('\x30' + '\x6f' + '\x33' + '\061' + chr(1065 - 1016), 8), nzTpIcepk0o8(chr(0b101 + 0o53) + chr(0b10011 + 0o134) + chr(0b110001) + chr(0b11010 + 0o34) + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1011 + 0o144) + chr(1319 - 1268) + chr(1117 - 1063) + chr(0b100000 + 0o21), 9538 - 9530), nzTpIcepk0o8('\x30' + '\157' + '\065' + chr(2396 - 2345), 49749 - 49741), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110011), 20841 - 20833), nzTpIcepk0o8('\x30' + '\x6f' + chr(49) + chr(53) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1100011 + 0o14) + chr(0b1011 + 0o50) + '\060' + chr(2064 - 2014), 0o10), nzTpIcepk0o8(chr(0b0 + 0o60) + chr(2062 - 1951) + '\x31' + chr(1630 - 1578) + chr(0b11000 + 0o34), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101110 + 0o1) + chr(0b101110 + 0o4) + chr(0b101110 + 0o2) + chr(0b10 + 0o56), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\061' + chr(0b110011) + '\065', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(11127 - 11016) + '\x31' + chr(0b110000) + '\x36', 22723 - 22715), nzTpIcepk0o8(chr(48) + '\157' + chr(49) + '\060' + chr(151 - 103), ord("\x08")), nzTpIcepk0o8(chr(0b10011 + 0o35) + '\x6f' + '\061' + chr(0b10101 + 0o40) + chr(0b110111), 8), nzTpIcepk0o8(chr(0b100101 + 0o13) + '\157' + chr(51) + chr(54) + chr(0b1101 + 0o44), 8), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110010) + '\067' + chr(54), 31226 - 31218)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(1371 - 1318) + '\x30', 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'i'), '\144' + '\x65' + '\143' + chr(111) + chr(0b1100100) + chr(0b1100101))(chr(0b1110101) + chr(0b1110100) + '\x66' + '\x2d' + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def BpmpVU6ew_wz(hXMPsSrOQzbh, r_D0HyqK4grO, bmmTXKdBuMbO=None, SUcYaF9gAJAW=nzTpIcepk0o8('\060' + '\x6f' + '\060', 0o10), bhvcCFR07maA=37.0, jif2BXBXDWe0=nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\060', 8), P6MCancmTVIW=None, dcIGdrKJIQqm=roI3spqORKae(ES5oEprVxulp(b'4\xec\xea\xac'), chr(100) + chr(0b1100101) + chr(0b1011011 + 0o10) + chr(111) + '\144' + '\145')('\x75' + chr(0b1110100) + chr(0b1100010 + 0o4) + chr(45) + chr(56)), N53N20X2V9t8=1.0, _fwxLQ0Lh__w=0.0):
P6MCancmTVIW = hXMPsSrOQzbh._set_material(r_D0HyqK4grO, P6MCancmTVIW, multi=nzTpIcepk0o8('\060' + '\x6f' + '\061', 0o10))
zF8oFOtHDCse = hXMPsSrOQzbh._prep_cmd_args(bhvcCFR07maA, dcIGdrKJIQqm, P6MCancmTVIW, jif2BXBXDWe0, N53N20X2V9t8, _fwxLQ0Lh__w, multi=nzTpIcepk0o8(chr(0b100 + 0o54) + '\157' + chr(1297 - 1248), 8))
if SUcYaF9gAJAW:
roI3spqORKae(zF8oFOtHDCse, roI3spqORKae(ES5oEprVxulp(b'\x0f\xd7\xd4\xfd\xffV\xf4\x00\x0fX<\xc1'), chr(0b1100100) + chr(101) + '\x63' + '\x6f' + chr(100) + chr(0b111001 + 0o54))(chr(117) + '\164' + chr(102) + chr(45) + chr(56)))(roI3spqORKae(ES5oEprVxulp(b'j\xe7\xe2\xae\xe2_\xd6\x1d\x04C\x0c'), chr(100) + chr(5706 - 5605) + chr(6009 - 5910) + chr(0b1101111) + '\x64' + '\145')(chr(0b0 + 0o165) + '\x74' + '\x66' + chr(0b101101) + chr(1738 - 1682)))
if bmmTXKdBuMbO is None:
bmmTXKdBuMbO = bbT2xIe5pzk7(nzTpIcepk0o8(chr(48) + '\157' + chr(1257 - 1208), 8), ftfygxgFas5X(r_D0HyqK4grO) + nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110001), 8))
vniSnlI09HNg = hXMPsSrOQzbh._multi_lines(r_D0HyqK4grO, bmmTXKdBuMbO)
roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'0\xbb\xb0\xf1\xe6\x00\x83[W\x07(\xc0'), chr(0b1100100) + '\x65' + '\143' + '\157' + chr(0b1100100) + chr(0b1001110 + 0o27))(chr(6007 - 5890) + '\x74' + chr(0b1010001 + 0o25) + chr(0b101101) + chr(56)))(roI3spqORKae(ES5oEprVxulp(b'*\xe5\xe2'), chr(100) + '\x65' + '\x63' + chr(0b1101111) + chr(0b1000110 + 0o36) + '\x65')(chr(117) + chr(0b1110100) + '\146' + chr(45) + chr(0b111000)), zF8oFOtHDCse, vniSnlI09HNg)
pDD0JFrFHFd1 = hXMPsSrOQzbh._process_mfe(hXMPsSrOQzbh._read_tempfile(roI3spqORKae(ES5oEprVxulp(b'*\xe5\xe2\xe7\xeaW\xd6'), chr(100) + chr(0b1110 + 0o127) + chr(99) + chr(0b1101111) + chr(9590 - 9490) + chr(6568 - 6467))(chr(117) + chr(0b1010010 + 0o42) + chr(0b1100110) + chr(863 - 818) + chr(0b101001 + 0o17))))
if SUcYaF9gAJAW:
return pDD0JFrFHFd1
else:
return pDD0JFrFHFd1[nzTpIcepk0o8('\060' + '\x6f' + '\x30', 8)] |
klavinslab/coral | coral/analysis/_structure/nupack.py | NUPACK.subopt | def subopt(self, strand, gap, temp=37.0, pseudo=False, material=None,
dangles='some', sodium=1.0, magnesium=0.0):
'''Compute the suboptimal structures within a defined energy gap of the
MFE. Runs the \'subopt\' command.
:param strand: Strand on which to run subopt. Strands must be either
coral.DNA or coral.RNA).
:type strand: coral.DNA or coral.RNA
:param gap: Energy gap within to restrict results, e.g. 0.1.
:type gap: float
:param temp: Temperature setting for the computation. Negative values
are not allowed.
:type temp: float
:param pseudo: Enable pseudoknots.
:type pseudo: bool
:param material: The material setting to use in the computation. If set
to None (the default), the material type is inferred
from the strands. Other settings available: 'dna' for
DNA parameters, 'rna' for RNA (1995) parameters, and
'rna1999' for the RNA 1999 parameters.
:type material: str
:param dangles: How to treat dangles in the computation. From the
user guide: For \'none\': Dangle energies are ignored.
For \'some\': \'A dangle energy is incorporated for
each unpaired base flanking a duplex\'. For 'all': all
dangle energy is considered.
:type dangles: str
:param sodium: Sodium concentration in solution (molar), only applies
to DNA.
:type sodium: float
:param magnesium: Magnesium concentration in solution (molar), only
applies to DNA>
:type magnesium: float
:returns: A list of dictionaries of the type returned by .mfe().
:rtype: list
'''
# Set the material (will be used to set command material flag)
material = self._set_material(strand, material)
# Set up command flags
cmd_args = self._prep_cmd_args(temp, dangles, material, pseudo, sodium,
magnesium, multi=False)
# Set up the input file and run the command. Note: no STDOUT
lines = [str(strand), str(gap)]
self._run('subopt', cmd_args, lines)
# Read the output from file
structures = self._process_mfe(self._read_tempfile('subopt.subopt'))
return structures | python | def subopt(self, strand, gap, temp=37.0, pseudo=False, material=None,
dangles='some', sodium=1.0, magnesium=0.0):
'''Compute the suboptimal structures within a defined energy gap of the
MFE. Runs the \'subopt\' command.
:param strand: Strand on which to run subopt. Strands must be either
coral.DNA or coral.RNA).
:type strand: coral.DNA or coral.RNA
:param gap: Energy gap within to restrict results, e.g. 0.1.
:type gap: float
:param temp: Temperature setting for the computation. Negative values
are not allowed.
:type temp: float
:param pseudo: Enable pseudoknots.
:type pseudo: bool
:param material: The material setting to use in the computation. If set
to None (the default), the material type is inferred
from the strands. Other settings available: 'dna' for
DNA parameters, 'rna' for RNA (1995) parameters, and
'rna1999' for the RNA 1999 parameters.
:type material: str
:param dangles: How to treat dangles in the computation. From the
user guide: For \'none\': Dangle energies are ignored.
For \'some\': \'A dangle energy is incorporated for
each unpaired base flanking a duplex\'. For 'all': all
dangle energy is considered.
:type dangles: str
:param sodium: Sodium concentration in solution (molar), only applies
to DNA.
:type sodium: float
:param magnesium: Magnesium concentration in solution (molar), only
applies to DNA>
:type magnesium: float
:returns: A list of dictionaries of the type returned by .mfe().
:rtype: list
'''
# Set the material (will be used to set command material flag)
material = self._set_material(strand, material)
# Set up command flags
cmd_args = self._prep_cmd_args(temp, dangles, material, pseudo, sodium,
magnesium, multi=False)
# Set up the input file and run the command. Note: no STDOUT
lines = [str(strand), str(gap)]
self._run('subopt', cmd_args, lines)
# Read the output from file
structures = self._process_mfe(self._read_tempfile('subopt.subopt'))
return structures | [
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"# Set t... | Compute the suboptimal structures within a defined energy gap of the
MFE. Runs the \'subopt\' command.
:param strand: Strand on which to run subopt. Strands must be either
coral.DNA or coral.RNA).
:type strand: coral.DNA or coral.RNA
:param gap: Energy gap within to restrict results, e.g. 0.1.
:type gap: float
:param temp: Temperature setting for the computation. Negative values
are not allowed.
:type temp: float
:param pseudo: Enable pseudoknots.
:type pseudo: bool
:param material: The material setting to use in the computation. If set
to None (the default), the material type is inferred
from the strands. Other settings available: 'dna' for
DNA parameters, 'rna' for RNA (1995) parameters, and
'rna1999' for the RNA 1999 parameters.
:type material: str
:param dangles: How to treat dangles in the computation. From the
user guide: For \'none\': Dangle energies are ignored.
For \'some\': \'A dangle energy is incorporated for
each unpaired base flanking a duplex\'. For 'all': all
dangle energy is considered.
:type dangles: str
:param sodium: Sodium concentration in solution (molar), only applies
to DNA.
:type sodium: float
:param magnesium: Magnesium concentration in solution (molar), only
applies to DNA>
:type magnesium: float
:returns: A list of dictionaries of the type returned by .mfe().
:rtype: list | [
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ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8('\060' + '\x6f' + chr(2642 - 2590) + chr(1136 - 1086), 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(0b1010 + 0o53) + chr(50), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(140 - 85) + chr(0b110 + 0o57), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x31' + '\x30', 0b1000), nzTpIcepk0o8(chr(954 - 906) + '\x6f' + chr(0b10111 + 0o33) + '\x34' + '\x34', 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(50) + '\x35' + chr(1835 - 1783), 0b1000), nzTpIcepk0o8(chr(1470 - 1422) + chr(111) + '\061' + chr(51) + '\065', 0o10), nzTpIcepk0o8(chr(119 - 71) + '\157' + chr(49) + chr(0b110000) + '\x31', 0b1000), nzTpIcepk0o8(chr(779 - 731) + '\157' + chr(2497 - 2447) + '\x37' + chr(0b10101 + 0o34), 13153 - 13145), nzTpIcepk0o8(chr(0b11110 + 0o22) + chr(0b1101111) + chr(0b100000 + 0o27) + chr(0b110100), 0o10), nzTpIcepk0o8('\060' + chr(5722 - 5611) + chr(49) + chr(54) + chr(1686 - 1634), 0b1000), nzTpIcepk0o8(chr(417 - 369) + chr(10919 - 10808) + chr(0b110011) + chr(631 - 583) + '\065', 38379 - 38371), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x31' + chr(55) + chr(0b110011), 51525 - 51517), nzTpIcepk0o8(chr(176 - 128) + chr(0b1101111) + chr(0b110010) + chr(0b1011 + 0o54) + chr(1809 - 1759), 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(51) + chr(0b110101) + chr(931 - 881), 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(51) + '\x30' + chr(0b1000 + 0o52), ord("\x08")), nzTpIcepk0o8(chr(1821 - 1773) + chr(0b1000101 + 0o52) + chr(0b110010 + 0o1) + chr(2395 - 2346) + '\067', 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(0b1001 + 0o53) + chr(48), 17957 - 17949), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(2393 - 2338) + '\x31', ord("\x08")), nzTpIcepk0o8(chr(0b1001 + 0o47) + chr(0b111011 + 0o64) + chr(0b110011) + chr(0b110100) + chr(0b1100 + 0o45), ord("\x08")), nzTpIcepk0o8(chr(2194 - 2146) + chr(0b1000100 + 0o53) + chr(0b1011 + 0o54) + '\x31', 8), nzTpIcepk0o8(chr(0b11100 + 0o24) + chr(0b111 + 0o150) + chr(51) + chr(0b11011 + 0o31) + chr(0b0 + 0o61), 8), nzTpIcepk0o8(chr(0b1100 + 0o44) + chr(7349 - 7238) + chr(0b10010 + 0o37) + chr(51), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(0b101001 + 0o10) + chr(141 - 87) + '\x35', 0o10), nzTpIcepk0o8('\060' + chr(0b101000 + 0o107) + chr(54) + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(9582 - 9471) + chr(0b10 + 0o57) + '\x34' + chr(0b100000 + 0o26), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + '\062' + chr(1737 - 1682) + '\066', 64365 - 64357), nzTpIcepk0o8(chr(1579 - 1531) + chr(0b1101111) + '\061' + '\x32' + chr(0b110111), 38796 - 38788), nzTpIcepk0o8(chr(2120 - 2072) + '\x6f' + chr(0b110010) + chr(55) + '\x36', 8), nzTpIcepk0o8('\x30' + chr(111) + '\x33' + '\067' + '\x35', 0o10), nzTpIcepk0o8(chr(0b101101 + 0o3) + '\x6f' + chr(0b110010 + 0o0) + chr(0b100000 + 0o23) + chr(53), 2581 - 2573), nzTpIcepk0o8(chr(793 - 745) + chr(111) + '\x36' + chr(0b110101), 0o10), nzTpIcepk0o8(chr(1066 - 1018) + chr(111) + chr(0b110000 + 0o1) + '\x32' + '\x37', 8), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(51) + chr(0b110101) + '\061', 12515 - 12507), nzTpIcepk0o8(chr(318 - 270) + '\157' + '\062' + chr(0b11010 + 0o31) + '\x31', 61839 - 61831), nzTpIcepk0o8(chr(0b110000) + chr(0b110111 + 0o70) + '\063' + '\x31' + chr(0b110011), 34920 - 34912), nzTpIcepk0o8(chr(0b101111 + 0o1) + chr(111) + chr(0b110010) + chr(1985 - 1934) + chr(0b110111), 7269 - 7261), nzTpIcepk0o8(chr(0b111 + 0o51) + '\157' + chr(893 - 842) + '\x32', 34700 - 34692), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(327 - 276) + '\063' + chr(0b10001 + 0o44), 53115 - 53107), nzTpIcepk0o8(chr(0b10100 + 0o34) + chr(10882 - 10771) + chr(51) + chr(55) + chr(0b100111 + 0o20), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b1000 + 0o50) + '\157' + chr(53) + '\060', ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x0c'), chr(3971 - 3871) + '\145' + chr(99) + chr(0b1101111) + chr(0b110010 + 0o62) + '\x65')(chr(117) + chr(7279 - 7163) + chr(0b1111 + 0o127) + chr(0b1100 + 0o41) + chr(2784 - 2728)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def gOUvVwhXggpa(hXMPsSrOQzbh, sOvPdpw6JkD6, TcZ0Rbmam82x, bhvcCFR07maA=37.0, jif2BXBXDWe0=nzTpIcepk0o8('\060' + chr(111) + '\060', ord("\x08")), P6MCancmTVIW=None, dcIGdrKJIQqm=roI3spqORKae(ES5oEprVxulp(b'QEPm'), chr(0b1000111 + 0o35) + chr(0b111100 + 0o51) + chr(0b0 + 0o143) + chr(0b111111 + 0o60) + chr(0b101101 + 0o67) + chr(0b10101 + 0o120))(chr(7579 - 7462) + chr(1808 - 1692) + chr(102) + '\x2d' + chr(655 - 599)), N53N20X2V9t8=1.0, _fwxLQ0Lh__w=0.0):
P6MCancmTVIW = hXMPsSrOQzbh._set_material(sOvPdpw6JkD6, P6MCancmTVIW)
zF8oFOtHDCse = hXMPsSrOQzbh._prep_cmd_args(bhvcCFR07maA, dcIGdrKJIQqm, P6MCancmTVIW, jif2BXBXDWe0, N53N20X2V9t8, _fwxLQ0Lh__w, multi=nzTpIcepk0o8(chr(48) + '\x6f' + '\x30', 8))
vniSnlI09HNg = [N9zlRy29S1SS(sOvPdpw6JkD6), N9zlRy29S1SS(TcZ0Rbmam82x)]
roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'U\x12\n0\xc5\x9dmu\x8b\x0c5\xf1'), chr(0b1011100 + 0o10) + chr(101) + '\x63' + '\157' + '\144' + chr(0b1100101))('\165' + '\x74' + chr(102) + chr(45) + '\070'))(roI3spqORKae(ES5oEprVxulp(b'Q__g\xd4\xd8'), chr(9328 - 9228) + chr(0b110110 + 0o57) + '\143' + chr(111) + '\x64' + chr(0b111010 + 0o53))(chr(0b11 + 0o162) + '\x74' + chr(0b1100110) + '\x2d' + '\070'), zF8oFOtHDCse, vniSnlI09HNg)
pDD0JFrFHFd1 = hXMPsSrOQzbh._process_mfe(hXMPsSrOQzbh._read_tempfile(roI3spqORKae(ES5oEprVxulp(b'Q__g\xd4\xd8s2\xcc^\x1b\xb5\x0f'), chr(0b1100100) + chr(0b10110 + 0o117) + chr(0b11001 + 0o112) + chr(0b1101111) + chr(0b1100100) + chr(101))('\165' + chr(116) + chr(102) + '\055' + '\x38')))
return pDD0JFrFHFd1 |
klavinslab/coral | coral/analysis/_structure/nupack.py | NUPACK.count | def count(self, strand, pseudo=False):
'''Enumerates the total number of secondary structures over the
structural ensemble Ω(π). Runs the \'count\' command.
:param strand: Strand on which to run count. Strands must be either
coral.DNA or coral.RNA).
:type strand: list
:param pseudo: Enable pseudoknots.
:type pseudo: bool
:returns: The count of the number of structures in the structural
ensemble.
:rtype: int
'''
# Set up command flags
if pseudo:
cmd_args = ['-pseudo']
else:
cmd_args = []
# Set up the input file and run the command
stdout = self._run('count', cmd_args, [str(strand)]).split('\n')
# Return the count
return int(float(stdout[-2])) | python | def count(self, strand, pseudo=False):
'''Enumerates the total number of secondary structures over the
structural ensemble Ω(π). Runs the \'count\' command.
:param strand: Strand on which to run count. Strands must be either
coral.DNA or coral.RNA).
:type strand: list
:param pseudo: Enable pseudoknots.
:type pseudo: bool
:returns: The count of the number of structures in the structural
ensemble.
:rtype: int
'''
# Set up command flags
if pseudo:
cmd_args = ['-pseudo']
else:
cmd_args = []
# Set up the input file and run the command
stdout = self._run('count', cmd_args, [str(strand)]).split('\n')
# Return the count
return int(float(stdout[-2])) | [
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/analysis/_structure/nupack.py#L548-L572 | train | Enumerates the total number of secondary structures over the the
ensemble Ω ( π. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(0b1101111) + chr(1548 - 1499) + '\061' + chr(0b110001), 8523 - 8515), nzTpIcepk0o8(chr(1438 - 1390) + chr(11042 - 10931) + chr(52) + chr(0b110010 + 0o0), 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(2352 - 2301) + chr(1355 - 1305) + chr(0b110110), 0b1000), nzTpIcepk0o8('\x30' + chr(6211 - 6100) + chr(0b101000 + 0o13) + '\060' + '\x30', 15526 - 15518), nzTpIcepk0o8(chr(2140 - 2092) + chr(111) + '\064' + '\x30', 58783 - 58775), nzTpIcepk0o8(chr(2136 - 2088) + chr(111) + '\066' + '\060', 0o10), nzTpIcepk0o8(chr(2145 - 2097) + chr(0b1101111) + chr(2437 - 2386) + chr(49) + '\x31', ord("\x08")), nzTpIcepk0o8(chr(1471 - 1423) + '\x6f' + '\062' + chr(0b101111 + 0o6) + '\x34', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(1167 - 1116) + '\x34' + chr(54), 11614 - 11606), nzTpIcepk0o8('\x30' + chr(0b101011 + 0o104) + '\x32' + '\x31' + chr(0b101110 + 0o5), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(49) + chr(0b110 + 0o61) + chr(0b101110 + 0o11), ord("\x08")), nzTpIcepk0o8(chr(1695 - 1647) + chr(111) + chr(0b100100 + 0o16) + '\x35' + '\x37', 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(0b100001 + 0o22) + chr(55) + '\064', ord("\x08")), nzTpIcepk0o8(chr(714 - 666) + chr(111) + chr(75 - 25) + chr(1534 - 1481) + chr(0b110111 + 0o0), 8), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(51) + chr(53), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(2292 - 2241) + chr(0b110111) + chr(0b10 + 0o61), 0o10), nzTpIcepk0o8('\060' + chr(0b1000011 + 0o54) + chr(52) + chr(2583 - 2532), 50062 - 50054), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b11101 + 0o26) + chr(2039 - 1985) + chr(0b101011 + 0o10), 0b1000), nzTpIcepk0o8(chr(1997 - 1949) + chr(9936 - 9825) + chr(1828 - 1777) + '\067' + '\065', 0o10), nzTpIcepk0o8(chr(241 - 193) + chr(0b1101111) + '\x32' + '\060', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b11101 + 0o25) + chr(298 - 243) + '\x36', 2366 - 2358), nzTpIcepk0o8('\060' + chr(2460 - 2349) + '\x33' + '\x33' + '\060', 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(2235 - 2185) + chr(0b110100) + '\x32', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x31' + chr(55) + chr(50), 0o10), nzTpIcepk0o8('\060' + chr(5321 - 5210) + '\x33' + chr(0b101000 + 0o17) + '\062', 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + '\063' + '\x32' + chr(2496 - 2442), 8), nzTpIcepk0o8(chr(1727 - 1679) + chr(0b1001110 + 0o41) + '\067', 20798 - 20790), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\067', 8), nzTpIcepk0o8(chr(0b110000) + chr(0b1001 + 0o146) + chr(947 - 896) + chr(0b110010) + chr(51), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + '\065' + chr(1145 - 1093), 15712 - 15704), nzTpIcepk0o8('\060' + chr(4855 - 4744) + chr(837 - 788) + '\x36' + chr(0b11011 + 0o30), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(50) + chr(0b100111 + 0o14) + chr(1336 - 1282), 0o10), nzTpIcepk0o8(chr(1932 - 1884) + '\x6f' + chr(50) + '\x30', 8), nzTpIcepk0o8(chr(48) + '\157' + '\x32' + '\065' + '\067', 8), nzTpIcepk0o8(chr(48) + '\x6f' + '\062' + '\065' + chr(51), 0o10), nzTpIcepk0o8(chr(0b1000 + 0o50) + chr(9384 - 9273) + '\061' + '\x34' + chr(53), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110010) + '\065' + chr(0b10000 + 0o45), 4850 - 4842), nzTpIcepk0o8('\x30' + chr(0b100111 + 0o110) + '\062' + chr(1628 - 1574), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b100111 + 0o110) + '\x37' + chr(0b110011), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + '\063' + chr(0b110010) + chr(0b110000), 26670 - 26662)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + '\157' + '\x35' + '\060', ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'g'), '\144' + '\145' + chr(9316 - 9217) + chr(0b1101111) + chr(0b0 + 0o144) + chr(0b111 + 0o136))('\x75' + '\164' + chr(0b1100110) + '\x2d' + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def sQSWKlURp7QK(hXMPsSrOQzbh, sOvPdpw6JkD6, jif2BXBXDWe0=nzTpIcepk0o8(chr(0b100 + 0o54) + '\x6f' + chr(343 - 295), 0b1000)):
if jif2BXBXDWe0:
zF8oFOtHDCse = [roI3spqORKae(ES5oEprVxulp(b'dR\xa5\xa5UT\xa6'), chr(0b1001110 + 0o26) + chr(101) + '\x63' + '\x6f' + chr(100) + chr(0b1000001 + 0o44))(chr(0b1010 + 0o153) + chr(11469 - 11353) + chr(7241 - 7139) + '\x2d' + chr(0b1000 + 0o60))]
else:
zF8oFOtHDCse = []
E4teKT3YJIcH = hXMPsSrOQzbh._run(roI3spqORKae(ES5oEprVxulp(b'*M\xa3\xaeT'), '\144' + '\145' + '\143' + '\157' + '\144' + '\x65')(chr(117) + '\164' + chr(0b101011 + 0o73) + '\x2d' + chr(0b100110 + 0o22)), zF8oFOtHDCse, [N9zlRy29S1SS(sOvPdpw6JkD6)]).LfRrQOxuDvnC(roI3spqORKae(ES5oEprVxulp(b'C'), chr(0b1011 + 0o131) + '\145' + '\x63' + chr(111) + chr(100) + '\x65')(chr(0b100101 + 0o120) + chr(0b1011100 + 0o30) + chr(102) + '\x2d' + chr(2148 - 2092)))
return nzTpIcepk0o8(jLW6pRf2DSRk(E4teKT3YJIcH[-nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b11111 + 0o23), ord("\x08"))])) |
klavinslab/coral | coral/analysis/_structure/nupack.py | NUPACK.count_multi | def count_multi(self, strands, permutation=None, pseudo=False):
'''Enumerates the total number of secondary structures over the
structural ensemble Ω(π) with an ordered permutation of strands. Runs
the \'count\' command.
:param strands: List of strands to use as inputs to count -multi.
:type strands: list
:param permutation: The circular permutation of strands to test in
complex. e.g. to test in the order that was input
for 4 strands, the permutation would be [1,2,3,4].
If set to None, defaults to the order of the
input strands.
:type permutation: list
:param temp: Temperature setting for the computation. Negative values
are not allowed.
:type temp: float
:param pseudo: Enable pseudoknots.
:type pseudo: bool
:param material: The material setting to use in the computation. If set
to None (the default), the material type is inferred
from the strands. Other settings available: 'dna' for
DNA parameters, 'rna' for RNA (1995) parameters, and
'rna1999' for the RNA 1999 parameters.
:type material: str
:returns: Dictionary with the following key:value pairs: 'energy':
free energy, 'pfunc': partition function.
:rtype: dict
'''
# Set up command flags
cmd_args = ['-multi']
if pseudo:
cmd_args.append('-pseudo')
# Set up the input file and run the command
if permutation is None:
permutation = range(1, len(strands) + 1)
lines = self._multi_lines(strands, permutation)
stdout = self._run('count', cmd_args, lines).split('\n')
return int(float(stdout[-2])) | python | def count_multi(self, strands, permutation=None, pseudo=False):
'''Enumerates the total number of secondary structures over the
structural ensemble Ω(π) with an ordered permutation of strands. Runs
the \'count\' command.
:param strands: List of strands to use as inputs to count -multi.
:type strands: list
:param permutation: The circular permutation of strands to test in
complex. e.g. to test in the order that was input
for 4 strands, the permutation would be [1,2,3,4].
If set to None, defaults to the order of the
input strands.
:type permutation: list
:param temp: Temperature setting for the computation. Negative values
are not allowed.
:type temp: float
:param pseudo: Enable pseudoknots.
:type pseudo: bool
:param material: The material setting to use in the computation. If set
to None (the default), the material type is inferred
from the strands. Other settings available: 'dna' for
DNA parameters, 'rna' for RNA (1995) parameters, and
'rna1999' for the RNA 1999 parameters.
:type material: str
:returns: Dictionary with the following key:value pairs: 'energy':
free energy, 'pfunc': partition function.
:rtype: dict
'''
# Set up command flags
cmd_args = ['-multi']
if pseudo:
cmd_args.append('-pseudo')
# Set up the input file and run the command
if permutation is None:
permutation = range(1, len(strands) + 1)
lines = self._multi_lines(strands, permutation)
stdout = self._run('count', cmd_args, lines).split('\n')
return int(float(stdout[-2])) | [
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:param strands: List of strands to use as inputs to count -multi.
:type strands: list
:param permutation: The circular permutation of strands to test in
complex. e.g. to test in the order that was input
for 4 strands, the permutation would be [1,2,3,4].
If set to None, defaults to the order of the
input strands.
:type permutation: list
:param temp: Temperature setting for the computation. Negative values
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:type temp: float
:param pseudo: Enable pseudoknots.
:type pseudo: bool
:param material: The material setting to use in the computation. If set
to None (the default), the material type is inferred
from the strands. Other settings available: 'dna' for
DNA parameters, 'rna' for RNA (1995) parameters, and
'rna1999' for the RNA 1999 parameters.
:type material: str
:returns: Dictionary with the following key:value pairs: 'energy':
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/analysis/_structure/nupack.py#L575-L615 | train | Enumerates the total number of secondary structures over the structureural ensemble Ω ( π ) with an ordered permutation of strands. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8('\060' + '\157' + chr(0b110100) + chr(0b110001), 48080 - 48072), nzTpIcepk0o8(chr(48) + chr(0b1101011 + 0o4) + chr(50) + chr(0b110100) + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b10110 + 0o33), 0b1000), nzTpIcepk0o8('\060' + chr(9301 - 9190) + chr(0b110011) + chr(0b1001 + 0o52) + chr(537 - 486), 0o10), nzTpIcepk0o8('\x30' + chr(3426 - 3315) + '\062' + '\060' + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(7237 - 7126) + chr(0b110001 + 0o2) + chr(48) + '\067', 42735 - 42727), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b10010 + 0o40) + chr(0b101000 + 0o16) + chr(0b110000), 36041 - 36033), nzTpIcepk0o8(chr(0b10101 + 0o33) + '\x6f' + '\063' + chr(50) + '\x33', 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b11110 + 0o24) + chr(327 - 273) + '\x34', 0o10), nzTpIcepk0o8('\x30' + '\x6f' + '\x32' + chr(55) + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(0b11110 + 0o22) + '\x6f' + chr(1310 - 1261) + chr(0b110010) + chr(57 - 6), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(454 - 404) + chr(2005 - 1957) + '\067', 0o10), nzTpIcepk0o8('\060' + '\157' + '\x33' + chr(0b110001), 29858 - 29850), nzTpIcepk0o8(chr(123 - 75) + chr(0b1011100 + 0o23) + chr(55) + '\x36', 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(51) + chr(1592 - 1544) + chr(51), 0b1000), nzTpIcepk0o8(chr(0b101 + 0o53) + '\157' + chr(0b110011) + chr(0b101111 + 0o7) + chr(0b11111 + 0o21), 26387 - 26379), nzTpIcepk0o8('\060' + chr(0b101 + 0o152) + chr(50) + '\064' + chr(0b110001), 7319 - 7311), nzTpIcepk0o8('\x30' + chr(111) + '\x33' + '\x31' + '\061', 5049 - 5041), nzTpIcepk0o8('\060' + chr(4771 - 4660) + chr(49) + chr(0b110011) + '\x37', 63576 - 63568), nzTpIcepk0o8(chr(1670 - 1622) + '\157' + '\x33' + chr(2312 - 2261) + chr(1343 - 1290), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b1 + 0o60) + '\x33' + chr(0b10100 + 0o37), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + '\062' + '\067', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b11101 + 0o24) + chr(0b110000) + chr(1391 - 1339), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b11000 + 0o31) + chr(0b10000 + 0o40) + chr(2033 - 1983), 0o10), nzTpIcepk0o8(chr(615 - 567) + chr(0b111111 + 0o60) + chr(0b110010) + '\x34' + chr(49), 8), nzTpIcepk0o8('\060' + chr(111) + '\x33' + chr(0b110101) + '\065', 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(0b11010 + 0o30) + chr(51) + chr(53), 41984 - 41976), nzTpIcepk0o8(chr(1475 - 1427) + chr(0b1011000 + 0o27) + '\x35' + chr(0b110110), 13724 - 13716), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\063' + chr(989 - 936) + '\062', 0o10), nzTpIcepk0o8('\x30' + chr(0b11101 + 0o122) + chr(0b110011) + chr(1374 - 1325) + chr(0b110010), 44557 - 44549), nzTpIcepk0o8(chr(1543 - 1495) + '\x6f' + chr(2398 - 2349) + '\064' + chr(0b10110 + 0o32), 0b1000), nzTpIcepk0o8(chr(2292 - 2244) + chr(111) + chr(0b11011 + 0o26) + chr(259 - 206) + chr(0b1001 + 0o47), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(0b110 + 0o54) + '\x36' + chr(0b110100), 8), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x33' + '\x35' + chr(0b100000 + 0o26), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + '\063' + chr(53) + chr(49), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + '\x33' + '\062' + '\063', 8), nzTpIcepk0o8('\x30' + chr(0b1 + 0o156) + chr(0b110001) + '\063', 0b1000), nzTpIcepk0o8(chr(2106 - 2058) + chr(111) + '\x32' + '\x35' + chr(0b110011), 38300 - 38292), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110010) + chr(0b110010) + chr(51), 0b1000), nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(0b1101111) + '\x33' + chr(0b110011) + chr(1702 - 1647), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + chr(3285 - 3174) + chr(722 - 669) + chr(48), 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x0f'), chr(9599 - 9499) + chr(7605 - 7504) + chr(99) + chr(0b1101111) + chr(100) + chr(982 - 881))(chr(0b1110101) + chr(116) + chr(0b1100110) + chr(0b101101) + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def IaZ4FLwuVgPz(hXMPsSrOQzbh, r_D0HyqK4grO, bmmTXKdBuMbO=None, jif2BXBXDWe0=nzTpIcepk0o8('\060' + chr(0b1010 + 0o145) + chr(48), 0o10)):
zF8oFOtHDCse = [roI3spqORKae(ES5oEprVxulp(b'\x0c\xcft\xb7\xf4\xae'), chr(100) + chr(5882 - 5781) + '\143' + '\157' + chr(100) + '\145')(chr(117) + '\164' + chr(0b1000011 + 0o43) + '\x2d' + chr(1594 - 1538))]
if jif2BXBXDWe0:
roI3spqORKae(zF8oFOtHDCse, roI3spqORKae(ES5oEprVxulp(b'i\xf6R\xef\xf8\xa0\xf7\xbc\xde\xd2\x06\xb2'), '\144' + chr(6308 - 6207) + chr(2549 - 2450) + chr(0b1101111) + chr(0b1111 + 0o125) + chr(8735 - 8634))(chr(0b1010010 + 0o43) + chr(0b1110100) + '\146' + '\055' + chr(665 - 609)))(roI3spqORKae(ES5oEprVxulp(b'\x0c\xd2r\xbe\xf5\xa3\xdf'), chr(0b1100100) + chr(7381 - 7280) + chr(0b1100011) + '\x6f' + '\144' + chr(0b1100101))(chr(0b1110101) + chr(0b1110100) + chr(0b1100110) + chr(0b101101) + '\070'))
if bmmTXKdBuMbO is None:
bmmTXKdBuMbO = bbT2xIe5pzk7(nzTpIcepk0o8(chr(48) + chr(111) + '\x31', 8), ftfygxgFas5X(r_D0HyqK4grO) + nzTpIcepk0o8(chr(1341 - 1293) + chr(0b10101 + 0o132) + chr(0b111 + 0o52), 8))
vniSnlI09HNg = hXMPsSrOQzbh._multi_lines(r_D0HyqK4grO, bmmTXKdBuMbO)
E4teKT3YJIcH = hXMPsSrOQzbh._run(roI3spqORKae(ES5oEprVxulp(b'B\xcdt\xb5\xf4'), chr(0b1100100) + '\x65' + chr(3236 - 3137) + '\x6f' + '\x64' + '\145')('\x75' + chr(0b1110100) + chr(6234 - 6132) + chr(1188 - 1143) + '\070'), zF8oFOtHDCse, vniSnlI09HNg).LfRrQOxuDvnC(roI3spqORKae(ES5oEprVxulp(b'+'), '\x64' + '\x65' + chr(0b1100011) + '\157' + chr(7283 - 7183) + chr(0b1100101))('\165' + '\x74' + chr(7442 - 7340) + chr(45) + chr(0b10110 + 0o42)))
return nzTpIcepk0o8(jLW6pRf2DSRk(E4teKT3YJIcH[-nzTpIcepk0o8(chr(48) + chr(111) + '\062', ord("\x08"))])) |
klavinslab/coral | coral/analysis/_structure/nupack.py | NUPACK.energy | def energy(self, strand, dotparens, temp=37.0, pseudo=False, material=None,
dangles='some', sodium=1.0, magnesium=0.0):
'''Calculate the free energy of a given sequence structure. Runs the
\'energy\' command.
:param strand: Strand on which to run energy. Strands must be either
coral.DNA or coral.RNA).
:type strand: coral.DNA or coral.RNA
:param dotparens: The structure in dotparens notation.
:type dotparens: str
:param temp: Temperature setting for the computation. Negative values
are not allowed.
:type temp: float
:param pseudo: Enable pseudoknots.
:type pseudo: bool
:param material: The material setting to use in the computation. If set
to None (the default), the material type is inferred
from the strands. Other settings available: 'dna' for
DNA parameters, 'rna' for RNA (1995) parameters, and
'rna1999' for the RNA 1999 parameters.
:type material: str
:param dangles: How to treat dangles in the computation. From the
user guide: For \'none\': Dangle energies are ignored.
For \'some\': \'A dangle energy is incorporated for
each unpaired base flanking a duplex\'. For 'all': all
dangle energy is considered.
:type dangles: str
:param sodium: Sodium concentration in solution (molar), only applies
to DNA.
:type sodium: float
:param magnesium: Magnesium concentration in solution (molar), only
applies to DNA>
:type magnesium: float
:returns: The free energy of the sequence with the specified secondary
structure.
:rtype: float
'''
# Set the material (will be used to set command material flag)
material = self._set_material(strand, material)
# Set up command flags
cmd_args = self._prep_cmd_args(temp, dangles, material, pseudo, sodium,
magnesium, multi=False)
# Set up the input file and run the command. Note: no STDOUT
lines = [str(strand), dotparens]
stdout = self._run('energy', cmd_args, lines).split('\n')
# Return the energy
return float(stdout[-2]) | python | def energy(self, strand, dotparens, temp=37.0, pseudo=False, material=None,
dangles='some', sodium=1.0, magnesium=0.0):
'''Calculate the free energy of a given sequence structure. Runs the
\'energy\' command.
:param strand: Strand on which to run energy. Strands must be either
coral.DNA or coral.RNA).
:type strand: coral.DNA or coral.RNA
:param dotparens: The structure in dotparens notation.
:type dotparens: str
:param temp: Temperature setting for the computation. Negative values
are not allowed.
:type temp: float
:param pseudo: Enable pseudoknots.
:type pseudo: bool
:param material: The material setting to use in the computation. If set
to None (the default), the material type is inferred
from the strands. Other settings available: 'dna' for
DNA parameters, 'rna' for RNA (1995) parameters, and
'rna1999' for the RNA 1999 parameters.
:type material: str
:param dangles: How to treat dangles in the computation. From the
user guide: For \'none\': Dangle energies are ignored.
For \'some\': \'A dangle energy is incorporated for
each unpaired base flanking a duplex\'. For 'all': all
dangle energy is considered.
:type dangles: str
:param sodium: Sodium concentration in solution (molar), only applies
to DNA.
:type sodium: float
:param magnesium: Magnesium concentration in solution (molar), only
applies to DNA>
:type magnesium: float
:returns: The free energy of the sequence with the specified secondary
structure.
:rtype: float
'''
# Set the material (will be used to set command material flag)
material = self._set_material(strand, material)
# Set up command flags
cmd_args = self._prep_cmd_args(temp, dangles, material, pseudo, sodium,
magnesium, multi=False)
# Set up the input file and run the command. Note: no STDOUT
lines = [str(strand), dotparens]
stdout = self._run('energy', cmd_args, lines).split('\n')
# Return the energy
return float(stdout[-2]) | [
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:type strand: coral.DNA or coral.RNA
:param dotparens: The structure in dotparens notation.
:type dotparens: str
:param temp: Temperature setting for the computation. Negative values
are not allowed.
:type temp: float
:param pseudo: Enable pseudoknots.
:type pseudo: bool
:param material: The material setting to use in the computation. If set
to None (the default), the material type is inferred
from the strands. Other settings available: 'dna' for
DNA parameters, 'rna' for RNA (1995) parameters, and
'rna1999' for the RNA 1999 parameters.
:type material: str
:param dangles: How to treat dangles in the computation. From the
user guide: For \'none\': Dangle energies are ignored.
For \'some\': \'A dangle energy is incorporated for
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:type dangles: str
:param sodium: Sodium concentration in solution (molar), only applies
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:type sodium: float
:param magnesium: Magnesium concentration in solution (molar), only
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:type magnesium: float
:returns: The free energy of the sequence with the specified secondary
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"command",
"."
] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/analysis/_structure/nupack.py#L618-L668 | train | Calculate the free energy of a given secondary sequence structure. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b110000) + chr(0b111010 + 0o65) + chr(54) + '\x32', 49715 - 49707), nzTpIcepk0o8('\060' + chr(111) + '\066' + chr(0b11 + 0o55), 61431 - 61423), nzTpIcepk0o8(chr(2232 - 2184) + chr(111) + chr(0b110011) + '\062' + '\x35', 33327 - 33319), nzTpIcepk0o8(chr(719 - 671) + chr(0b1101111) + '\x32' + chr(0b110000) + '\062', ord("\x08")), nzTpIcepk0o8('\x30' + chr(7206 - 7095) + chr(51) + '\067', 0b1000), nzTpIcepk0o8(chr(1461 - 1413) + chr(7323 - 7212) + '\062' + chr(0b110001) + chr(0b100110 + 0o15), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x31' + '\066' + chr(0b1100 + 0o52), 0b1000), nzTpIcepk0o8(chr(0b11010 + 0o26) + chr(0b1100010 + 0o15) + chr(50) + chr(0b110010) + chr(1251 - 1199), 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(50) + '\x30' + chr(0b1101 + 0o52), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(50) + '\066' + chr(0b110000), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x34' + chr(906 - 852), 0b1000), nzTpIcepk0o8(chr(0b10111 + 0o31) + '\x6f' + chr(0b110001) + chr(918 - 866) + chr(0b11001 + 0o30), 37809 - 37801), nzTpIcepk0o8(chr(0b100010 + 0o16) + chr(0b1101111) + chr(1070 - 1016) + chr(0b11010 + 0o30), 8), nzTpIcepk0o8(chr(0b110000) + chr(10023 - 9912) + chr(74 - 24) + chr(0b10011 + 0o41), 0b1000), nzTpIcepk0o8(chr(440 - 392) + '\157' + chr(1414 - 1365) + chr(0b110011) + chr(51), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101000 + 0o7) + chr(50) + chr(2468 - 2416) + '\x34', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(8814 - 8703) + '\x32' + chr(51) + '\x35', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x32' + chr(459 - 406) + chr(0b11000 + 0o32), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b11001 + 0o32) + chr(54) + chr(53), 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110101), 15027 - 15019), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x32' + '\065' + '\x33', 46916 - 46908), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x33' + '\x35' + chr(0b10010 + 0o40), 0o10), nzTpIcepk0o8('\060' + '\x6f' + '\x31' + chr(726 - 675), 45291 - 45283), nzTpIcepk0o8(chr(490 - 442) + chr(3110 - 2999) + chr(0b101011 + 0o7) + '\062' + chr(49), 57394 - 57386), nzTpIcepk0o8('\060' + chr(111) + '\x33' + chr(0b110110) + '\065', 8), nzTpIcepk0o8(chr(0b100110 + 0o12) + '\157' + chr(0b110011) + chr(54) + chr(0b110010), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110001) + chr(0b110110) + chr(0b1000 + 0o53), 35161 - 35153), nzTpIcepk0o8('\060' + '\157' + '\063' + chr(0b1100 + 0o45), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(0b10101 + 0o34) + chr(55) + chr(0b110011), 26511 - 26503), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(49) + '\x36' + '\060', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1100101 + 0o12) + chr(0b11000 + 0o31) + '\x34' + '\x33', 0o10), nzTpIcepk0o8(chr(0b10000 + 0o40) + chr(0b1101111) + '\062' + chr(0b110110) + '\x34', 0b1000), nzTpIcepk0o8(chr(0b10 + 0o56) + chr(0b111010 + 0o65) + chr(0b10 + 0o60) + chr(2303 - 2248) + chr(0b100100 + 0o16), 50047 - 50039), nzTpIcepk0o8('\060' + chr(3976 - 3865) + chr(0b110010) + '\x37', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b10011 + 0o134) + chr(53), 8), nzTpIcepk0o8(chr(0b11100 + 0o24) + chr(0b1101111) + chr(0b110001) + '\x34' + chr(48), 17886 - 17878), nzTpIcepk0o8(chr(48) + chr(0b1011010 + 0o25) + '\062' + '\067' + chr(2559 - 2505), 63646 - 63638), nzTpIcepk0o8('\060' + '\157' + chr(0b100100 + 0o20), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(10037 - 9926) + '\061' + '\065' + chr(0b10111 + 0o36), ord("\x08")), nzTpIcepk0o8('\x30' + chr(9258 - 9147) + chr(1583 - 1530) + '\062', ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + '\x6f' + '\x35' + '\x30', 12965 - 12957)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x1c'), chr(0b1100100) + chr(101) + chr(9604 - 9505) + chr(0b1101111) + '\x64' + chr(5774 - 5673))('\x75' + chr(0b1110100) + chr(6845 - 6743) + '\x2d' + chr(2538 - 2482)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def N74rCFbOFVLD(hXMPsSrOQzbh, sOvPdpw6JkD6, CflLPgy_HQLY, bhvcCFR07maA=37.0, jif2BXBXDWe0=nzTpIcepk0o8(chr(0b11 + 0o55) + chr(0b1101111) + chr(237 - 189), 14820 - 14812), P6MCancmTVIW=None, dcIGdrKJIQqm=roI3spqORKae(ES5oEprVxulp(b'A_\xb8\xe7'), chr(0b1010110 + 0o16) + chr(101) + chr(0b1100011) + chr(111) + chr(100) + chr(9122 - 9021))(chr(0b1110101) + chr(7472 - 7356) + chr(1669 - 1567) + chr(1923 - 1878) + chr(0b111000)), N53N20X2V9t8=1.0, _fwxLQ0Lh__w=0.0):
P6MCancmTVIW = hXMPsSrOQzbh._set_material(sOvPdpw6JkD6, P6MCancmTVIW)
zF8oFOtHDCse = hXMPsSrOQzbh._prep_cmd_args(bhvcCFR07maA, dcIGdrKJIQqm, P6MCancmTVIW, jif2BXBXDWe0, N53N20X2V9t8, _fwxLQ0Lh__w, multi=nzTpIcepk0o8('\x30' + '\157' + chr(0b110000), 8))
vniSnlI09HNg = [N9zlRy29S1SS(sOvPdpw6JkD6), CflLPgy_HQLY]
E4teKT3YJIcH = hXMPsSrOQzbh._run(roI3spqORKae(ES5oEprVxulp(b'W^\xb0\xf0x\xf2'), chr(1892 - 1792) + chr(2963 - 2862) + chr(3567 - 3468) + '\157' + chr(0b100010 + 0o102) + chr(3408 - 3307))(chr(117) + chr(6665 - 6549) + '\x66' + '\055' + '\070'), zF8oFOtHDCse, vniSnlI09HNg).LfRrQOxuDvnC(roI3spqORKae(ES5oEprVxulp(b'8'), chr(100) + '\x65' + chr(2912 - 2813) + chr(3924 - 3813) + chr(9285 - 9185) + '\x65')(chr(2806 - 2689) + '\164' + chr(9102 - 9000) + chr(45) + chr(0b111000)))
return jLW6pRf2DSRk(E4teKT3YJIcH[-nzTpIcepk0o8(chr(48) + chr(0b1001100 + 0o43) + chr(0b1010 + 0o50), 0b1000)]) |
klavinslab/coral | coral/analysis/_structure/nupack.py | NUPACK.complexes | def complexes(self, strands, max_size, ordered=False, pairs=False,
mfe=False, cutoff=0.001, degenerate=False, temp=37.0,
pseudo=False, material=None, dangles='some', sodium=1.0,
magnesium=0.0):
'''
:param strands: Strands on which to run energy. Strands must be either
coral.DNA or coral.RNA).
:type strands: list of coral.DNA or coral.RNA
:param max_size: Maximum complex size to consider (maximum number of
strand species in complex).
:type max_size: int
:param ordered: Consider distinct ordered complexes - all distinct
circular permutations of each complex.
:type ordered: bool
:param pairs: Calculate base-pairing observables as with .pairs().
:type pairs: bool
:param cutoff: A setting when pairs is set to True - only probabilities
above this threshold will be returned.
:type cutoff: float
:param degenerate: Applies only when \'mfe\' is set to True. If
set to True, the 'mfe' value associated with each
complex will be a list of degenerate MFEs (as in
the case of .mfe()).
:type degenerate: bool
:param temp: Temperature.
:type temp: float
:param pseudo: Enable pseudoknots.
:type pseudo: bool
:param material: The material setting to use in the computation. If set
to None (the default), the material type is inferred
from the strands. Other settings available: 'dna' for
DNA parameters, 'rna' for RNA (1995) parameters, and
'rna1999' for the RNA 1999 parameters.
:type material: str
:param dangles: How to treat dangles in the computation. From the
user guide: For \'none\': Dangle energies are ignored.
For \'some\': \'A dangle energy is incorporated for
each unpaired base flanking a duplex\'. For 'all': all
dangle energy is considered.
:type dangles: str
:param sodium: Sodium concentration in solution (molar), only applies
to DNA.
:type sodium: float
:param magnesium: Magnesium concentration in solution (molar), only
applies to DNA>
:type magnesium: float
:returns: A list of dictionaries containing at least 'energy',
'complex', and 'strands' keys. If 'ordered' is True, the
different possible ordered permutations of complexes are
considered. In addition, with 'ordered' set to True, an
additional 'order' key describing the exact order of strands
and a 'permutation' index (integer) are added. If 'pairs' is
True, there is an additional 'epairs' key containing the
base-pairing expectation values. If 'mfe' is selected, 'mfe,
'dotparens', and 'pairlist' keys in the same as .mfe(). In
addition, 'mfe' sets the -ordered flag, so the same keys as
when 'ordered' is set to True are added.
:rtype: float
'''
# TODO: Consider returning a pandas dataframe in this (and other)
# situations to make sorting/selection between results easier.
material = self._set_material(strands, material, multi=True)
cmd_args = self._prep_cmd_args(temp, dangles, material, pseudo, sodium,
magnesium, multi=False)
cmd_args.append('-quiet')
if mfe:
cmd_args.append('-mfe')
ordered = True
if degenerate:
cmd_args.append('-degenerate')
if ordered:
cmd_args.append('-ordered')
if pairs:
cmd_args.append('-pairs')
cmd_args.append('-cutoff')
cmd_args.append(cutoff)
dim = sum([len(s) for s in strands])
nstrands = len(strands)
# Set up the input file and run the command
lines = self._multi_lines(strands, [max_size])
self._run('complexes', cmd_args, lines)
# Read the output from file(s)
if ordered:
ocx_lines = self._read_tempfile('complexes.ocx').split('\n')
# Process each lines
output = []
for line in ocx_lines:
if line and not line.startswith('%'):
data = line.split('\t')
energy = float(data[-1])
complexes = [int(d) for d in data[2:2 + nstrands]]
permutation = int(data[1])
output.append({'energy': energy, 'complex': complexes,
'permutation': permutation})
key_lines = self._read_tempfile('complexes.ocx-key').split('\n')
data_lines = [l for l in key_lines if not l.startswith('%')]
data_lines.pop()
for i, line in enumerate(data_lines):
data = line.split('\t')
keys = [int(d) for d in data[2:-1]]
output[i]['order'] = keys
if pairs:
epairs_data = self._read_tempfile('complexes.ocx-epairs')
pairslist = self._process_epairs(epairs_data)
for i, pairs in enumerate(pairslist):
output[i]['epairs'] = self._pairs_to_np(pairs, dim)
# TODO: add ocx-ppairs as well
if mfe:
mfe_data = self._read_tempfile('complexes.ocx-mfe')
if degenerate:
return NotImplementedError('Not implemented for complexes')
else:
mfe_output = self._process_mfe(mfe_data, complexes=True)
for i, mfedat in enumerate(mfe_output):
output[i]['mfe'] = mfedat['mfe']
output[i]['dotparens'] = mfedat['dotparens']
output[i]['pairlist'] = mfedat['pairlist']
else:
cx_lines = self._read_tempfile('complexes.cx').split('\n')
# Remove empty last line
cx_lines.pop()
output = []
for line in cx_lines:
if not line.startswith('%'):
data = line.split('\t')
energy = float(data[-1])
complexes = [int(d) for d in data[1:1 + len(strands)]]
output.append({'energy': energy, 'complex': complexes})
if pairs:
# Process epairs
epairs_data = self._read_tempfile('complexes.cx-epairs')
pairslist = self._process_epairs(epairs_data)
for i, pairs in enumerate(pairslist):
proba_mat = self._pairs_to_np(pairs, dim)
output[i]['epairs'] = proba_mat
# Add strands (for downstream concentrations)
for cx in output:
cx['strands'] = [s.copy() for s in strands]
return output | python | def complexes(self, strands, max_size, ordered=False, pairs=False,
mfe=False, cutoff=0.001, degenerate=False, temp=37.0,
pseudo=False, material=None, dangles='some', sodium=1.0,
magnesium=0.0):
'''
:param strands: Strands on which to run energy. Strands must be either
coral.DNA or coral.RNA).
:type strands: list of coral.DNA or coral.RNA
:param max_size: Maximum complex size to consider (maximum number of
strand species in complex).
:type max_size: int
:param ordered: Consider distinct ordered complexes - all distinct
circular permutations of each complex.
:type ordered: bool
:param pairs: Calculate base-pairing observables as with .pairs().
:type pairs: bool
:param cutoff: A setting when pairs is set to True - only probabilities
above this threshold will be returned.
:type cutoff: float
:param degenerate: Applies only when \'mfe\' is set to True. If
set to True, the 'mfe' value associated with each
complex will be a list of degenerate MFEs (as in
the case of .mfe()).
:type degenerate: bool
:param temp: Temperature.
:type temp: float
:param pseudo: Enable pseudoknots.
:type pseudo: bool
:param material: The material setting to use in the computation. If set
to None (the default), the material type is inferred
from the strands. Other settings available: 'dna' for
DNA parameters, 'rna' for RNA (1995) parameters, and
'rna1999' for the RNA 1999 parameters.
:type material: str
:param dangles: How to treat dangles in the computation. From the
user guide: For \'none\': Dangle energies are ignored.
For \'some\': \'A dangle energy is incorporated for
each unpaired base flanking a duplex\'. For 'all': all
dangle energy is considered.
:type dangles: str
:param sodium: Sodium concentration in solution (molar), only applies
to DNA.
:type sodium: float
:param magnesium: Magnesium concentration in solution (molar), only
applies to DNA>
:type magnesium: float
:returns: A list of dictionaries containing at least 'energy',
'complex', and 'strands' keys. If 'ordered' is True, the
different possible ordered permutations of complexes are
considered. In addition, with 'ordered' set to True, an
additional 'order' key describing the exact order of strands
and a 'permutation' index (integer) are added. If 'pairs' is
True, there is an additional 'epairs' key containing the
base-pairing expectation values. If 'mfe' is selected, 'mfe,
'dotparens', and 'pairlist' keys in the same as .mfe(). In
addition, 'mfe' sets the -ordered flag, so the same keys as
when 'ordered' is set to True are added.
:rtype: float
'''
# TODO: Consider returning a pandas dataframe in this (and other)
# situations to make sorting/selection between results easier.
material = self._set_material(strands, material, multi=True)
cmd_args = self._prep_cmd_args(temp, dangles, material, pseudo, sodium,
magnesium, multi=False)
cmd_args.append('-quiet')
if mfe:
cmd_args.append('-mfe')
ordered = True
if degenerate:
cmd_args.append('-degenerate')
if ordered:
cmd_args.append('-ordered')
if pairs:
cmd_args.append('-pairs')
cmd_args.append('-cutoff')
cmd_args.append(cutoff)
dim = sum([len(s) for s in strands])
nstrands = len(strands)
# Set up the input file and run the command
lines = self._multi_lines(strands, [max_size])
self._run('complexes', cmd_args, lines)
# Read the output from file(s)
if ordered:
ocx_lines = self._read_tempfile('complexes.ocx').split('\n')
# Process each lines
output = []
for line in ocx_lines:
if line and not line.startswith('%'):
data = line.split('\t')
energy = float(data[-1])
complexes = [int(d) for d in data[2:2 + nstrands]]
permutation = int(data[1])
output.append({'energy': energy, 'complex': complexes,
'permutation': permutation})
key_lines = self._read_tempfile('complexes.ocx-key').split('\n')
data_lines = [l for l in key_lines if not l.startswith('%')]
data_lines.pop()
for i, line in enumerate(data_lines):
data = line.split('\t')
keys = [int(d) for d in data[2:-1]]
output[i]['order'] = keys
if pairs:
epairs_data = self._read_tempfile('complexes.ocx-epairs')
pairslist = self._process_epairs(epairs_data)
for i, pairs in enumerate(pairslist):
output[i]['epairs'] = self._pairs_to_np(pairs, dim)
# TODO: add ocx-ppairs as well
if mfe:
mfe_data = self._read_tempfile('complexes.ocx-mfe')
if degenerate:
return NotImplementedError('Not implemented for complexes')
else:
mfe_output = self._process_mfe(mfe_data, complexes=True)
for i, mfedat in enumerate(mfe_output):
output[i]['mfe'] = mfedat['mfe']
output[i]['dotparens'] = mfedat['dotparens']
output[i]['pairlist'] = mfedat['pairlist']
else:
cx_lines = self._read_tempfile('complexes.cx').split('\n')
# Remove empty last line
cx_lines.pop()
output = []
for line in cx_lines:
if not line.startswith('%'):
data = line.split('\t')
energy = float(data[-1])
complexes = [int(d) for d in data[1:1 + len(strands)]]
output.append({'energy': energy, 'complex': complexes})
if pairs:
# Process epairs
epairs_data = self._read_tempfile('complexes.cx-epairs')
pairslist = self._process_epairs(epairs_data)
for i, pairs in enumerate(pairslist):
proba_mat = self._pairs_to_np(pairs, dim)
output[i]['epairs'] = proba_mat
# Add strands (for downstream concentrations)
for cx in output:
cx['strands'] = [s.copy() for s in strands]
return output | [
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"pseudo... | :param strands: Strands on which to run energy. Strands must be either
coral.DNA or coral.RNA).
:type strands: list of coral.DNA or coral.RNA
:param max_size: Maximum complex size to consider (maximum number of
strand species in complex).
:type max_size: int
:param ordered: Consider distinct ordered complexes - all distinct
circular permutations of each complex.
:type ordered: bool
:param pairs: Calculate base-pairing observables as with .pairs().
:type pairs: bool
:param cutoff: A setting when pairs is set to True - only probabilities
above this threshold will be returned.
:type cutoff: float
:param degenerate: Applies only when \'mfe\' is set to True. If
set to True, the 'mfe' value associated with each
complex will be a list of degenerate MFEs (as in
the case of .mfe()).
:type degenerate: bool
:param temp: Temperature.
:type temp: float
:param pseudo: Enable pseudoknots.
:type pseudo: bool
:param material: The material setting to use in the computation. If set
to None (the default), the material type is inferred
from the strands. Other settings available: 'dna' for
DNA parameters, 'rna' for RNA (1995) parameters, and
'rna1999' for the RNA 1999 parameters.
:type material: str
:param dangles: How to treat dangles in the computation. From the
user guide: For \'none\': Dangle energies are ignored.
For \'some\': \'A dangle energy is incorporated for
each unpaired base flanking a duplex\'. For 'all': all
dangle energy is considered.
:type dangles: str
:param sodium: Sodium concentration in solution (molar), only applies
to DNA.
:type sodium: float
:param magnesium: Magnesium concentration in solution (molar), only
applies to DNA>
:type magnesium: float
:returns: A list of dictionaries containing at least 'energy',
'complex', and 'strands' keys. If 'ordered' is True, the
different possible ordered permutations of complexes are
considered. In addition, with 'ordered' set to True, an
additional 'order' key describing the exact order of strands
and a 'permutation' index (integer) are added. If 'pairs' is
True, there is an additional 'epairs' key containing the
base-pairing expectation values. If 'mfe' is selected, 'mfe,
'dotparens', and 'pairlist' keys in the same as .mfe(). In
addition, 'mfe' sets the -ordered flag, so the same keys as
when 'ordered' is set to True are added.
:rtype: float | [
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"... | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/analysis/_structure/nupack.py#L976-L1124 | train | Return a list of complexes for the base - pairing model. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(1817 - 1769) + chr(0b1101111) + chr(0b110001) + '\x37' + '\x33', 0b1000), nzTpIcepk0o8(chr(673 - 625) + chr(111) + '\062' + '\x30' + '\x31', 22474 - 22466), nzTpIcepk0o8('\x30' + '\157' + '\063' + chr(48), 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(1161 - 1111) + chr(2026 - 1976) + chr(0b10010 + 0o43), 23748 - 23740), nzTpIcepk0o8(chr(48) + '\157' + chr(0b10101 + 0o34) + '\x34' + '\x31', 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(0b110100 + 0o1) + '\060', 5160 - 5152), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(51) + '\063' + chr(0b110011 + 0o3), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(51) + chr(0b110111) + '\x36', ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(0b11010 + 0o27) + chr(0b110110) + '\x31', 37683 - 37675), nzTpIcepk0o8(chr(0b0 + 0o60) + chr(1840 - 1729) + '\066' + chr(0b1001 + 0o47), 0b1000), nzTpIcepk0o8('\060' + '\157' + '\x33' + '\064' + chr(0b110 + 0o52), 0o10), nzTpIcepk0o8('\060' + chr(2283 - 2172) + '\064' + '\064', 0o10), nzTpIcepk0o8('\x30' + chr(0b11011 + 0o124) + chr(0b110001) + chr(0b110101) + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110001) + '\064' + chr(51), 1786 - 1778), nzTpIcepk0o8(chr(1380 - 1332) + chr(0b1010010 + 0o35) + '\063' + chr(51) + chr(0b110011), ord("\x08")), nzTpIcepk0o8(chr(56 - 8) + '\x6f' + chr(0b11001 + 0o34) + chr(662 - 612), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b101101 + 0o4) + chr(48) + chr(0b110011), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1000011 + 0o54) + chr(2466 - 2415) + '\x36' + '\x31', 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110001) + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(1852 - 1804) + chr(0b1010010 + 0o35) + '\x33' + chr(2271 - 2219), 41421 - 41413), nzTpIcepk0o8('\060' + chr(0b100111 + 0o110) + chr(51) + '\061' + chr(55), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x33' + '\x31' + chr(48), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(51) + chr(54) + chr(0b110100), 0o10), nzTpIcepk0o8('\060' + chr(111) + '\x34' + chr(1081 - 1029), 8), nzTpIcepk0o8('\x30' + chr(111) + '\066' + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(0b110 + 0o52) + chr(3204 - 3093) + chr(0b10101 + 0o37) + chr(0b1000 + 0o53), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1000110 + 0o51) + '\061' + chr(54) + '\x34', ord("\x08")), nzTpIcepk0o8(chr(1489 - 1441) + chr(111) + chr(51) + chr(0b1001 + 0o53), 8), nzTpIcepk0o8('\x30' + '\157' + '\x32' + chr(1286 - 1233) + chr(0b110110), 0b1000), nzTpIcepk0o8(chr(1039 - 991) + chr(6447 - 6336) + chr(0b100011 + 0o17) + chr(1230 - 1177) + '\061', 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(50) + '\061' + chr(0b110101), 60593 - 60585), nzTpIcepk0o8('\060' + chr(1095 - 984) + chr(52) + chr(0b10000 + 0o45), ord("\x08")), nzTpIcepk0o8(chr(169 - 121) + '\157' + chr(0b110011) + chr(437 - 386) + chr(48), 0o10), nzTpIcepk0o8(chr(0b11101 + 0o23) + chr(6648 - 6537) + chr(595 - 546) + chr(553 - 503) + '\x34', 0b1000), nzTpIcepk0o8('\060' + '\x6f' + '\061' + chr(0b110001) + '\066', 0b1000), nzTpIcepk0o8('\060' + chr(0b1000111 + 0o50) + chr(2075 - 2026) + chr(0b110110) + chr(0b101010 + 0o7), 8), nzTpIcepk0o8(chr(0b101 + 0o53) + chr(0b1101111) + chr(1203 - 1153) + chr(2554 - 2502) + chr(52), 55711 - 55703), nzTpIcepk0o8('\060' + chr(0b100101 + 0o112) + chr(51) + chr(0b1011 + 0o52) + chr(52), 64143 - 64135), nzTpIcepk0o8(chr(0b10111 + 0o31) + '\x6f' + '\x32' + chr(0b100101 + 0o21) + '\x32', ord("\x08")), nzTpIcepk0o8(chr(1720 - 1672) + chr(0b1101111) + '\062' + chr(1603 - 1555) + chr(1622 - 1569), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110101) + chr(0b101001 + 0o7), 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'U'), chr(0b110100 + 0o60) + '\x65' + '\143' + chr(111) + chr(0b1011001 + 0o13) + '\145')(chr(1038 - 921) + chr(5920 - 5804) + chr(3769 - 3667) + chr(0b101101) + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def pVuUNS2vziT1(hXMPsSrOQzbh, r_D0HyqK4grO, QKiXFpVeEoZQ, BeOubuVvS_vx=nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(48), ord("\x08")), VxbmnfX6T_2s=nzTpIcepk0o8(chr(0b10001 + 0o37) + chr(4063 - 3952) + chr(48), 8), jszsUWiIS498=nzTpIcepk0o8(chr(0b10 + 0o56) + chr(10477 - 10366) + chr(48), 8), y_m39_E8rwSf=0.001, SUcYaF9gAJAW=nzTpIcepk0o8('\x30' + '\157' + '\x30', 8), bhvcCFR07maA=37.0, jif2BXBXDWe0=nzTpIcepk0o8(chr(1073 - 1025) + chr(11256 - 11145) + chr(0b101 + 0o53), 8), P6MCancmTVIW=None, dcIGdrKJIQqm=roI3spqORKae(ES5oEprVxulp(b'\x08\xeeu\xf0'), chr(8837 - 8737) + '\145' + '\x63' + chr(111) + '\x64' + '\x65')(chr(0b1001001 + 0o54) + chr(0b1110100) + chr(0b100101 + 0o101) + chr(0b11000 + 0o25) + '\070'), N53N20X2V9t8=1.0, _fwxLQ0Lh__w=0.0):
P6MCancmTVIW = hXMPsSrOQzbh._set_material(r_D0HyqK4grO, P6MCancmTVIW, multi=nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(49), 19323 - 19315))
zF8oFOtHDCse = hXMPsSrOQzbh._prep_cmd_args(bhvcCFR07maA, dcIGdrKJIQqm, P6MCancmTVIW, jif2BXBXDWe0, N53N20X2V9t8, _fwxLQ0Lh__w, multi=nzTpIcepk0o8(chr(0b11100 + 0o24) + chr(111) + chr(0b110000), 8))
roI3spqORKae(zF8oFOtHDCse, roI3spqORKae(ES5oEprVxulp(b'3\xd5K\xa1\x19O\x99\x91\x1b_\xb5\x11'), chr(0b1000001 + 0o43) + chr(0b1100101) + chr(99) + chr(0b10000 + 0o137) + chr(6098 - 5998) + '\145')('\x75' + '\164' + '\x66' + chr(0b101101) + chr(56)))(roI3spqORKae(ES5oEprVxulp(b'V\xf0m\xfc\x04\\'), chr(100) + '\x65' + chr(99) + chr(863 - 752) + chr(0b1100100) + chr(0b1100101))(chr(117) + chr(116) + '\x66' + chr(0b1010 + 0o43) + chr(0b1011 + 0o55)))
if jszsUWiIS498:
roI3spqORKae(zF8oFOtHDCse, roI3spqORKae(ES5oEprVxulp(b'3\xd5K\xa1\x19O\x99\x91\x1b_\xb5\x11'), '\x64' + chr(0b1100101) + '\x63' + chr(0b1101111) + '\144' + '\145')(chr(5951 - 5834) + chr(0b1000000 + 0o64) + '\x66' + chr(45) + chr(56)))(roI3spqORKae(ES5oEprVxulp(b'V\xec~\xf0'), chr(0b10010 + 0o122) + chr(8715 - 8614) + chr(99) + chr(111) + chr(0b1100100) + '\145')(chr(117) + chr(0b1000100 + 0o60) + '\146' + chr(0b110 + 0o47) + '\x38'))
BeOubuVvS_vx = nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\061', 8)
if SUcYaF9gAJAW:
roI3spqORKae(zF8oFOtHDCse, roI3spqORKae(ES5oEprVxulp(b'3\xd5K\xa1\x19O\x99\x91\x1b_\xb5\x11'), '\144' + '\x65' + '\x63' + '\157' + chr(0b1100100) + '\x65')('\165' + chr(9475 - 9359) + chr(2206 - 2104) + '\x2d' + '\x38'))(roI3spqORKae(ES5oEprVxulp(b'V\xe5}\xf2\x04F\xbb\x8c\x10D\x85'), '\144' + chr(0b1100101) + chr(0b11100 + 0o107) + chr(111) + chr(0b1100100) + chr(1036 - 935))('\165' + chr(1843 - 1727) + chr(9359 - 9257) + chr(45) + chr(0b11100 + 0o34)))
if BeOubuVvS_vx:
roI3spqORKae(zF8oFOtHDCse, roI3spqORKae(ES5oEprVxulp(b'3\xd5K\xa1\x19O\x99\x91\x1b_\xb5\x11'), '\144' + '\x65' + '\x63' + chr(111) + chr(0b1100100) + chr(101))('\165' + chr(0b1110100) + '\146' + chr(1434 - 1389) + chr(2614 - 2558)))(roI3spqORKae(ES5oEprVxulp(b'V\xeej\xf1\x04Z\xbb\x9a'), chr(0b1100100) + chr(101) + '\x63' + chr(111) + '\144' + '\145')(chr(0b1000100 + 0o61) + chr(116) + chr(0b1100110) + chr(45) + '\x38'))
if VxbmnfX6T_2s:
roI3spqORKae(zF8oFOtHDCse, roI3spqORKae(ES5oEprVxulp(b'3\xd5K\xa1\x19O\x99\x91\x1b_\xb5\x11'), '\144' + '\x65' + chr(0b101011 + 0o70) + '\x6f' + chr(0b1100100) + '\145')('\165' + chr(2630 - 2514) + chr(102) + chr(45) + chr(1378 - 1322)))(roI3spqORKae(ES5oEprVxulp(b'V\xf1y\xfc\x13['), chr(100) + chr(1749 - 1648) + chr(0b111111 + 0o44) + '\x6f' + '\x64' + '\x65')(chr(12830 - 12713) + chr(0b11001 + 0o133) + chr(0b1011110 + 0o10) + chr(1469 - 1424) + chr(0b10001 + 0o47)))
roI3spqORKae(zF8oFOtHDCse, roI3spqORKae(ES5oEprVxulp(b'3\xd5K\xa1\x19O\x99\x91\x1b_\xb5\x11'), '\144' + chr(0b1100101) + '\143' + chr(0b1000000 + 0o57) + chr(0b1100100) + chr(9980 - 9879))('\x75' + '\x74' + chr(0b1100110) + '\055' + '\x38'))(roI3spqORKae(ES5oEprVxulp(b'V\xe2m\xe1\x0eN\xb8'), chr(100) + '\145' + '\x63' + '\x6f' + '\144' + '\x65')('\165' + chr(0b1110100) + chr(102) + chr(45) + chr(0b111000)))
roI3spqORKae(zF8oFOtHDCse, roI3spqORKae(ES5oEprVxulp(b'3\xd5K\xa1\x19O\x99\x91\x1b_\xb5\x11'), chr(0b11110 + 0o106) + chr(0b100111 + 0o76) + '\x63' + '\x6f' + chr(4784 - 4684) + '\x65')(chr(0b1110101) + '\164' + chr(0b11111 + 0o107) + chr(0b101101) + '\070'))(y_m39_E8rwSf)
L5CH4CVaTec6 = oclC8DLjA_lV([ftfygxgFas5X(PmE5_h409JAA) for PmE5_h409JAA in r_D0HyqK4grO])
QGsyyLMqdxsU = ftfygxgFas5X(r_D0HyqK4grO)
vniSnlI09HNg = hXMPsSrOQzbh._multi_lines(r_D0HyqK4grO, [QKiXFpVeEoZQ])
roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x0c\xb9/\xad\x00\x19\xee\xcaC\x00\xa1\x10'), chr(0b101010 + 0o72) + chr(101) + chr(0b1100011) + '\x6f' + chr(0b1100011 + 0o1) + '\145')(chr(0b1110101) + chr(0b1011100 + 0o30) + '\x66' + '\x2d' + chr(0b111000)))(roI3spqORKae(ES5oEprVxulp(b'\x18\xeeu\xe5\rM\xa6\x9b\x02'), '\x64' + chr(101) + chr(0b10111 + 0o114) + chr(0b1000011 + 0o54) + chr(995 - 895) + chr(0b1100101))('\x75' + chr(6809 - 6693) + '\x66' + '\x2d' + chr(0b111000)), zF8oFOtHDCse, vniSnlI09HNg)
if BeOubuVvS_vx:
aShYXZyhIZZE = hXMPsSrOQzbh._read_tempfile(roI3spqORKae(ES5oEprVxulp(b'\x18\xeeu\xe5\rM\xa6\x9b\x02\x1e\x8fG\x15'), chr(100) + chr(0b1110 + 0o127) + '\x63' + chr(0b111111 + 0o60) + chr(0b100110 + 0o76) + chr(101))('\165' + '\164' + chr(0b1100110) + '\055' + chr(0b11100 + 0o34))).LfRrQOxuDvnC(roI3spqORKae(ES5oEprVxulp(b'q'), chr(3849 - 3749) + chr(6286 - 6185) + chr(1437 - 1338) + chr(0b1101111) + '\x64' + chr(6485 - 6384))(chr(1233 - 1116) + chr(0b11110 + 0o126) + '\x66' + chr(295 - 250) + chr(0b111000)))
toKQXlEvBKaK = []
for ffiOpFBWGmZU in aShYXZyhIZZE:
if ffiOpFBWGmZU and (not roI3spqORKae(ffiOpFBWGmZU, roI3spqORKae(ES5oEprVxulp(b'\x08\xf5y\xe7\x15[\xa9\x97\x05X'), '\x64' + chr(3134 - 3033) + '\x63' + chr(0b1101111) + chr(100) + '\x65')('\x75' + '\164' + chr(8169 - 8067) + chr(45) + chr(0b110 + 0o62)))(roI3spqORKae(ES5oEprVxulp(b'^'), chr(9936 - 9836) + chr(0b1001111 + 0o26) + chr(99) + chr(111) + chr(0b111001 + 0o53) + '\x65')(chr(0b1110101) + '\x74' + chr(134 - 32) + chr(1577 - 1532) + chr(3094 - 3038)))):
FfKOThdpoDTb = ffiOpFBWGmZU.LfRrQOxuDvnC(roI3spqORKae(ES5oEprVxulp(b'r'), '\144' + chr(101) + chr(0b1100011) + chr(0b101001 + 0o106) + chr(0b1011101 + 0o7) + chr(0b1100101))(chr(0b1100101 + 0o20) + chr(0b1110100) + chr(5042 - 4940) + chr(45) + chr(56)))
N74rCFbOFVLD = jLW6pRf2DSRk(FfKOThdpoDTb[-nzTpIcepk0o8(chr(48) + '\x6f' + chr(49), 8)])
pVuUNS2vziT1 = [nzTpIcepk0o8(vPPlOXQgR3SM) for vPPlOXQgR3SM in FfKOThdpoDTb[nzTpIcepk0o8(chr(0b10 + 0o56) + chr(0b1101111) + '\062', 44761 - 44753):nzTpIcepk0o8(chr(1295 - 1247) + chr(111) + '\062', 8) + QGsyyLMqdxsU]]
bmmTXKdBuMbO = nzTpIcepk0o8(FfKOThdpoDTb[nzTpIcepk0o8('\x30' + chr(7203 - 7092) + chr(0b110001), 8)])
roI3spqORKae(toKQXlEvBKaK, roI3spqORKae(ES5oEprVxulp(b'3\xd5K\xa1\x19O\x99\x91\x1b_\xb5\x11'), '\x64' + '\145' + '\143' + '\157' + chr(100) + chr(0b1100101))('\165' + '\x74' + '\x66' + chr(0b1111 + 0o36) + '\070'))({roI3spqORKae(ES5oEprVxulp(b'\x1e\xef}\xe7\x06Q'), '\144' + '\x65' + chr(4233 - 4134) + chr(0b1101111) + chr(0b1100100) + chr(0b1100100 + 0o1))(chr(0b1110101) + '\x74' + chr(102) + chr(949 - 904) + '\070'): N74rCFbOFVLD, roI3spqORKae(ES5oEprVxulp(b'\x18\xeeu\xe5\rM\xa6'), '\x64' + chr(7692 - 7591) + chr(99) + chr(0b1010011 + 0o34) + chr(0b1010 + 0o132) + chr(101))(chr(117) + '\164' + chr(0b1100110) + chr(45) + chr(56)): pVuUNS2vziT1, roI3spqORKae(ES5oEprVxulp(b'\x0b\xe4j\xf8\x14\\\xbf\x8a\x18_\x8e'), '\144' + chr(0b10111 + 0o116) + chr(0b0 + 0o143) + chr(0b1010100 + 0o33) + chr(100) + chr(0b101 + 0o140))(chr(117) + chr(0b11010 + 0o132) + chr(102) + chr(45) + chr(0b111000)): bmmTXKdBuMbO})
cWgIxKD8GydN = hXMPsSrOQzbh._read_tempfile(roI3spqORKae(ES5oEprVxulp(b'\x18\xeeu\xe5\rM\xa6\x9b\x02\x1e\x8fG\x15N\xb0O:'), chr(100) + chr(0b1100101) + chr(0b1001101 + 0o26) + chr(0b1001000 + 0o47) + chr(0b110110 + 0o56) + '\x65')(chr(0b1001101 + 0o50) + chr(0b1110100) + chr(102) + '\x2d' + '\070')).LfRrQOxuDvnC(roI3spqORKae(ES5oEprVxulp(b'q'), '\144' + chr(101) + '\x63' + '\x6f' + chr(0b101100 + 0o70) + '\145')('\165' + '\x74' + '\146' + '\055' + chr(56)))
zWrFex2hcHaX = [fPrVrKACaFCC for fPrVrKACaFCC in cWgIxKD8GydN if not fPrVrKACaFCC.startswith(roI3spqORKae(ES5oEprVxulp(b'^'), chr(0b1001000 + 0o34) + '\145' + chr(99) + chr(0b110000 + 0o77) + chr(3172 - 3072) + chr(101))(chr(117) + chr(0b1101111 + 0o5) + chr(102) + chr(45) + chr(3007 - 2951)))]
roI3spqORKae(zWrFex2hcHaX, roI3spqORKae(ES5oEprVxulp(b'\x0e\xc2G\xcc\x0eQ\xbc\x86Fz\xd0m'), '\144' + chr(101) + '\143' + chr(111) + chr(0b1100100) + chr(0b1000010 + 0o43))(chr(0b1110101) + chr(116) + chr(0b11011 + 0o113) + chr(1357 - 1312) + '\x38'))()
for (ZlbFMSG8gCoF, ffiOpFBWGmZU) in _kV_Bomx8PZ4(zWrFex2hcHaX):
FfKOThdpoDTb = ffiOpFBWGmZU.LfRrQOxuDvnC(roI3spqORKae(ES5oEprVxulp(b'r'), '\x64' + chr(0b10 + 0o143) + chr(99) + chr(0b1001 + 0o146) + chr(100) + chr(3642 - 3541))('\x75' + chr(116) + chr(102) + chr(0b10101 + 0o30) + '\x38'))
HOp0ZjSPeQln = [nzTpIcepk0o8(vPPlOXQgR3SM) for vPPlOXQgR3SM in FfKOThdpoDTb[nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110010), 8):-nzTpIcepk0o8(chr(48) + chr(0b1011011 + 0o24) + '\061', 8)]]
toKQXlEvBKaK[ZlbFMSG8gCoF][roI3spqORKae(ES5oEprVxulp(b'\x14\xf3|\xf0\x13'), '\144' + '\145' + chr(0b100000 + 0o103) + chr(0b1101111) + '\144' + '\x65')(chr(0b110101 + 0o100) + chr(116) + '\146' + chr(0b101100 + 0o1) + chr(200 - 144))] = HOp0ZjSPeQln
if VxbmnfX6T_2s:
bBYbdJL1NbLg = hXMPsSrOQzbh._read_tempfile(roI3spqORKae(ES5oEprVxulp(b'\x18\xeeu\xe5\rM\xa6\x9b\x02\x1e\x8fG\x15N\xbeZ"\x98~o'), chr(0b1100100) + chr(101) + '\x63' + chr(0b1000111 + 0o50) + chr(0b100010 + 0o102) + '\145')(chr(4588 - 4471) + chr(5267 - 5151) + chr(0b1100110) + chr(45) + chr(0b101 + 0o63)))
WInkkKdJGrrO = hXMPsSrOQzbh._process_epairs(bBYbdJL1NbLg)
for (ZlbFMSG8gCoF, VxbmnfX6T_2s) in _kV_Bomx8PZ4(WInkkKdJGrrO):
toKQXlEvBKaK[ZlbFMSG8gCoF][roI3spqORKae(ES5oEprVxulp(b'\x1e\xf1y\xfc\x13['), chr(0b101101 + 0o67) + '\145' + '\x63' + '\x6f' + chr(0b1100100) + chr(0b1100101))(chr(117) + '\x74' + chr(102) + '\x2d' + chr(56))] = hXMPsSrOQzbh._pairs_to_np(VxbmnfX6T_2s, L5CH4CVaTec6)
if jszsUWiIS498:
vVW6d_sPyWGC = hXMPsSrOQzbh._read_tempfile(roI3spqORKae(ES5oEprVxulp(b'\x18\xeeu\xe5\rM\xa6\x9b\x02\x1e\x8fG\x15N\xb6L&'), '\x64' + '\x65' + chr(0b1001 + 0o132) + chr(0b1101111) + chr(199 - 99) + '\x65')('\165' + chr(0b1110100) + '\x66' + '\x2d' + chr(2098 - 2042)))
if SUcYaF9gAJAW:
return Y1otPTwLRJvi(roI3spqORKae(ES5oEprVxulp(b'5\xeel\xb5\x08E\xae\x92\x14]\x85J\x19\x06\xbf\n%\x9e~<\xac\xa7\x99T[F\x0cy\xdd'), '\x64' + chr(0b101001 + 0o74) + '\143' + chr(5215 - 5104) + '\144' + chr(0b1011001 + 0o14))('\165' + chr(13270 - 13154) + chr(102) + chr(0b101101) + chr(56)))
else:
IKinQUWZeuRq = hXMPsSrOQzbh._process_mfe(vVW6d_sPyWGC, complexes=nzTpIcepk0o8(chr(0b101011 + 0o5) + chr(11052 - 10941) + chr(0b10000 + 0o41), 8))
for (ZlbFMSG8gCoF, ad2P5rThnxUp) in _kV_Bomx8PZ4(IKinQUWZeuRq):
toKQXlEvBKaK[ZlbFMSG8gCoF][roI3spqORKae(ES5oEprVxulp(b'\x16\xe7}'), '\144' + chr(5911 - 5810) + chr(0b1011111 + 0o4) + '\x6f' + chr(0b1100100) + chr(101))('\165' + chr(116) + chr(0b1100110) + chr(45) + chr(1092 - 1036))] = ad2P5rThnxUp[roI3spqORKae(ES5oEprVxulp(b'\x16\xe7}'), chr(0b1100100) + chr(0b1100101) + chr(99) + chr(0b1101111 + 0o0) + chr(5331 - 5231) + chr(0b1100101))('\165' + '\x74' + chr(0b1100110) + chr(0b110 + 0o47) + '\070')]
toKQXlEvBKaK[ZlbFMSG8gCoF][roI3spqORKae(ES5oEprVxulp(b'\x1f\xeel\xe5\x00Z\xbb\x90\x02'), chr(0b1001101 + 0o27) + chr(101) + chr(99) + chr(0b1101111) + chr(0b1100100) + chr(0b1000000 + 0o45))(chr(0b1110101) + '\x74' + chr(3902 - 3800) + chr(0b11 + 0o52) + chr(0b111000))] = ad2P5rThnxUp[roI3spqORKae(ES5oEprVxulp(b'\x1f\xeel\xe5\x00Z\xbb\x90\x02'), chr(3414 - 3314) + '\x65' + chr(0b1010001 + 0o22) + '\157' + '\x64' + chr(0b1100101))(chr(0b1110101) + '\164' + chr(0b1100110) + '\055' + '\070')]
toKQXlEvBKaK[ZlbFMSG8gCoF][roI3spqORKae(ES5oEprVxulp(b'\x0b\xe0q\xe7\rA\xad\x8a'), '\x64' + chr(0b1100101) + chr(0b101101 + 0o66) + chr(0b100100 + 0o113) + chr(0b1100100) + chr(0b1100101 + 0o0))(chr(8488 - 8371) + chr(6322 - 6206) + '\146' + chr(45) + '\070')] = ad2P5rThnxUp[roI3spqORKae(ES5oEprVxulp(b'\x0b\xe0q\xe7\rA\xad\x8a'), '\144' + chr(101) + chr(99) + chr(111) + chr(0b1100100) + chr(0b10100 + 0o121))(chr(0b1110101) + chr(116) + '\x66' + '\x2d' + '\x38')]
else:
ZpjeYGju4WsM = hXMPsSrOQzbh._read_tempfile(roI3spqORKae(ES5oEprVxulp(b'\x18\xeeu\xe5\rM\xa6\x9b\x02\x1e\x83\\'), chr(0b1100100) + '\145' + chr(0b1101 + 0o126) + '\157' + chr(6093 - 5993) + chr(8653 - 8552))(chr(0b1110101) + chr(7438 - 7322) + '\146' + chr(0b101101) + chr(2347 - 2291))).LfRrQOxuDvnC(roI3spqORKae(ES5oEprVxulp(b'q'), '\x64' + chr(0b111111 + 0o46) + '\x63' + '\157' + chr(0b111001 + 0o53) + chr(101))(chr(1162 - 1045) + chr(0b0 + 0o164) + '\146' + chr(0b101101) + chr(2731 - 2675)))
roI3spqORKae(ZpjeYGju4WsM, roI3spqORKae(ES5oEprVxulp(b'\x0e\xc2G\xcc\x0eQ\xbc\x86Fz\xd0m'), chr(2173 - 2073) + chr(0b1001110 + 0o27) + chr(99) + chr(111) + chr(0b1000110 + 0o36) + chr(0b111101 + 0o50))('\x75' + chr(116) + chr(0b1100110) + '\x2d' + chr(56)))()
toKQXlEvBKaK = []
for ffiOpFBWGmZU in ZpjeYGju4WsM:
if not roI3spqORKae(ffiOpFBWGmZU, roI3spqORKae(ES5oEprVxulp(b'\x08\xf5y\xe7\x15[\xa9\x97\x05X'), '\144' + '\x65' + '\x63' + '\157' + chr(100) + chr(0b111100 + 0o51))(chr(0b100011 + 0o122) + '\x74' + chr(102) + chr(0b101101) + chr(56)))(roI3spqORKae(ES5oEprVxulp(b'^'), chr(1262 - 1162) + chr(2684 - 2583) + '\x63' + chr(3598 - 3487) + chr(100) + chr(0b1100101))(chr(117) + '\x74' + chr(0b1001011 + 0o33) + '\055' + chr(0b101111 + 0o11))):
FfKOThdpoDTb = ffiOpFBWGmZU.LfRrQOxuDvnC(roI3spqORKae(ES5oEprVxulp(b'r'), '\144' + '\x65' + chr(99) + chr(0b1010010 + 0o35) + chr(0b1001101 + 0o27) + chr(0b1100101))(chr(0b10101 + 0o140) + chr(116) + chr(102) + '\055' + chr(0b1010 + 0o56)))
N74rCFbOFVLD = jLW6pRf2DSRk(FfKOThdpoDTb[-nzTpIcepk0o8(chr(48) + chr(0b100000 + 0o117) + chr(2287 - 2238), 8)])
pVuUNS2vziT1 = [nzTpIcepk0o8(vPPlOXQgR3SM) for vPPlOXQgR3SM in FfKOThdpoDTb[nzTpIcepk0o8('\060' + '\157' + chr(0b101111 + 0o2), 8):nzTpIcepk0o8(chr(0b110000) + chr(11083 - 10972) + chr(0b110001 + 0o0), 8) + ftfygxgFas5X(r_D0HyqK4grO)]]
roI3spqORKae(toKQXlEvBKaK, roI3spqORKae(ES5oEprVxulp(b'3\xd5K\xa1\x19O\x99\x91\x1b_\xb5\x11'), '\x64' + '\x65' + chr(0b1100011) + '\157' + '\144' + chr(0b1100101))(chr(0b101110 + 0o107) + chr(0b1110100) + chr(0b100101 + 0o101) + chr(0b101101) + chr(56)))({roI3spqORKae(ES5oEprVxulp(b'\x1e\xef}\xe7\x06Q'), chr(0b101110 + 0o66) + chr(0b10000 + 0o125) + '\x63' + '\157' + '\x64' + '\145')('\x75' + chr(116) + chr(0b1 + 0o145) + chr(45) + chr(0b111000)): N74rCFbOFVLD, roI3spqORKae(ES5oEprVxulp(b'\x18\xeeu\xe5\rM\xa6'), chr(0b1100100) + chr(7104 - 7003) + '\x63' + '\x6f' + chr(100) + chr(101))(chr(0b100010 + 0o123) + chr(8519 - 8403) + chr(102) + '\x2d' + chr(0b100000 + 0o30)): pVuUNS2vziT1})
if VxbmnfX6T_2s:
bBYbdJL1NbLg = hXMPsSrOQzbh._read_tempfile(roI3spqORKae(ES5oEprVxulp(b'\x18\xeeu\xe5\rM\xa6\x9b\x02\x1e\x83\\@\x06\xabK*\x83\x7f'), chr(0b1100100) + chr(0b1100101) + chr(0b1100011) + chr(0b1101111) + chr(0b1100100) + chr(0b1100101))('\x75' + chr(0b1001000 + 0o54) + chr(2264 - 2162) + '\x2d' + chr(2248 - 2192)))
WInkkKdJGrrO = hXMPsSrOQzbh._process_epairs(bBYbdJL1NbLg)
for (ZlbFMSG8gCoF, VxbmnfX6T_2s) in _kV_Bomx8PZ4(WInkkKdJGrrO):
ApclCwdOMLe8 = hXMPsSrOQzbh._pairs_to_np(VxbmnfX6T_2s, L5CH4CVaTec6)
toKQXlEvBKaK[ZlbFMSG8gCoF][roI3spqORKae(ES5oEprVxulp(b'\x1e\xf1y\xfc\x13['), chr(0b1100100) + chr(4109 - 4008) + chr(0b1100010 + 0o1) + '\157' + chr(0b10110 + 0o116) + '\x65')('\x75' + '\164' + chr(2186 - 2084) + chr(45) + chr(56))] = ApclCwdOMLe8
for wnHYGPseufQF in toKQXlEvBKaK:
wnHYGPseufQF[roI3spqORKae(ES5oEprVxulp(b'\x08\xf5j\xf4\x0fL\xad'), '\144' + chr(0b1100101) + chr(0b1000110 + 0o35) + chr(0b101101 + 0o102) + chr(2326 - 2226) + chr(7616 - 7515))(chr(0b1110101) + chr(8474 - 8358) + chr(102) + chr(0b101101) + chr(0b111000))] = [PmE5_h409JAA.copy() for PmE5_h409JAA in r_D0HyqK4grO]
return toKQXlEvBKaK |
klavinslab/coral | coral/analysis/_structure/nupack.py | NUPACK.concentrations | def concentrations(self, complexes, concs, ordered=False, pairs=False,
cutoff=0.001, temp=37.0):
'''
:param complexes: A list of the type returned by the complexes()
method.
:type complexes: list
:param concs: The concentration(s) of each strand species in the
initial complex. If they are all the same, a single
float can be used here.
:type concs: list of floats or float
:param ordered: Consider distinct ordered complexes - all distinct
circular permutations of each complex.
:type ordered: bool
:param pairs: Calculate base-pairing observables as with .pairs().
:type pairs: bool
:param cutoff: A setting when pairs is set to True - only probabilities
above this threshold will be returned.
:type cutoff: float
:param temp: Temperature in C.
:type temp: float
:returns: A list of dictionaries containing (at least) a
'concentrations' key. If 'pairs' is True, an 'fpairs' key
is added.
:rtype: list
'''
# Check inputs
nstrands = len(complexes[0]['strands'])
try:
if len(concs) != nstrands:
raise ValueError('concs argument not same length as strands.')
except TypeError:
concs = [concs for i in range(len(complexes['strands']))]
# Set up command-line arguments
cmd_args = ['-quiet']
if ordered:
cmd_args.append('-ordered')
# Write .con file
with open(os.path.join(self._tempdir, 'concentrations.con')) as f:
f.writelines(concs)
# Write .cx or .ocx file
header = ['%t Number of strands: {}'.format(nstrands),
'%\tid\tsequence']
for i, strand in enumerate(complexes['strands']):
header.append('%\t{}\t{}'.format(i + 1, strand))
header.append('%\tT = {}'.format(temp))
body = []
for i, cx in enumerate(complexes):
permutation = '\t'.join(complexes['complex'])
line = '{}\t{}\t{}'.format(i + 1, permutation, complexes['energy'])
body.append(line)
if ordered:
cxfile = os.path.join(self._tempdir, 'concentrations.ocx')
else:
cxfile = os.path.join(self._tempdir, 'concentrations.cx')
with open(cxfile) as f:
f.writelines(header + body)
# Run 'concentrations'
self._run('concentrations', cmd_args, None)
# Parse the .eq (concentrations) file
eq_lines = self._read_tempfile('concentrations.eq').split('\n')
tsv_lines = [l for l in eq_lines if not l.startswith('%')]
output = []
for i, line in enumerate(tsv_lines):
# It's a TSV
data = line.split('\t')
# Column 0 is an index
# Columns 1-nstrands is the complex
cx = [int(c) for c in data[1:nstrands]]
# Column nstrands + 1 is the complex energy
# Column nstrands + 2 is the equilibrium concentration
eq = float(data[nstrands + 2])
output[i] = {'complex': cx, 'concentration': eq}
if pairs:
# Read the .fpairs file
pairs = self._read_tempfile('concentrations.fpairs')
pairs_tsv = [l for l in pairs.split('\n') if not l.startswith('%')]
# Remove first line (n complexes)
dim = int(pairs_tsv.pop(0))
pprob = [[int(p[0]), int(p[1]), float(p[2])] for p in pairs_tsv]
# Convert to augmented numpy matrix
fpairs_mat = self.pairs_to_np(pprob, dim)
for i, out in enumerate(output):
output[i]['fpairs'] = fpairs_mat
return output | python | def concentrations(self, complexes, concs, ordered=False, pairs=False,
cutoff=0.001, temp=37.0):
'''
:param complexes: A list of the type returned by the complexes()
method.
:type complexes: list
:param concs: The concentration(s) of each strand species in the
initial complex. If they are all the same, a single
float can be used here.
:type concs: list of floats or float
:param ordered: Consider distinct ordered complexes - all distinct
circular permutations of each complex.
:type ordered: bool
:param pairs: Calculate base-pairing observables as with .pairs().
:type pairs: bool
:param cutoff: A setting when pairs is set to True - only probabilities
above this threshold will be returned.
:type cutoff: float
:param temp: Temperature in C.
:type temp: float
:returns: A list of dictionaries containing (at least) a
'concentrations' key. If 'pairs' is True, an 'fpairs' key
is added.
:rtype: list
'''
# Check inputs
nstrands = len(complexes[0]['strands'])
try:
if len(concs) != nstrands:
raise ValueError('concs argument not same length as strands.')
except TypeError:
concs = [concs for i in range(len(complexes['strands']))]
# Set up command-line arguments
cmd_args = ['-quiet']
if ordered:
cmd_args.append('-ordered')
# Write .con file
with open(os.path.join(self._tempdir, 'concentrations.con')) as f:
f.writelines(concs)
# Write .cx or .ocx file
header = ['%t Number of strands: {}'.format(nstrands),
'%\tid\tsequence']
for i, strand in enumerate(complexes['strands']):
header.append('%\t{}\t{}'.format(i + 1, strand))
header.append('%\tT = {}'.format(temp))
body = []
for i, cx in enumerate(complexes):
permutation = '\t'.join(complexes['complex'])
line = '{}\t{}\t{}'.format(i + 1, permutation, complexes['energy'])
body.append(line)
if ordered:
cxfile = os.path.join(self._tempdir, 'concentrations.ocx')
else:
cxfile = os.path.join(self._tempdir, 'concentrations.cx')
with open(cxfile) as f:
f.writelines(header + body)
# Run 'concentrations'
self._run('concentrations', cmd_args, None)
# Parse the .eq (concentrations) file
eq_lines = self._read_tempfile('concentrations.eq').split('\n')
tsv_lines = [l for l in eq_lines if not l.startswith('%')]
output = []
for i, line in enumerate(tsv_lines):
# It's a TSV
data = line.split('\t')
# Column 0 is an index
# Columns 1-nstrands is the complex
cx = [int(c) for c in data[1:nstrands]]
# Column nstrands + 1 is the complex energy
# Column nstrands + 2 is the equilibrium concentration
eq = float(data[nstrands + 2])
output[i] = {'complex': cx, 'concentration': eq}
if pairs:
# Read the .fpairs file
pairs = self._read_tempfile('concentrations.fpairs')
pairs_tsv = [l for l in pairs.split('\n') if not l.startswith('%')]
# Remove first line (n complexes)
dim = int(pairs_tsv.pop(0))
pprob = [[int(p[0]), int(p[1]), float(p[2])] for p in pairs_tsv]
# Convert to augmented numpy matrix
fpairs_mat = self.pairs_to_np(pprob, dim)
for i, out in enumerate(output):
output[i]['fpairs'] = fpairs_mat
return output | [
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method.
:type complexes: list
:param concs: The concentration(s) of each strand species in the
initial complex. If they are all the same, a single
float can be used here.
:type concs: list of floats or float
:param ordered: Consider distinct ordered complexes - all distinct
circular permutations of each complex.
:type ordered: bool
:param pairs: Calculate base-pairing observables as with .pairs().
:type pairs: bool
:param cutoff: A setting when pairs is set to True - only probabilities
above this threshold will be returned.
:type cutoff: float
:param temp: Temperature in C.
:type temp: float
:returns: A list of dictionaries containing (at least) a
'concentrations' key. If 'pairs' is True, an 'fpairs' key
is added.
:rtype: list | [
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"strand... | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/analysis/_structure/nupack.py#L1149-L1242 | train | This method returns a list of dictionaries containing the concentrations of each complex. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(171 - 123) + chr(0b1010111 + 0o30) + chr(0b110011) + chr(1896 - 1842) + '\064', 0b1000), nzTpIcepk0o8('\060' + chr(111) + '\x31' + chr(0b110110) + '\062', 0b1000), nzTpIcepk0o8(chr(1578 - 1530) + chr(0b1101111) + chr(2250 - 2199) + '\x30' + '\x36', 1213 - 1205), nzTpIcepk0o8('\060' + chr(0b1110 + 0o141) + chr(0b1 + 0o62) + '\x37' + '\x34', 32819 - 32811), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110001) + chr(0b110110) + chr(0b1000 + 0o55), 0o10), nzTpIcepk0o8(chr(319 - 271) + chr(0b1011110 + 0o21) + '\063' + chr(2160 - 2109) + '\x36', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1100011 + 0o14) + '\062' + chr(0b101000 + 0o15) + chr(1085 - 1034), ord("\x08")), nzTpIcepk0o8('\x30' + chr(3008 - 2897) + chr(0b110011) + '\061' + chr(55), 0b1000), nzTpIcepk0o8(chr(0b100101 + 0o13) + '\157' + chr(1051 - 1000) + chr(53) + '\067', 52750 - 52742), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(50) + chr(1245 - 1190) + chr(0b110000), 0o10), nzTpIcepk0o8(chr(802 - 754) + chr(0b11 + 0o154) + chr(0b100001 + 0o21) + '\062' + '\x31', 0o10), nzTpIcepk0o8(chr(48) + chr(10447 - 10336) + chr(201 - 151) + chr(0b101010 + 0o13) + '\x30', 44342 - 44334), nzTpIcepk0o8('\060' + '\x6f' + chr(0b101011 + 0o13) + chr(0b11010 + 0o26), 0b1000), nzTpIcepk0o8(chr(48) + chr(10232 - 10121) + chr(1369 - 1316), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\064' + chr(0b101010 + 0o7), 44728 - 44720), nzTpIcepk0o8(chr(1668 - 1620) + chr(0b1001001 + 0o46) + chr(0b11000 + 0o32) + chr(0b100100 + 0o14) + chr(2293 - 2240), 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(0b10011 + 0o40) + '\x36' + '\062', 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(51) + chr(0b11001 + 0o27) + chr(2166 - 2113), 45429 - 45421), nzTpIcepk0o8(chr(0b110000) + chr(0b1010111 + 0o30) + '\x31' + chr(0b110110) + '\x33', 13173 - 13165), nzTpIcepk0o8(chr(48) + chr(3661 - 3550) + '\066' + '\067', ord("\x08")), nzTpIcepk0o8(chr(1560 - 1512) + chr(0b1101111) + chr(49) + chr(0b1001 + 0o55) + chr(0b10111 + 0o40), 0o10), nzTpIcepk0o8(chr(1070 - 1022) + chr(0b1101111) + chr(0b1 + 0o61) + chr(1313 - 1258), 0b1000), nzTpIcepk0o8(chr(0b11000 + 0o30) + '\157' + chr(0b10110 + 0o36) + chr(1696 - 1642), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1 + 0o156) + chr(49) + chr(51) + chr(0b110110), 50973 - 50965), nzTpIcepk0o8(chr(0b110000) + chr(0b1011110 + 0o21) + '\x31' + chr(49) + '\064', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1000100 + 0o53) + '\063' + chr(2459 - 2404) + '\x31', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(49) + chr(49) + chr(848 - 799), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(1344 - 1295) + chr(75 - 22) + chr(52), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x33' + chr(52) + '\065', 7428 - 7420), nzTpIcepk0o8(chr(48) + chr(111) + '\063' + chr(571 - 516) + '\x32', 0o10), nzTpIcepk0o8(chr(73 - 25) + '\x6f' + '\x33' + chr(0b110100) + '\064', 33976 - 33968), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x34' + '\x32', 0b1000), nzTpIcepk0o8(chr(1399 - 1351) + '\x6f' + chr(0b110011) + '\x30' + chr(2796 - 2742), 8), nzTpIcepk0o8(chr(48) + chr(10997 - 10886) + chr(2178 - 2129) + chr(2181 - 2131) + chr(1675 - 1625), 0o10), nzTpIcepk0o8(chr(2265 - 2217) + '\157' + '\x32' + chr(0b110101) + '\x36', 40954 - 40946), nzTpIcepk0o8(chr(48) + chr(0b1100100 + 0o13) + chr(0b110010) + chr(0b110100) + '\066', ord("\x08")), nzTpIcepk0o8(chr(0b100101 + 0o13) + chr(0b110101 + 0o72) + chr(1885 - 1836) + chr(1630 - 1582) + chr(0b100110 + 0o13), 0o10), nzTpIcepk0o8(chr(1932 - 1884) + '\157' + '\062' + chr(0b111 + 0o54) + '\x34', 0o10), nzTpIcepk0o8(chr(0b11111 + 0o21) + chr(0b101111 + 0o100) + chr(49) + chr(0b110100) + '\x30', 40456 - 40448), nzTpIcepk0o8('\060' + '\x6f' + chr(50) + chr(795 - 741) + chr(55), 34408 - 34400)][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + chr(4849 - 4738) + chr(53) + chr(48), 6788 - 6780)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xda'), chr(8743 - 8643) + chr(101) + '\143' + '\157' + chr(100) + '\145')(chr(117) + chr(116) + '\146' + '\055' + chr(750 - 694)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def folbSXYfYVv_(hXMPsSrOQzbh, pVuUNS2vziT1, lYJrZUKNh3zS, BeOubuVvS_vx=nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110000), 0b1000), VxbmnfX6T_2s=nzTpIcepk0o8(chr(48) + '\157' + chr(0b100100 + 0o14), 8), y_m39_E8rwSf=0.001, bhvcCFR07maA=37.0):
QGsyyLMqdxsU = ftfygxgFas5X(pVuUNS2vziT1[nzTpIcepk0o8(chr(0b100000 + 0o20) + chr(0b1000110 + 0o51) + chr(1909 - 1861), 8)][roI3spqORKae(ES5oEprVxulp(b'\x87\x06\xb4\x9d\x1b\xba\xd8'), chr(0b100100 + 0o100) + chr(101) + chr(0b10000 + 0o123) + chr(0b1101111) + chr(0b111 + 0o135) + chr(0b111 + 0o136))(chr(0b1110101) + '\x74' + chr(0b1100110) + chr(45) + '\x38')])
try:
if ftfygxgFas5X(lYJrZUKNh3zS) != QGsyyLMqdxsU:
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b"\x97\x1d\xa8\x9f\x06\xfe\xca\xbd\x88\xcd\xfc\xcd^q\x01\xeb\x9d\xb1SD\x16zC~ \x9c'\x0b\x91\x92\xc4C\xb5r\xdd\xd23\xfd\x0e\xd3\x87\\"), '\x64' + '\145' + chr(4548 - 4449) + chr(1359 - 1248) + chr(0b1011001 + 0o13) + chr(101))('\x75' + chr(116) + chr(6677 - 6575) + '\055' + chr(56)))
except jZIjKu8IFANs:
lYJrZUKNh3zS = [lYJrZUKNh3zS for ZlbFMSG8gCoF in bbT2xIe5pzk7(ftfygxgFas5X(pVuUNS2vziT1[roI3spqORKae(ES5oEprVxulp(b'\x87\x06\xb4\x9d\x1b\xba\xd8'), chr(0b10010 + 0o122) + chr(0b1100101) + '\x63' + chr(0b100011 + 0o114) + '\x64' + '\145')(chr(117) + chr(116) + '\146' + '\x2d' + chr(56))]))]
zF8oFOtHDCse = [roI3spqORKae(ES5oEprVxulp(b'\xd9\x03\xb3\x95\x10\xaa'), chr(100) + chr(2008 - 1907) + chr(0b1100011) + chr(0b110111 + 0o70) + '\x64' + '\x65')(chr(7339 - 7222) + '\164' + chr(102) + chr(45) + chr(1486 - 1430))]
if BeOubuVvS_vx:
roI3spqORKae(zF8oFOtHDCse, roI3spqORKae(ES5oEprVxulp(b'\xbc&\x95\xc8\r\xb9\xec\xa0\x85\xd7\xc4\x9d'), chr(0b111001 + 0o53) + chr(101) + chr(0b1100011) + chr(3624 - 3513) + '\144' + chr(0b100011 + 0o102))(chr(0b111101 + 0o70) + '\164' + chr(102) + chr(1127 - 1082) + '\070'))(roI3spqORKae(ES5oEprVxulp(b'\xd9\x1d\xb4\x98\x10\xac\xce\xab'), '\x64' + chr(0b1000 + 0o135) + chr(99) + chr(111) + '\144' + chr(2740 - 2639))('\165' + '\164' + '\146' + '\x2d' + chr(0b11100 + 0o34)))
with DnU3Rq9N5ala(roI3spqORKae(aHUqKstZLeS6.path, roI3spqORKae(ES5oEprVxulp(b'\xadF\xbf\xb1L\x9c\xc8\xa9\xbb\xfb\xdf\xd9'), chr(100) + chr(8873 - 8772) + chr(99) + chr(0b1101111) + chr(100) + '\145')('\165' + chr(0b1110100) + chr(0b1100110) + chr(0b101011 + 0o2) + '\070'))(roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xab\x06\xa3\x91\x05\xba\xc2\xbd'), '\144' + chr(101) + chr(99) + '\157' + '\x64' + chr(5656 - 5555))(chr(117) + chr(0b1110100) + chr(102) + chr(45) + '\070')), roI3spqORKae(ES5oEprVxulp(b'\x97\x1d\xa8\x9f\x10\xb0\xdf\xbd\x8e\xcc\xf8\xc7^v\x0f\xe6\x9d\xab'), chr(0b1111 + 0o125) + chr(0b1100101) + chr(0b1100011) + chr(0b1101111) + '\x64' + '\x65')('\165' + chr(0b1110100) + '\x66' + chr(0b101101) + '\x38'))) as _R8IKF5IwAfX:
roI3spqORKae(_R8IKF5IwAfX, roI3spqORKae(ES5oEprVxulp(b'\x83\x00\xaf\x88\x10\xb2\xc2\xa1\x8a\xcb'), chr(0b1100100) + chr(0b1011001 + 0o14) + chr(2975 - 2876) + chr(111) + chr(0b1110 + 0o126) + '\x65')(chr(117) + chr(116) + '\x66' + chr(892 - 847) + chr(0b111000)))(lYJrZUKNh3zS)
jkp_M8Pp8CIt = [roI3spqORKae(ES5oEprVxulp(b'\xd1\x06\xe6\xb2\x00\xb3\xc9\xaa\x9d\x98\xfe\xce\x10vU\xf7\x93\xab\x17DM7]#'), chr(100) + '\145' + chr(899 - 800) + chr(0b1100000 + 0o17) + chr(0b1100100) + '\145')('\165' + '\x74' + chr(5930 - 5828) + '\x2d' + chr(1949 - 1893)).q33KG3foQ_CJ(QGsyyLMqdxsU), roI3spqORKae(ES5oEprVxulp(b'\xd1{\xaf\x98|\xad\xce\xbe\x9a\xdd\xff\xcbU'), chr(0b1100100) + chr(0b1100101) + chr(1301 - 1202) + chr(10601 - 10490) + chr(100) + chr(2272 - 2171))(chr(0b1110101) + chr(576 - 460) + '\x66' + '\055' + chr(0b110001 + 0o7))]
for (ZlbFMSG8gCoF, sOvPdpw6JkD6) in _kV_Bomx8PZ4(pVuUNS2vziT1[roI3spqORKae(ES5oEprVxulp(b'\x87\x06\xb4\x9d\x1b\xba\xd8'), '\x64' + '\x65' + chr(0b110110 + 0o55) + chr(111) + '\x64' + chr(0b111111 + 0o46))('\x75' + chr(116) + chr(0b1011000 + 0o16) + chr(1503 - 1458) + '\x38')]):
roI3spqORKae(jkp_M8Pp8CIt, roI3spqORKae(ES5oEprVxulp(b'\xbc&\x95\xc8\r\xb9\xec\xa0\x85\xd7\xc4\x9d'), '\144' + chr(2146 - 2045) + chr(4600 - 4501) + '\x6f' + chr(100) + chr(0b1100101))(chr(1808 - 1691) + chr(1535 - 1419) + '\x66' + '\055' + '\x38'))(roI3spqORKae(roI3spqORKae(ES5oEprVxulp(b'\xd1{\xbd\x81|\xa5\xd6'), chr(9314 - 9214) + '\x65' + chr(0b1100010 + 0o1) + chr(0b1010110 + 0o31) + chr(792 - 692) + '\145')('\165' + chr(0b1110100) + chr(0b1100110) + chr(740 - 695) + '\x38'), roI3spqORKae(ES5oEprVxulp(b'\x85A\xf5\xb72\xed\xcd\xa0\xbe\xe7\xd2\xe2'), chr(100) + chr(0b1010011 + 0o22) + chr(4731 - 4632) + chr(111) + chr(9748 - 9648) + '\145')(chr(117) + '\164' + '\146' + chr(0b101101) + chr(1118 - 1062)))(ZlbFMSG8gCoF + nzTpIcepk0o8('\x30' + '\157' + '\x31', ord("\x08")), sOvPdpw6JkD6))
roI3spqORKae(jkp_M8Pp8CIt, roI3spqORKae(ES5oEprVxulp(b'\xbc&\x95\xc8\r\xb9\xec\xa0\x85\xd7\xc4\x9d'), chr(100) + chr(256 - 155) + '\143' + chr(111) + '\144' + '\x65')('\x75' + chr(3292 - 3176) + '\x66' + chr(45) + chr(0b111000)))(roI3spqORKae(roI3spqORKae(ES5oEprVxulp(b'\xd1{\x92\xdcH\xfe\xd0\xb2'), chr(0b1100100) + chr(101) + chr(99) + '\157' + chr(0b111011 + 0o51) + '\x65')(chr(117) + chr(0b110111 + 0o75) + '\146' + '\055' + chr(0b100001 + 0o27)), roI3spqORKae(ES5oEprVxulp(b'\x85A\xf5\xb72\xed\xcd\xa0\xbe\xe7\xd2\xe2'), '\144' + chr(101) + chr(99) + chr(0b1101111) + '\x64' + chr(101))(chr(117) + chr(0b1110100) + chr(0b1100110) + '\x2d' + chr(56)))(bhvcCFR07maA))
ryRPGaxqs24n = []
for (ZlbFMSG8gCoF, wnHYGPseufQF) in _kV_Bomx8PZ4(pVuUNS2vziT1):
bmmTXKdBuMbO = roI3spqORKae(ES5oEprVxulp(b'\xfd'), '\144' + chr(101) + chr(0b1001 + 0o132) + chr(0b1000010 + 0o55) + chr(100) + chr(0b1100101))(chr(0b111101 + 0o70) + chr(8416 - 8300) + '\146' + '\055' + '\x38').Y4yM9BcfTCNq(pVuUNS2vziT1[roI3spqORKae(ES5oEprVxulp(b'\x97\x1d\xab\x8c\x19\xbb\xd3'), chr(0b1111 + 0o125) + '\145' + chr(0b101000 + 0o73) + '\157' + chr(0b1010110 + 0o16) + chr(101))('\x75' + '\164' + chr(0b101000 + 0o76) + chr(1887 - 1842) + chr(0b111000))])
ffiOpFBWGmZU = roI3spqORKae(ES5oEprVxulp(b'\x8f\x0f\xcf\x87\x08\xd7\xd0\xb2'), chr(100) + chr(0b1100101) + chr(0b1100011) + chr(2534 - 2423) + chr(0b11100 + 0o110) + '\x65')('\x75' + chr(116) + chr(102) + chr(1773 - 1728) + chr(0b110011 + 0o5)).q33KG3foQ_CJ(ZlbFMSG8gCoF + nzTpIcepk0o8(chr(48) + chr(4224 - 4113) + chr(0b111 + 0o52), 8), bmmTXKdBuMbO, pVuUNS2vziT1[roI3spqORKae(ES5oEprVxulp(b'\x91\x1c\xa3\x8e\x12\xa7'), '\144' + chr(4044 - 3943) + chr(0b101000 + 0o73) + chr(0b11101 + 0o122) + '\144' + chr(2053 - 1952))(chr(117) + chr(116) + '\x66' + chr(1121 - 1076) + chr(0b111000))])
roI3spqORKae(ryRPGaxqs24n, roI3spqORKae(ES5oEprVxulp(b'\xbc&\x95\xc8\r\xb9\xec\xa0\x85\xd7\xc4\x9d'), chr(100) + chr(4972 - 4871) + '\143' + chr(0b11111 + 0o120) + chr(0b1001100 + 0o30) + '\x65')('\x75' + '\x74' + chr(102) + chr(0b101101) + '\x38'))(ffiOpFBWGmZU)
if BeOubuVvS_vx:
CR1B25s92kqV = aHUqKstZLeS6.path.Y4yM9BcfTCNq(hXMPsSrOQzbh._tempdir, roI3spqORKae(ES5oEprVxulp(b'\x97\x1d\xa8\x9f\x10\xb0\xdf\xbd\x8e\xcc\xf8\xc7^v\x0f\xea\x91\xbd'), '\144' + chr(0b101010 + 0o73) + chr(99) + '\157' + chr(0b100111 + 0o75) + '\145')(chr(0b1010110 + 0o37) + '\x74' + '\146' + '\x2d' + chr(0b11011 + 0o35)))
else:
CR1B25s92kqV = aHUqKstZLeS6.path.Y4yM9BcfTCNq(hXMPsSrOQzbh._tempdir, roI3spqORKae(ES5oEprVxulp(b'\x97\x1d\xa8\x9f\x10\xb0\xdf\xbd\x8e\xcc\xf8\xc7^v\x0f\xe6\x8a'), chr(7070 - 6970) + chr(101) + chr(0b1100 + 0o127) + '\157' + chr(100) + chr(0b1000 + 0o135))('\x75' + chr(116) + chr(102) + chr(45) + chr(0b101110 + 0o12)))
with DnU3Rq9N5ala(CR1B25s92kqV) as _R8IKF5IwAfX:
roI3spqORKae(_R8IKF5IwAfX, roI3spqORKae(ES5oEprVxulp(b'\x83\x00\xaf\x88\x10\xb2\xc2\xa1\x8a\xcb'), chr(0b1100100) + '\x65' + chr(0b1110 + 0o125) + chr(111) + '\144' + chr(0b1100101))(chr(0b1110101) + '\x74' + chr(0b0 + 0o146) + chr(1453 - 1408) + '\x38'))(jkp_M8Pp8CIt + ryRPGaxqs24n)
roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x83J\xf1\xc4\x14\xef\x9b\xfb\xdd\x88\xd0\x9c'), chr(100) + chr(101) + chr(0b1011 + 0o130) + chr(0b1101111) + '\x64' + chr(101))('\165' + chr(0b1110 + 0o146) + chr(0b1000010 + 0o44) + chr(45) + chr(0b101000 + 0o20)))(roI3spqORKae(ES5oEprVxulp(b'\x97\x1d\xa8\x9f\x10\xb0\xdf\xbd\x8e\xcc\xf8\xc7^v'), chr(0b1 + 0o143) + '\x65' + '\x63' + '\x6f' + chr(4752 - 4652) + '\x65')(chr(0b1110101) + chr(0b1110100) + chr(1340 - 1238) + '\055' + chr(56)), zF8oFOtHDCse, None)
NaAbVC1KfhUQ = hXMPsSrOQzbh._read_tempfile(roI3spqORKae(ES5oEprVxulp(b'\x97\x1d\xa8\x9f\x10\xb0\xdf\xbd\x8e\xcc\xf8\xc7^v\x0f\xe0\x83'), chr(7241 - 7141) + '\x65' + chr(0b1100011) + '\157' + chr(617 - 517) + chr(6308 - 6207))(chr(9528 - 9411) + '\x74' + '\146' + chr(0b101101) + chr(2956 - 2900))).LfRrQOxuDvnC(roI3spqORKae(ES5oEprVxulp(b'\xfe'), chr(0b1100100) + chr(101) + '\143' + chr(111) + chr(3190 - 3090) + '\145')(chr(117) + chr(0b10 + 0o162) + chr(0b1100110) + '\055' + chr(0b100010 + 0o26)))
VyvPWQ5Z75B4 = [fPrVrKACaFCC for fPrVrKACaFCC in NaAbVC1KfhUQ if not fPrVrKACaFCC.startswith(roI3spqORKae(ES5oEprVxulp(b'\xd1'), chr(0b1010001 + 0o23) + '\145' + chr(9781 - 9682) + '\x6f' + '\144' + chr(4570 - 4469))(chr(11439 - 11322) + chr(0b1110100) + '\x66' + '\x2d' + '\x38'))]
toKQXlEvBKaK = []
for (ZlbFMSG8gCoF, ffiOpFBWGmZU) in _kV_Bomx8PZ4(VyvPWQ5Z75B4):
FfKOThdpoDTb = ffiOpFBWGmZU.LfRrQOxuDvnC(roI3spqORKae(ES5oEprVxulp(b'\xfd'), chr(0b111010 + 0o52) + '\x65' + '\x63' + chr(0b1101111) + chr(2360 - 2260) + '\x65')(chr(0b1110101) + chr(0b1110100) + chr(102) + chr(0b1000 + 0o45) + chr(56)))
wnHYGPseufQF = [nzTpIcepk0o8(teUmM7cKWZUa) for teUmM7cKWZUa in FfKOThdpoDTb[nzTpIcepk0o8('\060' + chr(4614 - 4503) + '\061', 8):QGsyyLMqdxsU]]
w3dGZFMKOIm_ = jLW6pRf2DSRk(FfKOThdpoDTb[QGsyyLMqdxsU + nzTpIcepk0o8(chr(48) + chr(0b1101100 + 0o3) + chr(50), 0b1000)])
toKQXlEvBKaK[ZlbFMSG8gCoF] = {roI3spqORKae(ES5oEprVxulp(b'\x97\x1d\xab\x8c\x19\xbb\xd3'), '\x64' + chr(0b1100101) + '\x63' + chr(10455 - 10344) + chr(100) + '\x65')(chr(0b1110101) + '\164' + '\x66' + chr(0b101101) + '\070'): wnHYGPseufQF, roI3spqORKae(ES5oEprVxulp(b'\x97\x1d\xa8\x9f\x10\xb0\xdf\xbd\x8e\xcc\xf8\xc7^'), '\144' + chr(0b1011 + 0o132) + chr(99) + chr(10092 - 9981) + chr(100) + chr(0b111101 + 0o50))(chr(0b1100000 + 0o25) + chr(7569 - 7453) + chr(3705 - 3603) + chr(45) + '\x38'): w3dGZFMKOIm_}
if VxbmnfX6T_2s:
VxbmnfX6T_2s = hXMPsSrOQzbh._read_tempfile(roI3spqORKae(ES5oEprVxulp(b'\x97\x1d\xa8\x9f\x10\xb0\xdf\xbd\x8e\xcc\xf8\xc7^v\x0f\xe3\x82\xa4\x1aE\x04'), chr(0b1111 + 0o125) + '\145' + chr(0b101100 + 0o67) + chr(111) + chr(100) + '\x65')(chr(0b1000100 + 0o61) + chr(0b1010001 + 0o43) + '\x66' + chr(0b101101) + '\070'))
Pab5DN5AeNLE = [fPrVrKACaFCC for fPrVrKACaFCC in VxbmnfX6T_2s.LfRrQOxuDvnC(roI3spqORKae(ES5oEprVxulp(b'\xfe'), '\144' + '\145' + chr(0b1100011) + '\157' + chr(100) + chr(0b1100101))('\x75' + '\164' + chr(102) + chr(1208 - 1163) + chr(0b100001 + 0o27))) if not fPrVrKACaFCC.startswith(roI3spqORKae(ES5oEprVxulp(b'\xd1'), chr(0b1100100) + chr(5096 - 4995) + chr(99) + chr(0b1101111) + '\x64' + '\x65')(chr(0b1110101) + '\x74' + chr(3386 - 3284) + chr(0b101 + 0o50) + chr(0b111000)))]
L5CH4CVaTec6 = nzTpIcepk0o8(Pab5DN5AeNLE.uC_Yoybx7J0I(nzTpIcepk0o8('\x30' + chr(10330 - 10219) + chr(732 - 684), 8)))
CPxvy9wnKNl9 = [[nzTpIcepk0o8(fSdw5wwLo9MO[nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(48), 8)]), nzTpIcepk0o8(fSdw5wwLo9MO[nzTpIcepk0o8(chr(48) + chr(12262 - 12151) + chr(1462 - 1413), 8)]), jLW6pRf2DSRk(fSdw5wwLo9MO[nzTpIcepk0o8('\060' + '\157' + chr(202 - 152), 8)])] for fSdw5wwLo9MO in Pab5DN5AeNLE]
v8FnMbu8cKac = hXMPsSrOQzbh.pairs_to_np(CPxvy9wnKNl9, L5CH4CVaTec6)
for (ZlbFMSG8gCoF, VwOu8WkJ9cpc) in _kV_Bomx8PZ4(toKQXlEvBKaK):
toKQXlEvBKaK[ZlbFMSG8gCoF][roI3spqORKae(ES5oEprVxulp(b'\x92\x02\xa7\x95\x07\xad'), chr(0b1100100) + chr(0b1100101) + chr(0b1100011) + chr(111) + '\x64' + chr(0b1011111 + 0o6))(chr(9114 - 8997) + chr(116) + chr(0b1100110) + '\x2d' + chr(0b101110 + 0o12))] = v8FnMbu8cKac
return toKQXlEvBKaK |
klavinslab/coral | coral/analysis/_structure/nupack.py | NUPACK.distributions | def distributions(self, complexes, counts, volume, maxstates=1e7,
ordered=False, temp=37.0):
'''Runs the \'distributions\' NUPACK command. Note: this is intended
for a relatively small number of species (on the order of ~20
total strands for complex size ~14).
:param complexes: A list of the type returned by the complexes()
method.
:type complexes: list
:param counts: A list of the exact number of molecules of each initial
species (the strands in the complexes command).
:type counts: list of ints
:param volume: The volume, in liters, of the container.
:type volume: float
:param maxstates: Maximum number of states to be enumerated, needed
as allowing too many states can lead to a segfault.
In NUPACK, this is referred to as lambda.
:type maxstates: float
:param ordered: Consider distinct ordered complexes - all distinct
circular permutations of each complex.
:type ordered: bool
:param temp: Temperature in C.
:type temp: float
:returns: A list of dictionaries containing (at least) a 'complexes'
key for the unique complex, an 'ev' key for the expected
value of the complex population and a 'probcols' list
indicating the probability that a given complex has
population 0, 1, ... max(pop) at equilibrium.
:rtype: list
:raises: LambdaError if maxstates is exceeded.
'''
# Check inputs
nstrands = len(complexes[0]['strands'])
if len(counts) != nstrands:
raise ValueError('counts argument not same length as strands.')
# Set up command-line arguments
cmd_args = []
if ordered:
cmd_args.append('-ordered')
# Write .count file
countpath = os.path.join(self._tempdir, 'distributions.count')
with open(countpath, 'w') as f:
f.writelines([str(c) for c in counts] + [str(volume)])
# Write .cx or .ocx file
header = ['%t Number of strands: {}'.format(nstrands),
'%\tid\tsequence']
for i, strand in enumerate(complexes['strands']):
header.append('%\t{}\t{}'.format(i + 1, strand))
header.append('%\tT = {}'.format(temp))
body = []
for i, cx in enumerate(complexes):
permutation = '\t'.join(complexes['complex'])
line = '{}\t{}\t{}'.format(i + 1, permutation, complexes['energy'])
body.append(line)
if ordered:
cxfile = os.path.join(self._tempdir, 'distributions.ocx')
else:
cxfile = os.path.join(self._tempdir, 'distributions.cx')
with open(cxfile) as f:
f.writelines(header + body)
# Run 'distributions'
stdout = self._run('distributions', cmd_args, None)
# Parse STDOUT
stdout_lines = stdout.split('\n')
if stdout_lines[0].startswith('Exceeded maximum number'):
raise LambdaError('Exceeded maxstates combinations.')
# pop_search = re.search('There are (*) pop', stdout_lines[0]).group(1)
# populations = int(pop_search)
# kT_search = re.search('of the box: (*) kT', stdout_lines[1]).group(1)
# kT = float(kT_search)
# Parse .dist file (comments header + TSV)
dist_lines = self._read_tempfile('distributions.dist').split('\n')
tsv_lines = [l for l in dist_lines if not l.startswith('%')]
tsv_lines.pop()
output = []
for i, line in enumerate(tsv_lines):
data = line.split('\t')
# Column 0 is an index
# Columns 1-nstrands are complexes
cx = [int(d) for d in data[1:nstrands]]
# Column nstrands + 1 is expected value of complex
ev = float(data[nstrands + 1])
# Columns nstrands + 2 and on are probability columns
probcols = [float(d) for d in data[nstrands + 2:]]
output[i]['complex'] = cx
output[i]['ev'] = ev
output[i]['probcols'] = probcols
return output | python | def distributions(self, complexes, counts, volume, maxstates=1e7,
ordered=False, temp=37.0):
'''Runs the \'distributions\' NUPACK command. Note: this is intended
for a relatively small number of species (on the order of ~20
total strands for complex size ~14).
:param complexes: A list of the type returned by the complexes()
method.
:type complexes: list
:param counts: A list of the exact number of molecules of each initial
species (the strands in the complexes command).
:type counts: list of ints
:param volume: The volume, in liters, of the container.
:type volume: float
:param maxstates: Maximum number of states to be enumerated, needed
as allowing too many states can lead to a segfault.
In NUPACK, this is referred to as lambda.
:type maxstates: float
:param ordered: Consider distinct ordered complexes - all distinct
circular permutations of each complex.
:type ordered: bool
:param temp: Temperature in C.
:type temp: float
:returns: A list of dictionaries containing (at least) a 'complexes'
key for the unique complex, an 'ev' key for the expected
value of the complex population and a 'probcols' list
indicating the probability that a given complex has
population 0, 1, ... max(pop) at equilibrium.
:rtype: list
:raises: LambdaError if maxstates is exceeded.
'''
# Check inputs
nstrands = len(complexes[0]['strands'])
if len(counts) != nstrands:
raise ValueError('counts argument not same length as strands.')
# Set up command-line arguments
cmd_args = []
if ordered:
cmd_args.append('-ordered')
# Write .count file
countpath = os.path.join(self._tempdir, 'distributions.count')
with open(countpath, 'w') as f:
f.writelines([str(c) for c in counts] + [str(volume)])
# Write .cx or .ocx file
header = ['%t Number of strands: {}'.format(nstrands),
'%\tid\tsequence']
for i, strand in enumerate(complexes['strands']):
header.append('%\t{}\t{}'.format(i + 1, strand))
header.append('%\tT = {}'.format(temp))
body = []
for i, cx in enumerate(complexes):
permutation = '\t'.join(complexes['complex'])
line = '{}\t{}\t{}'.format(i + 1, permutation, complexes['energy'])
body.append(line)
if ordered:
cxfile = os.path.join(self._tempdir, 'distributions.ocx')
else:
cxfile = os.path.join(self._tempdir, 'distributions.cx')
with open(cxfile) as f:
f.writelines(header + body)
# Run 'distributions'
stdout = self._run('distributions', cmd_args, None)
# Parse STDOUT
stdout_lines = stdout.split('\n')
if stdout_lines[0].startswith('Exceeded maximum number'):
raise LambdaError('Exceeded maxstates combinations.')
# pop_search = re.search('There are (*) pop', stdout_lines[0]).group(1)
# populations = int(pop_search)
# kT_search = re.search('of the box: (*) kT', stdout_lines[1]).group(1)
# kT = float(kT_search)
# Parse .dist file (comments header + TSV)
dist_lines = self._read_tempfile('distributions.dist').split('\n')
tsv_lines = [l for l in dist_lines if not l.startswith('%')]
tsv_lines.pop()
output = []
for i, line in enumerate(tsv_lines):
data = line.split('\t')
# Column 0 is an index
# Columns 1-nstrands are complexes
cx = [int(d) for d in data[1:nstrands]]
# Column nstrands + 1 is expected value of complex
ev = float(data[nstrands + 1])
# Columns nstrands + 2 and on are probability columns
probcols = [float(d) for d in data[nstrands + 2:]]
output[i]['complex'] = cx
output[i]['ev'] = ev
output[i]['probcols'] = probcols
return output | [
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"... | Runs the \'distributions\' NUPACK command. Note: this is intended
for a relatively small number of species (on the order of ~20
total strands for complex size ~14).
:param complexes: A list of the type returned by the complexes()
method.
:type complexes: list
:param counts: A list of the exact number of molecules of each initial
species (the strands in the complexes command).
:type counts: list of ints
:param volume: The volume, in liters, of the container.
:type volume: float
:param maxstates: Maximum number of states to be enumerated, needed
as allowing too many states can lead to a segfault.
In NUPACK, this is referred to as lambda.
:type maxstates: float
:param ordered: Consider distinct ordered complexes - all distinct
circular permutations of each complex.
:type ordered: bool
:param temp: Temperature in C.
:type temp: float
:returns: A list of dictionaries containing (at least) a 'complexes'
key for the unique complex, an 'ev' key for the expected
value of the complex population and a 'probcols' list
indicating the probability that a given complex has
population 0, 1, ... max(pop) at equilibrium.
:rtype: list
:raises: LambdaError if maxstates is exceeded. | [
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"size",... | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/analysis/_structure/nupack.py#L1245-L1343 | train | Runs the distributions NUPACK command. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8('\060' + chr(0b1101111) + '\x32' + chr(0b11001 + 0o36) + chr(0b110111), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(1749 - 1698) + '\x31' + '\x35', 40733 - 40725), nzTpIcepk0o8(chr(48) + chr(111) + '\x33' + chr(0b10010 + 0o45) + chr(2290 - 2239), 0b1000), nzTpIcepk0o8(chr(1695 - 1647) + '\157' + '\x31' + chr(0b110000) + chr(0b10101 + 0o37), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + '\x36' + '\063', 53158 - 53150), nzTpIcepk0o8(chr(0b1010 + 0o46) + chr(8708 - 8597) + chr(0b110011) + chr(0b110011) + chr(49), 8246 - 8238), nzTpIcepk0o8(chr(48) + '\157' + '\x37' + chr(52), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x32' + chr(2829 - 2774), 0o10), nzTpIcepk0o8('\060' + chr(7021 - 6910) + chr(0b11000 + 0o33) + chr(1416 - 1363) + '\060', 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x32' + chr(0b101100 + 0o13) + '\065', 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110001), 0b1000), nzTpIcepk0o8('\060' + '\157' + '\062' + chr(0b110010) + '\060', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b101010 + 0o11) + chr(0b110100) + chr(2239 - 2185), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(51) + chr(1402 - 1354) + '\064', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110001) + '\064' + chr(1084 - 1032), 0o10), nzTpIcepk0o8(chr(2243 - 2195) + '\157' + chr(49) + chr(53) + '\064', 0o10), nzTpIcepk0o8(chr(0b110000 + 0o0) + chr(0b10111 + 0o130) + chr(0b101101 + 0o5) + chr(0b1000 + 0o52), 57086 - 57078), nzTpIcepk0o8('\060' + chr(0b1011111 + 0o20) + chr(1071 - 1017) + '\x32', 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + '\063' + '\064' + chr(0b110011), 0o10), nzTpIcepk0o8(chr(814 - 766) + chr(111) + chr(50) + chr(1504 - 1455) + chr(1303 - 1254), 56103 - 56095), nzTpIcepk0o8(chr(48) + chr(111) + '\x32' + chr(2336 - 2286), 8), nzTpIcepk0o8('\x30' + chr(111) + chr(1809 - 1756) + chr(49), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110010 + 0o1) + chr(0b10001 + 0o40) + '\x36', 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b10011 + 0o37) + chr(50) + '\x31', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1010000 + 0o37) + '\061' + chr(2497 - 2447), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x33' + '\065' + chr(55), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(49), 8), nzTpIcepk0o8(chr(1037 - 989) + '\x6f' + chr(0b110011) + chr(2030 - 1982) + '\067', 0b1000), nzTpIcepk0o8(chr(0b10010 + 0o36) + chr(12150 - 12039) + chr(2280 - 2231) + chr(2676 - 2622) + chr(1491 - 1443), 0o10), nzTpIcepk0o8(chr(0b100111 + 0o11) + chr(4355 - 4244) + chr(0b110010) + '\x36' + chr(0b10110 + 0o34), 0o10), nzTpIcepk0o8('\060' + chr(6690 - 6579) + chr(0b1011 + 0o50) + chr(51) + '\064', 0b1000), nzTpIcepk0o8(chr(48) + '\157' + '\061' + chr(244 - 190) + chr(2158 - 2110), 8), nzTpIcepk0o8('\x30' + chr(0b1100110 + 0o11) + chr(50) + chr(49) + chr(339 - 289), 0b1000), nzTpIcepk0o8('\060' + chr(0b0 + 0o157) + chr(0b110111) + '\062', ord("\x08")), nzTpIcepk0o8('\060' + chr(8186 - 8075) + chr(0b100100 + 0o22) + chr(0b110001), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(50) + chr(0b10110 + 0o32) + chr(0b110000), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b11000 + 0o33) + '\x34' + chr(0b110011 + 0o0), 8), nzTpIcepk0o8('\060' + chr(5912 - 5801) + chr(49) + '\x31' + '\x33', 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(52) + '\067', ord("\x08")), nzTpIcepk0o8(chr(0b1101 + 0o43) + chr(111) + chr(329 - 278) + chr(222 - 170) + chr(2141 - 2093), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(7141 - 7030) + chr(0b110101) + '\x30', 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x91'), chr(100) + '\x65' + chr(99) + '\x6f' + '\144' + '\x65')('\165' + '\x74' + '\146' + chr(0b101101) + chr(0b1000 + 0o60)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def qjBntQNM7GdU(hXMPsSrOQzbh, pVuUNS2vziT1, gm2kNaWYNE_r, sbVhSlSPnlFP, BRVLeZ8XTQjM=10000000.0, BeOubuVvS_vx=nzTpIcepk0o8('\x30' + chr(11401 - 11290) + chr(0b11 + 0o55), 0b1000), bhvcCFR07maA=37.0):
QGsyyLMqdxsU = ftfygxgFas5X(pVuUNS2vziT1[nzTpIcepk0o8('\060' + chr(9310 - 9199) + chr(0b100100 + 0o14), 8)][roI3spqORKae(ES5oEprVxulp(b'\xcc\xb9\x89%]\xbdO'), chr(0b11110 + 0o106) + chr(0b1000001 + 0o44) + chr(0b1100011) + chr(0b11101 + 0o122) + chr(9461 - 9361) + chr(7896 - 7795))('\165' + '\x74' + '\x66' + chr(651 - 606) + chr(56))])
if ftfygxgFas5X(gm2kNaWYNE_r) != QGsyyLMqdxsU:
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'\xdc\xa2\x8e*G\xaa\x1cv\x9a\xdat\xfd\x83\xaa\x10L|]\x97\xa9aH\xa3\xf4*\x83d\xa9\x17\xc6\xb4P\xebI\x11\xf3\x979F\x8e\xdb\xbe\xd5'), '\144' + '\145' + '\x63' + '\x6f' + '\144' + chr(101))('\165' + '\164' + chr(1318 - 1216) + chr(848 - 803) + '\070'))
zF8oFOtHDCse = []
if BeOubuVvS_vx:
roI3spqORKae(zF8oFOtHDCse, roI3spqORKae(ES5oEprVxulp(b'\xf7\x99\xa8pK\xbe{x\x82\xd2T\xa5'), chr(0b1011111 + 0o5) + chr(101) + chr(99) + chr(0b1101111) + chr(9251 - 9151) + '\x65')(chr(117) + chr(7827 - 7711) + chr(9419 - 9317) + chr(45) + chr(871 - 815)))(roI3spqORKae(ES5oEprVxulp(b'\x92\xa2\x89 V\xabYs'), chr(0b1100100) + chr(101) + '\x63' + '\x6f' + chr(100) + chr(0b1001 + 0o134))('\x75' + chr(12804 - 12688) + '\146' + chr(0b101101) + chr(56)))
bnKZ8ayd1GYa = aHUqKstZLeS6.path.Y4yM9BcfTCNq(hXMPsSrOQzbh._tempdir, roI3spqORKae(ES5oEprVxulp(b'\xdb\xa4\x880A\xb0^b\x9c\xd4n\xfe\x95\xea\x07\x03g\\\x97'), '\x64' + '\145' + chr(596 - 497) + chr(0b1101111) + chr(0b1100100) + chr(0b1100101))(chr(0b1110101) + chr(0b1011011 + 0o31) + chr(102) + chr(78 - 33) + '\x38'))
with DnU3Rq9N5ala(bnKZ8ayd1GYa, roI3spqORKae(ES5oEprVxulp(b'\xc8'), chr(0b1100100) + chr(0b1010100 + 0o21) + chr(4280 - 4181) + '\x6f' + '\144' + chr(101))(chr(13202 - 13085) + '\164' + chr(0b1100110) + chr(45) + chr(56))) as _R8IKF5IwAfX:
roI3spqORKae(_R8IKF5IwAfX, roI3spqORKae(ES5oEprVxulp(b'\xc8\xbf\x920V\xb5Uy\x8d\xce'), chr(100) + chr(0b1100101) + '\x63' + '\157' + chr(9060 - 8960) + chr(0b1100101))('\x75' + chr(0b1110100) + '\x66' + chr(0b0 + 0o55) + chr(0b111000)))([N9zlRy29S1SS(teUmM7cKWZUa) for teUmM7cKWZUa in gm2kNaWYNE_r] + [N9zlRy29S1SS(sbVhSlSPnlFP)])
jkp_M8Pp8CIt = [roI3spqORKae(ES5oEprVxulp(b'\x9a\xb9\xdb\nF\xb4^r\x9a\x9dn\xf6\xc6\xb7\x10\x1es\\\x87\xfa(\t\xb5\xec'), chr(100) + '\145' + '\143' + chr(0b10101 + 0o132) + chr(0b10111 + 0o115) + '\145')(chr(12580 - 12463) + chr(0b1110100) + chr(0b1010 + 0o134) + '\x2d' + '\x38').q33KG3foQ_CJ(QGsyyLMqdxsU), roI3spqORKae(ES5oEprVxulp(b'\x9a\xc4\x92 :\xaaYf\x9d\xd8o\xf3\x83'), '\144' + chr(0b110000 + 0o65) + '\143' + '\157' + chr(100) + chr(0b1100101))(chr(0b1110101) + chr(116) + chr(1160 - 1058) + chr(0b10 + 0o53) + '\x38')]
for (ZlbFMSG8gCoF, sOvPdpw6JkD6) in _kV_Bomx8PZ4(pVuUNS2vziT1[roI3spqORKae(ES5oEprVxulp(b'\xcc\xb9\x89%]\xbdO'), '\144' + chr(0b1100101) + '\143' + chr(0b111011 + 0o64) + chr(2769 - 2669) + chr(101))('\x75' + chr(4772 - 4656) + chr(0b1000011 + 0o43) + chr(0b11000 + 0o25) + chr(0b101100 + 0o14))]):
roI3spqORKae(jkp_M8Pp8CIt, roI3spqORKae(ES5oEprVxulp(b'\xf7\x99\xa8pK\xbe{x\x82\xd2T\xa5'), chr(0b11 + 0o141) + chr(0b1100101) + chr(99) + chr(111) + chr(0b1100100) + chr(5768 - 5667))('\165' + chr(0b1110100) + chr(102) + chr(45) + chr(56)))(roI3spqORKae(roI3spqORKae(ES5oEprVxulp(b'\x9a\xc4\x809:\xa2A'), '\x64' + chr(0b100000 + 0o105) + '\x63' + '\157' + chr(100) + chr(0b1100101))(chr(11901 - 11784) + chr(0b1110100) + chr(0b111011 + 0o53) + '\055' + '\x38'), roI3spqORKae(ES5oEprVxulp(b'\xce\xfe\xc8\x0ft\xeaZx\xb9\xe2B\xda'), chr(100) + chr(101) + chr(0b1100011) + chr(0b1101111) + '\x64' + chr(0b1100101))('\x75' + chr(6216 - 6100) + chr(0b1100110) + chr(45) + chr(56)))(ZlbFMSG8gCoF + nzTpIcepk0o8(chr(1679 - 1631) + '\157' + chr(49), 8), sOvPdpw6JkD6))
roI3spqORKae(jkp_M8Pp8CIt, roI3spqORKae(ES5oEprVxulp(b'\xf7\x99\xa8pK\xbe{x\x82\xd2T\xa5'), chr(0b1000100 + 0o40) + '\145' + '\143' + chr(0b1101111) + '\144' + chr(855 - 754))(chr(0b1110101) + '\164' + '\146' + chr(0b101101) + chr(56)))(roI3spqORKae(roI3spqORKae(ES5oEprVxulp(b'\x9a\xc4\xafd\x0e\xf9Gj'), chr(100) + chr(0b1001001 + 0o34) + chr(99) + '\157' + chr(8519 - 8419) + chr(101))(chr(0b1010110 + 0o37) + '\164' + '\146' + chr(0b101101) + chr(0b111000)), roI3spqORKae(ES5oEprVxulp(b'\xce\xfe\xc8\x0ft\xeaZx\xb9\xe2B\xda'), chr(100) + chr(0b1100101) + chr(0b1011110 + 0o5) + chr(0b100100 + 0o113) + '\144' + '\x65')(chr(0b1110101) + chr(0b1001001 + 0o53) + chr(5488 - 5386) + chr(0b101101) + '\070'))(bhvcCFR07maA))
ryRPGaxqs24n = []
for (ZlbFMSG8gCoF, wnHYGPseufQF) in _kV_Bomx8PZ4(pVuUNS2vziT1):
bmmTXKdBuMbO = roI3spqORKae(ES5oEprVxulp(b'\xb6'), chr(0b101111 + 0o65) + '\145' + '\x63' + chr(0b101110 + 0o101) + chr(0b100000 + 0o104) + '\145')(chr(0b1100101 + 0o20) + '\164' + chr(2178 - 2076) + chr(0b101101) + '\x38').Y4yM9BcfTCNq(pVuUNS2vziT1[roI3spqORKae(ES5oEprVxulp(b'\xdc\xa2\x964_\xbcD'), chr(8094 - 7994) + chr(4402 - 4301) + chr(99) + chr(0b10010 + 0o135) + chr(0b1011100 + 0o10) + chr(6089 - 5988))(chr(7665 - 7548) + chr(116) + chr(102) + chr(0b1010 + 0o43) + chr(0b111000))])
ffiOpFBWGmZU = roI3spqORKae(ES5oEprVxulp(b'\xc4\xb0\xf2?N\xd0Gj'), '\x64' + chr(101) + '\143' + chr(0b1101111) + chr(5282 - 5182) + chr(0b1100101))('\x75' + chr(8738 - 8622) + chr(0b10101 + 0o121) + '\055' + '\x38').q33KG3foQ_CJ(ZlbFMSG8gCoF + nzTpIcepk0o8(chr(362 - 314) + chr(0b1010001 + 0o36) + '\x31', 8), bmmTXKdBuMbO, pVuUNS2vziT1[roI3spqORKae(ES5oEprVxulp(b'\xda\xa3\x9e6T\xa0'), chr(0b1000101 + 0o37) + chr(0b110111 + 0o56) + chr(0b1100011) + chr(0b110011 + 0o74) + '\x64' + '\x65')(chr(0b1110101) + chr(0b101011 + 0o111) + chr(0b1100110) + '\x2d' + chr(1284 - 1228))])
roI3spqORKae(ryRPGaxqs24n, roI3spqORKae(ES5oEprVxulp(b'\xf7\x99\xa8pK\xbe{x\x82\xd2T\xa5'), chr(0b1100100) + chr(0b1100101) + chr(0b1000110 + 0o35) + chr(5069 - 4958) + chr(100) + chr(0b1001101 + 0o30))(chr(0b1010101 + 0o40) + chr(12304 - 12188) + chr(0b10000 + 0o126) + '\x2d' + chr(56)))(ffiOpFBWGmZU)
if BeOubuVvS_vx:
CR1B25s92kqV = aHUqKstZLeS6.path.Y4yM9BcfTCNq(hXMPsSrOQzbh._tempdir, roI3spqORKae(ES5oEprVxulp(b'\xdb\xa4\x880A\xb0^b\x9c\xd4n\xfe\x95\xea\x0b\x0fj'), chr(0b1100100) + '\145' + '\143' + chr(908 - 797) + chr(100) + '\x65')(chr(0b110000 + 0o105) + '\x74' + chr(8048 - 7946) + '\055' + '\x38'))
else:
CR1B25s92kqV = aHUqKstZLeS6.path.Y4yM9BcfTCNq(hXMPsSrOQzbh._tempdir, roI3spqORKae(ES5oEprVxulp(b'\xdb\xa4\x880A\xb0^b\x9c\xd4n\xfe\x95\xea\x07\x14'), chr(0b101101 + 0o67) + chr(0b111110 + 0o47) + chr(0b1011011 + 0o10) + chr(0b1001 + 0o146) + chr(0b111 + 0o135) + chr(4595 - 4494))('\165' + '\164' + chr(9411 - 9309) + chr(0b101101) + chr(0b0 + 0o70)))
with DnU3Rq9N5ala(CR1B25s92kqV) as _R8IKF5IwAfX:
roI3spqORKae(_R8IKF5IwAfX, roI3spqORKae(ES5oEprVxulp(b'\xc8\xbf\x920V\xb5Uy\x8d\xce'), chr(0b100000 + 0o104) + chr(0b1100101) + '\143' + '\157' + chr(0b100100 + 0o100) + '\x65')(chr(0b1110101) + '\x74' + '\x66' + '\x2d' + '\070'))(jkp_M8Pp8CIt + ryRPGaxqs24n)
E4teKT3YJIcH = hXMPsSrOQzbh.w878a10420A4(roI3spqORKae(ES5oEprVxulp(b'\xdb\xa4\x880A\xb0^b\x9c\xd4n\xfe\x95'), chr(8304 - 8204) + chr(101) + chr(0b110100 + 0o57) + chr(0b1101111) + chr(0b110110 + 0o56) + chr(0b111111 + 0o46))(chr(0b1110101) + chr(116) + '\x66' + chr(0b101101) + '\070'), zF8oFOtHDCse, None)
c67wVwBZlnad = E4teKT3YJIcH.LfRrQOxuDvnC(roI3spqORKae(ES5oEprVxulp(b'\xb5'), chr(0b101011 + 0o71) + chr(101) + chr(0b1100011) + chr(0b1010010 + 0o35) + '\144' + '\x65')('\165' + chr(116) + chr(0b11001 + 0o115) + '\x2d' + chr(56)))
if roI3spqORKae(c67wVwBZlnad[nzTpIcepk0o8(chr(0b10000 + 0o40) + chr(8150 - 8039) + chr(0b110000), 8)], roI3spqORKae(ES5oEprVxulp(b'\xcc\xb9\x9a6G\xaaK~\x9c\xd5'), chr(0b10010 + 0o122) + '\x65' + chr(0b1100011) + chr(0b1101111) + chr(0b111 + 0o135) + '\145')('\165' + chr(6059 - 5943) + chr(0b1 + 0o145) + chr(45) + '\x38'))(roI3spqORKae(ES5oEprVxulp(b'\xfa\xb5\x98!V\xbdYs\xc8\xd0`\xe8\x8f\xa9\x11\x012\\\x96\xe4pL\xbc'), chr(4108 - 4008) + chr(2663 - 2562) + '\143' + '\x6f' + chr(0b1011111 + 0o5) + chr(0b1100101))(chr(117) + '\164' + '\x66' + chr(45) + '\070')):
raise imfWyifv1Z5z(roI3spqORKae(ES5oEprVxulp(b'\xfa\xb5\x98!V\xbdYs\xc8\xd0`\xe8\x95\xb0\x05\x18wA\xc3\xea}D\xac\xf8d\x8eu\xae\x1f\xdc\xaf^'), chr(6579 - 6479) + chr(7165 - 7064) + '\143' + chr(111) + chr(0b1011100 + 0o10) + chr(0b1100101))('\x75' + chr(116) + chr(0b10010 + 0o124) + chr(1001 - 956) + '\070'))
_7tzaw6wKXSl = hXMPsSrOQzbh._read_tempfile(roI3spqORKae(ES5oEprVxulp(b'\xdb\xa4\x880A\xb0^b\x9c\xd4n\xfe\x95\xea\x00\x05aF'), chr(0b111001 + 0o53) + '\x65' + chr(0b1000101 + 0o36) + chr(0b10111 + 0o130) + chr(1388 - 1288) + chr(0b1100101))(chr(117) + chr(0b1110100) + '\146' + chr(45) + '\070')).LfRrQOxuDvnC(roI3spqORKae(ES5oEprVxulp(b'\xb5'), chr(100) + chr(0b1100101) + '\x63' + '\157' + chr(1580 - 1480) + chr(0b1100101))(chr(117) + '\x74' + chr(0b101100 + 0o72) + '\x2d' + chr(56)))
VyvPWQ5Z75B4 = [fPrVrKACaFCC for fPrVrKACaFCC in _7tzaw6wKXSl if not fPrVrKACaFCC.startswith(roI3spqORKae(ES5oEprVxulp(b'\x9a'), chr(7381 - 7281) + chr(0b110 + 0o137) + chr(99) + chr(0b1101111) + chr(0b1100001 + 0o3) + chr(0b1100101))(chr(117) + '\164' + chr(0b1001000 + 0o36) + '\055' + '\x38'))]
roI3spqORKae(VyvPWQ5Z75B4, roI3spqORKae(ES5oEprVxulp(b'\xca\x8e\xa4\x1d\\\xa0^o\xdf\xf71\xd9'), chr(100) + chr(4003 - 3902) + chr(0b111 + 0o134) + '\157' + chr(9623 - 9523) + chr(0b1100101))(chr(0b1110101) + chr(10360 - 10244) + '\x66' + '\055' + '\070'))()
toKQXlEvBKaK = []
for (ZlbFMSG8gCoF, ffiOpFBWGmZU) in _kV_Bomx8PZ4(VyvPWQ5Z75B4):
FfKOThdpoDTb = ffiOpFBWGmZU.LfRrQOxuDvnC(roI3spqORKae(ES5oEprVxulp(b'\xb6'), '\x64' + '\x65' + chr(99) + '\157' + chr(0b1100100) + chr(0b1100101))('\165' + '\164' + chr(0b1010011 + 0o23) + chr(0b1001 + 0o44) + chr(56)))
wnHYGPseufQF = [nzTpIcepk0o8(vPPlOXQgR3SM) for vPPlOXQgR3SM in FfKOThdpoDTb[nzTpIcepk0o8(chr(0b100100 + 0o14) + chr(0b1101111) + chr(1579 - 1530), 8):QGsyyLMqdxsU]]
yEtjbPfxGrvU = jLW6pRf2DSRk(FfKOThdpoDTb[QGsyyLMqdxsU + nzTpIcepk0o8('\060' + chr(2408 - 2297) + chr(641 - 592), 8)])
D3yCWJJAqHeP = [jLW6pRf2DSRk(vPPlOXQgR3SM) for vPPlOXQgR3SM in FfKOThdpoDTb[QGsyyLMqdxsU + nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110010), 52608 - 52600):]]
toKQXlEvBKaK[ZlbFMSG8gCoF][roI3spqORKae(ES5oEprVxulp(b'\xdc\xa2\x964_\xbcD'), chr(0b111100 + 0o50) + chr(0b1100101) + chr(99) + '\157' + '\144' + chr(0b100110 + 0o77))('\x75' + '\164' + chr(5764 - 5662) + chr(45) + chr(2687 - 2631))] = wnHYGPseufQF
toKQXlEvBKaK[ZlbFMSG8gCoF][roI3spqORKae(ES5oEprVxulp(b'\xda\xbb'), '\144' + '\145' + '\143' + chr(0b111100 + 0o63) + chr(0b1011101 + 0o7) + chr(0b0 + 0o145))('\165' + '\x74' + chr(0b1100110) + chr(0b101001 + 0o4) + '\070')] = yEtjbPfxGrvU
toKQXlEvBKaK[ZlbFMSG8gCoF][roI3spqORKae(ES5oEprVxulp(b'\xcf\xbf\x94&P\xb6Pd'), '\x64' + '\145' + '\x63' + chr(0b1011011 + 0o24) + chr(0b11100 + 0o110) + chr(0b1100011 + 0o2))(chr(2334 - 2217) + chr(0b11110 + 0o126) + chr(0b1010001 + 0o25) + '\x2d' + '\x38')] = D3yCWJJAqHeP
return toKQXlEvBKaK |
klavinslab/coral | coral/analysis/_structure/nupack.py | NUPACK._multi_lines | def _multi_lines(self, strands, permutation):
'''Prepares lines to write to file for pfunc command input.
:param strand: Strand input (cr.DNA or cr.RNA).
:type strand: cr.DNA or cr.DNA
:param permutation: Permutation (e.g. [1, 2, 3, 4]) of the type used
by pfunc_multi.
:type permutation: list
'''
lines = []
# Write the total number of distinct strands
lines.append(str(len(strands)))
# Write the distinct strands
lines += [str(strand) for strand in strands]
# Write the permutation
lines.append(' '.join(str(p) for p in permutation))
return lines | python | def _multi_lines(self, strands, permutation):
'''Prepares lines to write to file for pfunc command input.
:param strand: Strand input (cr.DNA or cr.RNA).
:type strand: cr.DNA or cr.DNA
:param permutation: Permutation (e.g. [1, 2, 3, 4]) of the type used
by pfunc_multi.
:type permutation: list
'''
lines = []
# Write the total number of distinct strands
lines.append(str(len(strands)))
# Write the distinct strands
lines += [str(strand) for strand in strands]
# Write the permutation
lines.append(' '.join(str(p) for p in permutation))
return lines | [
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/analysis/_structure/nupack.py#L1346-L1363 | train | Prepares lines to write to file for command input. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(466 - 418) + chr(0b1101111) + chr(53) + chr(52), 0b1000), nzTpIcepk0o8(chr(48) + chr(482 - 371) + chr(0b110010) + chr(0b110110) + chr(48), 0b1000), nzTpIcepk0o8('\x30' + chr(6957 - 6846) + '\064', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b101101 + 0o102) + '\066' + '\x35', 25563 - 25555), nzTpIcepk0o8(chr(48) + '\157' + '\061' + chr(1091 - 1043) + '\063', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(49) + chr(0b110101) + chr(0b110011), 14099 - 14091), nzTpIcepk0o8('\060' + '\157' + '\061' + chr(2416 - 2362) + chr(0b1110 + 0o47), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(0b110010) + chr(2219 - 2170) + '\062', ord("\x08")), nzTpIcepk0o8(chr(0b10 + 0o56) + chr(7076 - 6965) + chr(0b101 + 0o56) + chr(52) + chr(1577 - 1528), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110010) + chr(51) + chr(0b11101 + 0o25), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(50) + chr(51) + chr(118 - 63), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1010110 + 0o31) + '\062' + chr(0b110010), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + '\x31' + chr(0b10100 + 0o36) + chr(0b101110 + 0o3), 0o10), nzTpIcepk0o8(chr(2234 - 2186) + chr(0b1101111 + 0o0) + '\061' + chr(0b110100) + '\060', 45057 - 45049), nzTpIcepk0o8(chr(0b100011 + 0o15) + chr(3251 - 3140) + chr(1949 - 1898) + chr(0b1101 + 0o47) + chr(396 - 344), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(49) + chr(0b110100) + '\x32', 63260 - 63252), nzTpIcepk0o8(chr(841 - 793) + chr(111) + chr(49) + chr(48) + chr(55), 25854 - 25846), nzTpIcepk0o8(chr(0b110000) + chr(0b100111 + 0o110) + chr(0b110011) + chr(48), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b1101 + 0o45) + chr(0b10011 + 0o42) + '\061', 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x32' + '\063' + chr(0b110110), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + '\067' + chr(0b110010), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b101011 + 0o6) + chr(2578 - 2526) + '\065', 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(50) + '\x30' + '\060', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(4938 - 4827) + chr(0b100000 + 0o21) + chr(0b110000) + chr(0b110100), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + '\x37', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(10884 - 10773) + chr(0b110011) + chr(0b1001 + 0o50) + chr(52), 0o10), nzTpIcepk0o8(chr(451 - 403) + '\157' + chr(879 - 829) + chr(345 - 296) + '\062', 8), nzTpIcepk0o8('\x30' + '\x6f' + '\x32' + '\x32' + chr(0b110010), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x32' + chr(0b10111 + 0o36) + '\062', ord("\x08")), nzTpIcepk0o8(chr(0b10011 + 0o35) + chr(9008 - 8897) + '\x31' + '\061' + chr(51), ord("\x08")), nzTpIcepk0o8(chr(2229 - 2181) + chr(0b1101111) + chr(0b11111 + 0o26) + '\063', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b111110 + 0o61) + chr(0b110010) + chr(0b110010) + chr(53), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(1733 - 1622) + chr(2181 - 2131) + '\064', ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(1754 - 1703) + '\066' + chr(0b1101 + 0o51), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(51) + '\062', ord("\x08")), nzTpIcepk0o8('\060' + chr(4371 - 4260) + chr(0b10011 + 0o44) + chr(2594 - 2542), 9237 - 9229), nzTpIcepk0o8('\x30' + chr(111) + chr(0b11010 + 0o35), 8), nzTpIcepk0o8('\x30' + chr(0b1101011 + 0o4) + chr(0b11011 + 0o30) + '\x30', 8), nzTpIcepk0o8('\x30' + '\157' + chr(639 - 588) + chr(0b110110 + 0o0) + chr(0b110110), 8), nzTpIcepk0o8(chr(1232 - 1184) + '\157' + chr(0b110011) + chr(0b1100 + 0o47) + chr(0b100000 + 0o26), 10819 - 10811)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b1100 + 0o44) + chr(0b11110 + 0o121) + chr(0b101001 + 0o14) + '\060', 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x02'), chr(6624 - 6524) + chr(0b1100101) + '\143' + '\157' + '\x64' + '\x65')('\x75' + chr(0b1011110 + 0o26) + '\x66' + '\x2d' + chr(88 - 32)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def M9cciJecyXGc(hXMPsSrOQzbh, r_D0HyqK4grO, bmmTXKdBuMbO):
vniSnlI09HNg = []
roI3spqORKae(vniSnlI09HNg, roI3spqORKae(ES5oEprVxulp(b"d\xe4W\x01;\x0c2\xe5\x8b\xf5\xca'"), '\144' + '\x65' + chr(6713 - 6614) + chr(0b1101111) + chr(0b1100100) + '\145')('\165' + '\164' + chr(0b100101 + 0o101) + '\x2d' + chr(56)))(N9zlRy29S1SS(ftfygxgFas5X(r_D0HyqK4grO)))
vniSnlI09HNg += [N9zlRy29S1SS(sOvPdpw6JkD6) for sOvPdpw6JkD6 in r_D0HyqK4grO]
roI3spqORKae(vniSnlI09HNg, roI3spqORKae(ES5oEprVxulp(b"d\xe4W\x01;\x0c2\xe5\x8b\xf5\xca'"), '\x64' + '\145' + chr(0b111000 + 0o53) + '\x6f' + chr(100) + chr(101))('\165' + chr(4703 - 4587) + chr(4212 - 4110) + chr(45) + '\070'))(roI3spqORKae(roI3spqORKae(ES5oEprVxulp(b'\x0c'), chr(4038 - 3938) + chr(101) + chr(99) + chr(0b1101111) + chr(0b1100100) + chr(101))(chr(117) + chr(0b1110100) + chr(102) + chr(0b101101) + '\070'), roI3spqORKae(ES5oEprVxulp(b'u\x84}xz)\x16\xec\xb5\xd9\xd1c'), chr(100) + chr(101) + '\x63' + chr(3818 - 3707) + chr(5587 - 5487) + '\x65')(chr(0b1001110 + 0o47) + chr(0b1110100) + chr(0b1100110) + chr(0b101101) + chr(56)))((N9zlRy29S1SS(fSdw5wwLo9MO) for fSdw5wwLo9MO in bmmTXKdBuMbO)))
return vniSnlI09HNg |
klavinslab/coral | coral/analysis/_structure/nupack.py | NUPACK._read_tempfile | def _read_tempfile(self, filename):
'''Read in and return file that's in the tempdir.
:param filename: Name of the file to read.
:type filename: str
'''
with open(os.path.join(self._tempdir, filename)) as f:
return f.read() | python | def _read_tempfile(self, filename):
'''Read in and return file that's in the tempdir.
:param filename: Name of the file to read.
:type filename: str
'''
with open(os.path.join(self._tempdir, filename)) as f:
return f.read() | [
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/analysis/_structure/nupack.py#L1366-L1374 | train | Read in and return file that s in the tempdir. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b100111 + 0o11) + '\x6f' + chr(0b110010) + chr(0b1000 + 0o50) + chr(55), 49345 - 49337), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b100001 + 0o22) + chr(0b110100) + chr(613 - 561), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(5356 - 5245) + chr(403 - 352) + '\x32' + chr(48), 0o10), nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(111) + chr(1267 - 1218) + '\063' + chr(0b11000 + 0o36), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(3388 - 3277) + chr(49) + '\x33' + chr(51), 0b1000), nzTpIcepk0o8('\x30' + chr(0b111111 + 0o60) + chr(0b110111) + '\064', 34147 - 34139), nzTpIcepk0o8(chr(48) + chr(11653 - 11542) + '\x32' + chr(0b10100 + 0o42) + chr(0b1101 + 0o44), 0o10), nzTpIcepk0o8(chr(0b100110 + 0o12) + chr(111) + chr(50) + chr(0b110101) + '\x34', ord("\x08")), nzTpIcepk0o8(chr(0b100 + 0o54) + chr(0b0 + 0o157) + chr(52), ord("\x08")), nzTpIcepk0o8('\060' + chr(10118 - 10007) + chr(0b110010) + chr(52) + chr(1168 - 1114), 0b1000), nzTpIcepk0o8(chr(0b10001 + 0o37) + chr(111) + chr(49) + '\x33' + chr(1041 - 990), 8), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(53) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(49) + '\061' + chr(52), 55894 - 55886), nzTpIcepk0o8(chr(162 - 114) + chr(0b1101111) + '\061' + chr(0b1100 + 0o52) + chr(0b110011 + 0o1), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(3653 - 3542) + '\063' + '\x34' + '\060', 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110101 + 0o2) + chr(1638 - 1587), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + '\062' + '\064' + chr(55), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(12029 - 11918) + '\063' + chr(1708 - 1654) + chr(0b101010 + 0o10), 44479 - 44471), nzTpIcepk0o8(chr(521 - 473) + '\157' + chr(50) + '\061' + chr(1856 - 1808), ord("\x08")), nzTpIcepk0o8(chr(0b101101 + 0o3) + chr(111) + chr(0b110011) + chr(0b110011) + '\x30', ord("\x08")), nzTpIcepk0o8(chr(785 - 737) + '\x6f' + '\061' + chr(55), ord("\x08")), nzTpIcepk0o8(chr(1054 - 1006) + '\x6f' + chr(53), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(1068 - 1018) + '\x30' + chr(0b110110), 0b1000), nzTpIcepk0o8(chr(1658 - 1610) + '\157' + chr(0b110110) + chr(0b10000 + 0o41), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + chr(0b110010) + '\063' + chr(0b101001 + 0o15), 10737 - 10729), nzTpIcepk0o8('\060' + chr(111) + chr(0b111 + 0o54) + chr(0b1101 + 0o45) + chr(0b110000), 8), nzTpIcepk0o8('\060' + chr(111) + chr(0b110100) + chr(53), 6580 - 6572), nzTpIcepk0o8(chr(0b101110 + 0o2) + chr(0b101000 + 0o107) + '\062' + chr(0b110110) + '\066', 0b1000), nzTpIcepk0o8('\060' + '\x6f' + '\063' + chr(53) + chr(0b110101), 0o10), nzTpIcepk0o8(chr(0b101110 + 0o2) + chr(7738 - 7627) + chr(0b110110) + chr(0b101100 + 0o10), 39989 - 39981), nzTpIcepk0o8(chr(179 - 131) + chr(2678 - 2567) + '\062' + chr(55) + chr(0b110110), 0o10), nzTpIcepk0o8(chr(1999 - 1951) + chr(111) + chr(653 - 600) + chr(48), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b101001 + 0o10) + chr(0b11110 + 0o31) + chr(2056 - 2001), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101 + 0o142) + chr(0b110010) + chr(0b110110), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(2114 - 2063) + '\061' + '\066', 9118 - 9110), nzTpIcepk0o8(chr(520 - 472) + chr(0b1001010 + 0o45) + chr(1217 - 1168) + '\067' + chr(1849 - 1799), 47591 - 47583), nzTpIcepk0o8(chr(791 - 743) + '\157' + '\x33' + chr(55) + '\x32', 18213 - 18205), nzTpIcepk0o8(chr(591 - 543) + chr(111) + '\x33' + chr(0b110011 + 0o3) + chr(0b110110), 54842 - 54834), nzTpIcepk0o8(chr(859 - 811) + chr(2237 - 2126) + '\062' + chr(0b101110 + 0o4) + chr(51), 23993 - 23985), nzTpIcepk0o8('\x30' + chr(3292 - 3181) + chr(0b101000 + 0o13) + chr(0b110110) + '\061', 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + chr(0b1101111) + '\x35' + '\060', 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xa9'), chr(0b110111 + 0o55) + '\x65' + chr(99) + chr(2352 - 2241) + chr(6532 - 6432) + '\145')(chr(117) + chr(0b101 + 0o157) + chr(9262 - 9160) + chr(1551 - 1506) + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def fztiz4KlnUzO(hXMPsSrOQzbh, FxZHtXEolYsL):
with DnU3Rq9N5ala(roI3spqORKae(aHUqKstZLeS6.path, roI3spqORKae(ES5oEprVxulp(b'\xde\xd0\xa9\x13b~\xd2\xcaP\xe5\x15]'), '\144' + chr(9892 - 9791) + chr(6838 - 6739) + chr(0b1101111) + chr(3110 - 3010) + '\x65')(chr(117) + '\164' + '\x66' + chr(45) + chr(0b101111 + 0o11)))(roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xd8\x90\xb53+X\xd8\xde'), '\x64' + chr(0b1100101) + '\x63' + '\x6f' + '\x64' + '\145')('\x75' + chr(0b1010 + 0o152) + chr(102) + '\x2d' + '\x38')), FxZHtXEolYsL)) as _R8IKF5IwAfX:
return roI3spqORKae(_R8IKF5IwAfX, roI3spqORKae(ES5oEprVxulp(b'\xe2\x8b\x8855t\x86\xf4Q\xc8lA'), '\x64' + chr(0b1100101) + chr(99) + chr(5584 - 5473) + chr(0b1011000 + 0o14) + '\145')('\165' + '\x74' + chr(7369 - 7267) + '\x2d' + chr(0b111000)))() |
klavinslab/coral | coral/analysis/_structure/nupack.py | NUPACK._pairs_to_np | def _pairs_to_np(self, pairlist, dim):
'''Given a set of pair probability lines, construct a numpy array.
:param pairlist: a list of pair probability triples
:type pairlist: list
:returns: An upper triangular matrix of pair probabilities augmented
with one extra column that represents the unpaired
probabilities.
:rtype: numpy.array
'''
mat = np.zeros((dim, dim + 1))
for line in pairlist:
i = int(line[0]) - 1
j = int(line[1]) - 1
prob = float(line[2])
mat[i, j] = prob
return mat | python | def _pairs_to_np(self, pairlist, dim):
'''Given a set of pair probability lines, construct a numpy array.
:param pairlist: a list of pair probability triples
:type pairlist: list
:returns: An upper triangular matrix of pair probabilities augmented
with one extra column that represents the unpaired
probabilities.
:rtype: numpy.array
'''
mat = np.zeros((dim, dim + 1))
for line in pairlist:
i = int(line[0]) - 1
j = int(line[1]) - 1
prob = float(line[2])
mat[i, j] = prob
return mat | [
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/analysis/_structure/nupack.py#L1376-L1393 | train | Given a set of pair probability lines construct a numpy array. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b11111 + 0o21) + chr(0b1011011 + 0o24) + '\x31' + '\067' + chr(51), ord("\x08")), nzTpIcepk0o8('\x30' + chr(843 - 732) + chr(54) + chr(1341 - 1292), 0b1000), nzTpIcepk0o8(chr(0b1111 + 0o41) + chr(0b1101111) + chr(0b100101 + 0o16) + chr(0b101110 + 0o5) + chr(0b110101), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b101011 + 0o7) + chr(0b110100) + chr(0b100100 + 0o16), 0b1000), nzTpIcepk0o8('\x30' + chr(7472 - 7361) + '\063' + '\x31' + chr(0b100100 + 0o17), 0o10), nzTpIcepk0o8(chr(838 - 790) + '\157' + '\x32' + '\x37' + chr(0b110111), 0o10), nzTpIcepk0o8(chr(0b10100 + 0o34) + chr(111) + chr(0b110000 + 0o2) + chr(386 - 336) + chr(0b110010), 31085 - 31077), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110001) + chr(55) + '\x37', 0o10), nzTpIcepk0o8('\060' + chr(0b10100 + 0o133) + '\x32' + '\x30' + '\061', ord("\x08")), nzTpIcepk0o8(chr(0b100001 + 0o17) + '\157' + chr(49) + '\x32' + chr(0b101100 + 0o11), 0b1000), nzTpIcepk0o8(chr(0b101001 + 0o7) + '\x6f' + chr(50) + '\060' + chr(48), ord("\x08")), nzTpIcepk0o8(chr(1599 - 1551) + '\157' + chr(51) + chr(0b101010 + 0o10) + chr(2090 - 2036), 36284 - 36276), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x34', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b10101 + 0o36) + chr(0b110101) + chr(51), 0b1000), nzTpIcepk0o8(chr(0b10111 + 0o31) + chr(0b10001 + 0o136) + chr(53) + '\x35', 40816 - 40808), nzTpIcepk0o8(chr(2179 - 2131) + chr(0b10101 + 0o132) + chr(50) + chr(1431 - 1381), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + '\061' + chr(50) + chr(0b1001 + 0o52), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(1281 - 1230), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + '\x31' + chr(0b110001) + '\066', 0b1000), nzTpIcepk0o8('\060' + chr(0b101010 + 0o105) + chr(138 - 89) + '\065' + chr(1955 - 1901), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(50) + chr(0b110111) + chr(970 - 922), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110001) + chr(1371 - 1323) + '\065', 0o10), nzTpIcepk0o8(chr(0b0 + 0o60) + chr(7812 - 7701) + chr(0b110111) + '\x33', 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(49) + chr(1180 - 1129) + '\x37', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(9104 - 8993) + '\061' + chr(0b110000) + chr(50), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(7908 - 7797) + chr(0b110001) + '\067' + chr(52), 29810 - 29802), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(49) + '\x30' + '\063', 0o10), nzTpIcepk0o8('\x30' + chr(1930 - 1819) + '\067' + '\067', 0b1000), nzTpIcepk0o8('\060' + chr(0b1111 + 0o140) + chr(50) + chr(2636 - 2583) + chr(48), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + '\062' + chr(640 - 585) + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + '\x37' + chr(49), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + '\062' + chr(0b111 + 0o53) + chr(50), 8), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x32' + '\x34' + '\064', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x31' + chr(0b110110) + '\065', 0o10), nzTpIcepk0o8(chr(48) + chr(8370 - 8259) + '\x33' + chr(1709 - 1656) + chr(0b101001 + 0o13), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1100010 + 0o15) + '\066' + chr(0b101011 + 0o12), 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(49) + '\x36' + '\x32', ord("\x08")), nzTpIcepk0o8(chr(865 - 817) + chr(111) + chr(0b110010) + chr(0b100 + 0o62) + chr(1246 - 1197), 34625 - 34617), nzTpIcepk0o8(chr(1519 - 1471) + chr(111) + '\062' + '\x33' + '\067', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110010) + '\x33' + chr(0b110001), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + '\157' + chr(2596 - 2543) + chr(2276 - 2228), ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'U'), chr(0b1011010 + 0o12) + chr(2217 - 2116) + '\143' + chr(7058 - 6947) + chr(0b1100100) + chr(101))(chr(0b1110101) + chr(116) + chr(6462 - 6360) + '\055' + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def FO7ZzMCid_Pf(hXMPsSrOQzbh, DS9tX9Lj5VA7, L5CH4CVaTec6):
K_Ma2k2FCM8b = nDF4gVNx0u9Q.UmwwEp7MzR6q((L5CH4CVaTec6, L5CH4CVaTec6 + nzTpIcepk0o8('\060' + chr(111) + chr(0b10101 + 0o34), 10709 - 10701)))
for ffiOpFBWGmZU in DS9tX9Lj5VA7:
ZlbFMSG8gCoF = nzTpIcepk0o8(ffiOpFBWGmZU[nzTpIcepk0o8('\x30' + '\157' + chr(2214 - 2166), 51717 - 51709)]) - nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(0b1100010 + 0o15) + chr(49), 8)
sChW4gUsXrIC = nzTpIcepk0o8(ffiOpFBWGmZU[nzTpIcepk0o8(chr(965 - 917) + chr(111) + chr(0b10010 + 0o37), 8)]) - nzTpIcepk0o8(chr(0b101111 + 0o1) + '\157' + chr(0b110001), 8)
FTVA28dcYVum = jLW6pRf2DSRk(ffiOpFBWGmZU[nzTpIcepk0o8(chr(0b10001 + 0o37) + chr(1084 - 973) + chr(50), 0o10)])
K_Ma2k2FCM8b[ZlbFMSG8gCoF, sChW4gUsXrIC] = FTVA28dcYVum
return K_Ma2k2FCM8b |
klavinslab/coral | coral/sequence/_dna.py | _flip_feature | def _flip_feature(self, feature, parent_len):
'''Adjust a feature's location when flipping DNA.
:param feature: The feature to flip.
:type feature: coral.Feature
:param parent_len: The length of the sequence to which the feature belongs.
:type parent_len: int
'''
copy = feature.copy()
# Put on the other strand
if copy.strand == 0:
copy.strand = 1
else:
copy.strand = 0
# Adjust locations - guarantee that start is always less than end
copy.start = parent_len - copy.start
copy.stop = parent_len - copy.stop
copy.start, copy.stop = copy.stop, copy.start
return copy | python | def _flip_feature(self, feature, parent_len):
'''Adjust a feature's location when flipping DNA.
:param feature: The feature to flip.
:type feature: coral.Feature
:param parent_len: The length of the sequence to which the feature belongs.
:type parent_len: int
'''
copy = feature.copy()
# Put on the other strand
if copy.strand == 0:
copy.strand = 1
else:
copy.strand = 0
# Adjust locations - guarantee that start is always less than end
copy.start = parent_len - copy.start
copy.stop = parent_len - copy.stop
copy.start, copy.stop = copy.stop, copy.start
return copy | [
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/sequence/_dna.py#L734-L753 | train | Flip a feature s location when flipping DNA. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b110000) + chr(0b100100 + 0o113) + chr(0b1011 + 0o52) + chr(0b11 + 0o63), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b111 + 0o56) + '\x37', ord("\x08")), nzTpIcepk0o8(chr(0b101101 + 0o3) + '\x6f' + chr(0b110101) + chr(0b110011), 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(50) + '\064' + chr(0b110100 + 0o0), ord("\x08")), nzTpIcepk0o8('\x30' + chr(2745 - 2634) + chr(0b11001 + 0o31) + chr(1856 - 1806) + chr(1368 - 1320), 19947 - 19939), nzTpIcepk0o8(chr(0b110000 + 0o0) + chr(5912 - 5801) + chr(0b110001) + chr(0b100 + 0o54) + chr(0b1010 + 0o53), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(1511 - 1460) + '\064' + chr(0b111 + 0o54), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(1366 - 1315) + chr(1604 - 1553) + '\064', 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + '\x36' + chr(0b1110 + 0o45), 0o10), nzTpIcepk0o8(chr(870 - 822) + chr(111) + chr(49) + chr(0b111 + 0o52) + chr(50), 0o10), nzTpIcepk0o8(chr(1053 - 1005) + '\x6f' + chr(0b101111 + 0o2) + chr(0b11100 + 0o30) + '\061', 0o10), nzTpIcepk0o8(chr(743 - 695) + chr(0b1101111) + '\061' + '\060' + chr(0b110101), 8), nzTpIcepk0o8('\x30' + '\x6f' + chr(2590 - 2537) + '\x36', 8), nzTpIcepk0o8(chr(0b10100 + 0o34) + chr(7544 - 7433) + chr(0b110010) + chr(0b10 + 0o64) + chr(0b1100 + 0o52), 0o10), nzTpIcepk0o8(chr(48) + '\157' + '\063' + chr(50) + '\x35', ord("\x08")), nzTpIcepk0o8(chr(1695 - 1647) + chr(0b1100 + 0o143) + chr(0b101000 + 0o12) + chr(1339 - 1289) + '\063', 0o10), nzTpIcepk0o8('\x30' + chr(11777 - 11666) + '\061' + chr(50) + chr(1466 - 1417), 54618 - 54610), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x33' + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b10100 + 0o37) + chr(53) + chr(55), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + '\x31' + chr(0b100010 + 0o23) + '\064', ord("\x08")), nzTpIcepk0o8(chr(685 - 637) + chr(3903 - 3792) + chr(0b110010) + chr(0b110001) + chr(55), 0o10), nzTpIcepk0o8(chr(211 - 163) + chr(111) + '\063' + '\066' + '\066', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b1010 + 0o47) + chr(489 - 434) + '\x37', 14613 - 14605), nzTpIcepk0o8('\x30' + '\157' + chr(823 - 768), 59874 - 59866), nzTpIcepk0o8(chr(48) + '\157' + chr(53) + '\x36', 8), nzTpIcepk0o8(chr(48) + '\x6f' + '\064' + chr(0b110011), 844 - 836), nzTpIcepk0o8('\060' + chr(7314 - 7203) + '\061' + chr(0b101 + 0o61) + '\067', 0o10), nzTpIcepk0o8(chr(1656 - 1608) + '\157' + '\063' + chr(794 - 746) + '\066', ord("\x08")), nzTpIcepk0o8(chr(0b100101 + 0o13) + chr(4832 - 4721) + chr(644 - 593) + '\067' + '\x32', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1000110 + 0o51) + chr(0b110011) + '\x37' + '\062', 8), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x32' + chr(1683 - 1635) + chr(0b110100 + 0o3), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1011110 + 0o21) + chr(49) + chr(54) + chr(0b1000 + 0o52), 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(49) + '\062' + chr(54), ord("\x08")), nzTpIcepk0o8(chr(1900 - 1852) + chr(11094 - 10983) + '\x31' + '\x33' + chr(50), 0b1000), nzTpIcepk0o8(chr(1878 - 1830) + chr(8693 - 8582) + chr(2017 - 1967) + '\x30' + chr(584 - 533), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(315 - 266) + chr(49) + '\x34', 11728 - 11720), nzTpIcepk0o8('\x30' + '\x6f' + '\063' + chr(51) + '\061', 0o10), nzTpIcepk0o8(chr(1592 - 1544) + '\x6f' + chr(0b110001) + chr(0b11101 + 0o24) + '\x32', 8), nzTpIcepk0o8(chr(0b11110 + 0o22) + chr(6284 - 6173) + chr(53) + chr(54), 8), nzTpIcepk0o8(chr(782 - 734) + chr(5075 - 4964) + '\061' + '\x30' + chr(53), 8)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + chr(0b1000001 + 0o56) + chr(2640 - 2587) + chr(0b101110 + 0o2), 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x00'), chr(4111 - 4011) + '\x65' + chr(0b100010 + 0o101) + chr(111) + chr(0b10010 + 0o122) + '\x65')(chr(0b1110101) + '\164' + chr(6299 - 6197) + chr(153 - 108) + chr(0b110111 + 0o1)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def Is42ITlbjPOM(hXMPsSrOQzbh, gNPUvMsk9RKn, wMnHN168dQmq):
aZTCj4v5QdfO = gNPUvMsk9RKn.copy()
if roI3spqORKae(aZTCj4v5QdfO, roI3spqORKae(ES5oEprVxulp(b']`]\xf4\xf45\x94\xeay!%s'), chr(100) + chr(1743 - 1642) + chr(6986 - 6887) + '\157' + chr(611 - 511) + chr(10027 - 9926))(chr(0b1110101) + chr(9552 - 9436) + '\146' + chr(45) + chr(0b110100 + 0o4))) == nzTpIcepk0o8(chr(0b100100 + 0o14) + '\157' + '\060', ord("\x08")):
aZTCj4v5QdfO.sOvPdpw6JkD6 = nzTpIcepk0o8(chr(334 - 286) + chr(0b100 + 0o153) + chr(413 - 364), 0b1000)
else:
aZTCj4v5QdfO.sOvPdpw6JkD6 = nzTpIcepk0o8(chr(0b101001 + 0o7) + '\157' + chr(48), 8)
aZTCj4v5QdfO.KQbHFTcl_LKy = wMnHN168dQmq - aZTCj4v5QdfO.KQbHFTcl_LKy
aZTCj4v5QdfO.dYJbBiYO_nGE = wMnHN168dQmq - aZTCj4v5QdfO.dYJbBiYO_nGE
(aZTCj4v5QdfO.KQbHFTcl_LKy, aZTCj4v5QdfO.dYJbBiYO_nGE) = (aZTCj4v5QdfO.dYJbBiYO_nGE, aZTCj4v5QdfO.KQbHFTcl_LKy)
return aZTCj4v5QdfO |
klavinslab/coral | coral/sequence/_dna.py | DNA.ape | def ape(self, ape_path=None):
'''Open in ApE if `ApE` is in your command line path.'''
# TODO: simplify - make ApE look in PATH only
cmd = 'ApE'
if ape_path is None:
# Check for ApE in PATH
ape_executables = []
for path in os.environ['PATH'].split(os.pathsep):
exepath = os.path.join(path, cmd)
ape_executables.append(os.access(exepath, os.X_OK))
if not any(ape_executables):
raise Exception('Ape not in PATH. Use ape_path kwarg.')
else:
cmd = ape_path
# Check whether ApE exists in PATH
tmp = tempfile.mkdtemp()
if self.name is not None and self.name:
filename = os.path.join(tmp, '{}.ape'.format(self.name))
else:
filename = os.path.join(tmp, 'tmp.ape')
coral.seqio.write_dna(self, filename)
process = subprocess.Popen([cmd, filename])
# Block until window is closed
try:
process.wait()
shutil.rmtree(tmp)
except KeyboardInterrupt:
shutil.rmtree(tmp) | python | def ape(self, ape_path=None):
'''Open in ApE if `ApE` is in your command line path.'''
# TODO: simplify - make ApE look in PATH only
cmd = 'ApE'
if ape_path is None:
# Check for ApE in PATH
ape_executables = []
for path in os.environ['PATH'].split(os.pathsep):
exepath = os.path.join(path, cmd)
ape_executables.append(os.access(exepath, os.X_OK))
if not any(ape_executables):
raise Exception('Ape not in PATH. Use ape_path kwarg.')
else:
cmd = ape_path
# Check whether ApE exists in PATH
tmp = tempfile.mkdtemp()
if self.name is not None and self.name:
filename = os.path.join(tmp, '{}.ape'.format(self.name))
else:
filename = os.path.join(tmp, 'tmp.ape')
coral.seqio.write_dna(self, filename)
process = subprocess.Popen([cmd, filename])
# Block until window is closed
try:
process.wait()
shutil.rmtree(tmp)
except KeyboardInterrupt:
shutil.rmtree(tmp) | [
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/sequence/_dna.py#L84-L111 | train | Open in ApE if ApE is in your command line path. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8('\x30' + '\157' + '\x31' + '\063', 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(0b110011) + chr(0b110001) + chr(278 - 224), 0o10), nzTpIcepk0o8('\060' + chr(0b100101 + 0o112) + chr(51) + chr(2277 - 2229), 37335 - 37327), nzTpIcepk0o8(chr(376 - 328) + chr(111) + chr(0b0 + 0o63) + chr(2606 - 2554) + '\063', 24778 - 24770), nzTpIcepk0o8(chr(0b100100 + 0o14) + chr(111) + chr(1578 - 1523) + '\x32', 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(51) + '\x32' + '\x32', 2312 - 2304), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\062' + chr(2058 - 2010), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b110110 + 0o71) + '\061' + chr(52) + chr(0b110000), 52175 - 52167), nzTpIcepk0o8(chr(1232 - 1184) + chr(1110 - 999) + '\063' + '\x32' + chr(54), 24332 - 24324), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110011) + chr(2227 - 2172) + chr(0b110110), 0b1000), nzTpIcepk0o8(chr(0b11001 + 0o27) + chr(0b1101111) + chr(50), 0o10), nzTpIcepk0o8(chr(1707 - 1659) + chr(111) + chr(2268 - 2215) + chr(0b0 + 0o61), 0b1000), nzTpIcepk0o8(chr(1080 - 1032) + chr(491 - 380) + chr(0b110001) + chr(49) + chr(0b100101 + 0o20), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(811 - 762) + '\063' + chr(0b100011 + 0o15), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b0 + 0o157) + chr(1083 - 1033) + chr(51) + chr(0b101 + 0o60), 0b1000), nzTpIcepk0o8('\060' + chr(111) + '\062' + chr(54) + chr(53), 22816 - 22808), nzTpIcepk0o8(chr(0b101011 + 0o5) + chr(0b1010100 + 0o33) + chr(0b110010) + chr(0b110110) + chr(0b110110), ord("\x08")), nzTpIcepk0o8(chr(0b101111 + 0o1) + chr(0b1100110 + 0o11) + chr(550 - 501) + chr(65 - 16) + chr(52), 19493 - 19485), nzTpIcepk0o8(chr(1303 - 1255) + '\x6f' + chr(0b1111 + 0o43) + '\x36' + chr(0b110011), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110001) + chr(53) + '\066', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(4052 - 3941) + '\062' + '\x30' + chr(739 - 691), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110011) + '\060' + '\060', 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(1999 - 1948) + '\063' + chr(0b110010), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110010) + chr(49) + '\x35', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\065' + chr(0b110110), 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(0b101011 + 0o7) + '\067' + '\067', 0b1000), nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(0b1101111) + chr(1008 - 959) + '\065' + '\067', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(2389 - 2339) + '\x31' + '\x37', 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(2097 - 2045) + chr(51), 16551 - 16543), nzTpIcepk0o8(chr(0b1100 + 0o44) + '\157' + '\x33' + chr(0b110000 + 0o5) + chr(0b111 + 0o57), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(7021 - 6910) + chr(49) + chr(0b10011 + 0o42) + chr(0b11100 + 0o24), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110001) + chr(0b110001) + '\063', 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + '\061' + chr(0b110010) + chr(51), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b110000 + 0o77) + chr(504 - 454), 8), nzTpIcepk0o8(chr(48) + '\157' + chr(0b1000 + 0o51) + chr(577 - 528) + chr(1149 - 1099), 28999 - 28991), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\061' + chr(642 - 588) + chr(2860 - 2805), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(1499 - 1450) + '\x35' + chr(0b111 + 0o51), 8), nzTpIcepk0o8('\x30' + chr(0b10100 + 0o133) + chr(0b110001) + chr(49) + chr(54), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(0b10001 + 0o42) + '\x34' + chr(0b101100 + 0o4), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x32' + chr(1273 - 1220), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b11101 + 0o23) + chr(111) + chr(53) + chr(0b10111 + 0o31), 58992 - 58984)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'%'), '\144' + chr(0b1100011 + 0o2) + chr(0b110011 + 0o60) + chr(9769 - 9658) + chr(0b1100100) + chr(0b1010110 + 0o17))(chr(12112 - 11995) + chr(0b1110100) + chr(0b11111 + 0o107) + chr(45) + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def c0f10MgmHZJl(hXMPsSrOQzbh, cPcJl8WaOp1U=None):
mD44XHfr1PSC = roI3spqORKae(ES5oEprVxulp(b'J\xbe]'), chr(100) + '\145' + chr(355 - 256) + '\157' + chr(100) + chr(0b110000 + 0o65))('\165' + chr(116) + chr(0b1011000 + 0o16) + chr(0b11011 + 0o22) + chr(0b111000))
if cPcJl8WaOp1U is None:
g0JVQUJ_hwhS = []
for _pSYqrosNb95 in roI3spqORKae(aHUqKstZLeS6.environ[roI3spqORKae(ES5oEprVxulp(b'[\x8fL\xab'), chr(9345 - 9245) + chr(0b1100101) + chr(99) + chr(0b1101111) + '\144' + chr(6322 - 6221))('\165' + chr(116) + '\x66' + '\x2d' + chr(2007 - 1951))], roI3spqORKae(ES5oEprVxulp(b'G\xa8J\x91k\x9dh\x15\x92\x88lj'), '\x64' + '\145' + chr(0b10100 + 0o117) + '\x6f' + '\144' + chr(5086 - 4985))('\165' + chr(0b111010 + 0o72) + chr(8322 - 8220) + chr(45) + chr(56)))(roI3spqORKae(aHUqKstZLeS6, roI3spqORKae(ES5oEprVxulp(b'{\xafl\x8bI\xb7`'), '\144' + chr(0b1100101) + chr(0b1100011) + '\157' + chr(0b1100100) + chr(0b101110 + 0o67))(chr(117) + chr(0b1110100) + '\146' + chr(0b100 + 0o51) + chr(0b111000)))):
krdNJAUTqDDe = aHUqKstZLeS6.path.Y4yM9BcfTCNq(_pSYqrosNb95, mD44XHfr1PSC)
roI3spqORKae(g0JVQUJ_hwhS, roI3spqORKae(ES5oEprVxulp(b'C\x9aK\xd7B\xb5W\x0f\xbc\x91W\x1c'), chr(0b1100100) + '\x65' + chr(99) + chr(11439 - 11328) + chr(0b1100100) + '\x65')(chr(117) + '\164' + '\146' + chr(1512 - 1467) + chr(0b1101 + 0o53)))(roI3spqORKae(aHUqKstZLeS6, roI3spqORKae(ES5oEprVxulp(b'I\xbe\\\x90h\xaaA\x11\x94\x86;M'), chr(0b101100 + 0o70) + '\145' + '\x63' + '\157' + '\x64' + chr(5056 - 4955))('\165' + chr(0b1101001 + 0o13) + chr(102) + chr(0b1001 + 0o44) + chr(0b111000)))(krdNJAUTqDDe, roI3spqORKae(aHUqKstZLeS6, roI3spqORKae(ES5oEprVxulp(b'S\x91W\xa8'), '\144' + chr(101) + chr(99) + chr(1995 - 1884) + '\x64' + chr(0b1100101))(chr(117) + chr(0b1110100) + chr(0b1100110) + chr(0b0 + 0o55) + chr(56)))))
if not VF4pKOObtlPc(g0JVQUJ_hwhS):
raise zfo2Sgkz3IVJ(roI3spqORKae(ES5oEprVxulp(b'J\xbe}\xc3T\xbdd@\xbf\x90"y\x0c\x0c\xd5\x9b\x96\x19\xc0\x0b\xa0\xa1\xaa\xe8q\xcf\x0e\xfbK\xce\x03<2p-Y'), '\x64' + chr(443 - 342) + chr(0b1010111 + 0o14) + '\x6f' + chr(100) + '\x65')('\165' + chr(0b101111 + 0o105) + chr(0b1000000 + 0o46) + chr(1587 - 1542) + chr(56)))
else:
mD44XHfr1PSC = cPcJl8WaOp1U
PT32xG247TS3 = VfV2QW3Td2UZ.mkdtemp()
if roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'X\x82N\xa1\x08\x90@!\x89\x93KL'), chr(0b1000101 + 0o37) + chr(0b1001100 + 0o31) + '\143' + '\157' + chr(7843 - 7743) + '\145')(chr(117) + chr(10215 - 10099) + chr(0b100000 + 0o106) + chr(45) + chr(0b101010 + 0o16))) is not None and roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'X\x82N\xa1\x08\x90@!\x89\x93KL'), chr(0b1001001 + 0o33) + chr(0b1100101) + chr(0b1100011) + chr(0b1101111) + chr(0b1100100) + chr(0b1100101))(chr(0b1101010 + 0o13) + chr(116) + '\x66' + chr(0b101101) + chr(0b10101 + 0o43))):
FxZHtXEolYsL = aHUqKstZLeS6.path.Y4yM9BcfTCNq(PT32xG247TS3, roI3spqORKae(ES5oEprVxulp(b'p\xb36\x82J\xb7'), chr(1609 - 1509) + chr(0b1100101) + chr(99) + '\x6f' + chr(0b10010 + 0o122) + chr(0b1100101))(chr(0b1110101) + chr(116) + '\x66' + chr(0b101101) + '\x38').q33KG3foQ_CJ(hXMPsSrOQzbh.SLVB2BPA_mIe))
else:
FxZHtXEolYsL = aHUqKstZLeS6.path.Y4yM9BcfTCNq(PT32xG247TS3, roI3spqORKae(ES5oEprVxulp(b'\x7f\xa3h\xcd[\xa2u'), chr(0b1100100) + '\x65' + chr(0b1001 + 0o132) + chr(2118 - 2007) + chr(0b110101 + 0o57) + '\x65')(chr(0b1110101) + '\x74' + chr(0b1100110) + chr(0b1111 + 0o36) + '\x38'))
roI3spqORKae(_bFWSozA7z0G.seqio, roI3spqORKae(ES5oEprVxulp(b'|\xbcq\x97_\x8dt\x0e\xb7'), chr(0b1100100) + '\x65' + chr(0b100101 + 0o76) + '\x6f' + chr(0b1100100) + '\x65')(chr(117) + '\x74' + chr(102) + '\055' + '\x38'))(hXMPsSrOQzbh, FxZHtXEolYsL)
conU5pBPX9i7 = eT8Y087E_kfd.Popen([mD44XHfr1PSC, FxZHtXEolYsL])
try:
roI3spqORKae(conU5pBPX9i7, roI3spqORKae(ES5oEprVxulp(b']\x8cv\x82w\xe2z\x19\xe7\xcacf'), chr(0b1001011 + 0o31) + chr(3411 - 3310) + chr(0b1101 + 0o126) + chr(0b1100001 + 0o16) + chr(100) + chr(9133 - 9032))('\165' + chr(116) + chr(102) + chr(0b101101) + chr(56)))()
roI3spqORKae(zcgTfC_NSHAo, roI3spqORKae(ES5oEprVxulp(b'y\xa3l\x91_\xb7'), '\x64' + '\x65' + '\x63' + chr(0b1101111) + '\x64' + '\145')('\165' + chr(116) + chr(623 - 521) + '\055' + '\x38'))(PT32xG247TS3)
except Fc8q2OvvlH7d:
roI3spqORKae(zcgTfC_NSHAo, roI3spqORKae(ES5oEprVxulp(b'y\xa3l\x91_\xb7'), chr(100) + '\x65' + chr(0b1100011) + '\157' + chr(0b1100100) + chr(7145 - 7044))(chr(117) + chr(10069 - 9953) + chr(0b1100110) + chr(104 - 59) + chr(0b111000)))(PT32xG247TS3) |
klavinslab/coral | coral/sequence/_dna.py | DNA.copy | def copy(self):
'''Create a copy of the current instance.
:returns: A safely-editable copy of the current sequence.
:rtype: coral.DNA
'''
# Significant performance improvements by skipping alphabet check
features_copy = [feature.copy() for feature in self.features]
copy = type(self)(self.top.seq, circular=self.circular,
features=features_copy, name=self.name,
bottom=self.bottom.seq, run_checks=False)
return copy | python | def copy(self):
'''Create a copy of the current instance.
:returns: A safely-editable copy of the current sequence.
:rtype: coral.DNA
'''
# Significant performance improvements by skipping alphabet check
features_copy = [feature.copy() for feature in self.features]
copy = type(self)(self.top.seq, circular=self.circular,
features=features_copy, name=self.name,
bottom=self.bottom.seq, run_checks=False)
return copy | [
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/sequence/_dna.py#L113-L125 | train | Create a safely - editable copy of the current instance. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b10011 + 0o35) + '\x6f' + chr(1954 - 1905) + chr(0b1100 + 0o45) + chr(1430 - 1375), ord("\x08")), nzTpIcepk0o8(chr(1950 - 1902) + '\157' + chr(0b110011) + chr(0b10010 + 0o40) + chr(51), 0b1000), nzTpIcepk0o8(chr(0b0 + 0o60) + chr(0b101010 + 0o105) + '\x32' + '\x35', ord("\x08")), nzTpIcepk0o8('\060' + chr(6808 - 6697) + '\061' + chr(0b110100) + chr(2364 - 2315), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110001) + chr(0b11000 + 0o33) + chr(0b110000), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(489 - 378) + chr(0b100 + 0o57) + chr(0b10001 + 0o40), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + '\063' + chr(52) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(570 - 522) + chr(111) + chr(49) + '\062' + chr(0b100011 + 0o15), 33999 - 33991), nzTpIcepk0o8(chr(767 - 719) + '\x6f' + chr(0b11011 + 0o26) + chr(1000 - 951) + chr(54), 0o10), nzTpIcepk0o8(chr(0b10000 + 0o40) + chr(111) + chr(0b110010) + '\061' + chr(54), ord("\x08")), nzTpIcepk0o8(chr(1584 - 1536) + chr(0b1101111) + chr(0b10 + 0o61) + chr(0b1001 + 0o53), 0b1000), nzTpIcepk0o8(chr(1064 - 1016) + chr(111) + '\062' + chr(0b10000 + 0o42) + '\x35', 0o10), nzTpIcepk0o8(chr(52 - 4) + chr(0b1101111) + chr(51) + chr(0b110010), 23284 - 23276), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110001) + chr(1308 - 1260) + chr(0b101101 + 0o3), 20189 - 20181), nzTpIcepk0o8(chr(1555 - 1507) + chr(0b1101111) + '\x35' + chr(1850 - 1801), ord("\x08")), nzTpIcepk0o8(chr(0b11001 + 0o27) + chr(0b1011 + 0o144) + '\x32' + '\066' + chr(0b1010 + 0o54), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(0b1100 + 0o45) + chr(1109 - 1057) + chr(0b1110 + 0o43), 8), nzTpIcepk0o8(chr(0b110000) + chr(0b11011 + 0o124) + chr(484 - 434) + chr(53) + chr(53), 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(0b110011) + chr(49) + chr(0b110010), 0o10), nzTpIcepk0o8('\060' + chr(10665 - 10554) + chr(0b101011 + 0o7) + chr(0b110000) + chr(0b11010 + 0o35), 0o10), nzTpIcepk0o8('\x30' + chr(0b1000100 + 0o53) + chr(55) + '\x32', 58190 - 58182), nzTpIcepk0o8('\x30' + chr(0b1101100 + 0o3) + chr(1926 - 1876) + '\x30' + '\x34', 2393 - 2385), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110110) + chr(55), ord("\x08")), nzTpIcepk0o8(chr(1763 - 1715) + chr(0b11011 + 0o124) + chr(51) + '\x31' + '\062', 8), nzTpIcepk0o8('\060' + chr(6917 - 6806) + chr(49) + chr(0b11101 + 0o24) + chr(52), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(50) + chr(578 - 529) + chr(0b110000 + 0o0), 53968 - 53960), nzTpIcepk0o8(chr(0b110000) + chr(0b101000 + 0o107) + '\061' + chr(0b101111 + 0o3) + chr(0b110110), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(658 - 547) + chr(0b100111 + 0o13) + chr(1348 - 1299) + chr(52), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(2410 - 2356) + chr(54), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(49) + chr(0b101000 + 0o16) + '\x36', 16569 - 16561), nzTpIcepk0o8('\060' + chr(0b1010110 + 0o31) + '\x33' + chr(0b10001 + 0o45), 0b1000), nzTpIcepk0o8(chr(0b11110 + 0o22) + chr(111) + chr(0b10100 + 0o37) + chr(2612 - 2557) + chr(49), 51261 - 51253), nzTpIcepk0o8(chr(0b110000) + chr(0b1011011 + 0o24) + '\x32' + '\067' + chr(48), 0b1000), nzTpIcepk0o8(chr(0b10 + 0o56) + chr(2683 - 2572) + chr(194 - 145) + chr(2428 - 2373) + chr(50), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + chr(1894 - 1843), 13193 - 13185), nzTpIcepk0o8('\060' + '\x6f' + chr(50) + '\x33' + '\x32', ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(0b110001) + chr(0b100100 + 0o21) + '\x31', 2447 - 2439), nzTpIcepk0o8(chr(48) + '\x6f' + '\x31' + chr(49) + chr(0b110000 + 0o0), 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(793 - 744) + chr(53) + '\067', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(2220 - 2168) + chr(51), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + chr(111) + chr(0b110101) + '\x30', ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'a'), chr(8032 - 7932) + '\x65' + chr(0b1100011) + chr(8810 - 8699) + '\144' + '\x65')('\x75' + chr(9441 - 9325) + chr(0b1100011 + 0o3) + chr(0b110 + 0o47) + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def aZTCj4v5QdfO(hXMPsSrOQzbh):
pHtoMMx8lLo8 = [gNPUvMsk9RKn.copy() for gNPUvMsk9RKn in hXMPsSrOQzbh.azxuCKSXk6dv]
aZTCj4v5QdfO = MJ07XsN5uFgW(hXMPsSrOQzbh)(hXMPsSrOQzbh.top.ftk9lc7G5FOo, circular=hXMPsSrOQzbh.z1jrZw1enaK_, features=pHtoMMx8lLo8, name=hXMPsSrOQzbh.SLVB2BPA_mIe, bottom=hXMPsSrOQzbh.bottom.ftk9lc7G5FOo, run_checks=nzTpIcepk0o8('\x30' + chr(0b100101 + 0o112) + chr(1535 - 1487), ord("\x08")))
return aZTCj4v5QdfO |
klavinslab/coral | coral/sequence/_dna.py | DNA.circularize | def circularize(self):
'''Circularize linear DNA.
:returns: A circularized version of the current sequence.
:rtype: coral.DNA
'''
if self.top[-1].seq == '-' and self.bottom[0].seq == '-':
raise ValueError('Cannot circularize - termini disconnected.')
if self.bottom[-1].seq == '-' and self.top[0].seq == '-':
raise ValueError('Cannot circularize - termini disconnected.')
copy = self.copy()
copy.circular = True
copy.top.circular = True
copy.bottom.circular = True
return copy | python | def circularize(self):
'''Circularize linear DNA.
:returns: A circularized version of the current sequence.
:rtype: coral.DNA
'''
if self.top[-1].seq == '-' and self.bottom[0].seq == '-':
raise ValueError('Cannot circularize - termini disconnected.')
if self.bottom[-1].seq == '-' and self.top[0].seq == '-':
raise ValueError('Cannot circularize - termini disconnected.')
copy = self.copy()
copy.circular = True
copy.top.circular = True
copy.bottom.circular = True
return copy | [
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"."
] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/sequence/_dna.py#L127-L143 | train | Circularize linear DNA. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8('\060' + '\157' + chr(1000 - 948) + '\060', 0o10), nzTpIcepk0o8(chr(48) + chr(3909 - 3798) + chr(0b110100) + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(1472 - 1424) + '\157' + chr(0b110010) + chr(0b1111 + 0o47) + '\x35', 0o10), nzTpIcepk0o8(chr(2064 - 2016) + chr(0b1101111) + chr(49) + '\064' + '\x34', 0o10), nzTpIcepk0o8('\x30' + '\x6f' + '\063' + chr(0b11111 + 0o27) + chr(0b110111), 9998 - 9990), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110110) + chr(673 - 624), 0o10), nzTpIcepk0o8('\060' + chr(0b1100101 + 0o12) + '\x31' + '\060' + chr(0b11000 + 0o34), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(689 - 640) + chr(0b110011) + '\060', 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(1374 - 1324) + chr(908 - 859), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b100010 + 0o115) + chr(0b110011) + chr(0b110010) + '\062', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(49) + chr(0b11101 + 0o25) + chr(484 - 435), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(0b10011 + 0o37) + '\x36' + chr(0b110010), 51778 - 51770), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110110) + chr(2155 - 2102), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b101001 + 0o106) + chr(51) + '\065' + chr(815 - 767), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(0b110011) + chr(0b101000 + 0o10), 0b1000), nzTpIcepk0o8(chr(1393 - 1345) + chr(111) + chr(0b110010) + chr(54) + chr(0b11110 + 0o24), 8), nzTpIcepk0o8(chr(1592 - 1544) + '\157' + chr(0b110011) + chr(0b110010) + '\x35', 0b1000), nzTpIcepk0o8(chr(2022 - 1974) + '\x6f' + chr(1199 - 1149) + '\x36' + chr(0b101011 + 0o14), 0o10), nzTpIcepk0o8(chr(2174 - 2126) + '\157' + chr(0b110001) + chr(0b110000 + 0o3), 63012 - 63004), nzTpIcepk0o8(chr(0b101011 + 0o5) + chr(0b1000110 + 0o51) + '\061', ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(2090 - 2039) + chr(0b110111) + chr(52), ord("\x08")), nzTpIcepk0o8('\x30' + chr(2625 - 2514) + '\062' + '\x37' + chr(0b110000), 55440 - 55432), nzTpIcepk0o8(chr(0b101001 + 0o7) + chr(0b1101111) + '\061' + chr(50) + chr(618 - 569), 8), nzTpIcepk0o8('\060' + chr(0b100001 + 0o116) + '\x33' + chr(110 - 55), 0o10), nzTpIcepk0o8(chr(1521 - 1473) + chr(111) + chr(0b100 + 0o57) + chr(0b110110) + chr(0b110010), 0o10), nzTpIcepk0o8(chr(0b101110 + 0o2) + chr(0b10 + 0o155) + chr(51) + '\066' + chr(1541 - 1493), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(5603 - 5492) + chr(144 - 93) + '\061' + chr(48), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + '\x31' + chr(0b100000 + 0o25) + chr(720 - 670), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(4283 - 4172) + '\x33' + '\x30', 8), nzTpIcepk0o8(chr(0b110000) + chr(0b1011100 + 0o23) + chr(0b110001) + '\061' + chr(51), 0o10), nzTpIcepk0o8('\x30' + chr(0b11 + 0o154) + chr(50) + chr(0b0 + 0o60) + chr(0b110000), 28554 - 28546), nzTpIcepk0o8(chr(1443 - 1395) + '\157' + chr(147 - 96), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(0b1 + 0o62), 8), nzTpIcepk0o8(chr(48) + '\x6f' + '\063' + '\x32' + chr(0b110011), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1010101 + 0o32) + chr(2087 - 2036) + '\x36' + '\066', 48055 - 48047), nzTpIcepk0o8(chr(48) + chr(0b11010 + 0o125) + chr(0b1100 + 0o52) + chr(48), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(52) + chr(0b110010), 0o10), nzTpIcepk0o8('\060' + '\x6f' + '\x35', 64045 - 64037), nzTpIcepk0o8('\x30' + '\x6f' + '\x33' + chr(0b11000 + 0o34), 0o10), nzTpIcepk0o8(chr(0b11001 + 0o27) + chr(0b1101111) + chr(0b110100 + 0o1) + chr(50), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + chr(111) + chr(2284 - 2231) + chr(234 - 186), ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x0e'), chr(0b1100100) + '\145' + chr(5663 - 5564) + chr(4625 - 4514) + chr(6981 - 6881) + chr(0b1011100 + 0o11))(chr(0b11000 + 0o135) + '\x74' + chr(0b1100110) + '\055' + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def zLJoDsYgf6YN(hXMPsSrOQzbh):
if roI3spqORKae(hXMPsSrOQzbh.top[-nzTpIcepk0o8(chr(2146 - 2098) + chr(111) + chr(870 - 821), 8)], roI3spqORKae(ES5oEprVxulp(b'FS\xde]\x9bRs\x1f$\x94\x1e\xdd'), '\144' + '\x65' + '\143' + chr(111) + chr(100) + chr(0b1100101))(chr(117) + '\x74' + chr(0b1100110) + '\055' + chr(56))) == roI3spqORKae(ES5oEprVxulp(b'\r'), chr(0b1100100) + '\145' + chr(0b110110 + 0o55) + '\x6f' + chr(7306 - 7206) + chr(5297 - 5196))(chr(0b1110101) + chr(8009 - 7893) + chr(7327 - 7225) + chr(0b101101) + chr(1346 - 1290)) and roI3spqORKae(hXMPsSrOQzbh.bottom[nzTpIcepk0o8(chr(0b1010 + 0o46) + chr(111) + chr(0b110000), ord("\x08"))], roI3spqORKae(ES5oEprVxulp(b'FS\xde]\x9bRs\x1f$\x94\x1e\xdd'), chr(0b1100100) + chr(101) + chr(0b1100011) + chr(0b10111 + 0o130) + '\144' + chr(101))('\x75' + chr(197 - 81) + chr(102) + '\x2d' + chr(429 - 373))) == roI3spqORKae(ES5oEprVxulp(b'\r'), chr(6828 - 6728) + chr(3676 - 3575) + chr(0b1100011) + '\x6f' + '\x64' + chr(0b110110 + 0o57))(chr(0b1000111 + 0o56) + chr(0b1110100) + '\146' + chr(0b101101) + chr(2524 - 2468)):
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'cF\xdb\n\x98Ed;x\xa02\xc7Y\x89j\xdb\xaf\xd2+,\xdc\xcc4m\x9f\x99\xa6\x038/\xe9p`\xbc\x98^GfhOD\t'), '\144' + chr(0b11110 + 0o107) + chr(0b1100011) + '\157' + chr(0b1100100) + chr(8359 - 8258))('\x75' + '\164' + '\146' + chr(1672 - 1627) + chr(0b111000)))
if roI3spqORKae(hXMPsSrOQzbh.bottom[-nzTpIcepk0o8(chr(0b10 + 0o56) + chr(0b1101111) + chr(0b11010 + 0o27), 8)], roI3spqORKae(ES5oEprVxulp(b'FS\xde]\x9bRs\x1f$\x94\x1e\xdd'), chr(4924 - 4824) + chr(0b1100101) + chr(0b1100011) + '\157' + chr(0b1000000 + 0o44) + '\145')('\x75' + chr(116) + '\x66' + chr(1581 - 1536) + chr(0b111000))) == roI3spqORKae(ES5oEprVxulp(b'\r'), chr(0b1100100) + chr(0b101 + 0o140) + chr(1351 - 1252) + chr(0b1110 + 0o141) + chr(1488 - 1388) + chr(101))('\x75' + chr(0b1110100) + chr(102) + '\055' + chr(0b111000)) and roI3spqORKae(hXMPsSrOQzbh.top[nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(48), 8)], roI3spqORKae(ES5oEprVxulp(b'FS\xde]\x9bRs\x1f$\x94\x1e\xdd'), chr(2886 - 2786) + '\145' + chr(7083 - 6984) + chr(0b1101111) + chr(0b1100100) + '\x65')(chr(0b1110101) + '\x74' + chr(6295 - 6193) + chr(0b110 + 0o47) + chr(0b101110 + 0o12))) == roI3spqORKae(ES5oEprVxulp(b'\r'), chr(100) + '\145' + chr(0b1100011) + chr(8457 - 8346) + '\144' + chr(101))(chr(12982 - 12865) + chr(0b100010 + 0o122) + chr(0b1100110) + chr(0b101 + 0o50) + chr(56)):
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'cF\xdb\n\x98Ed;x\xa02\xc7Y\x89j\xdb\xaf\xd2+,\xdc\xcc4m\x9f\x99\xa6\x038/\xe9p`\xbc\x98^GfhOD\t'), chr(100) + '\x65' + '\143' + '\x6f' + chr(0b111101 + 0o47) + chr(5237 - 5136))(chr(117) + '\164' + chr(0b1100110) + chr(45) + chr(0b101010 + 0o16)))
aZTCj4v5QdfO = hXMPsSrOQzbh.copy()
aZTCj4v5QdfO.z1jrZw1enaK_ = nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110001), 8)
aZTCj4v5QdfO.top.z1jrZw1enaK_ = nzTpIcepk0o8(chr(48) + chr(2137 - 2026) + chr(0b11001 + 0o30), 8)
aZTCj4v5QdfO.bottom.z1jrZw1enaK_ = nzTpIcepk0o8('\060' + chr(0b1101111) + '\x31', 8)
return aZTCj4v5QdfO |
klavinslab/coral | coral/sequence/_dna.py | DNA.display | def display(self):
'''Display a visualization of the sequence in an IPython notebook.'''
try:
from IPython.display import HTML
import uuid
except ImportError:
raise IPythonDisplayImportError
sequence_json = self.json()
d3cdn = '//d3js.org/d3.v3.min.js'
div_id = 'sequence_{}'.format(uuid.uuid1())
cur_dir = os.path.abspath(os.path.dirname(__file__))
d3_plasmid_path = os.path.join(cur_dir, 'd3-plasmid.js')
with open(d3_plasmid_path) as f:
d3_plasmid_js = f.read()
html = '<div id={div_id}></div>'.format(div_id=div_id)
js_databind = '''
<script>
require([\'{d3_cdn}\'], function(lib) {{
window.data = {data};'''.format(div_id=div_id, d3_cdn=d3cdn,
data=sequence_json)
js_viz = '''
d3sequence(window.data, \'{div_id}\')
}});
</script>
'''.format(div_id=div_id)
return HTML(html + js_databind + d3_plasmid_js + js_viz) | python | def display(self):
'''Display a visualization of the sequence in an IPython notebook.'''
try:
from IPython.display import HTML
import uuid
except ImportError:
raise IPythonDisplayImportError
sequence_json = self.json()
d3cdn = '//d3js.org/d3.v3.min.js'
div_id = 'sequence_{}'.format(uuid.uuid1())
cur_dir = os.path.abspath(os.path.dirname(__file__))
d3_plasmid_path = os.path.join(cur_dir, 'd3-plasmid.js')
with open(d3_plasmid_path) as f:
d3_plasmid_js = f.read()
html = '<div id={div_id}></div>'.format(div_id=div_id)
js_databind = '''
<script>
require([\'{d3_cdn}\'], function(lib) {{
window.data = {data};'''.format(div_id=div_id, d3_cdn=d3cdn,
data=sequence_json)
js_viz = '''
d3sequence(window.data, \'{div_id}\')
}});
</script>
'''.format(div_id=div_id)
return HTML(html + js_databind + d3_plasmid_js + js_viz) | [
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/sequence/_dna.py#L145-L176 | train | Display a visualization of the sequence in an IPython notebook. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b110000) + chr(0b1101001 + 0o6) + chr(0b110010) + chr(0b10111 + 0o35) + '\x34', 0b1000), nzTpIcepk0o8(chr(48) + chr(331 - 220) + '\066' + chr(0b110110), 0o10), nzTpIcepk0o8('\060' + chr(598 - 487) + '\x33' + chr(0b110101) + chr(0b110010), 20909 - 20901), nzTpIcepk0o8('\x30' + chr(8643 - 8532) + chr(50) + chr(51) + chr(52), 9935 - 9927), nzTpIcepk0o8(chr(690 - 642) + chr(111) + chr(50) + chr(0b10101 + 0o37) + chr(1611 - 1560), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110100) + '\060', 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(51) + chr(0b110011) + chr(0b1011 + 0o47), 58977 - 58969), nzTpIcepk0o8('\x30' + chr(111) + '\061' + '\065', 0o10), nzTpIcepk0o8('\x30' + '\x6f' + '\x33' + chr(55) + '\x35', 9035 - 9027), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110101) + chr(53), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(865 - 754) + chr(2175 - 2126) + chr(240 - 190) + chr(0b100001 + 0o26), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x31' + chr(2563 - 2512), ord("\x08")), nzTpIcepk0o8(chr(1683 - 1635) + chr(9134 - 9023) + chr(1960 - 1911), 56924 - 56916), nzTpIcepk0o8(chr(0b1101 + 0o43) + '\x6f' + chr(0b110100) + '\x35', ord("\x08")), nzTpIcepk0o8(chr(2248 - 2200) + '\157' + chr(1084 - 1030), 41439 - 41431), nzTpIcepk0o8(chr(1061 - 1013) + '\x6f' + chr(0b110010) + '\061' + chr(0b110100 + 0o1), ord("\x08")), nzTpIcepk0o8(chr(1203 - 1155) + chr(0b110101 + 0o72) + '\x36' + chr(0b1000 + 0o51), 49242 - 49234), nzTpIcepk0o8('\x30' + '\157' + chr(0b1100 + 0o47) + '\x31' + '\062', ord("\x08")), nzTpIcepk0o8(chr(0b100111 + 0o11) + '\157' + chr(51) + chr(1069 - 1015) + chr(1710 - 1656), ord("\x08")), nzTpIcepk0o8(chr(0b1100 + 0o44) + chr(10800 - 10689) + chr(1277 - 1228) + chr(0b110001) + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b111001 + 0o66) + chr(0b11111 + 0o26) + '\x37', 0b1000), nzTpIcepk0o8(chr(0b10001 + 0o37) + chr(111) + '\061' + '\x31' + chr(81 - 28), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110001) + chr(55) + chr(986 - 934), 36947 - 36939), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x35' + chr(1431 - 1383), 46715 - 46707), nzTpIcepk0o8('\060' + '\x6f' + '\x33' + chr(1037 - 986), 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(2009 - 1958) + chr(0b1101 + 0o43) + '\x31', 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110011) + chr(0b1110 + 0o43) + chr(0b110100), 0b1000), nzTpIcepk0o8('\060' + chr(5499 - 5388) + chr(0b110010 + 0o4) + chr(475 - 421), 8), nzTpIcepk0o8(chr(0b11011 + 0o25) + '\157' + chr(0b110001 + 0o2), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(3227 - 3116) + '\x32' + chr(53) + '\066', 0b1000), nzTpIcepk0o8('\060' + chr(0b100110 + 0o111) + chr(0b110001) + '\063' + chr(54), 0o10), nzTpIcepk0o8(chr(0b10000 + 0o40) + chr(0b1101111) + '\x32' + chr(0b1001 + 0o50) + chr(0b110110), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101100 + 0o3) + chr(0b110001 + 0o0) + chr(0b110010) + '\063', ord("\x08")), nzTpIcepk0o8('\x30' + chr(5481 - 5370) + chr(2531 - 2480) + '\064', 0b1000), nzTpIcepk0o8(chr(0b10101 + 0o33) + '\157' + chr(0b11010 + 0o27) + '\065' + chr(0b100110 + 0o13), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(1210 - 1161) + chr(53) + chr(53), ord("\x08")), nzTpIcepk0o8(chr(0b1011 + 0o45) + chr(111) + chr(0b101 + 0o54) + chr(1237 - 1187) + chr(2380 - 2329), 8), nzTpIcepk0o8(chr(48) + chr(0b1101000 + 0o7) + chr(0b100001 + 0o20) + '\x33' + chr(55), 0b1000), nzTpIcepk0o8(chr(220 - 172) + chr(0b1101111) + chr(2152 - 2102) + '\x34' + chr(0b110001), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(49) + '\x36', 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + chr(12142 - 12031) + '\065' + '\060', 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x8a'), chr(0b1001100 + 0o30) + '\x65' + chr(0b1010101 + 0o16) + chr(0b111010 + 0o65) + chr(0b100100 + 0o100) + chr(898 - 797))(chr(2993 - 2876) + chr(116) + '\146' + '\x2d' + chr(0b10101 + 0o43)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def Oux2FGbzTd3C(hXMPsSrOQzbh):
try:
(WF7Iu8LMkSNT,) = (roI3spqORKae(roI3spqORKae(rFFUeiYWzOhx(roI3spqORKae(ES5oEprVxulp(b'\xedf\x93\xe8\xcbO\xb4#\x99D${mD\x7f'), chr(100) + '\x65' + chr(0b101010 + 0o71) + '\x6f' + '\x64' + '\145')('\x75' + chr(0b1110100) + chr(0b110111 + 0o57) + chr(0b1000 + 0o45) + chr(0b11 + 0o65)), roI3spqORKae(ES5oEprVxulp(b'\xecb\xa7\xd0'), chr(0b1100100) + chr(7302 - 7201) + chr(99) + '\157' + chr(100) + chr(101))(chr(117) + '\164' + '\146' + chr(0b101101) + chr(0b101011 + 0o15))), roI3spqORKae(ES5oEprVxulp(b'\xc0_\x99\xec\xcfA\xa3'), chr(0b1001100 + 0o30) + chr(101) + '\143' + '\157' + chr(0b1100100) + chr(0b110000 + 0o65))(chr(0b1110101) + '\164' + chr(0b1100110) + chr(0b101101) + chr(3112 - 3056))), roI3spqORKae(ES5oEprVxulp(b'\xecb\xa7\xd0'), '\x64' + chr(101) + '\143' + chr(0b1101111) + '\x64' + '\145')('\165' + '\x74' + '\146' + chr(0b101101) + chr(2690 - 2634))),)
(m4Y3vm7KKv8P,) = (zGgTE_CdZfvi(roI3spqORKae(ES5oEprVxulp(b'\xd1C\x83\xf8'), '\144' + chr(0b1011100 + 0o11) + chr(0b1100011) + '\157' + chr(7543 - 7443) + chr(0b1100101))(chr(7343 - 7226) + chr(116) + chr(0b1011011 + 0o13) + chr(0b11110 + 0o17) + chr(3097 - 3041))),)
except fPFTJxVnGShv:
raise O75aOoEIFAus
wlNSwKIFi3ad = hXMPsSrOQzbh.LNUKEwZDIbyb()
HrsimIIp8dNp = roI3spqORKae(ES5oEprVxulp(b"\x8b\x19\x8e\xaf\xc9S\xf4b\x8fJxo2\x0bp\xbe\x1f\xa7\x9f$\x01'\x0f"), chr(0b101110 + 0o66) + chr(101) + '\143' + chr(0b10010 + 0o135) + chr(2076 - 1976) + '\x65')('\x75' + chr(12182 - 12066) + '\x66' + '\055' + chr(56))
bx8IbZW8ouQd = roI3spqORKae(ES5oEprVxulp(b'\xd7S\x9b\xe9\xc6N\xb9h\xa2V*'), chr(0b1100100) + chr(0b1000101 + 0o40) + '\143' + chr(111) + chr(0b101011 + 0o71) + '\145')(chr(0b101100 + 0o111) + chr(3833 - 3717) + chr(102) + '\x2d' + '\070').q33KG3foQ_CJ(m4Y3vm7KKv8P.uuid1())
vSNaZ48I6kso = aHUqKstZLeS6.path.abspath(aHUqKstZLeS6.path.qu5fsQlGSLfc(OHWDi_URd_WF))
s6kVFB0Vezwj = aHUqKstZLeS6.path.Y4yM9BcfTCNq(vSNaZ48I6kso, roI3spqORKae(ES5oEprVxulp(b'\xc0\x05\xc7\xec\xcfA\xa9`\x94Iyar'), chr(100) + chr(0b1011000 + 0o15) + chr(0b101100 + 0o67) + '\157' + chr(1009 - 909) + '\x65')(chr(117) + chr(6008 - 5892) + '\x66' + '\x2d' + chr(56)))
with DnU3Rq9N5ala(s6kVFB0Vezwj) as _R8IKF5IwAfX:
cT_voMHveVRq = _R8IKF5IwAfX.eoXknH7XUn7m()
ISqAO12SND9I = roI3spqORKae(ES5oEprVxulp(b'\x98R\x83\xea\x83I\xbe0\x86I>}^Lb\xf0\x0f\xf6\xd9.F;B'), '\x64' + chr(0b1100101) + chr(0b1100011) + chr(0b1101111) + chr(1223 - 1123) + chr(0b1100101))(chr(12911 - 12794) + chr(116) + '\x66' + chr(0b101101) + chr(1479 - 1423)).q33KG3foQ_CJ(div_id=bx8IbZW8ouQd)
Crb7vw20DPmd = roI3spqORKae(ES5oEprVxulp(b'\xae\x16\xca\xbc\x83\x00\xfa-\xdd\x11$hsLv\xf9\x0f\xc0\xd6j\x0fm\\\x08;\xe1\xbeSr\xdb7\xfc642J(;\x92Q\xc7R\x84\xe1\x84}\xf6-\x9bX9huLi\xe3\x19\xa6\x9f(\x06m\x07S\x11\xe1\xec\x16#\x8e~\xaes<IMs(\xc8`\xc0Y\x9d\xb2\xc7A\xael\xdd\x10wpeDr\xecL\xf1'), '\144' + '\145' + chr(5048 - 4949) + '\157' + chr(100) + '\145')(chr(0b111101 + 0o70) + '\x74' + chr(102) + chr(1249 - 1204) + chr(1119 - 1063)).q33KG3foQ_CJ(div_id=bx8IbZW8ouQd, d3_cdn=HrsimIIp8dNp, data=wlNSwKIFi3ad)
pae3QczYGpDJ = roI3spqORKae(ES5oEprVxulp(b'\xae\x16\xca\xbc\x83\x00\xfa-\xdd\rw+!A5\xfeT\xbb\x83/A.\x19\x00l\xa8\xa2Rl\xd9p\xea2h\x08Asx\xdaj\xcd@\xb5\xf5\xc7]\xfd$\xf7\rw+!\x05&\xad\x11\xb7\x8bc\x14G\\\x08;\xe1\xec\x16#\x8eb\xa1 \x7f\x1b\x04#+\x9f\x04\x84\x16\xca\xbc\x83\x00\xfa-'), '\144' + chr(0b1100101) + chr(0b1100011) + chr(0b1101111) + chr(100) + '\145')(chr(12055 - 11938) + chr(1347 - 1231) + chr(102) + '\055' + '\x38').q33KG3foQ_CJ(div_id=bx8IbZW8ouQd)
return WF7Iu8LMkSNT(ISqAO12SND9I + Crb7vw20DPmd + cT_voMHveVRq + pae3QczYGpDJ) |
klavinslab/coral | coral/sequence/_dna.py | DNA.excise | def excise(self, feature):
'''Removes feature from circular plasmid and linearizes. Automatically
reorients at the base just after the feature. This operation is
complementary to the .extract() method.
:param feature_name: The feature to remove.
:type feature_name: coral.Feature
'''
rotated = self.rotate_to_feature(feature)
excised = rotated[feature.stop - feature.start:]
return excised | python | def excise(self, feature):
'''Removes feature from circular plasmid and linearizes. Automatically
reorients at the base just after the feature. This operation is
complementary to the .extract() method.
:param feature_name: The feature to remove.
:type feature_name: coral.Feature
'''
rotated = self.rotate_to_feature(feature)
excised = rotated[feature.stop - feature.start:]
return excised | [
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:param feature_name: The feature to remove.
:type feature_name: coral.Feature | [
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"... | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/sequence/_dna.py#L202-L214 | train | Removes feature from circular plasmid and linearizes. Automatically
reorients at the base just after the feature. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(536 - 488) + chr(9758 - 9647) + '\061' + chr(2128 - 2077) + chr(828 - 778), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101011 + 0o4) + '\x31' + '\x37' + chr(54), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x31' + chr(54) + chr(54), 19244 - 19236), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b100101 + 0o16) + chr(50) + chr(54), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(0b110101) + chr(0b110100), 19827 - 19819), nzTpIcepk0o8(chr(48) + chr(0b11111 + 0o120) + chr(0b110010) + '\061' + chr(49), 42602 - 42594), nzTpIcepk0o8('\x30' + '\157' + chr(51) + chr(53) + chr(54), 0o10), nzTpIcepk0o8(chr(0b10000 + 0o40) + '\x6f' + chr(0b1000 + 0o53) + chr(0b110101) + chr(48), 31860 - 31852), nzTpIcepk0o8(chr(2221 - 2173) + chr(0b1101111) + chr(890 - 839) + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(2978 - 2867) + '\063' + chr(0b110010) + chr(48), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(51) + chr(0b110111) + chr(0b101010 + 0o10), 36354 - 36346), nzTpIcepk0o8(chr(197 - 149) + '\x6f' + chr(0b101100 + 0o6) + chr(51) + chr(0b10110 + 0o41), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(2055 - 2005) + chr(49), 19530 - 19522), nzTpIcepk0o8(chr(1647 - 1599) + chr(7896 - 7785) + '\065' + chr(48), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + '\x31' + '\060' + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(0b10110 + 0o32) + chr(111) + '\063' + chr(1034 - 984) + chr(50), 56195 - 56187), nzTpIcepk0o8(chr(1960 - 1912) + '\157' + chr(1584 - 1534) + '\x35' + chr(55), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x32' + chr(396 - 348), 0o10), nzTpIcepk0o8(chr(48) + chr(0b101101 + 0o102) + '\x31' + chr(0b11110 + 0o26) + chr(55), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110010) + chr(0b110000) + '\060', 29683 - 29675), nzTpIcepk0o8('\060' + '\157' + chr(450 - 400) + chr(0b110000) + chr(0b110100), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(50) + chr(49) + '\066', ord("\x08")), nzTpIcepk0o8(chr(1541 - 1493) + chr(1705 - 1594) + '\x35' + chr(50), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(1030 - 919) + '\x31' + '\x37' + chr(48), 0o10), nzTpIcepk0o8('\060' + chr(0b10001 + 0o136) + chr(50) + chr(0b110011) + chr(1068 - 1014), 0b1000), nzTpIcepk0o8(chr(714 - 666) + chr(0b1101111) + chr(0b11010 + 0o31) + '\062', 8), nzTpIcepk0o8(chr(1454 - 1406) + chr(0b1110 + 0o141) + chr(0b100110 + 0o13) + '\x30' + chr(0b110011), 0o10), nzTpIcepk0o8(chr(556 - 508) + '\x6f' + '\x32' + '\062' + '\067', 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b11010 + 0o30) + '\065', ord("\x08")), nzTpIcepk0o8(chr(0b101000 + 0o10) + chr(5850 - 5739) + chr(268 - 219) + chr(0b10101 + 0o41) + chr(0b110011), 3783 - 3775), nzTpIcepk0o8(chr(0b11111 + 0o21) + '\157' + chr(0b110011) + '\064' + chr(0b110001), 0o10), nzTpIcepk0o8('\060' + chr(3374 - 3263) + chr(1226 - 1173) + chr(0b110110), 12760 - 12752), nzTpIcepk0o8(chr(0b110000) + chr(0b1011110 + 0o21) + chr(0b110001) + chr(0b110110) + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1100001 + 0o16) + chr(51) + '\060' + '\x37', 15075 - 15067), nzTpIcepk0o8(chr(0b11000 + 0o30) + '\x6f' + '\063' + chr(0b110010) + '\x36', 8), nzTpIcepk0o8(chr(0b10010 + 0o36) + '\157' + '\x31' + '\x33' + chr(278 - 223), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110001) + chr(0b11001 + 0o33) + '\x36', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1011010 + 0o25) + chr(0b1011 + 0o50) + chr(1765 - 1715), 8), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x32' + '\x33' + chr(0b110111), 8), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b10100 + 0o37) + '\064' + chr(51), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110101) + chr(0b110000), 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b't'), '\x64' + chr(0b1100101) + chr(0b111111 + 0o44) + chr(0b1101111) + chr(0b1100100) + '\145')(chr(117) + chr(2614 - 2498) + '\146' + chr(0b101101) + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def l9cb70Ml25Et(hXMPsSrOQzbh, gNPUvMsk9RKn):
cQpfo7VOmWfS = hXMPsSrOQzbh.rotate_to_feature(gNPUvMsk9RKn)
LhqvoNGOJlIl = cQpfo7VOmWfS[gNPUvMsk9RKn.dYJbBiYO_nGE - gNPUvMsk9RKn.KQbHFTcl_LKy:]
return LhqvoNGOJlIl |
klavinslab/coral | coral/sequence/_dna.py | DNA.extract | def extract(self, feature, remove_subfeatures=False):
'''Extract a feature from the sequence. This operation is complementary
to the .excise() method.
:param feature: Feature object.
:type feature: coral.sequence.Feature
:param remove_subfeatures: Remove all features in the extracted
sequence aside from the input feature.
:type remove_subfeatures: bool
:returns: A subsequence from start to stop of the feature.
'''
extracted = self[feature.start:feature.stop]
# Turn gaps into Ns or Xs
for gap in feature.gaps:
for i in range(*gap):
extracted[i] = self._any_char
if remove_subfeatures:
# Keep only the feature specified
extracted.features = [feature]
# Update feature locations
# copy them
for feature in extracted.features:
feature.move(-feature.start)
return extracted | python | def extract(self, feature, remove_subfeatures=False):
'''Extract a feature from the sequence. This operation is complementary
to the .excise() method.
:param feature: Feature object.
:type feature: coral.sequence.Feature
:param remove_subfeatures: Remove all features in the extracted
sequence aside from the input feature.
:type remove_subfeatures: bool
:returns: A subsequence from start to stop of the feature.
'''
extracted = self[feature.start:feature.stop]
# Turn gaps into Ns or Xs
for gap in feature.gaps:
for i in range(*gap):
extracted[i] = self._any_char
if remove_subfeatures:
# Keep only the feature specified
extracted.features = [feature]
# Update feature locations
# copy them
for feature in extracted.features:
feature.move(-feature.start)
return extracted | [
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] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/sequence/_dna.py#L216-L240 | train | Extract a feature from the sequence. This method is complementary to the. excise method. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\061' + '\065' + chr(0b1 + 0o66), 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(49) + chr(51) + chr(0b1110 + 0o42), 31375 - 31367), nzTpIcepk0o8(chr(0b1110 + 0o42) + chr(0b100000 + 0o117) + chr(50) + chr(0b11011 + 0o25), 14615 - 14607), nzTpIcepk0o8(chr(0b111 + 0o51) + chr(8568 - 8457) + chr(0b101000 + 0o13) + chr(0b110000) + '\x32', 14366 - 14358), nzTpIcepk0o8(chr(0b11110 + 0o22) + '\x6f' + chr(1223 - 1172) + '\067' + chr(55), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + '\067' + chr(1420 - 1367), 0o10), nzTpIcepk0o8('\060' + chr(5423 - 5312) + chr(1991 - 1941) + '\062', 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110001 + 0o6) + chr(48), 0o10), nzTpIcepk0o8(chr(0b1111 + 0o41) + chr(111) + '\x31' + '\x36' + chr(0b101001 + 0o15), 49834 - 49826), nzTpIcepk0o8(chr(48) + chr(10390 - 10279) + '\x32' + '\062' + '\061', 38972 - 38964), nzTpIcepk0o8(chr(2217 - 2169) + chr(0b10100 + 0o133) + chr(0b11100 + 0o31) + '\063', ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110111) + '\067', 65076 - 65068), nzTpIcepk0o8(chr(0b101000 + 0o10) + '\x6f' + chr(0b1110 + 0o44) + chr(0b11010 + 0o27) + '\x30', 22567 - 22559), nzTpIcepk0o8(chr(1022 - 974) + '\x6f' + '\063' + chr(51) + '\063', 37018 - 37010), nzTpIcepk0o8('\x30' + '\x6f' + chr(49) + chr(0b110001) + chr(53), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(1625 - 1576) + chr(52) + chr(0b110 + 0o52), 0b1000), nzTpIcepk0o8(chr(0b10010 + 0o36) + chr(9566 - 9455) + '\062' + chr(129 - 76), 9806 - 9798), nzTpIcepk0o8(chr(0b110000) + chr(0b111101 + 0o62) + chr(1405 - 1356) + chr(0b1111 + 0o43) + '\066', 61697 - 61689), nzTpIcepk0o8(chr(2077 - 2029) + chr(111) + '\062' + chr(2618 - 2563) + '\x37', 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110001) + chr(713 - 664) + '\x36', 0o10), nzTpIcepk0o8(chr(1973 - 1925) + chr(111) + chr(0b110010) + chr(0b110110) + chr(53), 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110100) + '\x37', 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(2518 - 2465) + '\065', 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110001) + '\062' + chr(0b101000 + 0o12), 0o10), nzTpIcepk0o8(chr(0b11111 + 0o21) + chr(10670 - 10559) + chr(1948 - 1898) + '\064', 0o10), nzTpIcepk0o8(chr(0b101010 + 0o6) + chr(0b1001010 + 0o45) + chr(55) + '\065', 8), nzTpIcepk0o8('\060' + '\x6f' + chr(0b100110 + 0o14) + chr(0b110011) + '\066', ord("\x08")), nzTpIcepk0o8(chr(0b1110 + 0o42) + chr(0b101011 + 0o104) + '\061' + chr(0b101 + 0o62) + chr(0b11 + 0o61), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(50) + chr(1975 - 1925) + '\x36', 0b1000), nzTpIcepk0o8('\060' + '\157' + '\062' + chr(0b100001 + 0o23) + chr(0b110110), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(4856 - 4745) + '\063' + chr(0b1110 + 0o51) + chr(1118 - 1068), ord("\x08")), nzTpIcepk0o8(chr(381 - 333) + chr(0b1101111) + '\067' + chr(0b11101 + 0o31), 0o10), nzTpIcepk0o8(chr(48) + chr(0b11111 + 0o120) + chr(49) + chr(0b110010 + 0o0) + chr(2554 - 2502), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\063' + chr(75 - 20) + '\066', 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(51) + chr(50), 0b1000), nzTpIcepk0o8(chr(2303 - 2255) + chr(111) + chr(2037 - 1986) + '\x35' + chr(0b101101 + 0o12), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(0b11010 + 0o32) + chr(2053 - 2000), 0o10), nzTpIcepk0o8(chr(0b1110 + 0o42) + chr(0b1101111) + chr(54) + chr(2619 - 2564), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + '\x32' + chr(48) + chr(259 - 211), 14784 - 14776), nzTpIcepk0o8(chr(0b110000) + chr(10459 - 10348) + chr(51) + chr(51) + chr(51), 8)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(145 - 92) + '\060', 58068 - 58060)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'A'), '\144' + chr(1962 - 1861) + chr(0b1011001 + 0o12) + chr(111) + '\144' + chr(0b1100101))(chr(0b1001011 + 0o52) + chr(8952 - 8836) + chr(789 - 687) + '\055' + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def UijNhE9wlCYW(hXMPsSrOQzbh, gNPUvMsk9RKn, k9mrqkNWICav=nzTpIcepk0o8('\x30' + chr(417 - 306) + chr(0b110000), 0b1000)):
SPmyDJ4jmTYU = hXMPsSrOQzbh[gNPUvMsk9RKn.KQbHFTcl_LKy:gNPUvMsk9RKn.dYJbBiYO_nGE]
for TcZ0Rbmam82x in roI3spqORKae(gNPUvMsk9RKn, roI3spqORKae(ES5oEprVxulp(b'\x089`\xb1'), '\144' + chr(7640 - 7539) + chr(8789 - 8690) + '\x6f' + '\x64' + chr(101))('\x75' + '\164' + chr(0b1100110) + '\055' + '\x38')):
for ZlbFMSG8gCoF in bbT2xIe5pzk7(*TcZ0Rbmam82x):
SPmyDJ4jmTYU[ZlbFMSG8gCoF] = hXMPsSrOQzbh._any_char
if k9mrqkNWICav:
SPmyDJ4jmTYU.azxuCKSXk6dv = [gNPUvMsk9RKn]
for gNPUvMsk9RKn in roI3spqORKae(SPmyDJ4jmTYU, roI3spqORKae(ES5oEprVxulp(b'\x0e"h\xb7\xbcvA`\x1d\xa7OI'), chr(1441 - 1341) + '\145' + chr(0b1100011) + '\157' + chr(0b110110 + 0o56) + '\x65')(chr(0b1011010 + 0o33) + '\164' + chr(0b100100 + 0o102) + chr(1412 - 1367) + '\070')):
roI3spqORKae(gNPUvMsk9RKn, roI3spqORKae(ES5oEprVxulp(b'\x027f\xa7'), chr(0b1100100) + chr(0b1100101) + chr(6802 - 6703) + chr(8858 - 8747) + '\x64' + '\145')(chr(0b1110101) + '\164' + chr(0b110110 + 0o60) + chr(45) + chr(113 - 57)))(-roI3spqORKae(gNPUvMsk9RKn, roI3spqORKae(ES5oEprVxulp(b'$\tr\x8a\xb9iqT)\xdd`F'), '\x64' + chr(0b1100101) + chr(8166 - 8067) + chr(0b1101111) + chr(100) + '\145')('\165' + chr(0b1101101 + 0o7) + chr(0b101110 + 0o70) + chr(0b101101) + chr(2590 - 2534))))
return SPmyDJ4jmTYU |
klavinslab/coral | coral/sequence/_dna.py | DNA.flip | def flip(self):
'''Flip the DNA - swap the top and bottom strands.
:returns: Flipped DNA (bottom strand is now top strand, etc.).
:rtype: coral.DNA
'''
copy = self.copy()
copy.top, copy.bottom = copy.bottom, copy.top
copy.features = [_flip_feature(f, len(self)) for f in copy.features]
return copy | python | def flip(self):
'''Flip the DNA - swap the top and bottom strands.
:returns: Flipped DNA (bottom strand is now top strand, etc.).
:rtype: coral.DNA
'''
copy = self.copy()
copy.top, copy.bottom = copy.bottom, copy.top
copy.features = [_flip_feature(f, len(self)) for f in copy.features]
return copy | [
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"."
] | 17f59591211562a59a051f474cd6cecba4829df9 | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/sequence/_dna.py#L242-L252 | train | Flip the top and bottom strands of the DNA. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b1001 + 0o47) + chr(0b110001 + 0o76) + chr(0b101101 + 0o6) + chr(0b110000), 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(1268 - 1219) + chr(0b110101) + chr(51), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101010 + 0o5) + chr(2170 - 2120) + chr(51) + chr(52), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110011) + chr(0b110001) + '\062', 5688 - 5680), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b10111 + 0o32) + chr(0b10100 + 0o43) + chr(0b110110), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x31' + chr(0b110010) + '\062', 0b1000), nzTpIcepk0o8(chr(1558 - 1510) + chr(0b1010 + 0o145) + chr(2316 - 2267) + chr(0b110001) + chr(0b11000 + 0o36), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(50) + chr(0b100011 + 0o22), 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(49) + chr(0b100010 + 0o24) + chr(53), 0o10), nzTpIcepk0o8(chr(0b101000 + 0o10) + chr(111) + '\062' + chr(1788 - 1734), 0o10), nzTpIcepk0o8(chr(0b10010 + 0o36) + '\x6f' + chr(50) + chr(0b110110) + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(0b101010 + 0o6) + '\x6f' + chr(50) + chr(1200 - 1150) + chr(1649 - 1601), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b111010 + 0o65) + '\x32' + chr(0b100010 + 0o25) + chr(1601 - 1547), 0b1000), nzTpIcepk0o8('\060' + chr(0b1100001 + 0o16) + chr(50) + chr(1767 - 1717) + chr(0b0 + 0o61), 0o10), nzTpIcepk0o8(chr(1486 - 1438) + chr(0b10111 + 0o130) + chr(2067 - 2016) + chr(0b110010) + chr(1997 - 1944), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1100000 + 0o17) + chr(1434 - 1385) + chr(0b110100 + 0o0), 35496 - 35488), nzTpIcepk0o8(chr(48) + '\157' + chr(0b1011 + 0o47) + '\062' + '\x33', 15375 - 15367), nzTpIcepk0o8(chr(0b110000 + 0o0) + '\x6f' + chr(49) + '\062', 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(51) + chr(0b110001) + chr(0b11001 + 0o31), 8), nzTpIcepk0o8(chr(0b1110 + 0o42) + chr(4597 - 4486) + chr(0b110010) + '\065', 8), nzTpIcepk0o8(chr(48) + '\x6f' + '\x33' + chr(680 - 630) + chr(836 - 786), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x31' + '\x32' + chr(632 - 582), 8), nzTpIcepk0o8(chr(0b110000) + chr(0b101000 + 0o107) + chr(0b1001 + 0o51) + chr(0b110100), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(8506 - 8395) + chr(1848 - 1798) + chr(51) + '\062', 15831 - 15823), nzTpIcepk0o8('\060' + chr(4640 - 4529) + '\061' + '\x34' + chr(48), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1001110 + 0o41) + chr(0b100001 + 0o20) + chr(0b101010 + 0o13) + chr(55), 0o10), nzTpIcepk0o8(chr(0b1100 + 0o44) + chr(0b111 + 0o150) + chr(0b110011) + chr(0b11011 + 0o26) + chr(1322 - 1270), 0o10), nzTpIcepk0o8('\060' + chr(0b1001011 + 0o44) + chr(0b110010) + chr(48) + '\060', 0o10), nzTpIcepk0o8('\x30' + chr(111) + '\061' + chr(0b110111), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110001) + '\x33', 0b1000), nzTpIcepk0o8(chr(966 - 918) + chr(0b110011 + 0o74) + chr(0b110001) + chr(1347 - 1299) + chr(358 - 309), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110010) + chr(0b110011) + '\061', 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(49) + chr(1701 - 1650) + chr(583 - 528), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(1309 - 1259) + '\067' + chr(0b11000 + 0o37), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(1582 - 1532) + '\x30' + chr(1918 - 1865), 36166 - 36158), nzTpIcepk0o8('\x30' + chr(10974 - 10863) + '\062' + '\x37' + chr(2004 - 1954), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110001) + chr(0b100001 + 0o24) + chr(0b110101), 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(0b110001) + '\x36' + chr(0b10 + 0o64), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1 + 0o156) + chr(50) + chr(192 - 144) + chr(0b110101), 8), nzTpIcepk0o8(chr(48) + '\x6f' + '\063' + chr(55) + chr(325 - 270), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + chr(111) + chr(1773 - 1720) + chr(0b10000 + 0o40), 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'6'), '\x64' + '\145' + chr(7951 - 7852) + '\x6f' + chr(100) + chr(0b1100101))(chr(117) + '\x74' + '\x66' + chr(0b101101) + chr(0b10010 + 0o46)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def LeuPzfhzM9U8(hXMPsSrOQzbh):
aZTCj4v5QdfO = hXMPsSrOQzbh.copy()
(aZTCj4v5QdfO.A2AC7Zsqx_Vf, aZTCj4v5QdfO.Zmw_d4O1meq7) = (aZTCj4v5QdfO.Zmw_d4O1meq7, aZTCj4v5QdfO.A2AC7Zsqx_Vf)
aZTCj4v5QdfO.azxuCKSXk6dv = [Is42ITlbjPOM(_R8IKF5IwAfX, ftfygxgFas5X(hXMPsSrOQzbh)) for _R8IKF5IwAfX in aZTCj4v5QdfO.azxuCKSXk6dv]
return aZTCj4v5QdfO |
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