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openvax/varcode | varcode/effects/effect_ordering.py | cds_length_of_associated_transcript | def cds_length_of_associated_transcript(effect):
"""
Length of coding sequence of transcript associated with effect,
if there is one (otherwise return 0).
"""
return apply_to_transcript_if_exists(
effect=effect,
fn=lambda t: len(t.coding_sequence) if (t.complete and t.coding_sequence) else 0,
default=0) | python | def cds_length_of_associated_transcript(effect):
"""
Length of coding sequence of transcript associated with effect,
if there is one (otherwise return 0).
"""
return apply_to_transcript_if_exists(
effect=effect,
fn=lambda t: len(t.coding_sequence) if (t.complete and t.coding_sequence) else 0,
default=0) | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/effect_ordering.py#L146-L154 | train | Returns the length of the coding sequence of the associated transcript. | 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(111) + '\x33' + chr(2033 - 1982) + chr(397 - 342), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(88 - 37) + '\x37' + '\061', 0o10), nzTpIcepk0o8('\060' + '\157' + chr(1537 - 1488) + chr(2353 - 2303) + chr(0b110010), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + '\065', 0o10), nzTpIcepk0o8(chr(1232 - 1184) + chr(111) + chr(0b110011) + chr(0b110110) + chr(1872 - 1820), ord("\x08")), nzTpIcepk0o8(chr(270 - 222) + chr(0b110101 + 0o72) + chr(0b11111 + 0o22) + chr(0b10001 + 0o43) + chr(0b110101 + 0o2), 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(53), 8), nzTpIcepk0o8(chr(0b111 + 0o51) + chr(10176 - 10065) + '\x34', 0b1000), nzTpIcepk0o8('\x30' + chr(3244 - 3133) + chr(0b101000 + 0o14) + chr(51), 8774 - 8766), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x33' + '\x30' + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(240 - 192) + chr(111) + '\066' + chr(51), ord("\x08")), nzTpIcepk0o8(chr(2244 - 2196) + '\x6f' + chr(357 - 307), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110001) + chr(0b110011) + chr(0b110011), 24131 - 24123), nzTpIcepk0o8(chr(0b1011 + 0o45) + chr(0b110010 + 0o75) + chr(51) + chr(54) + '\x36', 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + '\x33' + chr(0b110111) + '\064', 34702 - 34694), nzTpIcepk0o8(chr(0b10010 + 0o36) + chr(6007 - 5896) + '\x31' + '\064' + '\064', ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + chr(49) + chr(2773 - 2719) + '\065', ord("\x08")), nzTpIcepk0o8('\x30' + chr(8968 - 8857) + chr(0b100 + 0o60) + chr(0b110110), ord("\x08")), nzTpIcepk0o8(chr(2232 - 2184) + chr(0b1101111) + '\062' + chr(0b110011) + chr(2313 - 2264), 0b1000), nzTpIcepk0o8('\x30' + chr(5806 - 5695) + chr(0b10010 + 0o40) + chr(0b110111 + 0o0) + chr(0b100011 + 0o16), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110001) + chr(0b110010) + chr(1615 - 1567), 0o10), nzTpIcepk0o8('\x30' + chr(0b1010110 + 0o31) + chr(51) + '\x33' + chr(0b110110), 0o10), nzTpIcepk0o8('\060' + chr(5314 - 5203) + chr(1169 - 1119) + chr(970 - 919), ord("\x08")), nzTpIcepk0o8(chr(0b100010 + 0o16) + '\x6f' + chr(0b101110 + 0o5) + '\x37' + chr(52), 8), nzTpIcepk0o8('\x30' + chr(111) + chr(51) + chr(0b110010 + 0o0) + chr(0b110000), 0b1000), nzTpIcepk0o8('\x30' + chr(8523 - 8412) + '\061' + chr(0b110001) + chr(0b10000 + 0o44), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + '\061' + '\061' + chr(903 - 850), 0o10), nzTpIcepk0o8(chr(336 - 288) + chr(111) + chr(49) + chr(1792 - 1739), ord("\x08")), nzTpIcepk0o8(chr(0b11000 + 0o30) + chr(111) + chr(0b110001) + chr(53) + '\x35', ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + '\x33' + chr(0b100101 + 0o15) + chr(0b100 + 0o55), 0o10), nzTpIcepk0o8('\x30' + chr(0b11100 + 0o123) + chr(0b10100 + 0o41) + chr(55), 382 - 374), nzTpIcepk0o8('\x30' + '\x6f' + '\x32' + chr(0b110110), 9918 - 9910), nzTpIcepk0o8(chr(0b100001 + 0o17) + chr(0b1101111) + chr(2145 - 2095), 8), nzTpIcepk0o8(chr(696 - 648) + chr(111) + chr(1604 - 1555) + chr(0b110000) + chr(49), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(1068 - 1018) + chr(0b110001) + chr(1626 - 1575), 21104 - 21096), nzTpIcepk0o8(chr(1319 - 1271) + chr(0b1101111) + '\x33' + chr(0b110101) + '\062', 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(100 - 51) + '\067' + chr(998 - 949), 0b1000), nzTpIcepk0o8(chr(0b11001 + 0o27) + '\x6f' + '\061' + chr(52) + chr(0b110001), 0b1000), nzTpIcepk0o8(chr(251 - 203) + chr(0b1011 + 0o144) + chr(278 - 227) + chr(0b101 + 0o57) + chr(1934 - 1885), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\063' + chr(55) + chr(838 - 784), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b101111 + 0o6) + '\x30', 53292 - 53284)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xf1'), '\144' + '\x65' + chr(3254 - 3155) + '\157' + '\x64' + chr(0b1100101))(chr(13491 - 13374) + chr(0b1110100) + '\146' + chr(0b101101) + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def sNTqK0jx1yku(WueclzVPVP7r):
return IlSN4xxGCzHm(effect=WueclzVPVP7r, fn=lambda h3Vc_4wxEbgd: ftfygxgFas5X(roI3spqORKae(h3Vc_4wxEbgd, roI3spqORKae(ES5oEprVxulp(b'\xbc\x966l\x9a\x00ZwF\xb3Fg5\x95\x99'), '\144' + chr(9557 - 9456) + chr(0b1100011) + '\x6f' + chr(382 - 282) + chr(0b100010 + 0o103))('\x75' + chr(0b1110011 + 0o1) + chr(10248 - 10146) + chr(1865 - 1820) + '\x38'))) if roI3spqORKae(h3Vc_4wxEbgd, roI3spqORKae(ES5oEprVxulp(b"\x8b\x9d'P\xa1\x0bPot\x92@4"), chr(0b1100100) + chr(0b10101 + 0o120) + chr(0b11000 + 0o113) + '\x6f' + chr(100) + chr(0b1011000 + 0o15))(chr(3460 - 3343) + chr(116) + chr(0b101 + 0o141) + chr(871 - 826) + chr(0b1110 + 0o52))) and roI3spqORKae(h3Vc_4wxEbgd, roI3spqORKae(ES5oEprVxulp(b'\xbc\x966l\x9a\x00ZwF\xb3Fg5\x95\x99'), '\144' + '\x65' + '\x63' + '\157' + '\144' + '\x65')(chr(8481 - 8364) + chr(116) + '\146' + chr(0b101101) + chr(56))) else nzTpIcepk0o8(chr(0b11 + 0o55) + '\157' + chr(1926 - 1878), 0o10), default=nzTpIcepk0o8('\x30' + chr(111) + chr(1166 - 1118), 8)) |
openvax/varcode | varcode/effects/effect_ordering.py | length_of_associated_transcript | def length_of_associated_transcript(effect):
"""
Length of spliced mRNA sequence of transcript associated with effect,
if there is one (otherwise return 0).
"""
return apply_to_transcript_if_exists(
effect=effect,
fn=lambda t: len(t.sequence),
default=0) | python | def length_of_associated_transcript(effect):
"""
Length of spliced mRNA sequence of transcript associated with effect,
if there is one (otherwise return 0).
"""
return apply_to_transcript_if_exists(
effect=effect,
fn=lambda t: len(t.sequence),
default=0) | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/effect_ordering.py#L157-L165 | train | Returns the length of spliced mRNA sequence of transcript associated with effect. | 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) + chr(2248 - 2195) + chr(50), 0o10), nzTpIcepk0o8('\060' + chr(0b1000001 + 0o56) + chr(0b110011) + chr(0b110010) + chr(2462 - 2408), ord("\x08")), nzTpIcepk0o8(chr(634 - 586) + chr(0b1100100 + 0o13) + '\x35', 0o10), nzTpIcepk0o8('\x30' + '\157' + '\x34' + '\x36', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(8671 - 8560) + chr(0b110011) + '\x30' + chr(52), 15867 - 15859), nzTpIcepk0o8(chr(1527 - 1479) + chr(111) + chr(0b110001) + chr(1405 - 1350) + chr(48), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(2673 - 2562) + '\x33' + chr(0b11111 + 0o21) + chr(2584 - 2531), 6329 - 6321), nzTpIcepk0o8(chr(0b11011 + 0o25) + '\157' + chr(1737 - 1687) + '\066' + chr(0b110111), 9704 - 9696), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110011) + chr(0b10110 + 0o41) + chr(51), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110111) + '\x35', ord("\x08")), nzTpIcepk0o8(chr(0b110000 + 0o0) + chr(0b1010001 + 0o36) + chr(51) + '\064' + chr(0b100 + 0o60), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + '\062' + chr(0b110100), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\062' + '\066' + chr(0b1110 + 0o43), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1010010 + 0o35) + '\062' + chr(0b110110) + chr(0b11 + 0o56), 8), nzTpIcepk0o8('\060' + chr(111) + '\066' + chr(144 - 90), 60779 - 60771), nzTpIcepk0o8(chr(48) + chr(0b11110 + 0o121) + '\x31' + chr(0b110100) + '\x31', 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b101001 + 0o10) + chr(0b100001 + 0o22) + '\x34', 0o10), nzTpIcepk0o8(chr(0b11010 + 0o26) + chr(5534 - 5423) + chr(0b10101 + 0o34) + '\x37' + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + '\063' + chr(0b110111) + chr(0b1110 + 0o47), 0b1000), nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(10091 - 9980) + chr(273 - 222) + chr(0b110010) + chr(0b110010), 61690 - 61682), nzTpIcepk0o8(chr(1587 - 1539) + chr(0b110010 + 0o75) + '\063' + chr(0b100001 + 0o20), 0o10), nzTpIcepk0o8(chr(0b101101 + 0o3) + chr(5685 - 5574) + chr(0b110001) + chr(0b110001) + '\065', ord("\x08")), nzTpIcepk0o8(chr(0b11111 + 0o21) + chr(12013 - 11902) + chr(1847 - 1793) + '\x36', 8), nzTpIcepk0o8('\060' + '\157' + chr(1083 - 1032) + chr(50) + chr(630 - 579), 37937 - 37929), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(212 - 163) + chr(909 - 854) + chr(0b100000 + 0o20), 8), nzTpIcepk0o8(chr(0b1 + 0o57) + '\x6f' + chr(0b11101 + 0o26) + chr(2184 - 2133), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110001) + chr(0b101100 + 0o10) + '\x30', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x31' + chr(1565 - 1516) + chr(55), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b110101 + 0o72) + chr(51) + '\x37' + chr(0b110011), 8), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(51) + '\061' + '\067', 0b1000), nzTpIcepk0o8('\060' + chr(0b10111 + 0o130) + chr(0b110001 + 0o0) + chr(0b10011 + 0o42) + chr(0b101010 + 0o13), 0o10), nzTpIcepk0o8('\060' + chr(7451 - 7340) + chr(50) + chr(0b110000) + '\x32', 65307 - 65299), nzTpIcepk0o8(chr(0b1000 + 0o50) + chr(0b10000 + 0o137) + '\x32' + chr(54) + chr(0b100100 + 0o20), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x30', 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(1426 - 1376) + chr(343 - 288) + chr(48), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b101111 + 0o100) + chr(1849 - 1799) + chr(54) + '\x37', 8), nzTpIcepk0o8(chr(0b110000) + chr(0b111011 + 0o64) + chr(0b110011) + '\065', 0o10), nzTpIcepk0o8(chr(0b10 + 0o56) + '\157' + '\x31' + '\064' + chr(0b110110), 0b1000), nzTpIcepk0o8(chr(324 - 276) + chr(8614 - 8503) + chr(0b0 + 0o61) + '\x34' + '\067', 21078 - 21070), nzTpIcepk0o8('\x30' + '\x6f' + chr(2248 - 2197) + chr(222 - 167) + '\x37', 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x35' + '\x30', 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x04'), '\x64' + '\145' + '\143' + chr(1148 - 1037) + chr(0b101110 + 0o66) + chr(8250 - 8149))('\x75' + chr(0b101111 + 0o105) + '\x66' + '\x2d' + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def GQvOW0LZKSh5(WueclzVPVP7r):
return IlSN4xxGCzHm(effect=WueclzVPVP7r, fn=lambda h3Vc_4wxEbgd: ftfygxgFas5X(roI3spqORKae(h3Vc_4wxEbgd, roI3spqORKae(ES5oEprVxulp(b"k\xb7CC\xabH\xa9\xc0\xc8\t\xa7'"), chr(5284 - 5184) + chr(101) + chr(99) + chr(111) + '\144' + chr(0b1100100 + 0o1))(chr(0b1110101) + chr(0b1001001 + 0o53) + chr(0b1001101 + 0o31) + chr(0b100111 + 0o6) + chr(0b111000)))), default=nzTpIcepk0o8('\x30' + '\157' + chr(0b100001 + 0o17), 8)) |
openvax/varcode | varcode/effects/effect_ordering.py | name_of_associated_transcript | def name_of_associated_transcript(effect):
"""
Name of transcript associated with effect,
if there is one (otherwise return "").
"""
return apply_to_transcript_if_exists(
effect=effect,
fn=lambda t: t.name,
default="") | python | def name_of_associated_transcript(effect):
"""
Name of transcript associated with effect,
if there is one (otherwise return "").
"""
return apply_to_transcript_if_exists(
effect=effect,
fn=lambda t: t.name,
default="") | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/effect_ordering.py#L168-L176 | train | Returns the name of the associated transcript. | 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) + '\066' + '\x36', 0b1000), nzTpIcepk0o8('\x30' + chr(8396 - 8285) + '\062' + chr(2735 - 2681) + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(0b101001 + 0o7) + chr(11604 - 11493) + chr(2160 - 2111) + chr(54), 6894 - 6886), nzTpIcepk0o8(chr(0b101001 + 0o7) + chr(7418 - 7307) + chr(2367 - 2316) + chr(1127 - 1073) + '\x34', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b100 + 0o57) + '\061' + chr(2545 - 2490), 0b1000), nzTpIcepk0o8(chr(471 - 423) + chr(0b1101111) + '\x33' + '\065' + '\064', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(9554 - 9443) + chr(358 - 309) + chr(0b110110) + chr(2277 - 2226), 57784 - 57776), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(153 - 104) + chr(49) + chr(188 - 140), 62263 - 62255), nzTpIcepk0o8('\060' + '\x6f' + chr(2378 - 2329) + chr(0b110111) + chr(0b100100 + 0o17), 24416 - 24408), nzTpIcepk0o8(chr(692 - 644) + chr(4527 - 4416) + chr(0b110010) + chr(629 - 577) + chr(1726 - 1675), 53723 - 53715), nzTpIcepk0o8(chr(574 - 526) + chr(0b1101111) + chr(51) + chr(0b110100) + '\065', 56388 - 56380), nzTpIcepk0o8('\060' + chr(111) + '\061' + chr(0b11010 + 0o33) + '\062', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1001010 + 0o45) + chr(512 - 463) + chr(0b10100 + 0o35) + chr(55), 3024 - 3016), nzTpIcepk0o8(chr(1480 - 1432) + chr(0b1101111) + chr(0b110110) + chr(2893 - 2839), 8), nzTpIcepk0o8(chr(0b111 + 0o51) + chr(0b1000001 + 0o56) + chr(0b110001 + 0o1) + '\x36' + '\064', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110010), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(2277 - 2228) + chr(55) + chr(0b110101), 0b1000), nzTpIcepk0o8('\x30' + chr(6756 - 6645) + chr(1855 - 1805) + '\x32', 5351 - 5343), nzTpIcepk0o8(chr(405 - 357) + chr(10046 - 9935) + '\x36' + '\062', 0o10), nzTpIcepk0o8(chr(0b10000 + 0o40) + chr(8523 - 8412) + chr(51) + chr(49) + chr(0b110010), 0o10), nzTpIcepk0o8(chr(931 - 883) + chr(0b1101111) + chr(0b101000 + 0o11) + chr(53) + chr(1135 - 1086), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110011) + chr(53) + '\062', 22715 - 22707), nzTpIcepk0o8(chr(0b101010 + 0o6) + chr(1038 - 927) + chr(1820 - 1771) + '\060' + '\x37', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(2705 - 2594) + chr(0b110010) + '\x32' + chr(54), 0b1000), nzTpIcepk0o8('\x30' + chr(9686 - 9575) + chr(518 - 465) + chr(516 - 463), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110011) + chr(0b11001 + 0o36) + '\x32', 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + '\063' + chr(348 - 298) + '\067', 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(49) + chr(48) + chr(0b11 + 0o63), ord("\x08")), nzTpIcepk0o8(chr(683 - 635) + chr(0b1101111) + chr(1085 - 1033) + chr(0b101101 + 0o3), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b11011 + 0o26) + chr(49) + chr(50), ord("\x08")), nzTpIcepk0o8(chr(2196 - 2148) + chr(3941 - 3830) + chr(49) + chr(0b110011) + chr(0b110001), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110001), 24561 - 24553), nzTpIcepk0o8(chr(272 - 224) + '\x6f' + chr(0b11011 + 0o33) + chr(52), 53804 - 53796), nzTpIcepk0o8('\060' + chr(111) + chr(0b101000 + 0o11) + chr(50) + chr(0b101101 + 0o5), 0o10), nzTpIcepk0o8('\x30' + chr(11007 - 10896) + '\062' + chr(0b11000 + 0o37) + chr(52), 57151 - 57143), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110001) + chr(0b100010 + 0o25) + chr(0b10101 + 0o36), 8), nzTpIcepk0o8(chr(0b110000) + chr(0b111001 + 0o66) + chr(1337 - 1285) + '\061', 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b1 + 0o62) + chr(1475 - 1426) + '\067', 8), nzTpIcepk0o8(chr(1058 - 1010) + chr(0b1000 + 0o147) + chr(51) + chr(53) + '\x34', 8), nzTpIcepk0o8('\060' + chr(111) + chr(1134 - 1083) + '\x35' + '\x33', ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + chr(0b1101111) + chr(53) + chr(1477 - 1429), 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x18'), chr(181 - 81) + chr(0b1100101) + chr(0b1000 + 0o133) + '\x6f' + chr(100) + chr(101))('\x75' + chr(0b10 + 0o162) + '\146' + '\x2d' + chr(0b100001 + 0o27)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def nDpr4fO2AeEC(WueclzVPVP7r):
return IlSN4xxGCzHm(effect=WueclzVPVP7r, fn=lambda h3Vc_4wxEbgd: roI3spqORKae(h3Vc_4wxEbgd, roI3spqORKae(ES5oEprVxulp(b'e\xfcX\xb6\xfd\xae#\t$\xce\xac\x0f'), chr(100) + chr(2881 - 2780) + '\143' + '\157' + chr(100) + chr(0b1010000 + 0o25))(chr(117) + chr(0b1110100) + chr(102) + chr(0b101101) + chr(0b1110 + 0o52))), default=roI3spqORKae(ES5oEprVxulp(b''), '\x64' + chr(7121 - 7020) + chr(0b1100011) + '\x6f' + chr(0b1001111 + 0o25) + chr(4698 - 4597))('\165' + '\164' + chr(0b1100110) + chr(1474 - 1429) + chr(56))) |
openvax/varcode | varcode/effects/effect_ordering.py | gene_id_of_associated_transcript | def gene_id_of_associated_transcript(effect):
"""
Ensembl gene ID of transcript associated with effect, returns
None if effect does not have transcript.
"""
return apply_to_transcript_if_exists(
effect=effect,
fn=lambda t: t.gene_id,
default=None) | python | def gene_id_of_associated_transcript(effect):
"""
Ensembl gene ID of transcript associated with effect, returns
None if effect does not have transcript.
"""
return apply_to_transcript_if_exists(
effect=effect,
fn=lambda t: t.gene_id,
default=None) | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/effect_ordering.py#L179-L187 | train | Ensembl gene ID of associated transcript with effect. | 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(10661 - 10550) + chr(0b110010) + chr(0b110001) + chr(2827 - 2772), 0o10), nzTpIcepk0o8(chr(1092 - 1044) + chr(0b1101111) + '\062' + chr(0b1001 + 0o56) + chr(53), 0o10), nzTpIcepk0o8('\x30' + chr(0b111010 + 0o65) + '\x33' + chr(50) + '\x32', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(11184 - 11073) + chr(629 - 574) + chr(0b1001 + 0o53), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\065', 4061 - 4053), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b101001 + 0o12) + '\062' + chr(48), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b1000 + 0o53), 0o10), nzTpIcepk0o8(chr(0b101111 + 0o1) + '\157' + '\061' + chr(0b10 + 0o60) + '\061', 0o10), nzTpIcepk0o8('\060' + chr(111) + '\x36' + chr(49), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(818 - 767) + '\066' + chr(51), 0o10), nzTpIcepk0o8('\x30' + chr(6445 - 6334) + chr(1887 - 1836) + chr(1912 - 1864) + chr(0b11011 + 0o27), 0o10), nzTpIcepk0o8(chr(0b10101 + 0o33) + chr(0b1101111) + chr(0b110011) + '\x33' + '\x35', 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(50) + chr(1452 - 1400) + '\x31', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x33' + '\062' + '\065', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(10423 - 10312) + chr(0b1 + 0o65) + '\x36', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(8024 - 7913) + chr(0b110111) + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(0b111 + 0o51) + '\157' + chr(0b110011) + chr(1426 - 1374) + chr(1776 - 1723), 48912 - 48904), nzTpIcepk0o8(chr(267 - 219) + chr(0b1101111) + chr(50) + '\x37' + chr(55), 0o10), nzTpIcepk0o8(chr(0b10101 + 0o33) + chr(0b1101111) + chr(260 - 210) + '\x35' + '\064', 0o10), nzTpIcepk0o8('\x30' + chr(2636 - 2525) + chr(0b100010 + 0o21) + chr(1879 - 1831) + chr(261 - 208), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1000111 + 0o50) + '\x31' + chr(50) + chr(0b1111 + 0o41), ord("\x08")), nzTpIcepk0o8(chr(0b10000 + 0o40) + '\157' + chr(0b110011) + chr(495 - 445) + chr(55), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(712 - 662) + chr(0b110010) + chr(0b100001 + 0o23), 50282 - 50274), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\063' + chr(2166 - 2112) + chr(52), 2237 - 2229), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(1653 - 1600) + chr(757 - 703), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b11111 + 0o25), 23689 - 23681), nzTpIcepk0o8(chr(48) + '\x6f' + '\062' + chr(672 - 621) + chr(0b101101 + 0o3), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(3877 - 3766) + '\061' + chr(48) + '\x31', 0b1000), nzTpIcepk0o8(chr(712 - 664) + chr(11157 - 11046) + chr(1012 - 963) + '\060' + chr(49), 8), nzTpIcepk0o8(chr(48) + chr(956 - 845) + chr(0b11000 + 0o31) + chr(0b1011 + 0o53) + '\x30', 0o10), nzTpIcepk0o8(chr(1976 - 1928) + '\x6f' + '\063' + chr(1382 - 1332) + '\060', 8), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(2414 - 2363) + chr(48) + chr(1414 - 1366), 34969 - 34961), nzTpIcepk0o8(chr(48) + chr(111) + chr(50) + '\x37' + '\x35', 8), nzTpIcepk0o8(chr(0b110000) + '\157' + '\063' + chr(274 - 226) + '\063', 0b1000), nzTpIcepk0o8(chr(0b110000 + 0o0) + chr(553 - 442) + chr(0b110010) + '\060' + chr(0b110001), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110001) + chr(48) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(471 - 423) + chr(111) + chr(49), 0b1000), nzTpIcepk0o8('\x30' + chr(8009 - 7898) + chr(51) + chr(305 - 255) + chr(0b11000 + 0o36), 0b1000), nzTpIcepk0o8(chr(1995 - 1947) + '\157' + chr(2318 - 2268) + chr(0b111 + 0o51) + chr(0b11110 + 0o23), 8), nzTpIcepk0o8('\060' + chr(0b100000 + 0o117) + chr(0b110011) + chr(0b110010) + chr(0b110010), 8)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + '\x6f' + chr(53) + '\060', 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xa1'), '\144' + chr(0b110110 + 0o57) + chr(5698 - 5599) + '\157' + chr(0b1100100) + '\145')(chr(0b110000 + 0o105) + chr(116) + chr(102) + chr(0b100101 + 0o10) + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def WA11YIivOKML(WueclzVPVP7r):
return IlSN4xxGCzHm(effect=WueclzVPVP7r, fn=lambda h3Vc_4wxEbgd: roI3spqORKae(h3Vc_4wxEbgd, roI3spqORKae(ES5oEprVxulp(b'\xe8\xd8\xbcYZ\xb9g'), chr(0b1100100) + '\145' + chr(7297 - 7198) + chr(0b1101111) + chr(1953 - 1853) + '\x65')(chr(6773 - 6656) + chr(0b1110100) + '\146' + chr(213 - 168) + '\070')), default=None) |
openvax/varcode | varcode/effects/effect_ordering.py | effect_has_complete_transcript | def effect_has_complete_transcript(effect):
"""
Parameters
----------
effect : subclass of MutationEffect
Returns True if effect has transcript and that transcript has complete CDS
"""
return apply_to_transcript_if_exists(
effect=effect,
fn=lambda t: t.complete,
default=False) | python | def effect_has_complete_transcript(effect):
"""
Parameters
----------
effect : subclass of MutationEffect
Returns True if effect has transcript and that transcript has complete CDS
"""
return apply_to_transcript_if_exists(
effect=effect,
fn=lambda t: t.complete,
default=False) | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/effect_ordering.py#L190-L201 | train | Returns True if effect has complete transcript False otherwise | 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(50), ord("\x08")), nzTpIcepk0o8(chr(1919 - 1871) + '\x6f' + '\x34' + '\x34', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110011) + '\x31', 49246 - 49238), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\061' + chr(0b111 + 0o60) + chr(50), ord("\x08")), nzTpIcepk0o8(chr(0b1111 + 0o41) + chr(7155 - 7044) + chr(1053 - 1004) + chr(54) + '\x32', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b101010 + 0o105) + chr(0b110010) + chr(0b11000 + 0o32), 0b1000), nzTpIcepk0o8(chr(1105 - 1057) + chr(3077 - 2966) + '\x31' + '\x36', 0o10), nzTpIcepk0o8(chr(430 - 382) + '\x6f' + '\x32' + chr(0b101111 + 0o1) + '\x34', ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110011) + chr(724 - 675) + chr(52), 0o10), nzTpIcepk0o8(chr(0b11000 + 0o30) + '\157' + '\x32' + chr(0b1111 + 0o42) + chr(1136 - 1084), 30648 - 30640), nzTpIcepk0o8('\x30' + chr(9763 - 9652) + chr(321 - 272) + chr(55) + chr(0b1010 + 0o53), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(280 - 225), 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(0b1110 + 0o45) + chr(0b1001 + 0o56) + '\x30', 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(50) + chr(0b110110) + chr(52), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\061' + '\x35' + '\x34', 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(0b10101 + 0o35) + '\x32' + '\x33', 0o10), nzTpIcepk0o8(chr(0b11011 + 0o25) + chr(243 - 132) + '\x33' + chr(48) + '\x32', ord("\x08")), nzTpIcepk0o8('\x30' + chr(5174 - 5063) + '\062' + chr(55) + '\x36', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + '\x31' + chr(1262 - 1208) + chr(0b11001 + 0o36), 61752 - 61744), nzTpIcepk0o8(chr(48) + chr(1961 - 1850) + chr(0b1 + 0o63) + chr(660 - 605), 0o10), nzTpIcepk0o8(chr(854 - 806) + chr(111) + chr(0b101100 + 0o7) + '\063' + chr(952 - 901), 32126 - 32118), nzTpIcepk0o8('\060' + chr(10842 - 10731) + chr(0b1110 + 0o45) + '\x37' + chr(0b110110), ord("\x08")), nzTpIcepk0o8(chr(0b101001 + 0o7) + chr(6306 - 6195) + chr(0b1100 + 0o46) + chr(0b110001) + '\061', 0o10), nzTpIcepk0o8(chr(848 - 800) + '\157' + '\065' + chr(0b101101 + 0o4), 0o10), nzTpIcepk0o8(chr(0b100100 + 0o14) + chr(3197 - 3086) + '\x33' + chr(0b100100 + 0o14) + chr(0b1011 + 0o46), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\063' + chr(0b110010) + chr(0b10101 + 0o34), 0b1000), nzTpIcepk0o8(chr(0b11101 + 0o23) + chr(111) + chr(0b110001) + '\067' + chr(1684 - 1629), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(767 - 714) + chr(51), 0o10), nzTpIcepk0o8(chr(2162 - 2114) + chr(111) + chr(0b110010) + chr(0b111 + 0o56) + '\066', 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x32' + chr(828 - 779) + '\060', 0b1000), nzTpIcepk0o8(chr(984 - 936) + chr(4283 - 4172) + chr(0b101110 + 0o7) + chr(0b100 + 0o57), 8), nzTpIcepk0o8(chr(0b11 + 0o55) + chr(0b1101111) + '\x31' + chr(1460 - 1412) + chr(0b110001), 41943 - 41935), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(49) + chr(241 - 189) + chr(728 - 675), 0b1000), nzTpIcepk0o8('\x30' + chr(2403 - 2292) + '\061' + '\062' + '\066', 0o10), nzTpIcepk0o8(chr(0b100000 + 0o20) + chr(111) + chr(1212 - 1163) + chr(0b110100) + chr(0b110001), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\065' + chr(427 - 379), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(49) + chr(0b110110) + chr(324 - 271), ord("\x08")), nzTpIcepk0o8(chr(1971 - 1923) + '\157' + '\061' + chr(0b110001), 0o10), nzTpIcepk0o8('\060' + '\x6f' + '\065' + chr(2184 - 2135), 8), nzTpIcepk0o8('\060' + '\x6f' + chr(51) + '\x35' + chr(0b101110 + 0o11), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + '\157' + '\x35' + chr(0b110000), 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b','), '\x64' + '\145' + '\143' + chr(111) + chr(5108 - 5008) + chr(9370 - 9269))(chr(0b1101010 + 0o13) + chr(0b1110100) + '\x66' + chr(0b101101) + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def nxhBqOFJ8jpS(WueclzVPVP7r):
return IlSN4xxGCzHm(effect=WueclzVPVP7r, fn=lambda h3Vc_4wxEbgd: roI3spqORKae(h3Vc_4wxEbgd, roI3spqORKae(ES5oEprVxulp(b"V@l/'~[\xef\x9b\xdc\x0e1"), '\144' + chr(0b1001110 + 0o27) + '\143' + '\157' + chr(0b1100100) + chr(101))('\x75' + '\x74' + '\x66' + '\055' + '\070')), default=nzTpIcepk0o8(chr(48) + '\x6f' + '\x30', 0b1000)) |
openvax/varcode | varcode/effects/effect_ordering.py | effect_associated_with_protein_coding_gene | def effect_associated_with_protein_coding_gene(effect):
"""
Parameters
----------
effect : subclass of MutationEffect
Returns True if effect is associated with a gene and that gene
has a protein_coding biotype.
"""
return apply_to_gene_if_exists(
effect=effect,
fn=lambda g: g.biotype == "protein_coding",
default=False) | python | def effect_associated_with_protein_coding_gene(effect):
"""
Parameters
----------
effect : subclass of MutationEffect
Returns True if effect is associated with a gene and that gene
has a protein_coding biotype.
"""
return apply_to_gene_if_exists(
effect=effect,
fn=lambda g: g.biotype == "protein_coding",
default=False) | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/effect_ordering.py#L204-L216 | train | Returns True if effect is associated with a gene and that gene has a protein_coding biotype. | 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(630 - 579) + chr(0b100010 + 0o16) + '\063', 1024 - 1016), nzTpIcepk0o8(chr(48) + chr(0b1101101 + 0o2) + chr(54) + chr(0b101100 + 0o7), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x32' + chr(0b110010) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(894 - 846) + chr(0b1101000 + 0o7) + chr(0b1000 + 0o51) + '\060' + chr(53), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110010) + chr(52) + chr(0b10010 + 0o36), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110001) + chr(0b101101 + 0o7) + chr(0b11 + 0o60), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(0b110010) + chr(2851 - 2797) + '\x33', 0o10), nzTpIcepk0o8(chr(0b110000 + 0o0) + chr(0b101001 + 0o106) + chr(49) + '\x35' + chr(0b110111 + 0o0), 0o10), nzTpIcepk0o8('\060' + '\157' + '\063' + chr(0b111 + 0o57) + chr(0b110001), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(11236 - 11125) + chr(52) + chr(0b101001 + 0o14), 55742 - 55734), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(49) + chr(53) + '\x32', ord("\x08")), nzTpIcepk0o8(chr(0b100000 + 0o20) + '\157' + '\x31' + chr(53) + '\062', 8), nzTpIcepk0o8(chr(0b1101 + 0o43) + chr(0b101100 + 0o103) + chr(52) + '\062', ord("\x08")), nzTpIcepk0o8(chr(0b11100 + 0o24) + chr(111) + '\066' + chr(0b110100), 61471 - 61463), nzTpIcepk0o8(chr(0b11 + 0o55) + '\157' + '\x32' + chr(0b110000) + '\x35', 0b1000), nzTpIcepk0o8('\x30' + chr(0b10001 + 0o136) + chr(54) + chr(0b110111), 42605 - 42597), nzTpIcepk0o8(chr(0b0 + 0o60) + '\x6f' + '\063' + chr(0b110101) + chr(0b110101), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b101101 + 0o102) + chr(0b110100) + '\065', 8), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(1685 - 1635) + chr(2778 - 2724) + '\061', 0o10), nzTpIcepk0o8('\060' + chr(0b1010111 + 0o30) + '\x31' + '\x34' + chr(0b110111 + 0o0), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(2332 - 2282) + chr(0b110011) + chr(0b110111), 37275 - 37267), nzTpIcepk0o8('\x30' + chr(111) + chr(49) + chr(0b11000 + 0o34) + chr(762 - 713), ord("\x08")), nzTpIcepk0o8('\x30' + chr(8727 - 8616) + chr(49) + chr(0b100111 + 0o20) + '\x32', 48403 - 48395), nzTpIcepk0o8('\060' + chr(979 - 868) + chr(0b110011) + chr(2163 - 2113) + '\x30', 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(0b10110 + 0o34) + chr(1927 - 1873), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110011) + chr(1266 - 1215), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b1011 + 0o50) + '\063' + chr(0b110001), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b1100 + 0o47) + chr(0b110111) + chr(0b100000 + 0o20), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(1596 - 1485) + '\062' + chr(49) + chr(1815 - 1763), 19700 - 19692), nzTpIcepk0o8('\x30' + chr(0b1011000 + 0o27) + chr(0b110111) + chr(0b101 + 0o61), 64615 - 64607), nzTpIcepk0o8(chr(1204 - 1156) + '\x6f' + chr(51) + chr(0b101111 + 0o2), 0b1000), nzTpIcepk0o8(chr(0b1000 + 0o50) + '\x6f' + chr(0b110010) + chr(48) + chr(2860 - 2806), ord("\x08")), nzTpIcepk0o8(chr(1330 - 1282) + chr(0b1101111) + chr(0b1011 + 0o50) + chr(0b110011) + '\067', 52811 - 52803), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(2113 - 2063) + '\062' + chr(2879 - 2824), 0o10), nzTpIcepk0o8(chr(0b100101 + 0o13) + chr(111) + chr(0b110011) + '\062' + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(0b100 + 0o54) + chr(0b1100010 + 0o15) + '\x31' + '\060', ord("\x08")), nzTpIcepk0o8(chr(1965 - 1917) + chr(0b1101111) + chr(0b110111) + '\066', 8), nzTpIcepk0o8(chr(48) + chr(3792 - 3681) + '\061' + chr(0b11 + 0o55) + chr(51), 60015 - 60007), nzTpIcepk0o8('\x30' + chr(0b1000111 + 0o50) + chr(0b11001 + 0o30) + chr(0b100001 + 0o22), 18251 - 18243), nzTpIcepk0o8(chr(0b1110 + 0o42) + chr(0b1101111) + chr(0b0 + 0o61) + chr(54) + chr(0b110011), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b1110 + 0o42) + chr(0b1101111) + chr(53) + chr(48), 46481 - 46473)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xed'), chr(3692 - 3592) + chr(7732 - 7631) + chr(99) + '\x6f' + chr(100) + chr(101))(chr(0b1110101) + '\164' + chr(102) + chr(920 - 875) + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def oswVU1fWvmLt(WueclzVPVP7r):
return wbQlcs8KXkFI(effect=WueclzVPVP7r, fn=lambda KQq7Z9J63zv1: roI3spqORKae(KQq7Z9J63zv1, roI3spqORKae(ES5oEprVxulp(b'\xa1Z\xfb1\xd9\x13\xd6'), chr(0b1100100) + '\145' + chr(0b1100011) + '\x6f' + chr(0b1000 + 0o134) + '\145')('\165' + chr(116) + chr(0b110101 + 0o61) + chr(45) + chr(0b111000))) == roI3spqORKae(ES5oEprVxulp(b'\xb3A\xfb1\xc5\n\xdd0\x92J\x0e\x03LS'), chr(100) + chr(101) + chr(0b1100011) + '\x6f' + '\x64' + chr(101))(chr(4988 - 4871) + chr(0b1110100) + chr(0b1011101 + 0o11) + chr(0b101101) + chr(0b110 + 0o62)), default=nzTpIcepk0o8('\060' + '\157' + '\060', 0b1000)) |
openvax/varcode | varcode/effects/effect_ordering.py | effect_associated_with_protein_coding_transcript | def effect_associated_with_protein_coding_transcript(effect):
"""
Parameters
----------
effect : subclass of MutationEffect
Returns True if effect is associated with a transcript and that transcript
has a protein_coding biotype.
"""
return apply_to_transcript_if_exists(
effect=effect,
fn=lambda t: t.biotype == "protein_coding",
default=False) | python | def effect_associated_with_protein_coding_transcript(effect):
"""
Parameters
----------
effect : subclass of MutationEffect
Returns True if effect is associated with a transcript and that transcript
has a protein_coding biotype.
"""
return apply_to_transcript_if_exists(
effect=effect,
fn=lambda t: t.biotype == "protein_coding",
default=False) | [
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Returns True if effect is associated with a transcript and that transcript
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"MutationEffect"
] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/effect_ordering.py#L219-L231 | train | Returns True if effect is associated with a protein coding transcript. | 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' + '\x6f' + '\x31' + chr(592 - 540) + chr(1862 - 1811), 57764 - 57756), nzTpIcepk0o8(chr(0b10 + 0o56) + chr(0b1101111) + '\061' + chr(1868 - 1813) + '\x36', 18376 - 18368), nzTpIcepk0o8(chr(48) + chr(2689 - 2578) + chr(750 - 700) + chr(0b10010 + 0o37) + chr(52), 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(1318 - 1268) + chr(54), 45708 - 45700), nzTpIcepk0o8(chr(48) + '\157' + '\061' + chr(0b110000 + 0o2) + chr(0b101101 + 0o6), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(4782 - 4671) + '\x35' + chr(55), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + '\x33' + chr(1393 - 1344) + chr(0b1010 + 0o53), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b111010 + 0o65) + chr(0b110011) + chr(772 - 724) + chr(50), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + '\x33' + '\063' + '\x35', 23088 - 23080), nzTpIcepk0o8(chr(48) + '\x6f' + '\x33' + chr(0b100 + 0o60) + chr(0b1110 + 0o44), 65410 - 65402), nzTpIcepk0o8(chr(1241 - 1193) + chr(0b1101111) + '\062' + '\060', 48581 - 48573), nzTpIcepk0o8('\060' + chr(111) + chr(0b110100) + '\066', 0b1000), nzTpIcepk0o8(chr(686 - 638) + chr(111) + chr(0b110001) + '\x33' + '\x36', 0o10), nzTpIcepk0o8(chr(2264 - 2216) + chr(9425 - 9314) + '\063' + chr(0b110101) + chr(0b110 + 0o60), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1100011 + 0o14) + chr(1446 - 1395) + chr(0b10 + 0o64) + chr(0b11110 + 0o24), 0o10), nzTpIcepk0o8(chr(0b100001 + 0o17) + chr(111) + '\x32' + chr(49) + chr(0b110011 + 0o0), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(51) + chr(0b11 + 0o57) + chr(698 - 650), 19493 - 19485), nzTpIcepk0o8('\060' + chr(1204 - 1093) + chr(0b10101 + 0o36) + chr(2580 - 2527) + chr(50), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(1805 - 1754) + '\061' + chr(0b101001 + 0o11), 0b1000), nzTpIcepk0o8('\x30' + chr(4365 - 4254) + chr(0b11110 + 0o24) + chr(0b1101 + 0o47) + chr(55), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1001110 + 0o41) + chr(0b101111 + 0o10) + '\060', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(54) + '\067', 1824 - 1816), nzTpIcepk0o8(chr(1941 - 1893) + chr(4917 - 4806) + '\x31' + '\067' + '\x37', 0o10), nzTpIcepk0o8(chr(899 - 851) + '\x6f' + chr(0b110011) + '\067' + chr(53), 14610 - 14602), nzTpIcepk0o8(chr(1390 - 1342) + chr(0b11100 + 0o123) + chr(1864 - 1815) + '\x31' + chr(50), 0b1000), nzTpIcepk0o8(chr(0b1101 + 0o43) + chr(111) + '\x32' + chr(0b11110 + 0o22) + '\060', 0o10), nzTpIcepk0o8(chr(48) + chr(10715 - 10604) + chr(1257 - 1207) + chr(0b110001), ord("\x08")), nzTpIcepk0o8('\060' + chr(7558 - 7447) + chr(51) + '\x35', 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(0b110010) + chr(0b110011) + chr(0b10001 + 0o37), 0b1000), nzTpIcepk0o8(chr(0b100010 + 0o16) + '\157' + chr(0b1110 + 0o43) + chr(0b10001 + 0o37) + chr(0b110000), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1100111 + 0o10) + '\062' + '\062' + '\063', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b11011 + 0o27) + chr(0b110111 + 0o0) + chr(1340 - 1292), 32328 - 32320), nzTpIcepk0o8(chr(48) + chr(0b1000011 + 0o54) + chr(0b110011) + '\x30' + '\065', 0b1000), nzTpIcepk0o8(chr(0b100001 + 0o17) + chr(111) + '\x31' + chr(1705 - 1650), ord("\x08")), nzTpIcepk0o8(chr(0b100111 + 0o11) + '\x6f' + chr(51) + chr(0b110010) + chr(53), 0b1000), nzTpIcepk0o8('\x30' + chr(3659 - 3548) + chr(0b110001) + chr(54), 0b1000), nzTpIcepk0o8(chr(2007 - 1959) + '\157' + chr(0b11001 + 0o30) + chr(1994 - 1942) + '\063', 8), nzTpIcepk0o8('\060' + chr(5261 - 5150) + chr(2338 - 2289) + chr(50) + '\067', 61563 - 61555), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b10010 + 0o41) + chr(847 - 795), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(1751 - 1702) + chr(0b110011) + '\060', 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + chr(0b1101111) + '\065' + '\060', ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'M'), chr(0b111110 + 0o46) + '\x65' + chr(5478 - 5379) + chr(0b111110 + 0o61) + chr(100) + chr(6894 - 6793))(chr(0b1110101) + chr(116) + '\x66' + chr(1749 - 1704) + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def nzsRXAKfamRg(WueclzVPVP7r):
return IlSN4xxGCzHm(effect=WueclzVPVP7r, fn=lambda h3Vc_4wxEbgd: roI3spqORKae(h3Vc_4wxEbgd, roI3spqORKae(ES5oEprVxulp(b'\x01\x17\xe3b*_\xa8'), chr(1877 - 1777) + chr(4435 - 4334) + chr(0b1100011) + chr(111) + chr(100) + chr(101))('\165' + chr(1204 - 1088) + '\146' + chr(0b101101) + chr(761 - 705))) == roI3spqORKae(ES5oEprVxulp(b'\x13\x0c\xe3b6F\xa3\x9d\xbe\x8dtO0\x89'), chr(0b1010100 + 0o20) + chr(0b10011 + 0o122) + chr(99) + chr(0b11010 + 0o125) + chr(100) + '\145')(chr(0b110101 + 0o100) + '\164' + chr(102) + chr(0b1000 + 0o45) + '\070'), default=nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x30', 0o10)) |
openvax/varcode | varcode/effects/effect_ordering.py | parse_transcript_number | def parse_transcript_number(effect):
"""
Try to parse the number at the end of a transcript name associated with
an effect.
e.g. TP53-001 returns the integer 1.
Parameters
----------
effect : subclass of MutationEffect
Returns int
"""
name = name_of_associated_transcript(effect)
if "-" not in name:
return 0
parts = name.split("-")
last_part = parts[-1]
if last_part.isdigit():
return int(last_part)
else:
return 0 | python | def parse_transcript_number(effect):
"""
Try to parse the number at the end of a transcript name associated with
an effect.
e.g. TP53-001 returns the integer 1.
Parameters
----------
effect : subclass of MutationEffect
Returns int
"""
name = name_of_associated_transcript(effect)
if "-" not in name:
return 0
parts = name.split("-")
last_part = parts[-1]
if last_part.isdigit():
return int(last_part)
else:
return 0 | [
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effect : subclass of MutationEffect
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/effect_ordering.py#L249-L270 | train | Try to parse the number at the end of a transcript name associated with
an effect. Returns 0 if the number is not 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' + chr(0b110010) + chr(0b110010) + chr(433 - 381), 0b1000), nzTpIcepk0o8(chr(0b10 + 0o56) + chr(0b1101101 + 0o2) + chr(1385 - 1336), 0b1000), nzTpIcepk0o8('\060' + chr(111) + '\062' + chr(910 - 860), ord("\x08")), nzTpIcepk0o8(chr(1837 - 1789) + chr(0b1101111) + chr(2334 - 2284) + chr(0b0 + 0o65) + chr(0b10001 + 0o41), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b101 + 0o54) + chr(2909 - 2854) + chr(0b110000), 7522 - 7514), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b101100 + 0o6) + chr(48) + chr(0b100000 + 0o27), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(771 - 722) + chr(1315 - 1267) + '\062', 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(0b1011 + 0o47) + chr(49) + chr(54), ord("\x08")), nzTpIcepk0o8(chr(0b11010 + 0o26) + chr(0b111001 + 0o66) + chr(928 - 877) + '\066' + '\062', ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(2131 - 2082) + '\067' + chr(55), 0b1000), nzTpIcepk0o8('\x30' + '\157' + '\062' + '\x35' + '\x30', 0o10), nzTpIcepk0o8(chr(0b10101 + 0o33) + chr(111) + chr(486 - 437) + chr(55) + chr(48), 8), nzTpIcepk0o8('\x30' + chr(111) + chr(0b11111 + 0o24) + chr(1725 - 1672) + '\067', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b10110 + 0o131) + chr(2038 - 1987) + chr(0b110111), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + '\061' + '\x36' + '\067', 0b1000), nzTpIcepk0o8(chr(48) + '\157' + '\062' + chr(803 - 754) + chr(1370 - 1318), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\062' + chr(0b110110) + chr(0b110010), 0b1000), nzTpIcepk0o8(chr(698 - 650) + '\x6f' + chr(51) + chr(0b110010) + '\062', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b10101 + 0o132) + chr(51) + chr(50) + '\066', 0o10), nzTpIcepk0o8(chr(0b100101 + 0o13) + chr(111) + chr(0b10101 + 0o35) + '\065' + '\064', ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(1141 - 1087) + chr(2885 - 2830), 59226 - 59218), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x33' + chr(596 - 544) + chr(0b110111), 0o10), nzTpIcepk0o8(chr(132 - 84) + chr(10500 - 10389) + chr(0b101100 + 0o5) + '\x33' + chr(51), 19961 - 19953), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110011 + 0o2) + chr(52), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + '\063' + '\060' + chr(0b100011 + 0o23), 0b1000), nzTpIcepk0o8(chr(48) + chr(3310 - 3199) + '\x31' + chr(0b1111 + 0o42) + chr(0b100010 + 0o16), 0b1000), nzTpIcepk0o8(chr(89 - 41) + '\157' + chr(49) + '\061' + chr(0b110001), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101010 + 0o5) + chr(367 - 318) + chr(1668 - 1616), 39636 - 39628), nzTpIcepk0o8(chr(48) + chr(11746 - 11635) + '\063' + chr(1033 - 979) + chr(50), 8), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(1047 - 997) + chr(0b11000 + 0o33) + chr(1694 - 1639), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + '\063' + '\065' + chr(0b11000 + 0o31), ord("\x08")), nzTpIcepk0o8(chr(0b101000 + 0o10) + chr(2723 - 2612) + chr(1272 - 1223) + chr(0b110011), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(0b100101 + 0o14) + '\061' + chr(50), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110001) + '\x35', 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(0b10001 + 0o40) + chr(0b11011 + 0o31) + chr(54), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110011) + chr(113 - 61) + chr(51), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + '\063' + chr(605 - 555) + chr(54), 8), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110110) + chr(48), ord("\x08")), nzTpIcepk0o8(chr(1920 - 1872) + '\157' + chr(1690 - 1641) + '\066', 0b1000), nzTpIcepk0o8('\060' + chr(11317 - 11206) + chr(98 - 48) + '\060' + chr(2139 - 2088), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x35' + chr(0b1001 + 0o47), 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xba'), chr(0b1100100) + chr(7310 - 7209) + chr(0b1100011) + chr(0b1010110 + 0o31) + chr(100) + '\145')('\x75' + chr(651 - 535) + chr(0b1100110) + chr(45) + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def farAVvWC6PLf(WueclzVPVP7r):
SLVB2BPA_mIe = nDpr4fO2AeEC(WueclzVPVP7r)
if roI3spqORKae(ES5oEprVxulp(b'\xb9'), '\144' + chr(0b1000 + 0o135) + chr(0b101010 + 0o71) + chr(0b1101111) + chr(8050 - 7950) + chr(101))(chr(117) + chr(8562 - 8446) + chr(0b1100110) + chr(1841 - 1796) + chr(0b11 + 0o65)) not in SLVB2BPA_mIe:
return nzTpIcepk0o8('\060' + chr(111) + chr(1345 - 1297), 0o10)
ws_9aXBYp0Zv = SLVB2BPA_mIe.LfRrQOxuDvnC(roI3spqORKae(ES5oEprVxulp(b'\xb9'), chr(5350 - 5250) + chr(0b1100101) + chr(99) + '\157' + '\144' + '\145')('\165' + '\x74' + chr(0b1100110) + '\055' + chr(2922 - 2866)))
u_Uc2bHOX3pQ = ws_9aXBYp0Zv[-nzTpIcepk0o8('\060' + chr(0b101001 + 0o106) + chr(0b110001), 8)]
if roI3spqORKae(u_Uc2bHOX3pQ, roI3spqORKae(ES5oEprVxulp(b'\xfdrv\xc3\x1f\xee6'), chr(6866 - 6766) + chr(101) + '\x63' + chr(0b1010011 + 0o34) + chr(100) + chr(0b1100101))('\165' + '\x74' + chr(0b1001010 + 0o34) + chr(45) + '\x38'))():
return nzTpIcepk0o8(u_Uc2bHOX3pQ)
else:
return nzTpIcepk0o8('\x30' + '\x6f' + chr(1175 - 1127), 8) |
openvax/varcode | varcode/effects/effect_ordering.py | multi_gene_effect_sort_key | def multi_gene_effect_sort_key(effect):
"""
This function acts as a sort key for choosing the highest priority
effect across multiple genes (so does not assume that effects might
involve the same start/stop codons).
Returns tuple with the following elements:
1) Integer priority of the effect type.
2) Does the associated gene have a "protein_coding" biotype?
False if no gene is associated with effect.
3) Does the associated transcript have a "protein_coding" biotype?
False if no transcript is associated with effect.
4) Is the associated transcript complete?
False if no transcript is associated with effect.
5) CDS length
This value will be 0 if the effect has no associated transcript
or if the transcript is noncoding or incomplete
6) Total length of the transcript
This value will be 0 intra/intergenic variants effects without
an associated transcript.
7) Number of exons
This value will be 0 intra/intergenic variants effects without
an associated transcript.
8) If everything is the same up this point then let's use the very
sloppy heuristic of preferring transcripts like "TP53-201" over
"TP53-206", so anything ending with "01" is considered better.
9) Lastly, if we end up with two transcripts like "TP53-202" and
"TP53-203", prefer the one with the lowest number in the name.
"""
return tuple([
effect_priority(effect),
effect_associated_with_protein_coding_gene(effect),
effect_associated_with_protein_coding_transcript(effect),
effect_has_complete_transcript(effect),
cds_length_of_associated_transcript(effect),
length_of_associated_transcript(effect),
number_exons_in_associated_transcript(effect),
transcript_name_ends_with_01(effect),
-parse_transcript_number(effect)
]) | python | def multi_gene_effect_sort_key(effect):
"""
This function acts as a sort key for choosing the highest priority
effect across multiple genes (so does not assume that effects might
involve the same start/stop codons).
Returns tuple with the following elements:
1) Integer priority of the effect type.
2) Does the associated gene have a "protein_coding" biotype?
False if no gene is associated with effect.
3) Does the associated transcript have a "protein_coding" biotype?
False if no transcript is associated with effect.
4) Is the associated transcript complete?
False if no transcript is associated with effect.
5) CDS length
This value will be 0 if the effect has no associated transcript
or if the transcript is noncoding or incomplete
6) Total length of the transcript
This value will be 0 intra/intergenic variants effects without
an associated transcript.
7) Number of exons
This value will be 0 intra/intergenic variants effects without
an associated transcript.
8) If everything is the same up this point then let's use the very
sloppy heuristic of preferring transcripts like "TP53-201" over
"TP53-206", so anything ending with "01" is considered better.
9) Lastly, if we end up with two transcripts like "TP53-202" and
"TP53-203", prefer the one with the lowest number in the name.
"""
return tuple([
effect_priority(effect),
effect_associated_with_protein_coding_gene(effect),
effect_associated_with_protein_coding_transcript(effect),
effect_has_complete_transcript(effect),
cds_length_of_associated_transcript(effect),
length_of_associated_transcript(effect),
number_exons_in_associated_transcript(effect),
transcript_name_ends_with_01(effect),
-parse_transcript_number(effect)
]) | [
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False if no gene is associated with effect.
3) Does the associated transcript have a "protein_coding" biotype?
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/effect_ordering.py#L273-L313 | train | This function returns a sort key for choosing the highest priority of an effect across multiple genes. | 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(0b10000 + 0o43) + '\x34' + chr(51), ord("\x08")), nzTpIcepk0o8(chr(0b10001 + 0o37) + chr(0b1101010 + 0o5) + '\x32' + '\067' + chr(0b110111), 36755 - 36747), nzTpIcepk0o8(chr(48) + '\x6f' + chr(49) + chr(0b1111 + 0o46) + '\x32', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x32' + chr(0b110010 + 0o0) + chr(0b100111 + 0o13), 0o10), nzTpIcepk0o8(chr(1385 - 1337) + chr(0b1101111) + chr(51) + chr(51) + '\x36', ord("\x08")), nzTpIcepk0o8(chr(2267 - 2219) + '\x6f' + chr(484 - 433) + chr(0b110111) + chr(0b100111 + 0o11), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110011) + chr(1367 - 1319) + '\x33', 0b1000), nzTpIcepk0o8(chr(0b100010 + 0o16) + chr(111) + chr(1131 - 1080) + chr(0b1010 + 0o46), 0o10), nzTpIcepk0o8(chr(1876 - 1828) + chr(0b1101111) + '\061' + '\066' + '\x31', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\062' + '\065' + '\063', 62538 - 62530), nzTpIcepk0o8(chr(48) + chr(0b10011 + 0o134) + '\x33' + chr(2062 - 2007), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(1839 - 1788) + chr(52) + chr(55), 0b1000), nzTpIcepk0o8(chr(0b1101 + 0o43) + chr(111) + '\x31' + chr(0b110111) + '\061', 24021 - 24013), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110010) + chr(0b100000 + 0o24) + '\x33', 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110101) + chr(50), 0b1000), nzTpIcepk0o8('\060' + chr(3854 - 3743) + chr(0b110010) + '\x36' + '\061', 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(710 - 660) + chr(397 - 347) + chr(51), ord("\x08")), nzTpIcepk0o8(chr(0b100000 + 0o20) + chr(12168 - 12057) + chr(0b110010) + '\061' + '\060', 0o10), nzTpIcepk0o8(chr(754 - 706) + '\x6f' + chr(51) + chr(90 - 36) + '\064', ord("\x08")), nzTpIcepk0o8(chr(359 - 311) + chr(0b1100101 + 0o12) + chr(0b110 + 0o57), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1010 + 0o145) + chr(324 - 275) + chr(0b110001) + '\062', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110011) + chr(0b110001) + chr(2634 - 2579), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b11011 + 0o124) + '\x32' + '\062' + chr(1621 - 1573), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + '\063' + chr(51) + chr(0b110000 + 0o5), 0b1000), nzTpIcepk0o8('\060' + chr(12004 - 11893) + chr(2123 - 2074) + '\060' + chr(2090 - 2037), 0o10), nzTpIcepk0o8('\060' + '\157' + '\063' + chr(0b1110 + 0o45) + chr(1720 - 1669), 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(49) + chr(2852 - 2797) + chr(2460 - 2406), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1010111 + 0o30) + '\x31' + chr(0b11001 + 0o36) + '\064', 49473 - 49465), nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(0b1101111) + chr(0b110011) + chr(0b1001 + 0o53) + chr(1417 - 1368), 17271 - 17263), nzTpIcepk0o8('\x30' + '\157' + '\x30', 0b1000), nzTpIcepk0o8('\x30' + chr(0b10101 + 0o132) + chr(0b110010) + '\x30', 38672 - 38664), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b101001 + 0o12) + chr(48) + chr(0b101010 + 0o15), 0b1000), nzTpIcepk0o8(chr(0b11100 + 0o24) + chr(11638 - 11527) + chr(50) + '\060' + '\x30', 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b11101 + 0o32) + chr(0b110100), 32813 - 32805), nzTpIcepk0o8(chr(48) + chr(0b100101 + 0o112) + chr(782 - 733) + chr(1229 - 1181) + '\066', 0o10), nzTpIcepk0o8(chr(1479 - 1431) + chr(111) + chr(51) + '\x32' + chr(0b1010 + 0o46), ord("\x08")), nzTpIcepk0o8(chr(0b1 + 0o57) + '\x6f' + chr(0b100101 + 0o16) + chr(0b110001) + chr(0b110001), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(50) + chr(48), 8), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110001) + '\x37', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111 + 0o0) + chr(51) + '\x30' + chr(1805 - 1753), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + 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'\xcd'), chr(100) + chr(101) + chr(0b100 + 0o137) + chr(111) + chr(3284 - 3184) + '\145')('\165' + chr(420 - 304) + '\146' + '\x2d' + chr(0b11010 + 0o36)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def IEpds8shfG9T(WueclzVPVP7r):
return nfNqtJL5aRaY([a6DfvLcv0V2D(WueclzVPVP7r), oswVU1fWvmLt(WueclzVPVP7r), nzsRXAKfamRg(WueclzVPVP7r), nxhBqOFJ8jpS(WueclzVPVP7r), sNTqK0jx1yku(WueclzVPVP7r), GQvOW0LZKSh5(WueclzVPVP7r), kuyP8J6540PE(WueclzVPVP7r), oHDVXZHtBjH1(WueclzVPVP7r), -farAVvWC6PLf(WueclzVPVP7r)]) |
openvax/varcode | varcode/effects/effect_ordering.py | select_between_exonic_splice_site_and_alternate_effect | def select_between_exonic_splice_site_and_alternate_effect(effect):
"""
If the given effect is an ExonicSpliceSite then it might contain
an alternate effect of higher priority. In that case, return the
alternate effect. Otherwise, this acts as an identity function.
"""
if effect.__class__ is not ExonicSpliceSite:
return effect
if effect.alternate_effect is None:
return effect
splice_priority = effect_priority(effect)
alternate_priority = effect_priority(effect.alternate_effect)
if splice_priority > alternate_priority:
return effect
else:
return effect.alternate_effect | python | def select_between_exonic_splice_site_and_alternate_effect(effect):
"""
If the given effect is an ExonicSpliceSite then it might contain
an alternate effect of higher priority. In that case, return the
alternate effect. Otherwise, this acts as an identity function.
"""
if effect.__class__ is not ExonicSpliceSite:
return effect
if effect.alternate_effect is None:
return effect
splice_priority = effect_priority(effect)
alternate_priority = effect_priority(effect.alternate_effect)
if splice_priority > alternate_priority:
return effect
else:
return effect.alternate_effect | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/effect_ordering.py#L316-L331 | train | Select the most appropriate effect between an ExonicSpliceSite and an alternate effect. | 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(406 - 358) + chr(111) + '\061' + '\x37' + chr(0b110 + 0o60), 33740 - 33732), nzTpIcepk0o8('\060' + chr(111) + chr(51) + '\067' + '\x33', ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + '\061' + chr(53) + chr(1413 - 1363), 40042 - 40034), nzTpIcepk0o8('\x30' + chr(0b101000 + 0o107) + chr(0b101 + 0o56) + chr(0b110001) + '\065', 38069 - 38061), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110100) + chr(0b10 + 0o63), 49224 - 49216), nzTpIcepk0o8(chr(0b11010 + 0o26) + chr(0b1001000 + 0o47) + chr(51) + chr(55) + chr(51), 8), nzTpIcepk0o8('\x30' + '\157' + '\x32' + chr(0b1000 + 0o50) + '\067', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b10000 + 0o137) + chr(49) + chr(0b100101 + 0o13) + chr(0b1111 + 0o45), 0o10), nzTpIcepk0o8('\x30' + '\157' + '\x32' + '\x36' + chr(0b1011 + 0o54), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110010) + '\x31' + chr(0b100 + 0o60), ord("\x08")), nzTpIcepk0o8(chr(0b100110 + 0o12) + chr(0b101001 + 0o106) + '\062' + chr(49) + chr(55), 53644 - 53636), nzTpIcepk0o8('\x30' + '\157' + chr(51) + '\067', 0b1000), nzTpIcepk0o8(chr(0b10001 + 0o37) + '\157' + chr(0b110011) + chr(2101 - 2050) + '\063', 0b1000), nzTpIcepk0o8(chr(48) + chr(7178 - 7067) + chr(51) + chr(1106 - 1057) + chr(51), 0o10), nzTpIcepk0o8('\x30' + chr(0b1011011 + 0o24) + chr(50) + chr(55), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(2293 - 2182) + chr(375 - 326) + '\063' + chr(52), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(9045 - 8934) + chr(1686 - 1637) + chr(52) + '\x36', 0o10), nzTpIcepk0o8(chr(0b101111 + 0o1) + chr(7967 - 7856) + chr(1145 - 1096) + '\067' + chr(0b10001 + 0o37), 50071 - 50063), nzTpIcepk0o8(chr(300 - 252) + chr(2943 - 2832) + chr(208 - 159) + chr(49), 36442 - 36434), nzTpIcepk0o8(chr(1448 - 1400) + chr(0b1001101 + 0o42) + chr(0b110001) + chr(1687 - 1633) + chr(1607 - 1555), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + '\x31' + '\061' + '\x34', 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(50) + chr(0b110010 + 0o0) + chr(0b110000), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(51) + '\x33' + chr(50), 18688 - 18680), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(51) + chr(50) + chr(50), 0o10), nzTpIcepk0o8(chr(893 - 845) + chr(111) + chr(0b110011 + 0o4) + '\x31', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(5329 - 5218) + chr(379 - 329) + '\063' + chr(1768 - 1717), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(1207 - 1158) + chr(0b100011 + 0o21) + chr(1140 - 1088), 46806 - 46798), nzTpIcepk0o8(chr(48) + chr(0b10000 + 0o137) + chr(0b101101 + 0o6) + chr(0b100101 + 0o20) + chr(52), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\067' + chr(130 - 81), 8), nzTpIcepk0o8(chr(0b1010 + 0o46) + '\x6f' + chr(0b110010) + chr(0b11101 + 0o23) + chr(52), 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(51) + chr(49) + '\x33', 8), nzTpIcepk0o8(chr(0b1101 + 0o43) + chr(111) + '\063' + '\063', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(2597 - 2546) + '\x32' + chr(725 - 670), 0o10), nzTpIcepk0o8('\060' + chr(0b110110 + 0o71) + '\061' + chr(1230 - 1180), 7854 - 7846), nzTpIcepk0o8(chr(48) + '\x6f' + chr(231 - 181) + chr(49), 0b1000), nzTpIcepk0o8('\x30' + chr(4630 - 4519) + '\x31' + chr(0b110110) + chr(0b11111 + 0o25), 8), nzTpIcepk0o8(chr(708 - 660) + '\157' + chr(50) + '\067', 8), nzTpIcepk0o8(chr(0b100001 + 0o17) + chr(0b1101111) + chr(49) + chr(0b10010 + 0o45) + chr(0b11110 + 0o22), 8), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110010) + '\x30' + chr(0b11001 + 0o27), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110010) + '\065' + chr(1899 - 1845), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + chr(0b1101111) + chr(448 - 395) + chr(765 - 717), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'P'), chr(0b1100 + 0o130) + chr(0b1100101) + '\x63' + chr(1058 - 947) + '\x64' + chr(101))(chr(117) + chr(0b11111 + 0o125) + chr(0b1100110) + '\x2d' + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def lge9193GJ0ch(WueclzVPVP7r):
if roI3spqORKae(WueclzVPVP7r, roI3spqORKae(ES5oEprVxulp(b'\x13\x88^\xf4Q\x99\xd6%\xe1\xc7\xf8^'), chr(6072 - 5972) + chr(101) + chr(3464 - 3365) + '\157' + chr(0b1010010 + 0o22) + '\x65')(chr(0b1110101) + chr(116) + '\x66' + chr(0b101101) + '\070')) is not j1aB_lXmg5Oq:
return WueclzVPVP7r
if roI3spqORKae(WueclzVPVP7r, roI3spqORKae(ES5oEprVxulp(b'\x1f\x97\x1e\xa8W\x95\xe60\xd2\xd3\xeay\xbd\xaet('), '\x64' + '\145' + chr(8437 - 8338) + chr(0b10000 + 0o137) + '\x64' + chr(0b1100101))(chr(0b1110101) + '\x74' + '\x66' + chr(0b101101) + '\x38')) is None:
return WueclzVPVP7r
AayaTwzLJRDe = a6DfvLcv0V2D(WueclzVPVP7r)
Ydw_OpZard0c = a6DfvLcv0V2D(WueclzVPVP7r.alternate_effect)
if AayaTwzLJRDe > Ydw_OpZard0c:
return WueclzVPVP7r
else:
return roI3spqORKae(WueclzVPVP7r, roI3spqORKae(ES5oEprVxulp(b'\x1f\x97\x1e\xa8W\x95\xe60\xd2\xd3\xeay\xbd\xaet('), chr(1482 - 1382) + chr(0b111001 + 0o54) + '\x63' + chr(111) + chr(0b100100 + 0o100) + '\x65')(chr(117) + chr(116) + '\146' + chr(0b101101) + '\070')) |
openvax/varcode | varcode/effects/effect_ordering.py | keep_max_priority_effects | def keep_max_priority_effects(effects):
"""
Given a list of effects, only keep the ones with the maximum priority
effect type.
Parameters
----------
effects : list of MutationEffect subclasses
Returns list of same length or shorter
"""
priority_values = map(effect_priority, effects)
max_priority = max(priority_values)
return [e for (e, p) in zip(effects, priority_values) if p == max_priority] | python | def keep_max_priority_effects(effects):
"""
Given a list of effects, only keep the ones with the maximum priority
effect type.
Parameters
----------
effects : list of MutationEffect subclasses
Returns list of same length or shorter
"""
priority_values = map(effect_priority, effects)
max_priority = max(priority_values)
return [e for (e, p) in zip(effects, priority_values) if p == max_priority] | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/effect_ordering.py#L334-L347 | train | Given a list of MutationEffect subclasses and only keep the ones with the maximum priority
effect type. | 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(0b1101101 + 0o2) + chr(0b11010 + 0o30) + chr(0b110001) + chr(52), 0b1000), nzTpIcepk0o8('\x30' + chr(6568 - 6457) + chr(51) + chr(2298 - 2248), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(51) + chr(49) + '\x36', 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(0b0 + 0o62) + '\060' + chr(0b101011 + 0o11), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(49) + '\x34' + '\066', 13419 - 13411), nzTpIcepk0o8(chr(48) + chr(0b1100101 + 0o12) + chr(49) + chr(0b110011) + '\065', 63696 - 63688), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\062' + '\x36' + chr(53), ord("\x08")), nzTpIcepk0o8(chr(939 - 891) + chr(111) + '\x33' + chr(52), 44421 - 44413), nzTpIcepk0o8('\060' + chr(10116 - 10005) + chr(52) + chr(1622 - 1569), 45379 - 45371), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(1108 - 1059) + '\060' + '\061', 23044 - 23036), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110011) + '\x31' + chr(0b110100 + 0o2), 8), nzTpIcepk0o8('\x30' + '\157' + chr(2275 - 2225), 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x36' + chr(0b10011 + 0o40), 15984 - 15976), nzTpIcepk0o8(chr(1900 - 1852) + chr(111) + '\x32' + chr(2636 - 2583) + chr(0b110000), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b10 + 0o64) + chr(1747 - 1697), ord("\x08")), nzTpIcepk0o8(chr(1969 - 1921) + chr(11436 - 11325) + chr(0b110001) + '\064', ord("\x08")), nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(0b1101111) + chr(0b110101) + chr(52), 19243 - 19235), nzTpIcepk0o8(chr(48) + chr(11855 - 11744) + chr(53), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x32' + '\x34' + chr(2114 - 2066), 0o10), nzTpIcepk0o8('\060' + chr(111) + '\063' + chr(50) + chr(179 - 130), 0b1000), nzTpIcepk0o8(chr(295 - 247) + chr(0b111001 + 0o66) + '\x31' + '\062' + '\x31', 45429 - 45421), nzTpIcepk0o8('\060' + '\x6f' + chr(2181 - 2129) + chr(95 - 43), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + '\x32' + chr(338 - 290), 25575 - 25567), nzTpIcepk0o8('\x30' + chr(111) + chr(0b11110 + 0o25) + '\x34' + chr(0b110000), 0o10), nzTpIcepk0o8(chr(187 - 139) + chr(0b110110 + 0o71) + chr(0b110011) + chr(50) + chr(0b110000), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(5854 - 5743) + chr(0b110001) + chr(0b110010) + '\x34', 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b0 + 0o62) + chr(0b110011) + chr(50), 0o10), nzTpIcepk0o8(chr(0b100 + 0o54) + '\157' + chr(0b110110) + chr(0b110010), 8), nzTpIcepk0o8('\x30' + '\x6f' + '\061' + chr(0b110 + 0o61) + '\065', 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110001 + 0o1) + chr(49) + '\065', 0o10), nzTpIcepk0o8(chr(0b11001 + 0o27) + chr(5648 - 5537) + '\062' + '\x34' + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(0b0 + 0o60) + chr(0b101000 + 0o107) + chr(0b10101 + 0o35) + chr(51) + chr(0b100001 + 0o24), 19638 - 19630), nzTpIcepk0o8(chr(48) + chr(0b1000010 + 0o55) + chr(0b110001) + chr(251 - 198), 33037 - 33029), nzTpIcepk0o8('\060' + chr(3985 - 3874) + chr(1426 - 1377) + chr(51) + '\x34', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1100001 + 0o16) + chr(2289 - 2238) + chr(49) + chr(193 - 139), 8), nzTpIcepk0o8('\x30' + chr(11628 - 11517) + '\x32' + chr(55) + chr(53), 0b1000), nzTpIcepk0o8('\x30' + '\157' + '\x31' + chr(1297 - 1242) + chr(50), 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + '\063' + chr(0b100110 + 0o15) + '\065', 0b1000), nzTpIcepk0o8(chr(1364 - 1316) + chr(0b1101111) + chr(49) + '\066', 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x32' + '\x30' + chr(0b101011 + 0o6), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + chr(0b1101111) + '\x35' + chr(48), 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xa2'), chr(0b1000111 + 0o35) + '\x65' + chr(0b1100 + 0o127) + '\157' + chr(5557 - 5457) + chr(0b1100101))(chr(117) + '\164' + chr(0b11010 + 0o114) + chr(131 - 86) + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def tXZbD8GcCqu0(WShYeokTxOn7):
jBG7lVZ7fVTx = VVP82lOIz6CD(a6DfvLcv0V2D, WShYeokTxOn7)
XDG7jQcaArTv = KV9ckIhroIia(jBG7lVZ7fVTx)
return [wgf0sgcu_xPL for (wgf0sgcu_xPL, fSdw5wwLo9MO) in TxMFWa_Xzviv(WShYeokTxOn7, jBG7lVZ7fVTx) if fSdw5wwLo9MO == XDG7jQcaArTv] |
openvax/varcode | varcode/effects/effect_ordering.py | filter_pipeline | def filter_pipeline(effects, filters):
"""
Apply each filter to the effect list sequentially. If any filter
returns zero values then ignore it. As soon as only one effect is left,
return it.
Parameters
----------
effects : list of MutationEffect subclass instances
filters : list of functions
Each function takes a list of effects and returns a list of effects
Returns list of effects
"""
for filter_fn in filters:
filtered_effects = filter_fn(effects)
if len(effects) == 1:
return effects
elif len(filtered_effects) > 1:
effects = filtered_effects
return effects | python | def filter_pipeline(effects, filters):
"""
Apply each filter to the effect list sequentially. If any filter
returns zero values then ignore it. As soon as only one effect is left,
return it.
Parameters
----------
effects : list of MutationEffect subclass instances
filters : list of functions
Each function takes a list of effects and returns a list of effects
Returns list of effects
"""
for filter_fn in filters:
filtered_effects = filter_fn(effects)
if len(effects) == 1:
return effects
elif len(filtered_effects) > 1:
effects = filtered_effects
return effects | [
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effects : list of MutationEffect subclass instances
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/effect_ordering.py#L394-L415 | train | Apply each filter to the effect list sequentially. | 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(1982 - 1932) + chr(0b110010) + '\x31', 0o10), nzTpIcepk0o8(chr(0b1 + 0o57) + chr(5430 - 5319) + '\x33' + chr(0b100111 + 0o11), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\062' + chr(0b1111 + 0o44), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x36' + chr(48), ord("\x08")), nzTpIcepk0o8(chr(0b100001 + 0o17) + '\x6f' + '\x33' + chr(0b1111 + 0o45) + chr(644 - 596), ord("\x08")), nzTpIcepk0o8(chr(656 - 608) + chr(5103 - 4992) + chr(553 - 503) + chr(0b110001) + chr(0b101100 + 0o5), 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(0b110110) + chr(0b111 + 0o52), 45084 - 45076), nzTpIcepk0o8(chr(0b10001 + 0o37) + '\157' + chr(0b1 + 0o61) + chr(0b1000 + 0o51) + '\062', 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110010) + chr(0b0 + 0o65), 16202 - 16194), nzTpIcepk0o8(chr(1675 - 1627) + '\157' + chr(50) + chr(2755 - 2701) + '\x32', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x32' + chr(48) + chr(1293 - 1238), ord("\x08")), nzTpIcepk0o8(chr(0b10101 + 0o33) + chr(0b100011 + 0o114) + '\x32' + '\x36' + chr(0b110100 + 0o2), 42050 - 42042), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\063' + '\067' + chr(49), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1001001 + 0o46) + chr(0b101100 + 0o5) + chr(55) + chr(54), ord("\x08")), nzTpIcepk0o8(chr(1309 - 1261) + chr(0b1001000 + 0o47) + chr(1465 - 1416) + chr(0b110001 + 0o1) + '\x36', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(7384 - 7273) + chr(0b11000 + 0o33) + chr(0b110000) + chr(0b110100), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1010100 + 0o33) + chr(1597 - 1546) + chr(0b1 + 0o60) + chr(51), 47554 - 47546), nzTpIcepk0o8(chr(1688 - 1640) + chr(0b1101111) + '\062' + chr(1572 - 1524) + chr(0b110010), 0o10), nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(111) + chr(50) + chr(0b11110 + 0o31) + chr(2814 - 2760), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101101 + 0o2) + '\062' + chr(53) + chr(420 - 365), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b11011 + 0o34), 0o10), nzTpIcepk0o8(chr(669 - 621) + chr(111) + '\063' + '\063' + chr(0b110001), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x33' + chr(1046 - 998) + '\x34', 8), nzTpIcepk0o8(chr(0b101 + 0o53) + chr(0b1101111) + '\x31' + chr(740 - 692) + chr(1459 - 1410), 63159 - 63151), nzTpIcepk0o8('\x30' + chr(111) + chr(51) + chr(0b110000) + chr(1051 - 1000), ord("\x08")), nzTpIcepk0o8(chr(367 - 319) + '\157' + chr(0b11111 + 0o22) + chr(50) + '\062', ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + '\x32' + chr(0b110011 + 0o0) + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110 + 0o54) + chr(0b110001) + chr(51), 44906 - 44898), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110011) + chr(53) + chr(55), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110011) + chr(1868 - 1815) + chr(2054 - 2005), 13100 - 13092), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x33' + chr(0b100100 + 0o14) + chr(0b110000), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101100 + 0o3) + chr(0b110011) + '\064' + chr(49), 61933 - 61925), nzTpIcepk0o8(chr(1744 - 1696) + chr(111) + chr(0b110001) + chr(0b1100 + 0o46) + chr(49), ord("\x08")), nzTpIcepk0o8('\x30' + chr(8854 - 8743) + '\x33' + chr(48) + chr(48), 8), nzTpIcepk0o8('\x30' + '\x6f' + chr(55) + chr(0b110100 + 0o2), 33853 - 33845), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x31' + chr(0b1 + 0o62) + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(858 - 747) + '\x33' + chr(0b110000 + 0o2), 0o10), nzTpIcepk0o8(chr(1762 - 1714) + chr(741 - 630) + chr(1473 - 1422) + chr(444 - 396) + chr(0b110001), 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110111) + chr(985 - 937), 0o10), nzTpIcepk0o8(chr(1755 - 1707) + chr(0b1101111) + chr(49) + chr(156 - 106) + '\x30', 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(1464 - 1416) + chr(111) + chr(53) + chr(0b110000), 3534 - 3526)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xbf'), chr(0b1100100) + chr(0b1100101) + chr(0b1100011) + '\157' + '\144' + chr(0b10010 + 0o123))(chr(117) + chr(0b1110100) + '\146' + chr(0b100011 + 0o12) + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def hhndKLIvnwYY(WShYeokTxOn7, jDRJWNV63hGm):
for tvDWtbR_eBn6 in jDRJWNV63hGm:
fpbq1_fubIG0 = tvDWtbR_eBn6(WShYeokTxOn7)
if ftfygxgFas5X(WShYeokTxOn7) == nzTpIcepk0o8(chr(48) + '\157' + chr(0b110001), 0b1000):
return WShYeokTxOn7
elif ftfygxgFas5X(fpbq1_fubIG0) > nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(49), 8):
WShYeokTxOn7 = fpbq1_fubIG0
return WShYeokTxOn7 |
openvax/varcode | varcode/effects/effect_ordering.py | top_priority_effect_for_single_gene | def top_priority_effect_for_single_gene(effects):
"""
For effects which are from the same gene, check to see if there
is a canonical transcript with both the maximum length CDS
and maximum length full transcript sequence.
If not, then use number of exons and transcript name as tie-breaking
features.
Parameters
----------
effects : list of MutationEffect subclass instances
Returns single effect object
"""
# first filter effects to keep those on
# 1) maximum priority effects
# 2) protein coding genes
# 3) protein coding transcripts
# 4) complete transcripts
#
# If any of these filters drop all the effects then we move on to the next
# filtering step.
effects = filter_pipeline(
effects=effects,
filters=[
keep_max_priority_effects,
keep_effects_on_protein_coding_genes,
keep_effects_on_protein_coding_transcripts,
keep_effects_on_complete_transcripts,
],
)
if len(effects) == 1:
return effects[0]
# compare CDS length and transcript lengths of remaining effects
# if one effect has the maximum of both categories then return it
cds_lengths = [cds_length_of_associated_transcript(e) for e in effects]
max_cds_length = max(cds_lengths)
# get set of indices of all effects with maximum CDS length
max_cds_length_indices = {
i
for (i, l) in enumerate(cds_lengths)
if l == max_cds_length
}
seq_lengths = [length_of_associated_transcript(e) for e in effects]
max_seq_length = max(seq_lengths)
# get set of indices for all effects whose associated transcript
# has maximum sequence length
max_seq_length_indices = {
i
for (i, l) in enumerate(seq_lengths)
if l == max_seq_length
}
# which effects have transcripts with both the longest CDS and
# longest full transcript sequence?
intersection_of_indices = \
max_cds_length_indices.intersection(max_seq_length_indices)
n_candidates = len(intersection_of_indices)
if n_candidates == 1:
best_index = intersection_of_indices.pop()
return effects[best_index]
elif n_candidates == 0:
# if set of max CDS effects and max sequence length effects is disjoint
# then let's try to do the tie-breaking sort over their union
union_of_indices = max_cds_length_indices.union(max_seq_length_indices)
candidate_effects = [effects[i] for i in union_of_indices]
else:
# if multiple effects have transcripts with the max CDS length and
# the max full sequence length then run the tie-breaking sort
# over all these candidates
candidate_effects = [effects[i] for i in intersection_of_indices]
# break ties by number of exons, whether name of transcript ends if "01",
# and all else being equal, prefer transcript names that end with lower
# numbers
return max(
candidate_effects,
key=tie_breaking_sort_key_for_single_gene_effects) | python | def top_priority_effect_for_single_gene(effects):
"""
For effects which are from the same gene, check to see if there
is a canonical transcript with both the maximum length CDS
and maximum length full transcript sequence.
If not, then use number of exons and transcript name as tie-breaking
features.
Parameters
----------
effects : list of MutationEffect subclass instances
Returns single effect object
"""
# first filter effects to keep those on
# 1) maximum priority effects
# 2) protein coding genes
# 3) protein coding transcripts
# 4) complete transcripts
#
# If any of these filters drop all the effects then we move on to the next
# filtering step.
effects = filter_pipeline(
effects=effects,
filters=[
keep_max_priority_effects,
keep_effects_on_protein_coding_genes,
keep_effects_on_protein_coding_transcripts,
keep_effects_on_complete_transcripts,
],
)
if len(effects) == 1:
return effects[0]
# compare CDS length and transcript lengths of remaining effects
# if one effect has the maximum of both categories then return it
cds_lengths = [cds_length_of_associated_transcript(e) for e in effects]
max_cds_length = max(cds_lengths)
# get set of indices of all effects with maximum CDS length
max_cds_length_indices = {
i
for (i, l) in enumerate(cds_lengths)
if l == max_cds_length
}
seq_lengths = [length_of_associated_transcript(e) for e in effects]
max_seq_length = max(seq_lengths)
# get set of indices for all effects whose associated transcript
# has maximum sequence length
max_seq_length_indices = {
i
for (i, l) in enumerate(seq_lengths)
if l == max_seq_length
}
# which effects have transcripts with both the longest CDS and
# longest full transcript sequence?
intersection_of_indices = \
max_cds_length_indices.intersection(max_seq_length_indices)
n_candidates = len(intersection_of_indices)
if n_candidates == 1:
best_index = intersection_of_indices.pop()
return effects[best_index]
elif n_candidates == 0:
# if set of max CDS effects and max sequence length effects is disjoint
# then let's try to do the tie-breaking sort over their union
union_of_indices = max_cds_length_indices.union(max_seq_length_indices)
candidate_effects = [effects[i] for i in union_of_indices]
else:
# if multiple effects have transcripts with the max CDS length and
# the max full sequence length then run the tie-breaking sort
# over all these candidates
candidate_effects = [effects[i] for i in intersection_of_indices]
# break ties by number of exons, whether name of transcript ends if "01",
# and all else being equal, prefer transcript names that end with lower
# numbers
return max(
candidate_effects,
key=tie_breaking_sort_key_for_single_gene_effects) | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/effect_ordering.py#L439-L526 | train | Returns the first non - empty mutation effect that is a canonical transcript with both the maximum length CDS and maximum length full transcript 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) + chr(111) + '\062' + '\061' + chr(0b110111), ord("\x08")), nzTpIcepk0o8('\x30' + chr(2277 - 2166) + '\062' + chr(53) + chr(0b11 + 0o62), ord("\x08")), nzTpIcepk0o8(chr(2275 - 2227) + chr(10892 - 10781) + '\x33' + chr(725 - 673) + chr(849 - 796), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111 + 0o0) + chr(553 - 504) + chr(0b100110 + 0o15) + '\066', 41711 - 41703), nzTpIcepk0o8(chr(1772 - 1724) + '\x6f' + '\x32' + '\065' + chr(0b110000), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101010 + 0o5) + '\061' + chr(49) + chr(0b100100 + 0o22), 17979 - 17971), nzTpIcepk0o8('\060' + chr(1399 - 1288) + '\x31' + chr(0b110001) + '\x33', 0b1000), nzTpIcepk0o8(chr(472 - 424) + chr(11600 - 11489) + '\061' + chr(51) + chr(0b11111 + 0o27), 8), nzTpIcepk0o8(chr(2008 - 1960) + chr(5483 - 5372) + chr(50) + chr(0b1010 + 0o54) + chr(1354 - 1301), 11642 - 11634), nzTpIcepk0o8(chr(0b1010 + 0o46) + chr(7451 - 7340) + '\063' + '\x30' + chr(126 - 76), 0o10), nzTpIcepk0o8(chr(0b101111 + 0o1) + chr(11310 - 11199) + chr(50) + chr(0b110011) + chr(1906 - 1854), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(187 - 138) + chr(0b110111) + '\x32', 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(2806 - 2753) + chr(0b110001), 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(51) + '\x31' + '\x32', 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b101011 + 0o7) + chr(0b110011 + 0o4) + chr(0b10001 + 0o46), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(10496 - 10385) + '\062' + chr(0b110000) + chr(0b10 + 0o56), 0b1000), nzTpIcepk0o8(chr(0b101 + 0o53) + '\x6f' + chr(2130 - 2081) + chr(0b110010) + chr(0b101100 + 0o12), 3691 - 3683), nzTpIcepk0o8(chr(1127 - 1079) + '\x6f' + '\062' + chr(1361 - 1313), 0o10), nzTpIcepk0o8(chr(0b11010 + 0o26) + '\157' + '\067' + chr(50), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(50) + chr(0b101110 + 0o3) + chr(0b100100 + 0o14), 22391 - 22383), nzTpIcepk0o8(chr(0b110000) + chr(0b110011 + 0o74) + chr(0b110010) + chr(303 - 250) + '\060', 8), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110101) + chr(2025 - 1974), 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(207 - 156) + chr(0b110100) + '\x35', 8), nzTpIcepk0o8(chr(677 - 629) + chr(0b111100 + 0o63) + '\x32' + chr(0b10100 + 0o35) + chr(0b101000 + 0o16), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(3113 - 3002) + '\x30', ord("\x08")), nzTpIcepk0o8(chr(0b100110 + 0o12) + '\x6f' + '\x36' + chr(0b11110 + 0o30), 25084 - 25076), nzTpIcepk0o8(chr(1419 - 1371) + chr(111) + chr(0b1110 + 0o43) + '\x30' + chr(190 - 135), 0o10), nzTpIcepk0o8('\x30' + '\157' + '\x33' + chr(1662 - 1613), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(9071 - 8960) + chr(0b110011) + chr(49) + '\067', 0b1000), nzTpIcepk0o8(chr(0b11110 + 0o22) + chr(111) + chr(0b110010) + '\x35' + chr(55), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(1209 - 1098) + chr(0b110001) + chr(0b100110 + 0o17) + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + '\x32' + '\x35' + chr(53), 8), nzTpIcepk0o8(chr(0b110000) + chr(0b11010 + 0o125) + '\x32' + '\067' + '\x37', 8), nzTpIcepk0o8(chr(0b110000) + chr(0b111101 + 0o62) + '\061' + '\x30' + chr(0b101010 + 0o7), 0b1000), nzTpIcepk0o8('\060' + chr(111) + '\063' + chr(1546 - 1498) + chr(55), 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(0b101010 + 0o7) + '\x34' + chr(925 - 877), 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(0b11010 + 0o31) + chr(0b110101) + chr(1964 - 1911), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + '\061' + chr(55) + chr(51), 14478 - 14470), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\061' + '\060' + '\063', 0b1000), nzTpIcepk0o8('\060' + chr(9642 - 9531) + chr(51) + chr(1127 - 1078) + '\x36', ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(111) + chr(2293 - 2240) + chr(0b1100 + 0o44), ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xa1'), chr(100) + '\145' + '\143' + '\x6f' + '\x64' + '\x65')(chr(117) + '\x74' + '\146' + chr(1596 - 1551) + chr(0b100010 + 0o26)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def iAmAoor_co4g(WShYeokTxOn7):
WShYeokTxOn7 = hhndKLIvnwYY(effects=WShYeokTxOn7, filters=[tXZbD8GcCqu0, BRL0BzYEVRz9, FUZZPmXKekts, q3UQnlJsBRyd])
if ftfygxgFas5X(WShYeokTxOn7) == nzTpIcepk0o8(chr(1602 - 1554) + chr(1009 - 898) + chr(0b11101 + 0o24), ord("\x08")):
return WShYeokTxOn7[nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b1101 + 0o43), 8)]
IeZB3KBvu_mt = [sNTqK0jx1yku(wgf0sgcu_xPL) for wgf0sgcu_xPL in WShYeokTxOn7]
UZ1ZJYPzn2_w = KV9ckIhroIia(IeZB3KBvu_mt)
OFranx5qXTo8 = {ZlbFMSG8gCoF for (ZlbFMSG8gCoF, fPrVrKACaFCC) in _kV_Bomx8PZ4(IeZB3KBvu_mt) if fPrVrKACaFCC == UZ1ZJYPzn2_w}
APU6ALztApa0 = [GQvOW0LZKSh5(wgf0sgcu_xPL) for wgf0sgcu_xPL in WShYeokTxOn7]
li8jMPysIgIe = KV9ckIhroIia(APU6ALztApa0)
ylhycMlk421C = {ZlbFMSG8gCoF for (ZlbFMSG8gCoF, fPrVrKACaFCC) in _kV_Bomx8PZ4(APU6ALztApa0) if fPrVrKACaFCC == li8jMPysIgIe}
FyDN74OZQLDt = OFranx5qXTo8.intersection(ylhycMlk421C)
dA0mHxtrkG8V = ftfygxgFas5X(FyDN74OZQLDt)
if dA0mHxtrkG8V == nzTpIcepk0o8('\x30' + '\157' + chr(0b100100 + 0o15), 8):
gqPYegDmN1nD = FyDN74OZQLDt.uC_Yoybx7J0I()
return WShYeokTxOn7[gqPYegDmN1nD]
elif dA0mHxtrkG8V == nzTpIcepk0o8(chr(48) + chr(11907 - 11796) + '\x30', 8):
iOq92WU9hH_n = OFranx5qXTo8.union(ylhycMlk421C)
V1fGAyO_JHqE = [WShYeokTxOn7[ZlbFMSG8gCoF] for ZlbFMSG8gCoF in iOq92WU9hH_n]
else:
V1fGAyO_JHqE = [WShYeokTxOn7[ZlbFMSG8gCoF] for ZlbFMSG8gCoF in FyDN74OZQLDt]
return KV9ckIhroIia(V1fGAyO_JHqE, key=Ysa3vOXcrfBl) |
openvax/varcode | varcode/effects/effect_ordering.py | top_priority_effect | def top_priority_effect(effects):
"""
Given a collection of variant transcript effects,
return the top priority object. ExonicSpliceSite variants require special
treatment since they actually represent two effects -- the splicing modification
and whatever else would happen to the exonic sequence if nothing else gets
changed. In cases where multiple transcripts give rise to multiple
effects, use a variety of filtering and sorting heuristics to pick
the canonical transcript.
"""
if len(effects) == 0:
raise ValueError("List of effects cannot be empty")
effects = map(
select_between_exonic_splice_site_and_alternate_effect,
effects)
effects_grouped_by_gene = apply_groupby(
effects, fn=gene_id_of_associated_transcript, skip_none=False)
if None in effects_grouped_by_gene:
effects_without_genes = effects_grouped_by_gene.pop(None)
else:
effects_without_genes = []
# if we had any effects associated with genes then choose one of those
if len(effects_grouped_by_gene) > 0:
effects_with_genes = [
top_priority_effect_for_single_gene(gene_effects)
for gene_effects in effects_grouped_by_gene.values()
]
return max(effects_with_genes, key=multi_gene_effect_sort_key)
else:
# if all effects were without genes then choose the best among those
assert len(effects_without_genes) > 0
return max(effects_without_genes, key=multi_gene_effect_sort_key) | python | def top_priority_effect(effects):
"""
Given a collection of variant transcript effects,
return the top priority object. ExonicSpliceSite variants require special
treatment since they actually represent two effects -- the splicing modification
and whatever else would happen to the exonic sequence if nothing else gets
changed. In cases where multiple transcripts give rise to multiple
effects, use a variety of filtering and sorting heuristics to pick
the canonical transcript.
"""
if len(effects) == 0:
raise ValueError("List of effects cannot be empty")
effects = map(
select_between_exonic_splice_site_and_alternate_effect,
effects)
effects_grouped_by_gene = apply_groupby(
effects, fn=gene_id_of_associated_transcript, skip_none=False)
if None in effects_grouped_by_gene:
effects_without_genes = effects_grouped_by_gene.pop(None)
else:
effects_without_genes = []
# if we had any effects associated with genes then choose one of those
if len(effects_grouped_by_gene) > 0:
effects_with_genes = [
top_priority_effect_for_single_gene(gene_effects)
for gene_effects in effects_grouped_by_gene.values()
]
return max(effects_with_genes, key=multi_gene_effect_sort_key)
else:
# if all effects were without genes then choose the best among those
assert len(effects_without_genes) > 0
return max(effects_without_genes, key=multi_gene_effect_sort_key) | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/effect_ordering.py#L529-L564 | train | Given a collection of variant transcript effects return the highest priority effect. | 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' + chr(49) + '\065' + '\067', 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(0b110011) + chr(52), 0b1000), nzTpIcepk0o8('\060' + chr(111) + '\062' + '\063' + chr(0b110010), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + '\061' + chr(0b110110) + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(54) + chr(0b10100 + 0o34), 0b1000), nzTpIcepk0o8(chr(533 - 485) + chr(0b1001 + 0o146) + chr(0b110010) + '\x30' + chr(261 - 207), ord("\x08")), nzTpIcepk0o8(chr(0b1101 + 0o43) + chr(0b1101111) + '\x33' + '\065' + chr(53), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(12033 - 11922) + chr(2295 - 2245) + chr(0b110101) + chr(0b110010 + 0o5), 0o10), nzTpIcepk0o8('\x30' + chr(9042 - 8931) + '\062' + chr(0b110100) + chr(0b1000 + 0o53), 0o10), nzTpIcepk0o8('\060' + chr(111) + '\062' + '\x32', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(9923 - 9812) + chr(417 - 366) + chr(0b1000 + 0o56) + chr(0b100111 + 0o16), 0b1000), nzTpIcepk0o8(chr(0b10 + 0o56) + '\x6f' + '\x31' + chr(48), 11579 - 11571), nzTpIcepk0o8(chr(0b11111 + 0o21) + '\x6f' + chr(0b110010) + chr(0b110010), 8), nzTpIcepk0o8('\x30' + '\157' + chr(999 - 950) + '\x31' + chr(0b101101 + 0o10), 54992 - 54984), nzTpIcepk0o8('\060' + chr(5718 - 5607) + chr(0b11001 + 0o36) + chr(51), 0o10), nzTpIcepk0o8(chr(1672 - 1624) + chr(1650 - 1539) + '\x31' + chr(745 - 693) + chr(0b110001), 35366 - 35358), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\061' + chr(0b110000), 8), nzTpIcepk0o8(chr(48) + chr(111) + chr(2487 - 2437) + chr(106 - 58) + chr(1913 - 1863), 24994 - 24986), nzTpIcepk0o8(chr(0b11 + 0o55) + chr(111) + chr(307 - 256) + '\060' + chr(55), 13177 - 13169), nzTpIcepk0o8(chr(1707 - 1659) + chr(0b1011111 + 0o20) + chr(1445 - 1394) + chr(0b10000 + 0o47), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1100001 + 0o16) + chr(0b100000 + 0o23) + '\061' + chr(54), 54253 - 54245), nzTpIcepk0o8('\060' + chr(11975 - 11864) + chr(51) + chr(50) + chr(0b11011 + 0o27), 23785 - 23777), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(49) + '\066' + chr(0b11011 + 0o25), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1110 + 0o141) + '\064' + chr(55), 0o10), nzTpIcepk0o8(chr(0b10110 + 0o32) + chr(0b1001 + 0o146) + '\x33' + '\x36' + chr(53), 8), nzTpIcepk0o8(chr(48) + chr(111) + chr(1649 - 1600) + '\x36' + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x33' + chr(0b10111 + 0o36) + chr(0b110101), 8), nzTpIcepk0o8(chr(0b101101 + 0o3) + chr(111) + chr(51) + chr(0b110000) + chr(49), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(50) + '\060' + chr(0b10001 + 0o40), 0b1000), nzTpIcepk0o8(chr(0b11 + 0o55) + chr(111) + chr(51) + chr(0b110011) + chr(0b101110 + 0o7), 0o10), nzTpIcepk0o8(chr(0b10011 + 0o35) + chr(0b1101111) + chr(427 - 374) + chr(1837 - 1789), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(10839 - 10728) + chr(0b101011 + 0o7) + chr(1282 - 1231) + '\064', 37554 - 37546), nzTpIcepk0o8('\060' + '\157' + chr(0b110100) + chr(2018 - 1968), 11007 - 10999), nzTpIcepk0o8('\x30' + chr(111) + '\x32' + '\065' + chr(49), ord("\x08")), nzTpIcepk0o8(chr(243 - 195) + chr(0b1000111 + 0o50) + chr(49) + chr(50) + '\062', 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + '\061' + chr(0b110100) + '\067', ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(50) + '\x37' + chr(0b1010 + 0o47), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x33' + '\066' + chr(2554 - 2502), 0o10), nzTpIcepk0o8(chr(48) + chr(0b10111 + 0o130) + chr(0b110010) + chr(0b110110) + '\066', 0o10), nzTpIcepk0o8(chr(184 - 136) + chr(8432 - 8321) + chr(1782 - 1732) + chr(0b10011 + 0o35) + '\063', 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + '\x6f' + chr(2503 - 2450) + chr(0b100011 + 0o15), 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'A'), '\x64' + chr(0b1100101) + chr(0b1000000 + 0o43) + chr(0b110000 + 0o77) + chr(4763 - 4663) + chr(101))('\165' + chr(0b100110 + 0o116) + chr(102) + chr(2016 - 1971) + chr(2940 - 2884)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def JVIu1bh86irm(WShYeokTxOn7):
if ftfygxgFas5X(WShYeokTxOn7) == nzTpIcepk0o8('\x30' + '\157' + chr(2220 - 2172), 0o10):
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'#u\xe9\x03\x10\xe9\x8b\x8f\xc6t\x93mq9HAk\xe3\xa9q\xa1\xa6PE\x90U\x88\xac\xf1\xa9Q'), '\144' + chr(101) + chr(8862 - 8763) + '\157' + chr(0b1100100) + chr(0b1100101))(chr(8494 - 8377) + chr(116) + chr(7673 - 7571) + chr(0b1111 + 0o36) + chr(56)))
WShYeokTxOn7 = VVP82lOIz6CD(lge9193GJ0ch, WShYeokTxOn7)
UgoLawEKkI7Z = F_CseZjwFS8f(WShYeokTxOn7, fn=WA11YIivOKML, skip_none=nzTpIcepk0o8('\060' + chr(10389 - 10278) + '\x30', 8))
if None in UgoLawEKkI7Z:
lJhps9iR2zNX = UgoLawEKkI7Z.uC_Yoybx7J0I(None)
else:
lJhps9iR2zNX = []
if ftfygxgFas5X(UgoLawEKkI7Z) > nzTpIcepk0o8(chr(48) + '\157' + chr(1083 - 1035), 8):
Pcxa6NBcoBr0 = [iAmAoor_co4g(O_kErST9C_wN) for O_kErST9C_wN in UgoLawEKkI7Z.CsodZJH6x9Tx()]
return KV9ckIhroIia(Pcxa6NBcoBr0, key=IEpds8shfG9T)
else:
assert ftfygxgFas5X(lJhps9iR2zNX) > nzTpIcepk0o8(chr(1298 - 1250) + chr(111) + chr(0b110000), 8)
return KV9ckIhroIia(lJhps9iR2zNX, key=IEpds8shfG9T) |
openvax/varcode | varcode/variant_collection.py | VariantCollection.to_dict | def to_dict(self):
"""
Since Collection.to_dict() returns a state dictionary with an
'elements' field we have to rename it to 'variants'.
"""
return dict(
variants=self.variants,
distinct=self.distinct,
sort_key=self.sort_key,
sources=self.sources,
source_to_metadata_dict=self.source_to_metadata_dict) | python | def to_dict(self):
"""
Since Collection.to_dict() returns a state dictionary with an
'elements' field we have to rename it to 'variants'.
"""
return dict(
variants=self.variants,
distinct=self.distinct,
sort_key=self.sort_key,
sources=self.sources,
source_to_metadata_dict=self.source_to_metadata_dict) | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/variant_collection.py#L83-L93 | train | Returns a dictionary with the state of the 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('\x30' + '\157' + chr(569 - 520) + chr(676 - 622) + chr(53), ord("\x08")), nzTpIcepk0o8(chr(193 - 145) + chr(6545 - 6434) + chr(0b110010) + chr(0b110000) + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(1675 - 1627) + chr(0b1101111) + chr(0b110011) + chr(0b10010 + 0o40), 0o10), nzTpIcepk0o8('\x30' + chr(0b1000111 + 0o50) + chr(0b100110 + 0o13) + '\x34' + '\061', 0b1000), nzTpIcepk0o8(chr(0b101001 + 0o7) + chr(0b100011 + 0o114) + chr(1407 - 1357) + '\062' + chr(51), 0b1000), nzTpIcepk0o8(chr(48) + chr(6482 - 6371) + '\061' + chr(0b100110 + 0o12) + chr(0b110111), 0o10), nzTpIcepk0o8('\060' + chr(0b1001011 + 0o44) + chr(51) + chr(55) + chr(52), 65187 - 65179), nzTpIcepk0o8(chr(48) + chr(9648 - 9537) + chr(51) + '\065' + '\064', 42822 - 42814), nzTpIcepk0o8(chr(1317 - 1269) + chr(0b1101111) + chr(0b110101) + chr(2503 - 2450), ord("\x08")), nzTpIcepk0o8(chr(0b11101 + 0o23) + '\157' + chr(0b110010) + chr(914 - 866) + chr(0b110110), 45115 - 45107), nzTpIcepk0o8('\x30' + '\157' + '\062' + chr(1478 - 1425) + '\064', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b100000 + 0o23) + chr(55) + chr(2552 - 2501), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b101001 + 0o10) + '\060' + '\066', 0o10), nzTpIcepk0o8('\060' + '\157' + chr(49) + '\062' + chr(51), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b10100 + 0o35) + '\066' + '\062', 24715 - 24707), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110011) + '\x36' + '\067', 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(50) + '\x37' + chr(0b110001), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b10110 + 0o33) + chr(0b110110) + '\066', ord("\x08")), nzTpIcepk0o8('\060' + chr(4785 - 4674) + chr(0b10111 + 0o34) + chr(53) + chr(55), 59294 - 59286), nzTpIcepk0o8(chr(227 - 179) + chr(111) + chr(0b110011) + '\066' + '\x30', 4486 - 4478), nzTpIcepk0o8('\x30' + chr(111) + '\x31' + chr(0b110000) + '\062', 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(1674 - 1626), 16672 - 16664), nzTpIcepk0o8('\x30' + '\x6f' + chr(55) + '\067', 2459 - 2451), nzTpIcepk0o8(chr(0b1110 + 0o42) + chr(111) + '\x31' + chr(0b110010) + chr(0b11100 + 0o25), 0o10), nzTpIcepk0o8(chr(0b11 + 0o55) + chr(5428 - 5317) + chr(52) + chr(0b11 + 0o64), 20897 - 20889), nzTpIcepk0o8(chr(48) + chr(111) + '\062' + chr(1932 - 1877) + '\062', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + '\061' + chr(51) + chr(0b101010 + 0o7), 0o10), nzTpIcepk0o8(chr(2122 - 2074) + chr(0b11100 + 0o123) + chr(53) + chr(55), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + '\063' + '\065' + chr(958 - 910), 14511 - 14503), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110101) + chr(911 - 862), 0o10), nzTpIcepk0o8(chr(0b10101 + 0o33) + '\x6f' + '\061' + chr(1585 - 1536) + chr(0b1111 + 0o47), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(49) + chr(0b110110) + chr(1085 - 1036), 0b1000), nzTpIcepk0o8(chr(0b11110 + 0o22) + chr(111) + chr(1721 - 1670) + chr(683 - 634) + chr(1341 - 1293), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110011) + '\065' + chr(50), 32554 - 32546), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b11001 + 0o32) + chr(548 - 493) + chr(54), 17043 - 17035), nzTpIcepk0o8(chr(2011 - 1963) + chr(0b10000 + 0o137) + chr(87 - 37) + '\x32' + '\064', 25533 - 25525), nzTpIcepk0o8('\x30' + chr(1917 - 1806) + chr(0b110011) + '\x32' + chr(54), ord("\x08")), nzTpIcepk0o8(chr(0b100011 + 0o15) + '\157' + chr(0b100 + 0o57) + '\x37' + chr(52), 8), nzTpIcepk0o8('\060' + chr(0b1101111) + '\062' + chr(146 - 91), 0b1000), nzTpIcepk0o8('\060' + chr(0b1011000 + 0o27) + chr(51) + chr(52), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + chr(9209 - 9098) + chr(53) + chr(0b110000), 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'['), '\x64' + '\x65' + chr(0b1100011) + chr(0b1000011 + 0o54) + chr(100) + chr(0b1101 + 0o130))(chr(117) + chr(0b1000 + 0o154) + chr(6342 - 6240) + chr(45) + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def WMDtuwiW7UsC(hXMPsSrOQzbh):
return znjnJWK64FDT(variants=roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x03\xe6h\x08\xf2)\x88\x9f'), chr(100) + '\145' + '\x63' + chr(8762 - 8651) + chr(100) + '\x65')(chr(0b1110101) + chr(4322 - 4206) + chr(0b1011010 + 0o14) + chr(77 - 32) + chr(0b111000))), distinct=roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x11\xeei\x15\xfa)\x9f\x98'), '\144' + chr(671 - 570) + chr(0b1000100 + 0o37) + chr(0b11111 + 0o120) + '\144' + chr(0b1100101))('\x75' + '\164' + chr(102) + chr(0b101101) + chr(56))), sort_key=roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'>\xfe`\x05\xa5\r\xbf\xb5i\xc8\x9d\x88'), chr(0b101000 + 0o74) + chr(0b10010 + 0o123) + chr(0b111111 + 0o44) + '\157' + chr(0b1001110 + 0o26) + chr(0b1100101))(chr(4002 - 3885) + chr(0b1110100) + '\146' + chr(614 - 569) + chr(0b111000))), sources=roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'1\xbeR5\xa32\x89\xdf\x1a\xf6\xe3\xb9'), chr(0b1100100) + chr(2197 - 2096) + chr(3909 - 3810) + '\157' + chr(100) + chr(0b110101 + 0o60))(chr(0b110101 + 0o100) + chr(0b1110100) + chr(102) + chr(0b1100 + 0o41) + chr(0b111000))), source_to_metadata_dict=roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x06\xe8o\x13\xf0"\xa3\x98B\xd9\xc1\x9e22\x16\x96\xcd\x17\xb0\x94+cK'), chr(100) + chr(0b1100101) + '\x63' + chr(3763 - 3652) + chr(100) + '\145')(chr(0b1110101) + chr(0b1000101 + 0o57) + '\x66' + '\x2d' + '\x38'))) |
openvax/varcode | varcode/variant_collection.py | VariantCollection.clone_with_new_elements | def clone_with_new_elements(self, new_elements):
"""
Create another VariantCollection of the same class and with
same state (including metadata) but possibly different entries.
Warning: metadata is a dictionary keyed by variants. This method
leaves that dictionary as-is, which may result in extraneous entries
or missing entries.
"""
kwargs = self.to_dict()
kwargs["variants"] = new_elements
return self.from_dict(kwargs) | python | def clone_with_new_elements(self, new_elements):
"""
Create another VariantCollection of the same class and with
same state (including metadata) but possibly different entries.
Warning: metadata is a dictionary keyed by variants. This method
leaves that dictionary as-is, which may result in extraneous entries
or missing entries.
"""
kwargs = self.to_dict()
kwargs["variants"] = new_elements
return self.from_dict(kwargs) | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/variant_collection.py#L95-L106 | train | Create another VariantCollection of the same class and with new elements. | 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(4191 - 4080) + chr(0b101101 + 0o5) + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1010101 + 0o32) + chr(0b100001 + 0o20) + chr(48) + chr(54), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b111001 + 0o66) + chr(0b1011 + 0o50) + chr(0b100000 + 0o23) + chr(48), 0o10), nzTpIcepk0o8(chr(0b101011 + 0o5) + '\157' + '\061' + '\x31' + chr(48), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(8326 - 8215) + chr(0b100110 + 0o13) + '\061', 0o10), nzTpIcepk0o8(chr(1065 - 1017) + chr(2202 - 2091) + '\066' + '\x36', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(1135 - 1024) + chr(55) + chr(1266 - 1211), 30192 - 30184), nzTpIcepk0o8('\060' + '\157' + chr(50) + chr(0b110000) + '\x33', 0b1000), nzTpIcepk0o8(chr(2176 - 2128) + '\x6f' + chr(0b110110), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(49) + chr(1090 - 1042) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(2636 - 2582), 8), nzTpIcepk0o8('\060' + chr(1038 - 927) + chr(51) + chr(48) + chr(50), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1100111 + 0o10) + '\063' + chr(0b110010) + chr(49), 0o10), nzTpIcepk0o8(chr(580 - 532) + '\x6f' + chr(49) + chr(48) + chr(0b111 + 0o60), 0o10), nzTpIcepk0o8('\060' + '\157' + '\x33' + '\063' + chr(0b10100 + 0o36), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + '\061' + chr(0b11110 + 0o24) + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(0b100001 + 0o17) + chr(10800 - 10689) + chr(0b110010) + '\x37' + '\x37', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\064' + chr(0b110111), 61720 - 61712), nzTpIcepk0o8(chr(2055 - 2007) + '\157' + chr(0b1000 + 0o52) + chr(0b110011) + '\x35', 0b1000), nzTpIcepk0o8(chr(48) + '\157' + '\x32' + chr(966 - 918) + chr(50), ord("\x08")), nzTpIcepk0o8(chr(0b1110 + 0o42) + chr(5624 - 5513) + chr(0b1010 + 0o47) + '\x30' + chr(54), 8), nzTpIcepk0o8(chr(0b110000) + chr(0b1000000 + 0o57) + chr(51) + '\x33' + chr(49), 54535 - 54527), nzTpIcepk0o8('\x30' + '\157' + '\065' + '\x31', 45684 - 45676), nzTpIcepk0o8(chr(48) + chr(5047 - 4936) + chr(0b101011 + 0o10) + '\065' + '\064', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b101001 + 0o106) + chr(0b110000 + 0o7) + chr(0b101100 + 0o6), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\066' + '\060', 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(0b11001 + 0o30) + chr(55) + '\x37', 0b1000), nzTpIcepk0o8(chr(0b100100 + 0o14) + chr(7769 - 7658) + chr(2313 - 2264) + chr(52) + '\x37', ord("\x08")), nzTpIcepk0o8(chr(103 - 55) + chr(9527 - 9416) + chr(89 - 40) + chr(0b101000 + 0o16) + chr(0b10 + 0o56), 0b1000), nzTpIcepk0o8(chr(0b100111 + 0o11) + chr(9273 - 9162) + chr(49) + chr(53) + chr(0b110010), 0o10), nzTpIcepk0o8('\x30' + chr(2270 - 2159) + '\061' + '\x32' + chr(2419 - 2365), 62878 - 62870), nzTpIcepk0o8(chr(0b10110 + 0o32) + chr(0b1000111 + 0o50) + chr(0b110011) + chr(51) + '\x34', 41068 - 41060), nzTpIcepk0o8(chr(0b10110 + 0o32) + chr(11601 - 11490) + chr(831 - 778) + chr(0b101101 + 0o7), ord("\x08")), nzTpIcepk0o8('\x30' + chr(4490 - 4379) + '\062' + chr(51) + '\x33', 0o10), nzTpIcepk0o8('\x30' + '\x6f' + '\x34' + chr(1896 - 1842), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1011000 + 0o27) + '\x36' + '\064', 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + '\x32' + chr(1113 - 1060) + chr(0b110001), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b11 + 0o56) + '\x30' + chr(0b11111 + 0o26), 20441 - 20433), nzTpIcepk0o8('\060' + chr(0b1101111) + '\061' + '\065' + chr(51), 15317 - 15309), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b11100 + 0o25) + chr(0b101110 + 0o10) + chr(53), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(53) + '\x30', ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b':'), chr(0b1100100) + chr(0b1100101) + '\143' + chr(0b11 + 0o154) + chr(1918 - 1818) + chr(0b1100101))(chr(0b110111 + 0o76) + chr(10550 - 10434) + chr(0b1011100 + 0o12) + chr(0b101101) + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def eiDoPwG2EJpy(hXMPsSrOQzbh, QER5VKmdmHtT):
q5n0sHDDTy90 = hXMPsSrOQzbh.to_dict()
q5n0sHDDTy90[roI3spqORKae(ES5oEprVxulp(b"b'\xaa!hXK\xf0"), '\144' + chr(0b1100101) + chr(0b1100011) + chr(0b1100110 + 0o11) + '\144' + '\145')(chr(4630 - 4513) + chr(9921 - 9805) + chr(102) + chr(0b101101) + '\x38')] = QER5VKmdmHtT
return roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'v$\xba\x02:xQ\xef\\;7\x98'), chr(0b1010111 + 0o15) + chr(0b1100101) + '\x63' + chr(8939 - 8828) + '\144' + chr(0b111111 + 0o46))(chr(7127 - 7010) + '\x74' + chr(8459 - 8357) + chr(0b101101) + chr(0b111000)))(q5n0sHDDTy90) |
openvax/varcode | varcode/variant_collection.py | VariantCollection.effects | def effects(self, raise_on_error=True):
"""
Parameters
----------
raise_on_error : bool, optional
If exception is raised while determining effect of variant on a
transcript, should it be raised? This default is True, meaning
errors result in raised exceptions, otherwise they are only logged.
"""
return EffectCollection([
effect
for variant in self
for effect in variant.effects(raise_on_error=raise_on_error)
]) | python | def effects(self, raise_on_error=True):
"""
Parameters
----------
raise_on_error : bool, optional
If exception is raised while determining effect of variant on a
transcript, should it be raised? This default is True, meaning
errors result in raised exceptions, otherwise they are only logged.
"""
return EffectCollection([
effect
for variant in self
for effect in variant.effects(raise_on_error=raise_on_error)
]) | [
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raise_on_error : bool, optional
If exception is raised while determining effect of variant on a
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/variant_collection.py#L108-L122 | train | Returns EffectCollection containing all effects of this Variant on a
transcript. | 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(2446 - 2395) + '\x34' + chr(2141 - 2092), 0o10), nzTpIcepk0o8('\060' + '\x6f' + '\061' + '\061' + chr(0b110010), 0b1000), nzTpIcepk0o8(chr(1997 - 1949) + chr(0b111100 + 0o63) + chr(2531 - 2477) + chr(0b1111 + 0o50), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b100 + 0o55) + '\060' + '\066', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b11000 + 0o127) + chr(105 - 55) + chr(0b110001) + chr(55), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1011000 + 0o27) + '\064' + chr(52), 0b1000), nzTpIcepk0o8(chr(0b101011 + 0o5) + '\x6f' + chr(49) + '\x32' + '\x33', 0o10), nzTpIcepk0o8('\x30' + chr(0b1100101 + 0o12) + '\062' + chr(0b110101) + '\061', ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + '\061' + chr(50) + chr(49), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1100 + 0o143) + chr(2360 - 2311) + '\x30' + chr(49), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\061' + chr(996 - 948) + '\x33', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b101010 + 0o105) + '\x31' + '\060' + chr(1533 - 1481), ord("\x08")), nzTpIcepk0o8(chr(607 - 559) + chr(111) + '\x33' + '\x37' + chr(0b0 + 0o60), 0o10), nzTpIcepk0o8(chr(2180 - 2132) + chr(11368 - 11257) + chr(1936 - 1887) + chr(55) + chr(0b11011 + 0o25), 18574 - 18566), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110010) + chr(54) + '\067', 31617 - 31609), nzTpIcepk0o8(chr(0b10000 + 0o40) + '\157' + '\062' + chr(1215 - 1160) + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(706 - 655) + '\061' + chr(52), 47192 - 47184), nzTpIcepk0o8(chr(0b10010 + 0o36) + chr(0b101001 + 0o106) + '\063' + chr(2971 - 2916) + chr(0b110100), 43625 - 43617), nzTpIcepk0o8(chr(0b110 + 0o52) + '\x6f' + chr(0b11 + 0o56) + chr(55) + '\x31', 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(0b100111 + 0o13) + chr(49) + chr(0b110100 + 0o3), 8), nzTpIcepk0o8('\060' + chr(0b1101111) + '\061' + chr(52) + chr(0b100100 + 0o17), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(1451 - 1340) + chr(49) + chr(0b110001) + chr(0b110010), 8), nzTpIcepk0o8(chr(0b11 + 0o55) + '\x6f' + chr(0b110010) + chr(593 - 541) + chr(1468 - 1420), ord("\x08")), nzTpIcepk0o8(chr(2297 - 2249) + chr(0b1101111) + '\x32' + '\x32' + '\x32', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(51) + '\065' + '\063', ord("\x08")), nzTpIcepk0o8('\060' + chr(1654 - 1543) + chr(0b110001) + chr(552 - 501) + '\x35', 0o10), nzTpIcepk0o8(chr(506 - 458) + chr(0b111 + 0o150) + '\x32' + chr(0b10011 + 0o42) + '\x33', 0b1000), nzTpIcepk0o8(chr(1030 - 982) + chr(5455 - 5344) + chr(2762 - 2709) + chr(0b1101 + 0o44), 12245 - 12237), nzTpIcepk0o8(chr(48) + chr(0b101101 + 0o102) + chr(50) + chr(51) + chr(49), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b111101 + 0o62) + '\x31' + chr(0b110011) + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(0b101001 + 0o7) + chr(0b1101111) + chr(51) + chr(0b110100) + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110001) + '\061' + '\063', 3698 - 3690), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(50) + chr(0b110010) + '\066', 62066 - 62058), nzTpIcepk0o8('\x30' + '\157' + '\067' + '\x31', 0b1000), nzTpIcepk0o8('\060' + chr(0b100110 + 0o111) + chr(0b110110), 26709 - 26701), nzTpIcepk0o8(chr(48) + '\157' + chr(49) + chr(571 - 520) + '\065', 8), nzTpIcepk0o8('\060' + '\157' + chr(0b1001 + 0o51) + chr(49) + chr(0b110111), 8), nzTpIcepk0o8(chr(630 - 582) + '\157' + chr(1585 - 1534) + '\060' + chr(0b1010 + 0o55), 33906 - 33898), nzTpIcepk0o8(chr(716 - 668) + chr(4024 - 3913) + '\063' + '\060' + chr(0b110010), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x32' + '\x32' + chr(1823 - 1769), 8)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + chr(2370 - 2259) + chr(53) + chr(297 - 249), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xcf'), '\144' + chr(101) + chr(99) + chr(6399 - 6288) + '\x64' + '\145')(chr(117) + '\x74' + chr(102) + '\x2d' + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def WShYeokTxOn7(hXMPsSrOQzbh, QW8XFQ5ICIcT=nzTpIcepk0o8(chr(0b1000 + 0o50) + '\157' + '\061', 0o10)):
return aUmLUkPZ7w_n([WueclzVPVP7r for ZXJSPKxkIyZK in hXMPsSrOQzbh for WueclzVPVP7r in roI3spqORKae(ZXJSPKxkIyZK, roI3spqORKae(ES5oEprVxulp(b'\x84,Q#\xecP '), chr(100) + chr(1969 - 1868) + chr(0b1010001 + 0o22) + chr(0b110100 + 0o73) + chr(0b1001110 + 0o26) + '\145')(chr(0b100110 + 0o117) + '\164' + chr(0b1010100 + 0o22) + chr(45) + '\x38'))(raise_on_error=QW8XFQ5ICIcT)]) |
openvax/varcode | varcode/variant_collection.py | VariantCollection.gene_counts | def gene_counts(self):
"""
Returns number of elements overlapping each gene name. Expects the
derived class (VariantCollection or EffectCollection) to have
an implementation of groupby_gene_name.
"""
return {
gene_name: len(group)
for (gene_name, group)
in self.groupby_gene_name().items()
} | python | def gene_counts(self):
"""
Returns number of elements overlapping each gene name. Expects the
derived class (VariantCollection or EffectCollection) to have
an implementation of groupby_gene_name.
"""
return {
gene_name: len(group)
for (gene_name, group)
in self.groupby_gene_name().items()
} | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/variant_collection.py#L145-L155 | train | Returns the number of elements overlapping each gene name. Expects the sequence to have
an implementation of groupby_gene_name. | 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(50) + chr(1751 - 1700) + chr(1570 - 1522), 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(49) + chr(51) + '\067', 15971 - 15963), nzTpIcepk0o8(chr(0b110 + 0o52) + chr(111) + chr(50) + chr(0b110111) + chr(1430 - 1382), 0b1000), nzTpIcepk0o8(chr(0b10 + 0o56) + chr(0b1101111) + chr(410 - 361) + '\062' + '\x35', 0b1000), nzTpIcepk0o8(chr(0b11 + 0o55) + chr(111) + '\x33' + chr(0b1000 + 0o55) + '\064', 0b1000), nzTpIcepk0o8('\060' + chr(11031 - 10920) + chr(0b110001) + '\x34' + chr(0b110000), 46189 - 46181), nzTpIcepk0o8(chr(0b100 + 0o54) + chr(0b1101111) + chr(51) + chr(812 - 760) + chr(1955 - 1901), 26910 - 26902), nzTpIcepk0o8(chr(0b10100 + 0o34) + '\x6f' + chr(0b100101 + 0o16) + chr(49) + chr(0b1010 + 0o55), 7448 - 7440), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b101111 + 0o4) + '\x34', 0o10), nzTpIcepk0o8(chr(0b101110 + 0o2) + chr(0b1100011 + 0o14) + chr(2338 - 2289), 0b1000), nzTpIcepk0o8('\x30' + chr(0b110 + 0o151) + chr(0b110010) + chr(0b110111) + '\062', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\061' + chr(0b110011) + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b1010 + 0o51) + chr(2026 - 1977) + chr(0b10000 + 0o45), 41084 - 41076), nzTpIcepk0o8(chr(0b100100 + 0o14) + chr(111) + chr(654 - 604) + '\067' + '\063', 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(0b110011) + chr(331 - 278) + chr(55), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(51) + '\x36' + chr(0b110100), 30535 - 30527), nzTpIcepk0o8(chr(48) + '\157' + '\061' + chr(0b110100) + chr(49), 0o10), nzTpIcepk0o8('\060' + chr(7136 - 7025) + chr(0b11110 + 0o23) + '\065' + chr(0b0 + 0o67), 0o10), nzTpIcepk0o8(chr(48) + chr(0b11010 + 0o125) + chr(52) + chr(1721 - 1666), ord("\x08")), nzTpIcepk0o8(chr(0b101011 + 0o5) + chr(111) + '\x31' + chr(0b1101 + 0o43) + chr(0b110011), 45760 - 45752), nzTpIcepk0o8(chr(616 - 568) + chr(111) + chr(0b100010 + 0o17) + chr(0b110111) + '\062', 0b1000), nzTpIcepk0o8(chr(48) + chr(6110 - 5999) + chr(0b110001) + chr(52) + chr(0b110110), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(2971 - 2916) + '\x33', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b10001 + 0o45) + chr(50), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + '\062' + '\066' + chr(0b10010 + 0o40), 12674 - 12666), nzTpIcepk0o8(chr(0b110000 + 0o0) + chr(4184 - 4073) + chr(55) + chr(54), 0b1000), nzTpIcepk0o8('\060' + chr(0b11011 + 0o124) + chr(49) + chr(0b11010 + 0o31) + '\x35', 0b1000), nzTpIcepk0o8(chr(2073 - 2025) + chr(7747 - 7636) + chr(0b101 + 0o55) + chr(0b110001) + '\x37', 0o10), nzTpIcepk0o8(chr(0b100 + 0o54) + chr(111) + '\062' + chr(50) + chr(0b11010 + 0o31), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1010100 + 0o33) + '\065' + chr(0b101010 + 0o7), 0o10), nzTpIcepk0o8('\060' + '\157' + '\063' + '\060' + chr(0b110011), 43756 - 43748), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(51) + chr(0b101000 + 0o15) + '\067', 8), nzTpIcepk0o8('\x30' + '\157' + chr(54) + '\x34', 48565 - 48557), nzTpIcepk0o8('\x30' + chr(111) + '\063' + '\066' + chr(52), 8), nzTpIcepk0o8('\060' + chr(111) + '\063' + '\x30' + '\x32', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110111) + chr(1097 - 1043), 8), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110001) + '\063' + chr(0b100100 + 0o20), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110001) + chr(48) + chr(53), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + '\063' + chr(0b110110) + chr(0b100000 + 0o23), ord("\x08")), nzTpIcepk0o8(chr(0b11010 + 0o26) + chr(0b101110 + 0o101) + '\067' + chr(1097 - 1048), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(111) + '\065' + chr(0b10100 + 0o34), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xb6'), '\x64' + chr(7009 - 6908) + chr(0b1100011) + '\x6f' + '\144' + chr(665 - 564))(chr(0b1110101) + chr(0b1001001 + 0o53) + chr(0b100010 + 0o104) + '\x2d' + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def vOxy_uoBcGbE(hXMPsSrOQzbh):
return {c1JfYxGQnmfV: ftfygxgFas5X(F9lJ8RbIonqb) for (c1JfYxGQnmfV, F9lJ8RbIonqb) in roI3spqORKae(hXMPsSrOQzbh.groupby_gene_name(), roI3spqORKae(ES5oEprVxulp(b'\xc1\x00\xd6\x1b\xa9\x1a\xae\xfb/w\xe21'), chr(0b1100100) + chr(2007 - 1906) + '\143' + chr(0b110110 + 0o71) + '\x64' + chr(101))('\x75' + chr(0b1101000 + 0o14) + chr(102) + chr(45) + chr(0b100111 + 0o21)))()} |
openvax/varcode | varcode/variant_collection.py | VariantCollection.filter_by_transcript_expression | def filter_by_transcript_expression(
self,
transcript_expression_dict,
min_expression_value=0.0):
"""
Filters variants down to those which have overlap a transcript whose
expression value in the transcript_expression_dict argument is greater
than min_expression_value.
Parameters
----------
transcript_expression_dict : dict
Dictionary mapping Ensembl transcript IDs to expression estimates
(either FPKM or TPM)
min_expression_value : float
Threshold above which we'll keep an effect in the result collection
"""
return self.filter_any_above_threshold(
multi_key_fn=lambda variant: variant.transcript_ids,
value_dict=transcript_expression_dict,
threshold=min_expression_value) | python | def filter_by_transcript_expression(
self,
transcript_expression_dict,
min_expression_value=0.0):
"""
Filters variants down to those which have overlap a transcript whose
expression value in the transcript_expression_dict argument is greater
than min_expression_value.
Parameters
----------
transcript_expression_dict : dict
Dictionary mapping Ensembl transcript IDs to expression estimates
(either FPKM or TPM)
min_expression_value : float
Threshold above which we'll keep an effect in the result collection
"""
return self.filter_any_above_threshold(
multi_key_fn=lambda variant: variant.transcript_ids,
value_dict=transcript_expression_dict,
threshold=min_expression_value) | [
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transcript_expression_dict : dict
Dictionary mapping Ensembl transcript IDs to expression estimates
(either FPKM or TPM)
min_expression_value : float
Threshold above which we'll keep an effect in the result collection | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/variant_collection.py#L175-L196 | train | Returns a new VariantCollection containing only those variants which have overlap a transcript whose transcript_expression_value in the transcript_expression_dict argument is greater than min_expression_value. | 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(4719 - 4608) + chr(0b110001) + '\x33' + '\x37', 0b1000), nzTpIcepk0o8(chr(358 - 310) + '\157' + chr(50) + chr(0b110100) + chr(48), ord("\x08")), nzTpIcepk0o8(chr(0b11101 + 0o23) + chr(0b1101111) + chr(51) + '\x31' + '\x35', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110100) + chr(0b110100), 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(1037 - 988) + '\x35' + '\062', 0o10), nzTpIcepk0o8('\060' + '\157' + chr(49) + '\066' + chr(0b100 + 0o61), 60324 - 60316), nzTpIcepk0o8('\x30' + chr(0b1000010 + 0o55) + chr(793 - 742) + chr(0b110011) + '\065', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1 + 0o156) + chr(49) + chr(0b110011) + chr(1800 - 1748), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + '\x36' + chr(54), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b10011 + 0o36) + chr(0b11000 + 0o35) + '\067', 0b1000), nzTpIcepk0o8('\060' + chr(11029 - 10918) + '\x37' + '\x32', 0b1000), nzTpIcepk0o8(chr(0b100000 + 0o20) + '\157' + '\063' + chr(49) + chr(0b101000 + 0o12), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1100000 + 0o17) + chr(1393 - 1342) + chr(0b100011 + 0o15) + '\x30', 0o10), nzTpIcepk0o8(chr(1071 - 1023) + '\x6f' + chr(0b1000 + 0o51) + '\062' + chr(0b10100 + 0o37), 12424 - 12416), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(1669 - 1618) + '\066' + chr(49), 47925 - 47917), nzTpIcepk0o8('\x30' + '\x6f' + '\x35' + chr(0b111 + 0o52), ord("\x08")), nzTpIcepk0o8(chr(0b11110 + 0o22) + '\157' + chr(1945 - 1894) + chr(0b110101) + chr(0b110010), 0o10), nzTpIcepk0o8('\x30' + '\157' + '\x31' + '\062' + chr(0b110010), 0o10), nzTpIcepk0o8(chr(488 - 440) + chr(0b1101 + 0o142) + '\x32' + chr(0b101011 + 0o12) + chr(0b100011 + 0o21), 0o10), nzTpIcepk0o8('\x30' + chr(111) + '\063' + chr(1074 - 1022) + chr(0b110110), 0o10), nzTpIcepk0o8(chr(464 - 416) + '\x6f' + chr(1655 - 1606) + chr(0b1100 + 0o47) + chr(49), 16903 - 16895), nzTpIcepk0o8(chr(48) + chr(7886 - 7775) + chr(881 - 830) + chr(50) + '\061', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(7452 - 7341) + '\x33' + chr(0b110101) + chr(51), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1000 + 0o147) + chr(740 - 691) + '\060' + chr(75 - 21), 52230 - 52222), nzTpIcepk0o8('\060' + chr(111) + '\062' + '\x31' + '\062', 64678 - 64670), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(50) + chr(51) + chr(52), 0b1000), nzTpIcepk0o8('\060' + '\157' + '\061' + chr(2197 - 2144) + '\065', 0o10), nzTpIcepk0o8('\060' + chr(0b10110 + 0o131) + chr(2257 - 2204) + chr(0b1001 + 0o54), 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(393 - 344) + '\x30' + chr(0b110110), 8), nzTpIcepk0o8(chr(48) + '\157' + chr(49), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(278 - 229) + chr(0b100110 + 0o16), 0o10), nzTpIcepk0o8(chr(1093 - 1045) + chr(1749 - 1638) + chr(53) + '\x33', 54854 - 54846), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\062' + chr(0b110100) + chr(403 - 352), 45253 - 45245), nzTpIcepk0o8(chr(424 - 376) + '\157' + chr(0b110001) + chr(0b111 + 0o54) + '\x30', 23558 - 23550), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b11011 + 0o31) + chr(50), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(7634 - 7523) + chr(1718 - 1667) + chr(48) + chr(0b110011 + 0o4), 0b1000), nzTpIcepk0o8(chr(0b10 + 0o56) + chr(111) + '\x31' + '\066' + '\x30', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(3106 - 2995) + chr(0b110010) + chr(0b101010 + 0o14) + '\x34', ord("\x08")), nzTpIcepk0o8(chr(130 - 82) + '\x6f' + chr(0b1110 + 0o43) + '\x32' + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(0b101 + 0o53) + chr(0b11110 + 0o121) + chr(0b110001) + chr(1468 - 1415) + chr(0b100010 + 0o20), 8)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x35' + '\060', 7956 - 7948)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'q'), '\144' + chr(101) + chr(1132 - 1033) + chr(0b1101111) + chr(1061 - 961) + '\x65')(chr(10816 - 10699) + '\164' + chr(0b1100110) + chr(0b101000 + 0o5) + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def rDv2O8kB1bUs(hXMPsSrOQzbh, ToguHn7Cf1Cy, TSqDQe75vpsb=0.0):
return roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'9\xc9\xa1P\x0f\x07\x82=X\x16e\xab\xa2<\x87L\xb5&\xc4\x94<\xa2\x83)\xe6\xf8'), chr(0b101101 + 0o67) + '\145' + chr(99) + chr(3536 - 3425) + chr(100) + chr(3125 - 3024))(chr(219 - 102) + chr(3386 - 3270) + chr(0b1101 + 0o131) + chr(1469 - 1424) + chr(56)))(multi_key_fn=lambda ZXJSPKxkIyZK: roI3spqORKae(ZXJSPKxkIyZK, roI3spqORKae(ES5oEprVxulp(b'+\xd2\xacJ\x19\x16\xaf5F\x1be\xa3\xa4 '), chr(9773 - 9673) + chr(0b1100101) + '\x63' + '\x6f' + '\144' + '\x65')(chr(0b1000001 + 0o64) + '\164' + chr(0b110111 + 0o57) + '\x2d' + chr(56))), value_dict=ToguHn7Cf1Cy, threshold=TSqDQe75vpsb) |
openvax/varcode | varcode/variant_collection.py | VariantCollection.filter_by_gene_expression | def filter_by_gene_expression(
self,
gene_expression_dict,
min_expression_value=0.0):
"""
Filters variants down to those which have overlap a gene whose
expression value in the transcript_expression_dict argument is greater
than min_expression_value.
Parameters
----------
gene_expression_dict : dict
Dictionary mapping Ensembl gene IDs to expression estimates
(either FPKM or TPM)
min_expression_value : float
Threshold above which we'll keep an effect in the result collection
"""
return self.filter_any_above_threshold(
multi_key_fn=lambda effect: effect.gene_ids,
value_dict=gene_expression_dict,
threshold=min_expression_value) | python | def filter_by_gene_expression(
self,
gene_expression_dict,
min_expression_value=0.0):
"""
Filters variants down to those which have overlap a gene whose
expression value in the transcript_expression_dict argument is greater
than min_expression_value.
Parameters
----------
gene_expression_dict : dict
Dictionary mapping Ensembl gene IDs to expression estimates
(either FPKM or TPM)
min_expression_value : float
Threshold above which we'll keep an effect in the result collection
"""
return self.filter_any_above_threshold(
multi_key_fn=lambda effect: effect.gene_ids,
value_dict=gene_expression_dict,
threshold=min_expression_value) | [
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gene_expression_dict : dict
Dictionary mapping Ensembl gene IDs to expression estimates
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/variant_collection.py#L198-L219 | train | Returns a new Collection containing only variants which have overlap a gene whose
expression value in the transcript_expression_dict argument is greater than min_expression_value. | 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(0b101 + 0o53) + chr(10265 - 10154) + chr(50) + chr(0b100111 + 0o15) + chr(50), 26753 - 26745), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110110) + chr(0b110110), ord("\x08")), nzTpIcepk0o8(chr(661 - 613) + '\157' + chr(51) + chr(0b110101), 0o10), nzTpIcepk0o8(chr(0b10110 + 0o32) + chr(111) + chr(50) + '\x30' + chr(52), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b10 + 0o155) + '\061' + chr(516 - 467) + '\063', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b110100 + 0o73) + chr(83 - 32) + chr(1918 - 1868) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x31' + '\066' + '\066', 1114 - 1106), nzTpIcepk0o8(chr(2238 - 2190) + chr(0b1101111) + '\061' + chr(0b110000) + '\x35', 63398 - 63390), nzTpIcepk0o8(chr(0b110000) + chr(0b1010101 + 0o32) + chr(50) + chr(0b1001 + 0o52) + chr(0b101111 + 0o7), 37874 - 37866), nzTpIcepk0o8('\x30' + chr(6215 - 6104) + '\061' + '\062' + '\063', 0b1000), nzTpIcepk0o8('\x30' + chr(0b1011110 + 0o21) + '\x31' + chr(0b1110 + 0o51) + chr(48), 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(0b10011 + 0o41) + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(432 - 377) + chr(267 - 215), 63966 - 63958), nzTpIcepk0o8('\x30' + chr(111) + chr(0b101110 + 0o5) + chr(48) + chr(0b1 + 0o66), 0o10), nzTpIcepk0o8(chr(0b10011 + 0o35) + '\x6f' + '\061' + '\x37' + '\x37', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b10100 + 0o133) + chr(54), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + '\066' + chr(0b100001 + 0o17), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + '\062' + '\067' + '\064', 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110010) + '\062' + chr(0b11111 + 0o24), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(52) + chr(0b10 + 0o63), 0o10), nzTpIcepk0o8(chr(965 - 917) + chr(9771 - 9660) + '\062' + '\x31' + '\x31', ord("\x08")), nzTpIcepk0o8('\060' + chr(274 - 163) + '\x37' + chr(0b11111 + 0o21), 0o10), nzTpIcepk0o8(chr(2199 - 2151) + '\x6f' + '\x32' + chr(0b110110) + chr(54), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(0b10001 + 0o37) + chr(111) + chr(0b110011) + chr(0b110011) + '\060', 0b1000), nzTpIcepk0o8(chr(1555 - 1507) + '\x6f' + chr(0b1 + 0o62) + chr(0b101010 + 0o10) + chr(332 - 279), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110011) + '\x36' + '\062', 38163 - 38155), nzTpIcepk0o8(chr(1628 - 1580) + chr(111) + chr(2093 - 2042) + '\066' + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(1277 - 1229) + '\x6f' + chr(0b1101 + 0o44) + chr(2391 - 2339) + '\x32', 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x34' + chr(51), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(1666 - 1617) + '\066' + chr(52), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(50) + '\x32' + '\064', ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(51) + chr(0b110100) + chr(50), 0o10), nzTpIcepk0o8(chr(0b11 + 0o55) + '\157' + chr(0b1000 + 0o52) + '\x37' + chr(2333 - 2284), 0o10), nzTpIcepk0o8(chr(48) + chr(4660 - 4549) + '\063' + chr(0b110101) + chr(0b100010 + 0o17), 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(0b10100 + 0o35) + '\x35' + chr(755 - 700), 0o10), nzTpIcepk0o8(chr(48) + chr(10152 - 10041) + chr(0b11000 + 0o33) + chr(1233 - 1185) + chr(2635 - 2582), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(1853 - 1803) + '\067', ord("\x08")), nzTpIcepk0o8(chr(1050 - 1002) + '\x6f' + chr(0b101011 + 0o6) + '\061' + chr(50), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b101011 + 0o104) + chr(0b1010 + 0o47) + chr(0b110001) + '\x34', ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b10110 + 0o32) + chr(111) + chr(0b110101) + chr(0b1 + 0o57), 39932 - 39924)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x8c'), '\x64' + chr(0b1010101 + 0o20) + '\143' + chr(4906 - 4795) + chr(6512 - 6412) + '\145')(chr(0b11101 + 0o130) + chr(0b11111 + 0o125) + chr(102) + '\055' + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def NLYV3y2R5am3(hXMPsSrOQzbh, g55hwTtIL77B, TSqDQe75vpsb=0.0):
return roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b"\xc4_q\xf0.\xa6)$\xf0*'F^\xa8\tco\xc8\xfbW\xecK\xdej\xb4\xb1"), chr(0b1100100) + chr(9379 - 9278) + chr(1722 - 1623) + chr(0b1100111 + 0o10) + chr(0b1000 + 0o134) + chr(101))('\165' + '\164' + chr(0b1100110) + chr(1118 - 1073) + chr(1497 - 1441)))(multi_key_fn=lambda WueclzVPVP7r: roI3spqORKae(WueclzVPVP7r, roI3spqORKae(ES5oEprVxulp(b'\xc5Ss\xe1\x14\xbd\x126'), chr(100) + chr(101) + '\143' + chr(3986 - 3875) + '\144' + chr(0b1100101))(chr(12052 - 11935) + '\164' + chr(0b1100110) + chr(335 - 290) + chr(0b1110 + 0o52))), value_dict=g55hwTtIL77B, threshold=TSqDQe75vpsb) |
openvax/varcode | varcode/variant_collection.py | VariantCollection.exactly_equal | def exactly_equal(self, other):
'''
Comparison between VariantCollection instances that takes into account
the info field of Variant instances.
Returns
----------
True if the variants in this collection equal the variants in the other
collection. The Variant.info fields are included in the comparison.
'''
return (
self.__class__ == other.__class__ and
len(self) == len(other) and
all(x.exactly_equal(y) for (x, y) in zip(self, other))) | python | def exactly_equal(self, other):
'''
Comparison between VariantCollection instances that takes into account
the info field of Variant instances.
Returns
----------
True if the variants in this collection equal the variants in the other
collection. The Variant.info fields are included in the comparison.
'''
return (
self.__class__ == other.__class__ and
len(self) == len(other) and
all(x.exactly_equal(y) for (x, y) in zip(self, other))) | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/variant_collection.py#L221-L234 | train | Returns True if the variants in this collection are exactly equal. | 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(0b10 + 0o56) + chr(111) + chr(0b11101 + 0o26) + chr(0b110001) + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(49) + '\x30' + chr(349 - 297), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101101 + 0o2) + '\063' + chr(931 - 881) + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(1173 - 1125) + '\x6f' + '\061' + chr(0b101000 + 0o13) + chr(0b110001), ord("\x08")), nzTpIcepk0o8('\060' + chr(10033 - 9922) + chr(0b110010) + chr(927 - 875) + '\062', 10471 - 10463), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x32' + '\066', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b11010 + 0o30) + chr(0b10110 + 0o40) + chr(54), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(51) + chr(0b1101 + 0o46) + '\x33', 34134 - 34126), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\062' + chr(0b110110 + 0o1), ord("\x08")), nzTpIcepk0o8('\x30' + chr(6286 - 6175) + chr(0b110010) + chr(0b110100) + chr(1150 - 1100), 8), nzTpIcepk0o8('\x30' + chr(0b1010 + 0o145) + '\x32' + chr(0b110011) + chr(53), 0b1000), nzTpIcepk0o8(chr(0b11 + 0o55) + '\157' + chr(49) + chr(55) + chr(54), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b101111 + 0o2) + chr(48) + '\063', 29748 - 29740), nzTpIcepk0o8(chr(237 - 189) + chr(9083 - 8972) + chr(1570 - 1516) + chr(0b11111 + 0o21), 0b1000), nzTpIcepk0o8('\060' + '\x6f' + '\x33' + '\060' + chr(0b110110), 37076 - 37068), nzTpIcepk0o8(chr(0b1110 + 0o42) + '\x6f' + '\061' + chr(0b110101) + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101101 + 0o2) + '\x32' + '\x34', 0b1000), nzTpIcepk0o8(chr(0b10011 + 0o35) + chr(111) + chr(0b110011) + '\x37' + '\060', 0o10), nzTpIcepk0o8(chr(48) + chr(0b10000 + 0o137) + chr(0b11001 + 0o31) + chr(0b110111) + chr(0b101110 + 0o4), 0o10), nzTpIcepk0o8(chr(0b101101 + 0o3) + chr(11568 - 11457) + chr(0b10 + 0o61) + '\x30' + chr(886 - 831), 0o10), nzTpIcepk0o8(chr(0b101100 + 0o4) + '\x6f' + chr(0b100010 + 0o17) + chr(880 - 827) + chr(877 - 824), ord("\x08")), nzTpIcepk0o8(chr(0b11000 + 0o30) + '\157' + chr(1608 - 1558) + chr(0b110110) + chr(0b100 + 0o56), ord("\x08")), nzTpIcepk0o8(chr(0b10000 + 0o40) + chr(0b1101111 + 0o0) + '\x33' + '\067' + '\066', 0o10), nzTpIcepk0o8(chr(2153 - 2105) + '\x6f' + '\066' + chr(0b110101), 0o10), nzTpIcepk0o8(chr(0b11101 + 0o23) + chr(0b1101111) + chr(49) + chr(0b100100 + 0o20) + chr(0b1001 + 0o50), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x31' + chr(0b110100) + '\061', 8), nzTpIcepk0o8(chr(0b110000 + 0o0) + '\x6f' + chr(1001 - 951) + '\067' + '\061', 0b1000), nzTpIcepk0o8(chr(954 - 906) + chr(111) + chr(0b10111 + 0o33) + chr(0b110100) + chr(0b11101 + 0o24), 50754 - 50746), nzTpIcepk0o8(chr(0b1 + 0o57) + chr(0b1101111) + chr(50) + chr(1765 - 1711) + '\061', ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + '\x33' + '\066' + '\x33', 0o10), nzTpIcepk0o8(chr(0b111 + 0o51) + chr(0b100001 + 0o116) + chr(51) + chr(0b1010 + 0o54) + chr(2466 - 2413), 0b1000), nzTpIcepk0o8(chr(800 - 752) + '\157' + '\062' + '\062', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b10110 + 0o131) + '\063' + '\x34' + '\060', 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(2596 - 2542) + chr(0b110110), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(1215 - 1160), 37474 - 37466), nzTpIcepk0o8('\x30' + chr(3157 - 3046) + '\066' + '\x34', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b101010 + 0o7) + chr(0b101101 + 0o3) + '\062', 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110011) + '\x35' + '\061', 0o10), nzTpIcepk0o8(chr(1698 - 1650) + chr(0b100101 + 0o112) + chr(1109 - 1060) + '\x32' + '\x36', 30567 - 30559), nzTpIcepk0o8('\x30' + '\x6f' + '\063' + chr(0b100100 + 0o16) + '\x33', 46163 - 46155)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(1582 - 1534) + chr(111) + chr(1510 - 1457) + chr(0b1010 + 0o46), ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xe4'), chr(100) + '\145' + '\x63' + chr(0b1101111) + chr(0b111111 + 0o45) + chr(0b1100101))('\165' + chr(116) + '\x66' + chr(45) + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def lkHPohbU81qy(hXMPsSrOQzbh, iDZKqp9Clygk):
return roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xa77\xe4`\xd6t\xe7\xbaA\xe9\xea?'), chr(4400 - 4300) + '\145' + chr(99) + '\157' + chr(100) + '\x65')(chr(117) + chr(939 - 823) + chr(0b1100110) + chr(0b101101) + chr(1466 - 1410))) == roI3spqORKae(iDZKqp9Clygk, roI3spqORKae(ES5oEprVxulp(b'\xa77\xe4`\xd6t\xe7\xbaA\xe9\xea?'), chr(0b1100100) + '\x65' + '\x63' + chr(0b1101111) + chr(100) + '\x65')(chr(0b1110101) + chr(1943 - 1827) + chr(0b1010000 + 0o26) + chr(45) + chr(56))) and ftfygxgFas5X(hXMPsSrOQzbh) == ftfygxgFas5X(iDZKqp9Clygk) and qX60lO1lgHA5((roI3spqORKae(bI5jsQ9OkQtj, roI3spqORKae(ES5oEprVxulp(b'\xaf<\xb1:\xd6z\xcf\x84r\xd3\xe8\x1f/'), chr(0b1100100) + chr(0b1100101) + chr(411 - 312) + chr(0b1101111) + '\x64' + '\145')(chr(3427 - 3310) + chr(116) + '\146' + chr(0b100001 + 0o14) + chr(56)))(Fi3yzxctM1zW) for (bI5jsQ9OkQtj, Fi3yzxctM1zW) in TxMFWa_Xzviv(hXMPsSrOQzbh, iDZKqp9Clygk))) |
openvax/varcode | varcode/variant_collection.py | VariantCollection._merge_metadata_dictionaries | def _merge_metadata_dictionaries(cls, dictionaries):
"""
Helper function for combining variant collections: given multiple
dictionaries mapping:
source name -> (variant -> (attribute -> value))
Returns dictionary with union of all variants and sources.
"""
# three levels of nested dictionaries!
# {source name: {variant: {attribute: value}}}
combined_dictionary = {}
for source_to_metadata_dict in dictionaries:
for source_name, variant_to_metadata_dict in source_to_metadata_dict.items():
combined_dictionary.setdefault(source_name, {})
combined_source_dict = combined_dictionary[source_name]
for variant, metadata_dict in variant_to_metadata_dict.items():
combined_source_dict.setdefault(variant, {})
combined_source_dict[variant].update(metadata_dict)
return combined_dictionary | python | def _merge_metadata_dictionaries(cls, dictionaries):
"""
Helper function for combining variant collections: given multiple
dictionaries mapping:
source name -> (variant -> (attribute -> value))
Returns dictionary with union of all variants and sources.
"""
# three levels of nested dictionaries!
# {source name: {variant: {attribute: value}}}
combined_dictionary = {}
for source_to_metadata_dict in dictionaries:
for source_name, variant_to_metadata_dict in source_to_metadata_dict.items():
combined_dictionary.setdefault(source_name, {})
combined_source_dict = combined_dictionary[source_name]
for variant, metadata_dict in variant_to_metadata_dict.items():
combined_source_dict.setdefault(variant, {})
combined_source_dict[variant].update(metadata_dict)
return combined_dictionary | [
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dictionaries mapping:
source name -> (variant -> (attribute -> value))
Returns dictionary with union of all variants and sources. | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/variant_collection.py#L237-L255 | train | Helper function for combining variant collections given multiple
dictionaries mapping source name to variant name and metadata 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(0b110 + 0o52) + chr(0b1101111) + chr(0b110011) + chr(0b110000) + chr(2915 - 2861), ord("\x08")), nzTpIcepk0o8('\x30' + chr(9095 - 8984) + chr(0b10111 + 0o33) + chr(0b110101) + '\x32', ord("\x08")), nzTpIcepk0o8(chr(443 - 395) + '\157' + '\x31' + chr(50) + chr(87 - 33), 0b1000), nzTpIcepk0o8(chr(0b100100 + 0o14) + chr(0b111001 + 0o66) + chr(0b1110 + 0o43) + '\x30' + chr(0b110010), 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(50) + chr(48) + chr(0b100000 + 0o20), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(0b100111 + 0o14) + chr(0b1110 + 0o42) + chr(0b101010 + 0o12), 0o10), nzTpIcepk0o8(chr(65 - 17) + chr(111) + chr(0b110010) + chr(0b110110), 36321 - 36313), nzTpIcepk0o8(chr(0b110000) + chr(0b100100 + 0o113) + '\x31' + chr(0b110001) + chr(1690 - 1636), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(7308 - 7197) + chr(0b110001) + chr(54) + '\x35', 41139 - 41131), nzTpIcepk0o8(chr(48) + '\157' + '\061' + chr(0b110 + 0o53), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110010) + '\060' + '\063', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\062' + chr(54) + chr(0b101111 + 0o7), ord("\x08")), nzTpIcepk0o8(chr(0b0 + 0o60) + chr(111) + '\063' + chr(2016 - 1967) + chr(57 - 2), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(2343 - 2293) + chr(695 - 642) + chr(0b110000), 0o10), nzTpIcepk0o8(chr(1271 - 1223) + '\157' + '\063' + '\x35' + chr(585 - 533), 0b1000), nzTpIcepk0o8(chr(0b110000 + 0o0) + chr(111) + chr(1056 - 1008), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110100) + chr(0b100111 + 0o20), 36559 - 36551), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110001) + '\063' + chr(0b1010 + 0o55), 0o10), nzTpIcepk0o8('\060' + chr(0b101001 + 0o106) + '\062' + chr(0b111 + 0o56) + chr(0b11100 + 0o25), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + '\061' + chr(0b110111) + '\x31', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(346 - 235) + '\065', 0o10), nzTpIcepk0o8('\060' + '\157' + chr(0b1110 + 0o45) + chr(0b110000) + '\x35', 0b1000), nzTpIcepk0o8(chr(223 - 175) + '\157' + '\061' + chr(0b110010) + chr(0b100001 + 0o21), 0o10), nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(111) + '\062' + chr(0b100100 + 0o16) + '\066', 6197 - 6189), nzTpIcepk0o8(chr(0b110 + 0o52) + '\x6f' + '\062' + '\067' + chr(52), 49717 - 49709), nzTpIcepk0o8('\x30' + chr(111) + chr(51) + chr(0b110110) + chr(54), 65509 - 65501), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(54) + '\x35', 0o10), nzTpIcepk0o8('\060' + chr(10227 - 10116) + chr(0b110001) + '\067' + '\062', ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + '\063' + '\062' + chr(54), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\062' + chr(2045 - 1992) + '\x31', 8), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(54) + chr(0b110101), 8), nzTpIcepk0o8('\x30' + chr(111) + chr(0b10 + 0o62) + chr(0b110010), 22291 - 22283), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(1991 - 1940) + chr(0b110010) + chr(54), 8), nzTpIcepk0o8('\060' + '\157' + '\x31' + chr(51), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1011111 + 0o20) + chr(2149 - 2099) + '\063' + '\x34', ord("\x08")), nzTpIcepk0o8(chr(1076 - 1028) + chr(5054 - 4943) + '\063' + chr(0b110001) + chr(1775 - 1725), ord("\x08")), nzTpIcepk0o8(chr(0b10111 + 0o31) + chr(11744 - 11633) + chr(51) + chr(48) + '\x31', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + '\063' + '\x37' + '\x32', 0b1000), nzTpIcepk0o8(chr(402 - 354) + chr(0b1111 + 0o140) + chr(0b100010 + 0o20) + '\066' + chr(0b110011), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(50) + chr(51) + chr(0b110010), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b1100 + 0o51) + chr(0b110000), 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xe8'), chr(0b1100100) + '\x65' + chr(99) + chr(111) + chr(0b1000100 + 0o40) + chr(0b1010101 + 0o20))(chr(4709 - 4592) + chr(116) + chr(0b1100110) + '\055' + chr(1927 - 1871)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def PFFxsDmv5KEg(_1vzISbJ_R2i, fL2CngqwmsHX):
zvQFoQtimEp1 = {}
for T80_NkicwSyK in fL2CngqwmsHX:
for (y9XN18XNF8kG, cNI86v5y5cEJ) in roI3spqORKae(T80_NkicwSyK, roI3spqORKae(ES5oEprVxulp(b'\x9f\xf58\x0c\xc5\xbe^zF\x7f\xdb\xdf'), '\144' + chr(0b1100101) + chr(0b1100011) + chr(111) + chr(0b1100100) + chr(3035 - 2934))(chr(117) + chr(0b1110100) + chr(102) + chr(0b11001 + 0o24) + chr(0b111000)))():
roI3spqORKae(zvQFoQtimEp1, roI3spqORKae(ES5oEprVxulp(b'\xbc\xcff\x08\xcd\xb1]w\x07f\xd4\xe5'), chr(0b1100100) + chr(0b1100101) + '\x63' + '\x6f' + chr(0b1100100) + chr(0b1100101))(chr(0b1110101) + chr(116) + chr(0b101111 + 0o67) + chr(1329 - 1284) + '\x38'))(y9XN18XNF8kG, {})
ryUIAMiTlGU6 = zvQFoQtimEp1[y9XN18XNF8kG]
for (ZXJSPKxkIyZK, IADDJ5HSAyHj) in roI3spqORKae(cNI86v5y5cEJ, roI3spqORKae(ES5oEprVxulp(b'\x9f\xf58\x0c\xc5\xbe^zF\x7f\xdb\xdf'), chr(3704 - 3604) + '\145' + chr(99) + chr(0b101000 + 0o107) + '\x64' + chr(1210 - 1109))('\165' + '\x74' + '\x66' + '\055' + chr(3068 - 3012)))():
roI3spqORKae(ryUIAMiTlGU6, roI3spqORKae(ES5oEprVxulp(b'\xbc\xcff\x08\xcd\xb1]w\x07f\xd4\xe5'), chr(529 - 429) + '\x65' + chr(99) + chr(111) + chr(0b1100100) + chr(0b111001 + 0o54))(chr(12151 - 12034) + '\164' + '\146' + chr(45) + '\070'))(ZXJSPKxkIyZK, {})
roI3spqORKae(ryUIAMiTlGU6[ZXJSPKxkIyZK], roI3spqORKae(ES5oEprVxulp(b'\x8c\xf5=p\xc9\x9dT\x7f\x16l\xf2\xd8'), chr(100) + '\x65' + chr(8250 - 8151) + chr(0b110010 + 0o75) + chr(0b1000110 + 0o36) + chr(0b1100101))(chr(117) + '\164' + '\x66' + chr(1274 - 1229) + '\070'))(IADDJ5HSAyHj)
return zvQFoQtimEp1 |
openvax/varcode | varcode/variant_collection.py | VariantCollection._combine_variant_collections | def _combine_variant_collections(cls, combine_fn, variant_collections, kwargs):
"""
Create a single VariantCollection from multiple different collections.
Parameters
----------
cls : class
Should be VariantCollection
combine_fn : function
Function which takes any number of sets of variants and returns
some combination of them (typically union or intersection).
variant_collections : tuple of VariantCollection
kwargs : dict
Optional dictionary of keyword arguments to pass to the initializer
for VariantCollection.
"""
kwargs["variants"] = combine_fn(*[set(vc) for vc in variant_collections])
kwargs["source_to_metadata_dict"] = cls._merge_metadata_dictionaries(
[vc.source_to_metadata_dict for vc in variant_collections])
kwargs["sources"] = set.union(*([vc.sources for vc in variant_collections]))
for key, value in variant_collections[0].to_dict().items():
# If some optional parameter isn't explicitly specified as an
# argument to union() or intersection() then use the same value
# as the first VariantCollection.
#
# I'm doing this so that the meaning of VariantCollection.union
# and VariantCollection.intersection with a single argument is
# the identity function (rather than setting optional parameters
# to their default values.
if key not in kwargs:
kwargs[key] = value
return cls(**kwargs) | python | def _combine_variant_collections(cls, combine_fn, variant_collections, kwargs):
"""
Create a single VariantCollection from multiple different collections.
Parameters
----------
cls : class
Should be VariantCollection
combine_fn : function
Function which takes any number of sets of variants and returns
some combination of them (typically union or intersection).
variant_collections : tuple of VariantCollection
kwargs : dict
Optional dictionary of keyword arguments to pass to the initializer
for VariantCollection.
"""
kwargs["variants"] = combine_fn(*[set(vc) for vc in variant_collections])
kwargs["source_to_metadata_dict"] = cls._merge_metadata_dictionaries(
[vc.source_to_metadata_dict for vc in variant_collections])
kwargs["sources"] = set.union(*([vc.sources for vc in variant_collections]))
for key, value in variant_collections[0].to_dict().items():
# If some optional parameter isn't explicitly specified as an
# argument to union() or intersection() then use the same value
# as the first VariantCollection.
#
# I'm doing this so that the meaning of VariantCollection.union
# and VariantCollection.intersection with a single argument is
# the identity function (rather than setting optional parameters
# to their default values.
if key not in kwargs:
kwargs[key] = value
return cls(**kwargs) | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/variant_collection.py#L258-L293 | train | Create a single VariantCollection from multiple VariantCollection objects. | 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(0b101011 + 0o7) + '\060' + chr(1733 - 1678), 0b1000), nzTpIcepk0o8(chr(574 - 526) + '\x6f' + chr(0b110001) + chr(0b110110) + '\x32', 9731 - 9723), nzTpIcepk0o8(chr(0b1001 + 0o47) + '\157' + chr(1785 - 1731) + '\x35', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b1010 + 0o47) + '\x36' + chr(0b110111), 0o10), nzTpIcepk0o8('\060' + chr(3781 - 3670) + chr(0b1010 + 0o51) + '\x33' + chr(0b100100 + 0o16), 54779 - 54771), nzTpIcepk0o8(chr(48) + chr(0b11001 + 0o126) + '\063' + '\064' + chr(0b11001 + 0o32), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(12245 - 12134) + chr(0b110011) + chr(0b110000) + chr(744 - 692), 0b1000), nzTpIcepk0o8(chr(0b11111 + 0o21) + chr(8993 - 8882) + chr(295 - 245) + chr(48) + chr(55), 8), nzTpIcepk0o8(chr(48) + chr(9563 - 9452) + chr(0b100110 + 0o16) + chr(0b101100 + 0o13), 32442 - 32434), nzTpIcepk0o8(chr(311 - 263) + '\x6f' + chr(104 - 55) + '\x37' + chr(0b110110), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(9877 - 9766) + '\x32' + '\x35' + chr(55), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\061' + '\065' + chr(0b11001 + 0o30), 36187 - 36179), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x33' + chr(0b110001) + chr(0b110011), ord("\x08")), nzTpIcepk0o8(chr(1298 - 1250) + chr(111) + chr(0b110011) + chr(55) + chr(0b110000), 61838 - 61830), nzTpIcepk0o8('\x30' + chr(111) + '\x31' + chr(0b110111) + chr(0b110010 + 0o5), 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(50), 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(2270 - 2217) + chr(0b110111), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x32' + '\064' + chr(0b110001 + 0o1), ord("\x08")), nzTpIcepk0o8(chr(817 - 769) + chr(0b1101111) + chr(0b110001) + chr(53) + chr(0b101000 + 0o16), 0b1000), nzTpIcepk0o8(chr(0b1111 + 0o41) + chr(0b1001 + 0o146) + chr(0b110010) + chr(55) + '\065', 0o10), nzTpIcepk0o8(chr(0b101111 + 0o1) + chr(0b1000 + 0o147) + '\x35' + chr(165 - 115), ord("\x08")), nzTpIcepk0o8(chr(0b11000 + 0o30) + '\157' + chr(0b110010) + chr(49) + chr(0b100010 + 0o25), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1011111 + 0o20) + '\066' + chr(532 - 484), 0b1000), nzTpIcepk0o8('\x30' + chr(111) + '\x33' + chr(0b110010) + chr(1238 - 1183), 10867 - 10859), nzTpIcepk0o8('\060' + '\157' + chr(49) + '\060', 0b1000), nzTpIcepk0o8('\060' + '\x6f' + '\x31', 19450 - 19442), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110001) + chr(0b110110) + chr(938 - 888), 8), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b1111 + 0o42) + '\065' + chr(48), 63990 - 63982), nzTpIcepk0o8('\x30' + chr(595 - 484) + '\x33' + chr(466 - 413) + chr(0b10010 + 0o43), 2827 - 2819), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(583 - 530) + '\061', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(2599 - 2548) + '\064' + '\063', 8), nzTpIcepk0o8(chr(0b10110 + 0o32) + chr(111) + chr(751 - 702) + chr(0b11110 + 0o24) + chr(0b110111), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(50) + chr(0b110011), 38324 - 38316), nzTpIcepk0o8('\060' + '\x6f' + chr(2268 - 2217) + '\x30', 0o10), nzTpIcepk0o8(chr(48) + chr(1876 - 1765) + chr(1646 - 1596) + '\x36' + chr(0b1011 + 0o53), 0o10), nzTpIcepk0o8(chr(48) + chr(5426 - 5315) + chr(51) + chr(50) + '\x30', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1000001 + 0o56) + chr(0b110001) + chr(49) + '\064', 25505 - 25497), nzTpIcepk0o8(chr(747 - 699) + chr(8001 - 7890) + chr(445 - 396) + chr(0b110011) + '\060', 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(230 - 181) + chr(0b110010 + 0o2) + chr(0b110011), 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(0b110110) + chr(48), 8)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b0 + 0o60) + chr(4993 - 4882) + chr(0b100011 + 0o22) + chr(48), 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xa9'), '\x64' + '\x65' + '\143' + chr(0b1101111) + chr(9891 - 9791) + chr(101))('\x75' + '\164' + '\x66' + '\055' + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def NlewkgfA7NCu(_1vzISbJ_R2i, Fo2ah1ohQ6mm, DglPiRaxt3Cu, q5n0sHDDTy90):
q5n0sHDDTy90[roI3spqORKae(ES5oEprVxulp(b'\xf1\x13G\x1e\xbb\x8d\xb0\xf4'), chr(0b1100100) + chr(0b101110 + 0o67) + chr(0b1100011) + chr(0b1101111) + '\x64' + chr(0b1100101))(chr(0b1110101) + '\164' + chr(102) + chr(45) + chr(0b10100 + 0o44))] = Fo2ah1ohQ6mm(*[Bvi71nNyvlqO(lGFBAPrKVYJd) for lGFBAPrKVYJd in DglPiRaxt3Cu])
q5n0sHDDTy90[roI3spqORKae(ES5oEprVxulp(b'\xf4\x1d@\x05\xb9\x86\x9b\xf3H!\xc2\x0c\xbf\x99\x1bc[\xc31\xd9C\xecD'), chr(0b1100100) + '\x65' + '\x63' + chr(0b1101111 + 0o0) + chr(2010 - 1910) + '\145')(chr(0b1010011 + 0o42) + '\x74' + chr(0b1100110) + chr(0b11001 + 0o24) + chr(56))] = _1vzISbJ_R2i._merge_metadata_dictionaries([lGFBAPrKVYJd.source_to_metadata_dict for lGFBAPrKVYJd in DglPiRaxt3Cu])
q5n0sHDDTy90[roI3spqORKae(ES5oEprVxulp(b'\xf4\x1d@\x05\xb9\x86\xb7'), chr(0b11000 + 0o114) + chr(265 - 164) + chr(0b1010110 + 0o15) + '\x6f' + chr(0b1100100) + chr(0b1100101))('\x75' + chr(8957 - 8841) + chr(102) + chr(0b1000 + 0o45) + '\070')] = Bvi71nNyvlqO.union(*[lGFBAPrKVYJd.D9HT0uu37pOB for lGFBAPrKVYJd in DglPiRaxt3Cu])
for (QYodcsDtoGq7, uV9iBiw0y_Mp) in roI3spqORKae(DglPiRaxt3Cu[nzTpIcepk0o8(chr(855 - 807) + chr(0b111 + 0o150) + chr(48), 0o10)].to_dict(), roI3spqORKae(ES5oEprVxulp(b'\xde-[9\x9f\x99\x8c\xb3\x14\x08\xf7\x00'), chr(2000 - 1900) + chr(0b1100101) + '\x63' + chr(6905 - 6794) + chr(0b111101 + 0o47) + chr(0b1100101))('\165' + '\x74' + chr(0b1100110) + chr(497 - 452) + '\x38'))():
if QYodcsDtoGq7 not in q5n0sHDDTy90:
q5n0sHDDTy90[QYodcsDtoGq7] = uV9iBiw0y_Mp
return _1vzISbJ_R2i(**q5n0sHDDTy90) |
openvax/varcode | varcode/variant_collection.py | VariantCollection.union | def union(self, *others, **kwargs):
"""
Returns the union of variants in a several VariantCollection objects.
"""
return self._combine_variant_collections(
combine_fn=set.union,
variant_collections=(self,) + others,
kwargs=kwargs) | python | def union(self, *others, **kwargs):
"""
Returns the union of variants in a several VariantCollection objects.
"""
return self._combine_variant_collections(
combine_fn=set.union,
variant_collections=(self,) + others,
kwargs=kwargs) | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/variant_collection.py#L295-L302 | train | Returns the union of two VariantCollection objects. | 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(0b110 + 0o61) + '\x32', ord("\x08")), nzTpIcepk0o8('\060' + chr(11726 - 11615) + '\x35' + chr(50), 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(0b110110) + chr(52), 10622 - 10614), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110010) + '\x30' + '\x35', 64436 - 64428), nzTpIcepk0o8('\x30' + chr(1491 - 1380) + chr(0b110001) + chr(1710 - 1658), 0b1000), nzTpIcepk0o8('\060' + chr(0b1001000 + 0o47) + chr(0b10011 + 0o41) + '\x36', 42393 - 42385), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b11000 + 0o37) + chr(0b110010 + 0o2), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(2271 - 2160) + chr(0b110110), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(3979 - 3868) + '\061' + chr(473 - 424), 45755 - 45747), nzTpIcepk0o8('\x30' + chr(111) + '\x32' + '\065' + chr(0b101010 + 0o10), 0b1000), nzTpIcepk0o8(chr(2238 - 2190) + chr(0b1101111) + chr(0b11000 + 0o31) + '\x33' + '\061', 42532 - 42524), nzTpIcepk0o8('\x30' + chr(3968 - 3857) + chr(49) + chr(0b110010) + '\x30', 12061 - 12053), nzTpIcepk0o8('\060' + '\157' + '\x31' + chr(0b110101) + chr(2872 - 2817), 43101 - 43093), nzTpIcepk0o8(chr(48) + chr(111) + '\063' + chr(0b11 + 0o56) + chr(53), 0b1000), nzTpIcepk0o8(chr(1069 - 1021) + '\157' + '\x31' + '\x30' + chr(1857 - 1806), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + '\x31' + chr(52) + '\065', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1100001 + 0o16) + chr(51) + '\x35' + chr(0b110110), ord("\x08")), nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(12136 - 12025) + chr(0b110000 + 0o5) + chr(48), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(883 - 834) + chr(51) + '\060', 0o10), nzTpIcepk0o8(chr(0b101110 + 0o2) + chr(111) + chr(51) + chr(1359 - 1305) + '\x30', 0b1000), nzTpIcepk0o8(chr(1408 - 1360) + '\x6f' + chr(0b110011) + '\065' + '\x37', 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + '\063' + chr(0b110100) + chr(0b101011 + 0o11), 0o10), nzTpIcepk0o8('\060' + chr(0b10 + 0o155) + '\062' + '\x34' + '\x31', ord("\x08")), nzTpIcepk0o8(chr(0b101 + 0o53) + chr(111) + chr(912 - 862) + chr(0b10111 + 0o40), 0o10), nzTpIcepk0o8('\x30' + chr(5846 - 5735) + chr(451 - 398) + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x33' + chr(1731 - 1677) + chr(832 - 781), 0b1000), nzTpIcepk0o8(chr(0b10011 + 0o35) + chr(0b1101111) + '\063' + chr(52) + '\064', 8), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b1101 + 0o45) + chr(2987 - 2932) + '\x36', 0o10), nzTpIcepk0o8(chr(0b10110 + 0o32) + chr(111) + chr(2529 - 2478) + chr(527 - 479) + chr(55), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110001) + chr(53) + chr(0b1011 + 0o52), 0b1000), nzTpIcepk0o8(chr(0b10110 + 0o32) + chr(7125 - 7014) + '\x31' + chr(0b10100 + 0o35) + chr(2219 - 2166), 13495 - 13487), nzTpIcepk0o8('\060' + chr(0b101011 + 0o104) + chr(1561 - 1510) + chr(420 - 370) + chr(0b1110 + 0o44), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + '\x31' + '\x30', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(10125 - 10014) + '\062' + chr(0b110100) + '\x32', 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110010) + '\x37' + '\x34', 0o10), nzTpIcepk0o8('\060' + chr(111) + '\066' + chr(819 - 764), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(0b10 + 0o57) + chr(1831 - 1783) + chr(0b110101), 40613 - 40605), nzTpIcepk0o8(chr(0b10 + 0o56) + '\157' + chr(50) + '\x37' + '\062', 8), nzTpIcepk0o8('\x30' + '\157' + '\061' + '\063' + chr(54), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110011) + chr(135 - 81) + chr(53), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + chr(5038 - 4927) + '\065' + '\x30', 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x94'), '\x64' + '\x65' + chr(0b100101 + 0o76) + chr(0b11100 + 0o123) + '\144' + '\145')('\165' + '\x74' + chr(0b10000 + 0o126) + chr(0b101101) + chr(391 - 335)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def ChS0HsK05yCu(hXMPsSrOQzbh, *XlJQggBAVmIr, **q5n0sHDDTy90):
return roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xe5I[\xe8nORcV\xdc8"\x06\xac-\x11\xb1K7\x9c\x83\x81\xc2cB\x9c\x8a\xcd'), '\x64' + chr(101) + '\143' + '\x6f' + chr(0b11100 + 0o110) + chr(0b1100101))('\165' + chr(0b1110100) + '\x66' + chr(45) + chr(56)))(combine_fn=roI3spqORKae(Bvi71nNyvlqO, roI3spqORKae(ES5oEprVxulp(b'\xcfD]\xeab'), chr(360 - 260) + chr(101) + chr(99) + '\157' + chr(264 - 164) + '\x65')(chr(0b1110101) + '\164' + chr(0b101110 + 0o70) + '\055' + chr(0b111000))), variant_collections=(hXMPsSrOQzbh,) + XlJQggBAVmIr, kwargs=q5n0sHDDTy90) |
openvax/varcode | varcode/variant_collection.py | VariantCollection.intersection | def intersection(self, *others, **kwargs):
"""
Returns the intersection of variants in several VariantCollection objects.
"""
return self._combine_variant_collections(
combine_fn=set.intersection,
variant_collections=(self,) + others,
kwargs=kwargs) | python | def intersection(self, *others, **kwargs):
"""
Returns the intersection of variants in several VariantCollection objects.
"""
return self._combine_variant_collections(
combine_fn=set.intersection,
variant_collections=(self,) + others,
kwargs=kwargs) | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/variant_collection.py#L304-L311 | train | Returns the intersection of two VariantCollection objects. | 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(1303 - 1255) + '\x6f' + '\063' + chr(0b110100) + chr(966 - 916), 55695 - 55687), nzTpIcepk0o8(chr(1421 - 1373) + chr(111) + chr(476 - 427) + chr(0b10001 + 0o37) + '\x30', 24242 - 24234), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(2394 - 2344) + '\x37' + '\x37', 11332 - 11324), nzTpIcepk0o8(chr(0b0 + 0o60) + '\x6f' + chr(0b110010) + chr(0b110001), 0o10), nzTpIcepk0o8('\060' + chr(8187 - 8076) + chr(0b11111 + 0o26) + '\066', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b11100 + 0o123) + '\063' + chr(1685 - 1634) + chr(0b110100 + 0o3), 0b1000), nzTpIcepk0o8(chr(0b11000 + 0o30) + chr(111) + '\x33' + chr(49) + chr(345 - 293), ord("\x08")), nzTpIcepk0o8(chr(0b10000 + 0o40) + '\157' + chr(0b100 + 0o56) + '\066' + '\060', 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(51) + chr(0b1111 + 0o41) + chr(0b10100 + 0o42), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x31' + '\061' + '\x35', 0o10), nzTpIcepk0o8('\x30' + chr(0b111000 + 0o67) + '\064' + chr(55), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110111) + chr(51), 16297 - 16289), nzTpIcepk0o8(chr(0b110000) + chr(760 - 649) + chr(50) + chr(1553 - 1505), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + '\x31' + chr(0b110101) + chr(328 - 274), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(50) + chr(0b110101) + '\x32', 0o10), nzTpIcepk0o8('\x30' + chr(3353 - 3242) + chr(0b100100 + 0o16) + chr(0b110100) + '\066', 0o10), nzTpIcepk0o8(chr(0b1110 + 0o42) + chr(0b1101111) + chr(2237 - 2186) + chr(0b1100 + 0o44) + chr(0b110011), ord("\x08")), nzTpIcepk0o8(chr(235 - 187) + chr(0b100100 + 0o113) + '\x33' + chr(0b1000 + 0o52) + '\x30', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b110 + 0o151) + chr(0b1001 + 0o50) + '\061' + '\066', 5518 - 5510), nzTpIcepk0o8(chr(0b1110 + 0o42) + '\x6f' + '\x31' + '\x34' + chr(0b10 + 0o62), 0o10), nzTpIcepk0o8(chr(605 - 557) + chr(0b1101111) + chr(0b110101) + '\064', ord("\x08")), nzTpIcepk0o8(chr(0b11 + 0o55) + chr(111) + chr(51) + chr(53) + '\x35', 37373 - 37365), nzTpIcepk0o8(chr(0b110000) + chr(10476 - 10365) + '\x32' + '\x32', 0o10), nzTpIcepk0o8(chr(0b100010 + 0o16) + chr(12046 - 11935) + chr(1342 - 1292) + chr(509 - 459) + '\065', 0o10), nzTpIcepk0o8(chr(0b1010 + 0o46) + '\157' + chr(0b110111) + chr(53), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x33' + chr(341 - 291) + chr(55), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1000101 + 0o52) + chr(49) + chr(0b1010 + 0o46) + chr(0b110101), 0b1000), nzTpIcepk0o8('\060' + chr(0b1000 + 0o147) + chr(0b11000 + 0o33) + '\x36' + chr(587 - 539), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x31' + chr(0b11111 + 0o24) + chr(54), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(746 - 697) + chr(0b11110 + 0o22) + chr(97 - 48), 12549 - 12541), nzTpIcepk0o8(chr(1428 - 1380) + chr(111) + chr(0b101100 + 0o6), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(4609 - 4498) + chr(0b110111) + chr(51), 8), nzTpIcepk0o8(chr(0b110000) + chr(5267 - 5156) + chr(49) + chr(0b110101) + '\067', ord("\x08")), nzTpIcepk0o8(chr(1533 - 1485) + chr(111) + '\x37' + chr(0b100100 + 0o20), 12364 - 12356), nzTpIcepk0o8(chr(48) + '\157' + chr(0b10010 + 0o44) + chr(50), ord("\x08")), nzTpIcepk0o8(chr(0b101 + 0o53) + '\157' + chr(0b101111 + 0o3) + chr(0b110110) + chr(0b11000 + 0o31), 0o10), nzTpIcepk0o8(chr(656 - 608) + chr(0b1101111) + chr(0b110011) + '\066' + '\x33', 0o10), nzTpIcepk0o8(chr(0b10011 + 0o35) + chr(11521 - 11410) + chr(49) + '\x32' + chr(0b101010 + 0o7), 0b1000), nzTpIcepk0o8(chr(0b1100 + 0o44) + chr(111) + '\063' + chr(0b110111) + '\x31', 0o10), nzTpIcepk0o8('\x30' + chr(111) + '\x32' + chr(0b110010) + chr(0b110110), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(1581 - 1533) + '\x6f' + '\065' + chr(1636 - 1588), ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xcc'), chr(0b10010 + 0o122) + chr(0b1010101 + 0o20) + chr(99) + chr(0b1010 + 0o145) + chr(0b10100 + 0o120) + chr(101))(chr(7951 - 7834) + '\164' + chr(102) + chr(45) + chr(0b110011 + 0o5)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def FNRQJPyBENBp(hXMPsSrOQzbh, *XlJQggBAVmIr, **q5n0sHDDTy90):
return roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xbd#\xd0|L\xb6\xa2\xd5\x99;FIy\x0f\xc4\xd2\x9c\xb3!\x08@\x88q\xe1T\xb8+\x83'), '\144' + chr(101) + chr(0b1100011) + chr(0b1101111) + chr(0b1100100) + chr(101))(chr(0b1110101) + '\x74' + chr(102) + chr(0b101101) + chr(1193 - 1137)))(combine_fn=roI3spqORKae(Bvi71nNyvlqO, roI3spqORKae(ES5oEprVxulp(b'\x8b.\xcbt\\\xac\xa9\xd3\xb2$HU'), chr(100) + chr(0b1001011 + 0o32) + chr(99) + chr(0b1101111) + '\x64' + chr(3228 - 3127))('\165' + '\x74' + chr(518 - 416) + '\055' + chr(0b111000))), variant_collections=(hXMPsSrOQzbh,) + XlJQggBAVmIr, kwargs=q5n0sHDDTy90) |
openvax/varcode | varcode/variant_collection.py | VariantCollection.to_dataframe | def to_dataframe(self):
"""Build a DataFrame from this variant collection"""
def row_from_variant(variant):
return OrderedDict([
("chr", variant.contig),
("start", variant.original_start),
("ref", variant.original_ref),
("alt", variant.original_alt),
("gene_name", ";".join(variant.gene_names)),
("gene_id", ";".join(variant.gene_ids))
])
rows = [row_from_variant(v) for v in self]
if len(rows) == 0:
# TODO: return a DataFrame with the appropriate columns
return pd.DataFrame()
return pd.DataFrame.from_records(rows, columns=rows[0].keys()) | python | def to_dataframe(self):
"""Build a DataFrame from this variant collection"""
def row_from_variant(variant):
return OrderedDict([
("chr", variant.contig),
("start", variant.original_start),
("ref", variant.original_ref),
("alt", variant.original_alt),
("gene_name", ";".join(variant.gene_names)),
("gene_id", ";".join(variant.gene_ids))
])
rows = [row_from_variant(v) for v in self]
if len(rows) == 0:
# TODO: return a DataFrame with the appropriate columns
return pd.DataFrame()
return pd.DataFrame.from_records(rows, columns=rows[0].keys()) | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/variant_collection.py#L313-L328 | train | Build a DataFrame from this variant collection | 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(51) + '\063' + chr(0b11011 + 0o30), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(2108 - 2059) + '\x34' + chr(52), 4838 - 4830), nzTpIcepk0o8(chr(0b11101 + 0o23) + chr(111) + chr(0b101000 + 0o13) + chr(51) + chr(48), 0o10), nzTpIcepk0o8('\x30' + '\157' + '\062' + chr(52) + '\x37', ord("\x08")), nzTpIcepk0o8(chr(1802 - 1754) + chr(0b1101111) + chr(0b110110), 0o10), nzTpIcepk0o8('\060' + chr(0b1011110 + 0o21) + '\065' + '\064', 0b1000), nzTpIcepk0o8(chr(355 - 307) + chr(111) + chr(1561 - 1510) + chr(0b10 + 0o61) + chr(0b1000 + 0o55), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b101001 + 0o106) + chr(51) + chr(50) + '\x32', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(49) + chr(49) + chr(781 - 728), 21950 - 21942), nzTpIcepk0o8('\x30' + '\x6f' + '\x37' + '\063', 0b1000), nzTpIcepk0o8('\060' + chr(0b1000011 + 0o54) + chr(0b110001) + chr(0b110111) + '\066', ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(1852 - 1801) + '\063' + chr(2567 - 2515), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(9024 - 8913) + '\x31' + chr(0b1001 + 0o51) + chr(0b110111), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(628 - 577) + chr(0b110110) + '\x34', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b100001 + 0o21) + '\061' + '\x36', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\061' + '\x30' + '\062', 0b1000), nzTpIcepk0o8('\x30' + chr(8100 - 7989) + chr(175 - 126) + chr(0b1011 + 0o53) + chr(48), ord("\x08")), nzTpIcepk0o8(chr(0b10010 + 0o36) + chr(0b1000 + 0o147) + chr(0b110001) + chr(0b110100) + '\066', 0o10), nzTpIcepk0o8('\060' + chr(0b1001100 + 0o43) + chr(2340 - 2285) + '\x31', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1100010 + 0o15) + '\066' + chr(50), ord("\x08")), nzTpIcepk0o8('\060' + chr(8788 - 8677) + chr(0b110010) + chr(2073 - 2024) + chr(1704 - 1654), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b110010 + 0o75) + chr(49) + '\060' + chr(715 - 660), ord("\x08")), nzTpIcepk0o8(chr(0b11101 + 0o23) + chr(3046 - 2935) + chr(50) + chr(310 - 262) + chr(0b110001), ord("\x08")), nzTpIcepk0o8(chr(1287 - 1239) + '\x6f' + chr(0b1001 + 0o55) + chr(0b110000), 42531 - 42523), nzTpIcepk0o8('\x30' + chr(0b1100 + 0o143) + '\x33' + chr(0b11000 + 0o33) + '\066', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1000000 + 0o57) + chr(447 - 396) + '\x34' + '\060', ord("\x08")), nzTpIcepk0o8(chr(142 - 94) + chr(0b1101111 + 0o0) + '\062' + chr(1510 - 1458) + chr(0b101010 + 0o15), 8), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110001) + chr(48) + chr(0b101001 + 0o13), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b11000 + 0o127) + chr(2035 - 1986) + '\x37' + '\x34', ord("\x08")), nzTpIcepk0o8(chr(0b1111 + 0o41) + chr(0b1101111) + chr(0b110001 + 0o2) + chr(1986 - 1932) + '\x37', ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110001) + chr(52) + chr(2732 - 2679), 55957 - 55949), nzTpIcepk0o8('\060' + '\x6f' + '\x31' + '\x37' + chr(0b110000), 0o10), nzTpIcepk0o8(chr(0b11111 + 0o21) + chr(3516 - 3405) + chr(0b110111) + '\062', 13567 - 13559), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110001) + chr(1092 - 1041) + chr(0b110110), 0b1000), nzTpIcepk0o8(chr(250 - 202) + chr(11467 - 11356) + chr(566 - 515) + chr(0b110110) + chr(0b110100), 8), nzTpIcepk0o8('\x30' + '\x6f' + '\x33' + '\x34' + chr(55), 0b1000), nzTpIcepk0o8(chr(0b101001 + 0o7) + chr(0b110010 + 0o75) + '\061' + chr(0b10101 + 0o34) + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(0b101000 + 0o10) + '\x6f' + chr(0b110011) + chr(0b1000 + 0o52) + chr(0b11101 + 0o27), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(2245 - 2192) + chr(2938 - 2883), 0b1000), nzTpIcepk0o8(chr(0b10000 + 0o40) + chr(5600 - 5489) + '\062' + chr(2931 - 2876) + chr(50), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(320 - 272) + chr(4549 - 4438) + chr(1302 - 1249) + '\x30', 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xf5'), '\x64' + '\145' + chr(0b110101 + 0o56) + chr(4654 - 4543) + chr(0b1100100) + chr(10095 - 9994))(chr(0b110101 + 0o100) + '\x74' + chr(4860 - 4758) + chr(0b1010 + 0o43) + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def ZQVHZJY0d7Ug(hXMPsSrOQzbh):
def YKSkiNhw4aQH(ZXJSPKxkIyZK):
return Ov4KLivfl4p6([(roI3spqORKae(ES5oEprVxulp(b'\xb8\x0c\xaa'), chr(100) + '\145' + chr(0b1100011) + '\157' + chr(100) + '\x65')(chr(117) + chr(116) + chr(0b1100110) + chr(0b101100 + 0o1) + chr(811 - 755)), roI3spqORKae(ZXJSPKxkIyZK, roI3spqORKae(ES5oEprVxulp(b'\xb8\x0b\xb6\xd3oK'), chr(0b1100100) + '\145' + chr(99) + chr(0b1100001 + 0o16) + chr(2376 - 2276) + chr(3902 - 3801))('\x75' + chr(0b1100111 + 0o15) + chr(102) + chr(1622 - 1577) + chr(1969 - 1913)))), (roI3spqORKae(ES5oEprVxulp(b'\xa8\x10\xb9\xd5r'), '\x64' + chr(2073 - 1972) + '\x63' + chr(0b111100 + 0o63) + chr(0b1100100) + chr(101))(chr(117) + '\164' + '\146' + chr(652 - 607) + chr(56)), roI3spqORKae(ZXJSPKxkIyZK, roI3spqORKae(ES5oEprVxulp(b'\xb4\x16\xb1\xc0oB\xbc\xbe\x12H\n\xbd%\x80'), chr(0b1100100) + '\145' + chr(99) + chr(111) + '\x64' + chr(499 - 398))('\165' + chr(0b1110100) + '\146' + '\x2d' + '\070'))), (roI3spqORKae(ES5oEprVxulp(b'\xa9\x01\xbe'), chr(0b10001 + 0o123) + chr(0b111001 + 0o54) + '\143' + '\157' + chr(100) + '\x65')(chr(0b1110101) + '\x74' + '\146' + chr(1026 - 981) + chr(0b111000)), roI3spqORKae(ZXJSPKxkIyZK, roI3spqORKae(ES5oEprVxulp(b'\xb4\x16\xb1\xc0oB\xbc\xbe\x12I\x1b\xba'), chr(100) + chr(0b1011110 + 0o7) + chr(0b1100011) + chr(0b101100 + 0o103) + chr(5056 - 4956) + chr(0b110111 + 0o56))('\x75' + '\x74' + chr(102) + chr(0b101101) + chr(2103 - 2047)))), (roI3spqORKae(ES5oEprVxulp(b'\xba\x08\xac'), '\144' + chr(7297 - 7196) + chr(3013 - 2914) + '\x6f' + chr(100) + chr(9724 - 9623))('\165' + chr(0b1100110 + 0o16) + chr(371 - 269) + '\x2d' + chr(0b101001 + 0o17)), roI3spqORKae(ZXJSPKxkIyZK, roI3spqORKae(ES5oEprVxulp(b'\xb4\x16\xb1\xc0oB\xbc\xbe\x12Z\x12\xa8'), '\144' + '\x65' + chr(0b1100011) + '\157' + '\144' + chr(0b11011 + 0o112))(chr(2048 - 1931) + chr(116) + chr(0b1100110) + '\055' + chr(0b111000)))), (roI3spqORKae(ES5oEprVxulp(b'\xbc\x01\xb6\xc2YB\xbc\xbf('), chr(5550 - 5450) + chr(0b1100101) + chr(0b1100011) + chr(0b111010 + 0o65) + chr(0b11101 + 0o107) + chr(0b101101 + 0o70))('\165' + chr(0b1110100) + chr(0b111010 + 0o54) + '\x2d' + chr(0b0 + 0o70)), roI3spqORKae(roI3spqORKae(ES5oEprVxulp(b'\xe0'), chr(2456 - 2356) + chr(0b1100101) + '\x63' + '\x6f' + chr(100) + chr(0b1010110 + 0o17))(chr(0b0 + 0o165) + chr(0b10101 + 0o137) + chr(0b1001100 + 0o32) + chr(0b101011 + 0o2) + chr(56)), roI3spqORKae(ES5oEprVxulp(b'\x82P\xa1\xea?n\xbe\xb4\x19x0\xad'), '\x64' + '\145' + '\143' + chr(0b1101111) + '\144' + '\145')('\165' + '\164' + chr(102) + '\055' + '\x38'))(roI3spqORKae(ZXJSPKxkIyZK, roI3spqORKae(ES5oEprVxulp(b'\xbc\x01\xb6\xc2YB\xbc\xbf(H'), '\144' + '\x65' + chr(99) + chr(0b100101 + 0o112) + chr(2166 - 2066) + chr(2930 - 2829))('\165' + chr(13111 - 12995) + chr(0b11 + 0o143) + chr(0b101101) + '\x38')))), (roI3spqORKae(ES5oEprVxulp(b'\xbc\x01\xb6\xc2YE\xb9'), '\144' + chr(101) + chr(0b1100011) + '\157' + '\x64' + chr(0b110111 + 0o56))(chr(0b1110101) + chr(116) + '\146' + '\x2d' + '\x38'), roI3spqORKae(roI3spqORKae(ES5oEprVxulp(b'\xe0'), chr(3584 - 3484) + chr(101) + '\x63' + chr(0b1101111) + '\144' + chr(0b110111 + 0o56))(chr(0b101111 + 0o106) + chr(0b1000100 + 0o60) + '\146' + chr(1779 - 1734) + chr(0b111000)), roI3spqORKae(ES5oEprVxulp(b'\x82P\xa1\xea?n\xbe\xb4\x19x0\xad'), '\144' + '\145' + chr(99) + chr(0b1010010 + 0o35) + chr(0b1100100) + '\145')(chr(0b1110101) + chr(116) + '\x66' + chr(1776 - 1731) + chr(56)))(roI3spqORKae(ZXJSPKxkIyZK, roI3spqORKae(ES5oEprVxulp(b'\xbc\x01\xb6\xc2YE\xb9\xa1'), chr(6675 - 6575) + chr(0b1100010 + 0o3) + '\x63' + chr(111) + '\144' + chr(0b1100101))(chr(0b1000110 + 0o57) + chr(0b1010100 + 0o40) + '\x66' + chr(1616 - 1571) + '\x38'))))])
AUW_CJJJXKka = [YKSkiNhw4aQH(r7AA1pbLjb44) for r7AA1pbLjb44 in hXMPsSrOQzbh]
if ftfygxgFas5X(AUW_CJJJXKka) == nzTpIcepk0o8(chr(0b111 + 0o51) + '\157' + chr(0b1010 + 0o46), 0o10):
return roI3spqORKae(HLKt4sa1j9hm, roI3spqORKae(ES5oEprVxulp(b'\x9f\x05\xac\xc6@^\xbc\xbf('), '\x64' + '\145' + chr(0b1000011 + 0o40) + chr(8486 - 8375) + chr(0b1010111 + 0o15) + chr(1526 - 1425))(chr(117) + chr(116) + chr(1187 - 1085) + chr(45) + '\070'))()
return roI3spqORKae(HLKt4sa1j9hm.DataFrame, roI3spqORKae(ES5oEprVxulp(b'\xbd\x16\xb7\xcaY^\xb8\xb1"I\x1a\xaf'), chr(0b1101 + 0o127) + chr(0b1100 + 0o131) + chr(5671 - 5572) + '\157' + chr(0b1100100) + chr(0b0 + 0o145))('\x75' + chr(116) + chr(0b1100110) + '\x2d' + chr(0b111000)))(AUW_CJJJXKka, columns=roI3spqORKae(AUW_CJJJXKka[nzTpIcepk0o8('\060' + chr(5073 - 4962) + chr(0b10010 + 0o36), 8)], roI3spqORKae(ES5oEprVxulp(b'\xb0\x01\xa1\xd4'), chr(0b111101 + 0o47) + chr(4517 - 4416) + '\x63' + chr(0b1101111) + chr(3176 - 3076) + chr(6616 - 6515))('\x75' + chr(2287 - 2171) + '\x66' + chr(1109 - 1064) + chr(56)))()) |
openvax/varcode | varcode/string_helpers.py | trim_shared_prefix | def trim_shared_prefix(ref, alt):
"""
Sometimes mutations are given with a shared prefix between the reference
and alternate strings. Examples: C>CT (nucleotides) or GYFP>G (amino acids).
This function trims the common prefix and returns the disjoint ref
and alt strings, along with the shared prefix.
"""
n_ref = len(ref)
n_alt = len(alt)
n_min = min(n_ref, n_alt)
i = 0
while i < n_min and ref[i] == alt[i]:
i += 1
# guaranteed that ref and alt agree on all the characters
# up to i'th position, so it doesn't matter which one we pull
# the prefix out of
prefix = ref[:i]
ref_suffix = ref[i:]
alt_suffix = alt[i:]
return ref_suffix, alt_suffix, prefix | python | def trim_shared_prefix(ref, alt):
"""
Sometimes mutations are given with a shared prefix between the reference
and alternate strings. Examples: C>CT (nucleotides) or GYFP>G (amino acids).
This function trims the common prefix and returns the disjoint ref
and alt strings, along with the shared prefix.
"""
n_ref = len(ref)
n_alt = len(alt)
n_min = min(n_ref, n_alt)
i = 0
while i < n_min and ref[i] == alt[i]:
i += 1
# guaranteed that ref and alt agree on all the characters
# up to i'th position, so it doesn't matter which one we pull
# the prefix out of
prefix = ref[:i]
ref_suffix = ref[i:]
alt_suffix = alt[i:]
return ref_suffix, alt_suffix, prefix | [
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and alternate strings. Examples: C>CT (nucleotides) or GYFP>G (amino acids).
This function trims the common prefix and returns the disjoint ref
and alt strings, along with the shared prefix. | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/string_helpers.py#L18-L39 | train | This function trims the common prefix between the reference and alternate strings. | 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(1156 - 1108) + chr(111) + chr(51) + chr(49) + chr(0b110100), 56667 - 56659), nzTpIcepk0o8(chr(0b110000) + chr(12189 - 12078) + chr(0b10100 + 0o36) + '\x30' + chr(0b100011 + 0o21), 61394 - 61386), nzTpIcepk0o8(chr(390 - 342) + chr(0b110011 + 0o74) + '\065' + chr(0b110100), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(48), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(53) + '\x30', 56265 - 56257), nzTpIcepk0o8('\060' + '\x6f' + '\x31' + '\063' + chr(49), 0b1000), nzTpIcepk0o8(chr(0b11000 + 0o30) + chr(0b1101111) + '\063' + chr(0b10000 + 0o45), 0o10), nzTpIcepk0o8(chr(0b1111 + 0o41) + chr(1076 - 965) + chr(2333 - 2283) + chr(615 - 564) + chr(1399 - 1350), ord("\x08")), nzTpIcepk0o8('\x30' + chr(10345 - 10234) + '\062', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b101111 + 0o100) + chr(0b110001) + chr(2219 - 2166) + chr(49), 0b1000), nzTpIcepk0o8(chr(719 - 671) + chr(0b1101111) + '\x32' + chr(1861 - 1806) + '\062', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1011 + 0o144) + chr(0b110000 + 0o3) + '\067' + chr(0b100110 + 0o17), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\062' + chr(50) + '\x35', 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(0b10010 + 0o41) + '\067' + chr(49), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(2299 - 2250) + chr(0b100100 + 0o21), 0o10), nzTpIcepk0o8(chr(1632 - 1584) + '\x6f' + '\x32' + '\x30' + chr(0b110110), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b100100 + 0o17) + '\062' + chr(49), 0b1000), nzTpIcepk0o8(chr(0b11010 + 0o26) + chr(0b1101111) + '\066' + chr(48), 3115 - 3107), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\062' + chr(48) + chr(0b100100 + 0o14), 0b1000), nzTpIcepk0o8(chr(1370 - 1322) + '\157' + chr(0b101101 + 0o4) + chr(0b110010 + 0o0) + chr(52), 26863 - 26855), nzTpIcepk0o8(chr(0b1101 + 0o43) + chr(111) + chr(0b10 + 0o57) + chr(0b10111 + 0o34) + chr(1032 - 979), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b0 + 0o157) + chr(2270 - 2219) + chr(739 - 687) + '\x31', 0b1000), nzTpIcepk0o8('\x30' + chr(0b11100 + 0o123) + chr(0b110011) + '\063' + chr(50), ord("\x08")), nzTpIcepk0o8(chr(0b101011 + 0o5) + '\157' + '\x32' + '\x36' + chr(0b110101), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + '\061' + '\060', ord("\x08")), nzTpIcepk0o8(chr(0b11010 + 0o26) + chr(5312 - 5201) + chr(0b110001 + 0o2) + '\x34', 3158 - 3150), nzTpIcepk0o8(chr(48) + chr(111) + '\062' + chr(1835 - 1785) + '\060', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1000111 + 0o50) + chr(51) + '\061' + chr(53), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110001) + chr(48) + chr(0b10010 + 0o44), 0o10), nzTpIcepk0o8(chr(48) + chr(0b10101 + 0o132) + chr(2204 - 2155) + '\x37' + '\066', ord("\x08")), nzTpIcepk0o8(chr(1822 - 1774) + chr(1811 - 1700) + chr(737 - 682) + '\063', 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\061', 0b1000), nzTpIcepk0o8(chr(0b100 + 0o54) + chr(111) + chr(2355 - 2305) + chr(51) + '\066', ord("\x08")), nzTpIcepk0o8('\060' + chr(6537 - 6426) + chr(0b100011 + 0o20) + '\x33' + '\067', 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(51) + chr(1539 - 1490) + chr(0b110100), 8), nzTpIcepk0o8(chr(511 - 463) + '\x6f' + chr(0b11110 + 0o23) + '\061' + '\x31', ord("\x08")), nzTpIcepk0o8(chr(0b1111 + 0o41) + chr(3333 - 3222) + '\062' + chr(0b110100) + chr(742 - 692), 30540 - 30532), nzTpIcepk0o8(chr(48) + '\x6f' + '\062' + '\062' + chr(0b110 + 0o56), 0b1000), nzTpIcepk0o8(chr(806 - 758) + '\x6f' + chr(0b110011) + chr(0b110101) + chr(1765 - 1710), ord("\x08")), nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(111) + chr(330 - 281) + chr(0b10111 + 0o32) + chr(0b1101 + 0o52), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(9970 - 9859) + chr(625 - 572) + chr(0b110000), 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xe2'), '\x64' + chr(101) + chr(99) + chr(0b100 + 0o153) + chr(100) + chr(0b1100101))(chr(13015 - 12898) + chr(0b1110100) + '\x66' + '\x2d' + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def F1E8Unal0je5(CmNScfxJ1Uih, YVIVvpvk_rzo):
H0vRGyprMf_l = ftfygxgFas5X(CmNScfxJ1Uih)
CRM06y2Nk0Uf = ftfygxgFas5X(YVIVvpvk_rzo)
D2oEFA65NThH = XURpmPuEWCNF(H0vRGyprMf_l, CRM06y2Nk0Uf)
ZlbFMSG8gCoF = nzTpIcepk0o8('\x30' + '\x6f' + chr(0b10001 + 0o37), 8)
while ZlbFMSG8gCoF < D2oEFA65NThH and CmNScfxJ1Uih[ZlbFMSG8gCoF] == YVIVvpvk_rzo[ZlbFMSG8gCoF]:
ZlbFMSG8gCoF += nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b101011 + 0o6), 8)
ZJwZgaHE72Po = CmNScfxJ1Uih[:ZlbFMSG8gCoF]
J3Js1vxfuA2C = CmNScfxJ1Uih[ZlbFMSG8gCoF:]
tSsEwp4z4vw7 = YVIVvpvk_rzo[ZlbFMSG8gCoF:]
return (J3Js1vxfuA2C, tSsEwp4z4vw7, ZJwZgaHE72Po) |
openvax/varcode | varcode/string_helpers.py | trim_shared_suffix | def trim_shared_suffix(ref, alt):
"""
Reuse the `trim_shared_prefix` function above to implement similar
functionality for string suffixes.
Given ref='ABC' and alt='BC', we first revese both strings:
reverse_ref = 'CBA'
reverse_alt = 'CB'
and then the result of calling trim_shared_prefix will be:
('A', '', 'CB')
We then reverse all three of the result strings to get back
the shared suffix and both prefixes leading up to it:
('A', '', 'BC')
"""
n_ref = len(ref)
n_alt = len(alt)
n_min = min(n_ref, n_alt)
i = 0
while i < n_min and ref[-i - 1] == alt[-i - 1]:
i += 1
# i is length of shared suffix.
if i == 0:
return (ref, alt, '')
return (ref[:-i], alt[:-i], ref[-i:]) | python | def trim_shared_suffix(ref, alt):
"""
Reuse the `trim_shared_prefix` function above to implement similar
functionality for string suffixes.
Given ref='ABC' and alt='BC', we first revese both strings:
reverse_ref = 'CBA'
reverse_alt = 'CB'
and then the result of calling trim_shared_prefix will be:
('A', '', 'CB')
We then reverse all three of the result strings to get back
the shared suffix and both prefixes leading up to it:
('A', '', 'BC')
"""
n_ref = len(ref)
n_alt = len(alt)
n_min = min(n_ref, n_alt)
i = 0
while i < n_min and ref[-i - 1] == alt[-i - 1]:
i += 1
# i is length of shared suffix.
if i == 0:
return (ref, alt, '')
return (ref[:-i], alt[:-i], ref[-i:]) | [
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and then the result of calling trim_shared_prefix will be:
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/string_helpers.py#L42-L66 | train | This function trims the shared suffix from two strings. | 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(0b101100 + 0o7) + '\x31' + '\065', 23269 - 23261), nzTpIcepk0o8(chr(0b100 + 0o54) + chr(111) + '\061' + chr(52) + chr(2233 - 2183), 19840 - 19832), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110001 + 0o1) + chr(322 - 272) + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(0b1011 + 0o45) + chr(669 - 558) + chr(51) + chr(200 - 145) + chr(0b1111 + 0o46), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b100110 + 0o14) + chr(1342 - 1293) + '\062', 12058 - 12050), nzTpIcepk0o8(chr(189 - 141) + '\157' + chr(50) + chr(0b110010) + '\x35', 0b1000), nzTpIcepk0o8(chr(0b1100 + 0o44) + chr(111) + chr(0b101001 + 0o12) + '\x31', 37889 - 37881), nzTpIcepk0o8(chr(0b11110 + 0o22) + chr(0b1101111) + '\063' + chr(51), 0b1000), nzTpIcepk0o8(chr(48) + chr(4616 - 4505) + chr(694 - 643) + chr(0b110011) + chr(227 - 178), 0b1000), nzTpIcepk0o8(chr(0b101101 + 0o3) + chr(111) + chr(0b110111) + chr(48), 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110011) + chr(198 - 145) + chr(0b11001 + 0o32), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(1251 - 1202) + chr(0b110100) + chr(0b100001 + 0o25), 27805 - 27797), nzTpIcepk0o8('\060' + chr(111) + chr(1362 - 1312) + '\x36' + chr(0b101000 + 0o12), ord("\x08")), nzTpIcepk0o8(chr(1574 - 1526) + chr(0b1101111) + '\064' + chr(55), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110010) + '\063' + '\x36', 0o10), nzTpIcepk0o8('\x30' + chr(0b1001000 + 0o47) + '\061' + '\x37' + '\x36', 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(50) + chr(0b110110) + '\x32', 8), nzTpIcepk0o8(chr(0b101011 + 0o5) + '\157' + '\062' + chr(0b110111) + '\066', 39626 - 39618), nzTpIcepk0o8(chr(1135 - 1087) + chr(11229 - 11118) + chr(0b110001) + chr(2548 - 2497) + '\x36', 0o10), nzTpIcepk0o8('\x30' + chr(8286 - 8175) + chr(0b11101 + 0o32) + chr(0b100101 + 0o22), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(4038 - 3927) + chr(0b1101 + 0o46) + '\065' + '\067', 19269 - 19261), nzTpIcepk0o8('\x30' + '\157' + chr(51) + chr(209 - 161) + chr(0b100100 + 0o14), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b100001 + 0o22) + chr(0b110001) + '\x36', 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b1010 + 0o55) + chr(48), 8), nzTpIcepk0o8(chr(0b11 + 0o55) + chr(0b1101111) + '\066' + '\064', 0b1000), nzTpIcepk0o8(chr(0b11000 + 0o30) + chr(0b1101111) + chr(2269 - 2219) + chr(0b10 + 0o64) + chr(2224 - 2174), 8), nzTpIcepk0o8(chr(70 - 22) + '\x6f' + chr(0b110011) + chr(0b10001 + 0o44) + chr(1590 - 1536), 0b1000), nzTpIcepk0o8(chr(1543 - 1495) + chr(0b1101111) + '\x33' + chr(0b1010 + 0o46) + chr(1530 - 1479), 0b1000), nzTpIcepk0o8(chr(1591 - 1543) + '\x6f' + chr(50) + chr(0b10110 + 0o33) + '\x37', ord("\x08")), nzTpIcepk0o8(chr(691 - 643) + '\x6f' + '\x33' + chr(52) + '\x32', ord("\x08")), nzTpIcepk0o8(chr(0b1100 + 0o44) + '\x6f' + chr(0b110011) + chr(2040 - 1988) + chr(53), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\062' + '\x33', 49504 - 49496), nzTpIcepk0o8('\060' + chr(111) + chr(50) + '\x37' + chr(0b101101 + 0o12), 0b1000), nzTpIcepk0o8('\060' + chr(0b100101 + 0o112) + chr(0b101100 + 0o7) + chr(0b10111 + 0o37) + chr(54), 0o10), nzTpIcepk0o8('\060' + chr(2935 - 2824) + chr(0b110011) + chr(52) + '\x37', 45041 - 45033), nzTpIcepk0o8('\060' + '\157' + '\x32' + '\x33' + '\x35', 0b1000), nzTpIcepk0o8(chr(1572 - 1524) + chr(111) + chr(0b110010) + chr(49) + chr(0b110000), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1000010 + 0o55) + chr(51) + chr(0b101101 + 0o10), 0b1000), nzTpIcepk0o8(chr(0b110 + 0o52) + '\x6f' + chr(0b11001 + 0o32) + chr(2253 - 2205) + chr(0b10101 + 0o36), 8), nzTpIcepk0o8('\x30' + chr(0b1000 + 0o147) + chr(0b100100 + 0o17) + '\x35' + '\062', ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b101001 + 0o7) + chr(2267 - 2156) + chr(53) + chr(48), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xe3'), '\144' + '\145' + chr(0b101111 + 0o64) + '\157' + chr(6122 - 6022) + chr(0b100100 + 0o101))(chr(3531 - 3414) + chr(6179 - 6063) + chr(9208 - 9106) + chr(500 - 455) + chr(0b100 + 0o64)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def Wnzm2ltDMRYd(CmNScfxJ1Uih, YVIVvpvk_rzo):
H0vRGyprMf_l = ftfygxgFas5X(CmNScfxJ1Uih)
CRM06y2Nk0Uf = ftfygxgFas5X(YVIVvpvk_rzo)
D2oEFA65NThH = XURpmPuEWCNF(H0vRGyprMf_l, CRM06y2Nk0Uf)
ZlbFMSG8gCoF = nzTpIcepk0o8(chr(48) + chr(111) + '\x30', 0o10)
while ZlbFMSG8gCoF < D2oEFA65NThH and CmNScfxJ1Uih[-ZlbFMSG8gCoF - nzTpIcepk0o8('\060' + '\x6f' + chr(49), 0b1000)] == YVIVvpvk_rzo[-ZlbFMSG8gCoF - nzTpIcepk0o8('\x30' + chr(0b1101111) + '\061', 8)]:
ZlbFMSG8gCoF += nzTpIcepk0o8('\060' + '\157' + chr(0b110001), 8)
if ZlbFMSG8gCoF == nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110000), 8):
return (CmNScfxJ1Uih, YVIVvpvk_rzo, roI3spqORKae(ES5oEprVxulp(b''), '\144' + chr(0b1100101) + chr(0b10001 + 0o122) + chr(1585 - 1474) + '\144' + chr(531 - 430))('\165' + '\164' + chr(0b1100110) + chr(0b101101) + chr(1009 - 953)))
return (CmNScfxJ1Uih[:-ZlbFMSG8gCoF], YVIVvpvk_rzo[:-ZlbFMSG8gCoF], CmNScfxJ1Uih[-ZlbFMSG8gCoF:]) |
openvax/varcode | varcode/string_helpers.py | trim_shared_flanking_strings | def trim_shared_flanking_strings(ref, alt):
"""
Given two nucleotide or amino acid strings, identify
if they have a common prefix, a common suffix, and return
their unique components along with the prefix and suffix.
For example, if the input ref = "SYFFQGR" and alt = "SYMLLFIFQGR"
then the result will be:
("F", "MLLFI", "SY", "FQGR")
"""
ref, alt, prefix = trim_shared_prefix(ref, alt)
ref, alt, suffix = trim_shared_suffix(ref, alt)
return ref, alt, prefix, suffix | python | def trim_shared_flanking_strings(ref, alt):
"""
Given two nucleotide or amino acid strings, identify
if they have a common prefix, a common suffix, and return
their unique components along with the prefix and suffix.
For example, if the input ref = "SYFFQGR" and alt = "SYMLLFIFQGR"
then the result will be:
("F", "MLLFI", "SY", "FQGR")
"""
ref, alt, prefix = trim_shared_prefix(ref, alt)
ref, alt, suffix = trim_shared_suffix(ref, alt)
return ref, alt, prefix, suffix | [
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then the result will be:
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/string_helpers.py#L69-L81 | train | Given two nucleotide or amino acid strings identify the common prefix and suffix of the two nucleotide strings and return the unique components along with the prefix and suffix. | 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) + '\157' + chr(0b110001) + chr(0b10001 + 0o46) + '\x36', ord("\x08")), nzTpIcepk0o8(chr(1956 - 1908) + chr(0b1101111) + '\x32' + chr(1803 - 1753) + '\062', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1000 + 0o147) + chr(0b100100 + 0o21) + '\x36', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(928 - 879) + '\x30' + '\061', 32542 - 32534), nzTpIcepk0o8(chr(0b100001 + 0o17) + chr(0b1100111 + 0o10) + chr(649 - 599) + chr(1610 - 1555) + chr(0b1001 + 0o53), 0b1000), nzTpIcepk0o8('\x30' + chr(0b11111 + 0o120) + chr(0b110001) + chr(0b101111 + 0o2) + chr(2577 - 2523), ord("\x08")), nzTpIcepk0o8(chr(1722 - 1674) + chr(111) + chr(0b110001) + chr(0b110011) + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(2335 - 2224) + chr(0b110011) + '\064' + '\x33', ord("\x08")), nzTpIcepk0o8(chr(1175 - 1127) + '\157' + '\x32' + chr(51), 0o10), nzTpIcepk0o8(chr(168 - 120) + chr(6266 - 6155) + chr(54) + chr(1975 - 1926), 0o10), nzTpIcepk0o8(chr(48) + '\157' + '\x32' + chr(0b110100) + chr(0b100101 + 0o22), ord("\x08")), nzTpIcepk0o8(chr(1671 - 1623) + chr(111) + chr(384 - 333) + chr(0b10001 + 0o41) + chr(0b110110), 54485 - 54477), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110001) + '\067' + '\x31', 55786 - 55778), nzTpIcepk0o8(chr(1901 - 1853) + chr(0b1101111) + chr(2468 - 2417) + chr(0b110100) + chr(705 - 653), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(50) + '\x31' + '\x33', 21716 - 21708), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\061' + chr(49) + chr(50), 0b1000), nzTpIcepk0o8(chr(0b100001 + 0o17) + '\157' + chr(1201 - 1152) + '\x36' + '\x36', 0b1000), nzTpIcepk0o8(chr(0b101010 + 0o6) + chr(6059 - 5948) + '\061' + chr(0b11 + 0o62) + chr(733 - 679), 0o10), nzTpIcepk0o8(chr(1394 - 1346) + chr(111) + chr(50) + '\x30', 23036 - 23028), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b10 + 0o57) + chr(52) + chr(1604 - 1551), 0o10), nzTpIcepk0o8('\x30' + chr(4021 - 3910) + chr(0b11011 + 0o31) + chr(214 - 165), 0o10), nzTpIcepk0o8(chr(1651 - 1603) + chr(0b1000111 + 0o50) + chr(51) + chr(0b110000) + chr(0b11 + 0o63), ord("\x08")), nzTpIcepk0o8(chr(1783 - 1735) + '\157' + '\062' + chr(51) + chr(311 - 256), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(0b110010) + '\x32', 19735 - 19727), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110001) + chr(52) + chr(0b1000 + 0o53), ord("\x08")), nzTpIcepk0o8('\060' + chr(8200 - 8089) + '\061' + '\x33' + chr(0b10 + 0o61), 28822 - 28814), nzTpIcepk0o8(chr(48) + '\x6f' + chr(55) + '\x34', 0o10), nzTpIcepk0o8(chr(0b101 + 0o53) + chr(111) + chr(1797 - 1748) + chr(1873 - 1819) + chr(55), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + '\x32' + chr(0b1 + 0o61), 8), nzTpIcepk0o8('\x30' + '\x6f' + '\062' + chr(1604 - 1555) + chr(0b101 + 0o56), 8), nzTpIcepk0o8('\060' + '\x6f' + chr(0b101 + 0o54) + chr(0b110100) + chr(0b110 + 0o52), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x32' + chr(55) + chr(611 - 560), 31746 - 31738), nzTpIcepk0o8(chr(0b11100 + 0o24) + '\157' + chr(0b110010) + chr(52) + chr(48), 0b1000), nzTpIcepk0o8(chr(0b100001 + 0o17) + chr(0b1101111) + '\061' + chr(0b100111 + 0o14) + chr(1193 - 1144), 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(50) + chr(0b110011) + chr(0b1010 + 0o47), 27603 - 27595), nzTpIcepk0o8(chr(0b110000) + chr(0b100011 + 0o114) + chr(1476 - 1421) + '\060', 0b1000), nzTpIcepk0o8('\060' + '\157' + '\x32' + chr(50) + '\x31', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1100000 + 0o17) + chr(51) + chr(54) + '\x37', 0o10), nzTpIcepk0o8(chr(0b11101 + 0o23) + chr(0b10100 + 0o133) + '\062' + chr(59 - 5) + chr(0b110110), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1000010 + 0o55) + chr(0b110010) + chr(0b110010) + chr(0b11 + 0o62), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + chr(0b1110 + 0o141) + 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'P'), chr(5323 - 5223) + chr(0b1100101) + chr(0b1010 + 0o131) + '\x6f' + chr(6911 - 6811) + chr(3782 - 3681))('\x75' + chr(0b1110100) + '\x66' + '\x2d' + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def Ajs8ZJ4OfLbv(CmNScfxJ1Uih, YVIVvpvk_rzo):
(CmNScfxJ1Uih, YVIVvpvk_rzo, ZJwZgaHE72Po) = F1E8Unal0je5(CmNScfxJ1Uih, YVIVvpvk_rzo)
(CmNScfxJ1Uih, YVIVvpvk_rzo, biRCFepsLie5) = Wnzm2ltDMRYd(CmNScfxJ1Uih, YVIVvpvk_rzo)
return (CmNScfxJ1Uih, YVIVvpvk_rzo, ZJwZgaHE72Po, biRCFepsLie5) |
openvax/varcode | varcode/cli/effects_script.py | main | def main(args_list=None):
"""
Script which loads variants and annotates them with overlapping genes
and predicted coding effects.
Example usage:
varcode
--vcf mutect.vcf \
--vcf strelka.vcf \
--maf tcga_brca.maf \
--variant chr1 498584 C G \
--json-variants more_variants.json
"""
print_version_info()
if args_list is None:
args_list = sys.argv[1:]
args = arg_parser.parse_args(args_list)
variants = variant_collection_from_args(args)
effects = variants.effects()
if args.only_coding:
effects = effects.drop_silent_and_noncoding()
if args.one_per_variant:
variant_to_effect_dict = effects.top_priority_effect_per_variant()
effects = effects.clone_with_new_elements(list(variant_to_effect_dict.values()))
effects_dataframe = effects.to_dataframe()
logger.info('\n%s', effects)
if args.output_csv:
effects_dataframe.to_csv(args.output_csv, index=False) | python | def main(args_list=None):
"""
Script which loads variants and annotates them with overlapping genes
and predicted coding effects.
Example usage:
varcode
--vcf mutect.vcf \
--vcf strelka.vcf \
--maf tcga_brca.maf \
--variant chr1 498584 C G \
--json-variants more_variants.json
"""
print_version_info()
if args_list is None:
args_list = sys.argv[1:]
args = arg_parser.parse_args(args_list)
variants = variant_collection_from_args(args)
effects = variants.effects()
if args.only_coding:
effects = effects.drop_silent_and_noncoding()
if args.one_per_variant:
variant_to_effect_dict = effects.top_priority_effect_per_variant()
effects = effects.clone_with_new_elements(list(variant_to_effect_dict.values()))
effects_dataframe = effects.to_dataframe()
logger.info('\n%s', effects)
if args.output_csv:
effects_dataframe.to_csv(args.output_csv, index=False) | [
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and predicted coding effects.
Example usage:
varcode
--vcf mutect.vcf \
--vcf strelka.vcf \
--maf tcga_brca.maf \
--variant chr1 498584 C G \
--json-variants more_variants.json | [
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"."
] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/cli/effects_script.py#L48-L77 | train | This is the main entry point for the VariantCollection script. | 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(1572 - 1524) + chr(111) + chr(50) + chr(51) + '\x32', 0o10), nzTpIcepk0o8(chr(48) + chr(4548 - 4437) + chr(548 - 498) + chr(54), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(674 - 563) + '\062' + '\061' + '\062', ord("\x08")), nzTpIcepk0o8(chr(0b101010 + 0o6) + chr(111) + '\x33' + chr(2182 - 2131) + '\x33', 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110001) + '\x31' + '\061', 0b1000), nzTpIcepk0o8('\060' + chr(0b100 + 0o153) + '\x31' + '\064' + '\063', 0b1000), nzTpIcepk0o8(chr(48) + chr(10607 - 10496) + chr(0b110011) + '\062' + chr(2425 - 2370), 38340 - 38332), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x33' + chr(0b1 + 0o57) + '\062', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x32', 0o10), nzTpIcepk0o8(chr(48) + chr(0b100110 + 0o111) + chr(0b110010) + '\x36' + chr(2396 - 2341), ord("\x08")), nzTpIcepk0o8(chr(1110 - 1062) + '\x6f' + chr(0b110010) + chr(50) + '\x36', ord("\x08")), nzTpIcepk0o8('\x30' + chr(8279 - 8168) + chr(874 - 823) + '\063' + chr(626 - 574), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(3051 - 2940) + chr(0b110111) + '\x36', 0b1000), nzTpIcepk0o8(chr(48) + chr(3231 - 3120) + chr(494 - 444) + '\061' + chr(0b110001), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b100101 + 0o14) + '\060' + '\065', 0b1000), nzTpIcepk0o8(chr(0b10001 + 0o37) + '\x6f' + chr(51) + '\064' + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\061' + chr(98 - 49) + '\062', 0b1000), nzTpIcepk0o8(chr(2293 - 2245) + chr(4088 - 3977) + chr(0b110010) + '\061' + '\x36', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1011110 + 0o21) + '\062' + chr(0b110101) + '\x37', 4090 - 4082), nzTpIcepk0o8('\060' + chr(0b101100 + 0o103) + chr(0b1111 + 0o43) + chr(0b101 + 0o55) + chr(826 - 775), 20213 - 20205), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(49) + '\064' + chr(822 - 767), 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(51) + '\062' + chr(1804 - 1752), ord("\x08")), nzTpIcepk0o8(chr(0b10101 + 0o33) + chr(0b1101111) + chr(0b110011) + '\066' + chr(190 - 140), 65455 - 65447), nzTpIcepk0o8(chr(0b110000) + chr(0b1000011 + 0o54) + chr(1771 - 1716) + '\x35', ord("\x08")), nzTpIcepk0o8(chr(979 - 931) + chr(0b10101 + 0o132) + chr(0b110011) + '\062' + chr(2233 - 2178), 8), nzTpIcepk0o8(chr(2034 - 1986) + '\157' + '\064' + chr(0b100101 + 0o15), 0b1000), nzTpIcepk0o8(chr(0b1011 + 0o45) + '\x6f' + '\x33' + chr(1846 - 1796) + chr(0b110000), 26392 - 26384), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110011) + chr(49) + chr(49), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(55), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + '\061' + '\061' + chr(0b110111), 8812 - 8804), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b100111 + 0o12) + chr(0b110111) + chr(0b101101 + 0o3), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(1446 - 1397) + '\x35' + chr(0b1010 + 0o46), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110111), 8), nzTpIcepk0o8('\x30' + '\x6f' + chr(185 - 135) + '\061', ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + chr(0b111 + 0o52) + chr(0b111 + 0o54) + chr(429 - 381), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(1010 - 961) + '\x30', 0o10), nzTpIcepk0o8(chr(230 - 182) + '\157' + chr(947 - 896) + chr(49) + '\066', 17285 - 17277), nzTpIcepk0o8('\060' + chr(10710 - 10599) + '\x31' + chr(0b11 + 0o57) + chr(0b11111 + 0o22), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + '\061' + chr(0b110010) + chr(1788 - 1739), 8), nzTpIcepk0o8('\x30' + chr(11242 - 11131) + '\x32' + '\062' + chr(52), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + '\157' + '\x35' + chr(0b100110 + 0o12), ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xb4'), chr(0b101011 + 0o71) + chr(101) + '\x63' + chr(7138 - 7027) + chr(0b100110 + 0o76) + '\145')('\x75' + '\x74' + chr(0b1100110) + chr(594 - 549) + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def BXHXH_QeD6rL(W0Qx8Cb9RSce=None):
Gy2oPTGw_8GJ()
if W0Qx8Cb9RSce is None:
W0Qx8Cb9RSce = bpyfpu4kTbwL.ajIDWyXMBa3b[nzTpIcepk0o8(chr(651 - 603) + chr(0b1101111) + '\x31', 58044 - 58036):]
eemPYp2vtTSr = bCPkA5flNgHN.JvKYHysdS3LV(W0Qx8Cb9RSce)
Loszd1LxpkfW = Y9HTnP3pboWJ(eemPYp2vtTSr)
WShYeokTxOn7 = Loszd1LxpkfW.effects()
if roI3spqORKae(eemPYp2vtTSr, roI3spqORKae(ES5oEprVxulp(b'\xf5x\xe6\xa2\x16\x00\xb8\xa6k\xd9\xf1'), '\x64' + chr(0b1011001 + 0o14) + chr(0b1100011) + chr(111) + chr(0b1100100) + chr(3287 - 3186))('\165' + '\164' + chr(1599 - 1497) + '\x2d' + '\070')):
WShYeokTxOn7 = WShYeokTxOn7.drop_silent_and_noncoding()
if roI3spqORKae(eemPYp2vtTSr, roI3spqORKae(ES5oEprVxulp(b'\xf5x\xef\x849\x06\xa5\x9dt\xd6\xe4\xb5_\xe71'), '\144' + '\x65' + chr(0b10011 + 0o120) + '\157' + chr(0b111111 + 0o45) + chr(0b1100101))(chr(0b1110101) + chr(116) + chr(0b1000000 + 0o46) + '\x2d' + '\070')):
wIYUbBfy0qRQ = WShYeokTxOn7.top_priority_effect_per_variant()
WShYeokTxOn7 = WShYeokTxOn7.clone_with_new_elements(H4NoA26ON7iG(wIYUbBfy0qRQ.CsodZJH6x9Tx()))
caASAPaRnMy_ = WShYeokTxOn7.to_dataframe()
roI3spqORKae(iKLp4UdyhCfx, roI3spqORKae(ES5oEprVxulp(b'\xf3n\xc4\xa3p/\xa0\x9d3\xd0\xe4\x93'), chr(100) + '\145' + chr(99) + chr(0b1101111) + chr(7028 - 6928) + '\x65')('\165' + chr(0b1010110 + 0o36) + chr(7992 - 7890) + chr(0b11000 + 0o25) + '\x38'))(roI3spqORKae(ES5oEprVxulp(b'\x903\xf9'), chr(0b101000 + 0o74) + '\145' + chr(99) + chr(0b1101111) + chr(100) + '\x65')(chr(0b1000111 + 0o56) + chr(0b1011011 + 0o31) + chr(0b11 + 0o143) + chr(0b1000 + 0o45) + chr(0b111 + 0o61)), WShYeokTxOn7)
if roI3spqORKae(eemPYp2vtTSr, roI3spqORKae(ES5oEprVxulp(b'\xf5c\xfe\xab<\x17\x88\xa1q\xc1'), chr(8242 - 8142) + '\x65' + chr(0b111110 + 0o45) + '\x6f' + chr(0b1100100) + chr(0b1000 + 0o135))(chr(0b100 + 0o161) + chr(116) + chr(3141 - 3039) + chr(327 - 282) + '\x38')):
roI3spqORKae(caASAPaRnMy_, roI3spqORKae(ES5oEprVxulp(b'\xeey\xd5\xb8:\x15'), '\144' + chr(0b100011 + 0o102) + chr(0b101 + 0o136) + '\157' + '\x64' + chr(101))(chr(117) + '\x74' + chr(102) + '\055' + chr(0b111000)))(roI3spqORKae(eemPYp2vtTSr, roI3spqORKae(ES5oEprVxulp(b'\xf5c\xfe\xab<\x17\x88\xa1q\xc1'), '\x64' + chr(0b1100101) + '\x63' + chr(111) + '\x64' + '\145')('\x75' + chr(116) + '\x66' + chr(0b101101) + chr(0b111000))), index=nzTpIcepk0o8(chr(0b110000) + chr(0b1010010 + 0o35) + '\060', 0o10)) |
openvax/varcode | varcode/effects/effect_prediction_coding_in_frame.py | get_codons | def get_codons(
variant,
trimmed_cdna_ref,
trimmed_cdna_alt,
sequence_from_start_codon,
cds_offset):
"""
Returns indices of first and last reference codons affected by the variant,
as well as the actual sequence of the mutated codons which replace those
reference codons.
Parameters
----------
variant : Variant
trimmed_cdna_ref : str
Trimmed reference cDNA nucleotides affected by the variant
trimmed_cdna_alt : str
Trimmed alternate cDNA nucleotides which replace the reference
sequence_from_start_codon : str
cDNA nucleotide coding sequence
cds_offset : int
Integer offset into the coding sequence where ref is replace with alt
"""
# index (starting from 0) of first affected reference codon
ref_codon_start_offset = cds_offset // 3
# which nucleotide of the first codon got changed?
nucleotide_offset_into_first_ref_codon = cds_offset % 3
n_ref_nucleotides = len(trimmed_cdna_ref)
if n_ref_nucleotides == 0:
if nucleotide_offset_into_first_ref_codon == 2:
# if we're inserting between codons
ref_codon_end_offset = ref_codon_start_offset
else:
# inserting inside a reference codon
ref_codon_end_offset = ref_codon_start_offset + 1
ref_codons = sequence_from_start_codon[
ref_codon_start_offset * 3:ref_codon_end_offset * 3]
# split the reference codon into nucleotides before/after insertion
prefix = ref_codons[:nucleotide_offset_into_first_ref_codon + 1]
suffix = ref_codons[nucleotide_offset_into_first_ref_codon + 1:]
else:
ref_codon_end_offset = (cds_offset + n_ref_nucleotides - 1) // 3 + 1
# codons in the reference sequence
ref_codons = sequence_from_start_codon[
ref_codon_start_offset * 3:ref_codon_end_offset * 3]
# We construct the new codons by taking the unmodified prefix
# of the first ref codon, the unmodified suffix of the last ref codon
# and sticking the alt nucleotides in between.
# Since this is supposed to be an in-frame mutation, the concatenated
# nucleotide string is expected to have a length that is a multiple of
# three.
prefix = ref_codons[:nucleotide_offset_into_first_ref_codon]
offset_in_last_ref_codon = (cds_offset + n_ref_nucleotides - 1) % 3
if offset_in_last_ref_codon == 0:
suffix = ref_codons[-2:]
elif offset_in_last_ref_codon == 1:
suffix = ref_codons[-1:]
else:
suffix = ""
mutant_codons = prefix + trimmed_cdna_alt + suffix
assert len(mutant_codons) % 3 == 0, \
"Expected in-frame mutation but got %s (length = %d)" % (
mutant_codons, len(mutant_codons))
return ref_codon_start_offset, ref_codon_end_offset, mutant_codons | python | def get_codons(
variant,
trimmed_cdna_ref,
trimmed_cdna_alt,
sequence_from_start_codon,
cds_offset):
"""
Returns indices of first and last reference codons affected by the variant,
as well as the actual sequence of the mutated codons which replace those
reference codons.
Parameters
----------
variant : Variant
trimmed_cdna_ref : str
Trimmed reference cDNA nucleotides affected by the variant
trimmed_cdna_alt : str
Trimmed alternate cDNA nucleotides which replace the reference
sequence_from_start_codon : str
cDNA nucleotide coding sequence
cds_offset : int
Integer offset into the coding sequence where ref is replace with alt
"""
# index (starting from 0) of first affected reference codon
ref_codon_start_offset = cds_offset // 3
# which nucleotide of the first codon got changed?
nucleotide_offset_into_first_ref_codon = cds_offset % 3
n_ref_nucleotides = len(trimmed_cdna_ref)
if n_ref_nucleotides == 0:
if nucleotide_offset_into_first_ref_codon == 2:
# if we're inserting between codons
ref_codon_end_offset = ref_codon_start_offset
else:
# inserting inside a reference codon
ref_codon_end_offset = ref_codon_start_offset + 1
ref_codons = sequence_from_start_codon[
ref_codon_start_offset * 3:ref_codon_end_offset * 3]
# split the reference codon into nucleotides before/after insertion
prefix = ref_codons[:nucleotide_offset_into_first_ref_codon + 1]
suffix = ref_codons[nucleotide_offset_into_first_ref_codon + 1:]
else:
ref_codon_end_offset = (cds_offset + n_ref_nucleotides - 1) // 3 + 1
# codons in the reference sequence
ref_codons = sequence_from_start_codon[
ref_codon_start_offset * 3:ref_codon_end_offset * 3]
# We construct the new codons by taking the unmodified prefix
# of the first ref codon, the unmodified suffix of the last ref codon
# and sticking the alt nucleotides in between.
# Since this is supposed to be an in-frame mutation, the concatenated
# nucleotide string is expected to have a length that is a multiple of
# three.
prefix = ref_codons[:nucleotide_offset_into_first_ref_codon]
offset_in_last_ref_codon = (cds_offset + n_ref_nucleotides - 1) % 3
if offset_in_last_ref_codon == 0:
suffix = ref_codons[-2:]
elif offset_in_last_ref_codon == 1:
suffix = ref_codons[-1:]
else:
suffix = ""
mutant_codons = prefix + trimmed_cdna_alt + suffix
assert len(mutant_codons) % 3 == 0, \
"Expected in-frame mutation but got %s (length = %d)" % (
mutant_codons, len(mutant_codons))
return ref_codon_start_offset, ref_codon_end_offset, mutant_codons | [
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] | Returns indices of first and last reference codons affected by the variant,
as well as the actual sequence of the mutated codons which replace those
reference codons.
Parameters
----------
variant : Variant
trimmed_cdna_ref : str
Trimmed reference cDNA nucleotides affected by the variant
trimmed_cdna_alt : str
Trimmed alternate cDNA nucleotides which replace the reference
sequence_from_start_codon : str
cDNA nucleotide coding sequence
cds_offset : int
Integer offset into the coding sequence where ref is replace with alt | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/effect_prediction_coding_in_frame.py#L36-L107 | train | Returns the indices of first and last reference codons affected by the variant and the actual sequence of the mutated codons. | 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(1256 - 1208) + chr(0b1101111) + chr(0b100110 + 0o20) + '\x36', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(50) + chr(48) + '\x33', 60979 - 60971), nzTpIcepk0o8('\x30' + chr(9364 - 9253) + chr(0b10000 + 0o43) + '\064' + chr(0b110101), 44132 - 44124), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b111 + 0o54) + '\x32' + chr(51), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110011) + chr(48) + chr(0b110010), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101110 + 0o1) + chr(1249 - 1199) + chr(0b100101 + 0o17) + chr(0b10010 + 0o43), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(52) + '\x32', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1011101 + 0o22) + '\x32' + chr(0b110010) + '\067', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(7842 - 7731) + chr(206 - 156) + chr(0b110111) + chr(1389 - 1338), 0o10), nzTpIcepk0o8(chr(48) + chr(0b100001 + 0o116) + chr(0b110010) + chr(52) + '\066', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\063' + chr(473 - 423) + chr(53), 64170 - 64162), nzTpIcepk0o8(chr(2163 - 2115) + '\x6f' + chr(2348 - 2299) + '\067' + '\x37', 0o10), nzTpIcepk0o8(chr(959 - 911) + chr(0b1101111) + chr(2239 - 2185), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b101110 + 0o101) + chr(0b110001) + chr(49) + chr(49), ord("\x08")), nzTpIcepk0o8('\060' + chr(12233 - 12122) + chr(0b110010) + chr(0b11 + 0o55) + chr(114 - 63), 8), nzTpIcepk0o8(chr(0b100011 + 0o15) + '\x6f' + chr(51) + '\060', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b11100 + 0o123) + chr(752 - 703) + chr(1474 - 1422) + '\x36', 40838 - 40830), nzTpIcepk0o8('\060' + chr(0b1001010 + 0o45) + '\063' + '\062' + '\x30', 26830 - 26822), nzTpIcepk0o8(chr(0b11110 + 0o22) + chr(0b11110 + 0o121) + chr(1098 - 1048) + chr(52) + chr(1888 - 1834), 8), nzTpIcepk0o8(chr(48) + chr(0b1011111 + 0o20) + '\x33' + chr(0b101110 + 0o6) + chr(504 - 450), 6935 - 6927), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(51) + '\067' + chr(0b110010), 0b1000), nzTpIcepk0o8(chr(0b101111 + 0o1) + chr(111) + chr(50), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110011) + chr(0b110100) + chr(2555 - 2501), 8), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(49) + '\x30' + '\067', 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(1280 - 1230) + '\061' + '\x32', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1010010 + 0o35) + chr(0b101000 + 0o13) + '\x33' + '\067', 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(2141 - 2091) + chr(50) + '\x36', 11903 - 11895), nzTpIcepk0o8('\060' + '\x6f' + chr(54) + '\x31', 9704 - 9696), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(49) + chr(422 - 369) + '\x33', 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110010) + chr(50) + chr(0b11001 + 0o30), ord("\x08")), nzTpIcepk0o8(chr(0b100111 + 0o11) + chr(111) + chr(1583 - 1534) + chr(0b110110) + '\x36', 0o10), nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(12096 - 11985) + chr(0b110001) + '\062' + chr(906 - 857), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b10110 + 0o131) + chr(0b11000 + 0o33) + chr(0b11001 + 0o34) + chr(0b1101 + 0o43), 0o10), nzTpIcepk0o8(chr(0b11100 + 0o24) + '\157' + chr(0b1001 + 0o52) + '\x37' + '\061', 0o10), nzTpIcepk0o8('\060' + chr(0b110110 + 0o71) + chr(1035 - 985) + '\x32' + '\x33', 0b1000), nzTpIcepk0o8('\060' + chr(0b1101010 + 0o5) + chr(51) + '\x31' + chr(626 - 574), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(0b100110 + 0o20) + chr(0b110010), 24880 - 24872), nzTpIcepk0o8(chr(48) + chr(12161 - 12050) + chr(54) + chr(50), 8), nzTpIcepk0o8(chr(0b101000 + 0o10) + '\x6f' + '\x37', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1100101 + 0o12) + '\063' + chr(0b110100) + '\060', 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + chr(0b1101001 + 0o6) + chr(53) + '\060', 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x18'), chr(2987 - 2887) + chr(0b1100101) + chr(829 - 730) + chr(433 - 322) + '\144' + chr(0b1100101))('\x75' + '\x74' + chr(102) + chr(1904 - 1859) + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def gg3MRF0sZgLZ(ZXJSPKxkIyZK, cduq82jeGeab, lIDGpzyU3VyV, _2B_8srBhfQc, ObtvnJg0h2SR):
yAcVglMCOnSW = ObtvnJg0h2SR // nzTpIcepk0o8('\x30' + '\157' + '\063', 0o10)
zSyFur52hn_0 = ObtvnJg0h2SR % nzTpIcepk0o8('\x30' + chr(2609 - 2498) + '\063', 8)
o8spGqEHRf7k = ftfygxgFas5X(cduq82jeGeab)
if o8spGqEHRf7k == nzTpIcepk0o8(chr(48) + '\157' + '\060', 0b1000):
if zSyFur52hn_0 == nzTpIcepk0o8(chr(0b110000) + chr(3413 - 3302) + '\x32', 8):
ldyQQqthZOTP = yAcVglMCOnSW
else:
ldyQQqthZOTP = yAcVglMCOnSW + nzTpIcepk0o8(chr(0b110000) + chr(514 - 403) + '\x31', 0o10)
STbBylJuPgCc = _2B_8srBhfQc[yAcVglMCOnSW * nzTpIcepk0o8(chr(0b110000) + chr(2012 - 1901) + chr(0b11110 + 0o25), 8):ldyQQqthZOTP * nzTpIcepk0o8(chr(48) + chr(111) + '\x33', 8)]
ZJwZgaHE72Po = STbBylJuPgCc[:zSyFur52hn_0 + nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b100 + 0o55), 8)]
biRCFepsLie5 = STbBylJuPgCc[zSyFur52hn_0 + nzTpIcepk0o8(chr(0b110000) + '\157' + '\x31', 8):]
else:
ldyQQqthZOTP = (ObtvnJg0h2SR + o8spGqEHRf7k - nzTpIcepk0o8('\060' + chr(0b1101111) + '\x31', 8)) // nzTpIcepk0o8('\060' + chr(8263 - 8152) + '\x33', 8) + nzTpIcepk0o8(chr(0b101000 + 0o10) + chr(0b1101111) + chr(0b110001), 8)
STbBylJuPgCc = _2B_8srBhfQc[yAcVglMCOnSW * nzTpIcepk0o8('\x30' + chr(0b11101 + 0o122) + chr(0b110011), 8):ldyQQqthZOTP * nzTpIcepk0o8(chr(0b110000) + chr(6871 - 6760) + chr(0b110011), 8)]
ZJwZgaHE72Po = STbBylJuPgCc[:zSyFur52hn_0]
z9JnW2YVBjnC = (ObtvnJg0h2SR + o8spGqEHRf7k - nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(2232 - 2183), 8)) % nzTpIcepk0o8(chr(0b1101 + 0o43) + chr(0b100001 + 0o116) + chr(2127 - 2076), 8)
if z9JnW2YVBjnC == nzTpIcepk0o8(chr(0b100101 + 0o13) + chr(0b1101111) + chr(48), 8):
biRCFepsLie5 = STbBylJuPgCc[-nzTpIcepk0o8(chr(1569 - 1521) + chr(11127 - 11016) + chr(50), 8):]
elif z9JnW2YVBjnC == nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(2386 - 2337), 8):
biRCFepsLie5 = STbBylJuPgCc[-nzTpIcepk0o8(chr(48) + '\157' + chr(0b1 + 0o60), 8):]
else:
biRCFepsLie5 = roI3spqORKae(ES5oEprVxulp(b''), '\x64' + chr(101) + chr(0b100110 + 0o75) + '\x6f' + chr(0b1100100) + chr(101))(chr(0b1110101) + chr(0b101101 + 0o107) + chr(0b1100110) + '\055' + chr(0b11010 + 0o36))
c6suuBZR9Vka = ZJwZgaHE72Po + lIDGpzyU3VyV + biRCFepsLie5
assert ftfygxgFas5X(c6suuBZR9Vka) % nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110011), 8) == nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x30', 8), roI3spqORKae(ES5oEprVxulp(b's\xfb\x95\xb6\xa1\xd1G\xf3\x9b\xcf\xbbR`;\xe2u\x03\xf0\xcb\x93\x8ec\x92.\xe5\xb1\xb6S\x1e\xe5V6\x87\x8d\xb3\xe9A\x12/\x8cS\xed\x82\xa7\xaa\x85\x1f\xb7\x9e\xc2\xfc'), '\x64' + chr(0b1011011 + 0o12) + '\x63' + '\157' + chr(8139 - 8039) + chr(2774 - 2673))(chr(2920 - 2803) + chr(7052 - 6936) + chr(102) + '\055' + '\x38') % (c6suuBZR9Vka, ftfygxgFas5X(c6suuBZR9Vka))
return (yAcVglMCOnSW, ldyQQqthZOTP, c6suuBZR9Vka) |
openvax/varcode | varcode/effects/effect_prediction_coding_in_frame.py | predict_in_frame_coding_effect | def predict_in_frame_coding_effect(
variant,
transcript,
trimmed_cdna_ref,
trimmed_cdna_alt,
sequence_from_start_codon,
cds_offset):
"""Coding effect of an in-frame nucleotide change
Parameters
----------
variant : Variant
transcript : Transcript
trimmed_cdna_ref : str
Reference nucleotides from the coding sequence of the transcript
trimmed_cdna_alt : str
Nucleotides to insert in place of the reference nucleotides
sequence_from_start_codon : Bio.Seq or str
Transcript sequence from the CDS start codon (including the 3' UTR).
This sequence includes the 3' UTR since a mutation may delete the stop
codon and we'll have to translate past the normal end of the CDS to
determine the new protein sequence.
cds_offset : int
Index of first ref nucleotide, starting from 0 = beginning of coding
sequence. If variant is a pure insertion (no ref nucleotides) then this
argument indicates the offset *after* which to insert the alt
nucleotides.
"""
ref_codon_start_offset, ref_codon_end_offset, mutant_codons = get_codons(
variant=variant,
trimmed_cdna_ref=trimmed_cdna_ref,
trimmed_cdna_alt=trimmed_cdna_alt,
sequence_from_start_codon=sequence_from_start_codon,
cds_offset=cds_offset)
mutation_affects_start_codon = (ref_codon_start_offset == 0)
if mutation_affects_start_codon and mutant_codons[:3] not in START_CODONS:
# if we changed a start codon to something else then
# we no longer know where the protein begins (or even in
# what frame).
# TODO: use the Kozak consensus sequence or a predictive model
# to identify the most likely start site
return StartLoss(
variant=variant,
transcript=transcript)
# rely on Ensembl's annotation of the protein sequence since we can't
# easily predict whether the starting nucleotide is a methionine
# (most common) or leucine
aa_ref = transcript.protein_sequence[ref_codon_start_offset:ref_codon_end_offset]
reference_protein_length = len(transcript.protein_sequence)
aa_alt, mutant_stop_codon_index, using_three_prime_utr = \
translate_in_frame_mutation(
transcript=transcript,
ref_codon_start_offset=ref_codon_start_offset,
ref_codon_end_offset=ref_codon_end_offset,
mutant_codons=mutant_codons)
mutant_codons_contain_stop = mutant_stop_codon_index != -1
# trim shared subsequences at the start and end of reference
# and mutated amino acid sequences
aa_ref, aa_alt, shared_prefix, shared_suffix = \
trim_shared_flanking_strings(
aa_ref,
aa_alt)
n_aa_ref = len(aa_ref)
n_aa_alt = len(aa_alt)
n_aa_shared = len(shared_prefix)
is_insertion = (ref_codon_start_offset == ref_codon_end_offset)
# index of first amino acid which is different from the reference
aa_mutation_start_offset = (
ref_codon_start_offset + n_aa_shared + is_insertion)
if mutant_codons_contain_stop:
mutant_stop_codon_index += n_aa_shared
if mutation_affects_start_codon and (aa_ref == aa_alt):
# Substitution between start codons gets special treatment since,
# though superficially synonymous, this could still potentially
# cause a start loss / change in reading frame and might be worth
# closer scrutiny
return AlternateStartCodon(
variant=variant,
transcript=transcript,
ref_codon=transcript.sequence[:3],
alt_codon=mutant_codons[:3])
n_ref_amino_acids_after_mutated_site = (
reference_protein_length - aa_mutation_start_offset - 1)
if mutant_codons_contain_stop and (
n_aa_alt <= n_ref_amino_acids_after_mutated_site):
# if the new coding sequence contains a stop codon, then this is a
# PrematureStop mutation if it decreases the length of the protein
return PrematureStop(
variant=variant,
transcript=transcript,
aa_mutation_start_offset=aa_mutation_start_offset,
aa_ref=aa_ref,
aa_alt=aa_alt)
if (aa_mutation_start_offset > reference_protein_length) or (
n_aa_ref == n_aa_alt == 0):
# if inserted nucleotides go after original stop codon or if nothing
# is changed in the amino acid sequence then this is a Silent variant
return Silent(
variant=variant,
transcript=transcript,
aa_pos=aa_mutation_start_offset,
aa_ref=shared_prefix + shared_suffix)
elif using_three_prime_utr:
# if non-silent mutation is at the end of the protein then
# should be a stop-loss
return StopLoss(
variant,
transcript,
aa_ref=aa_ref,
aa_alt=aa_alt)
elif n_aa_alt == 0:
return Deletion(
variant,
transcript,
aa_mutation_start_offset=aa_mutation_start_offset,
aa_ref=aa_ref)
elif n_aa_ref == 0:
return Insertion(
variant,
transcript,
aa_mutation_start_offset=aa_mutation_start_offset,
aa_alt=aa_alt)
elif n_aa_ref == n_aa_alt == 1:
# simple substitution e.g. p.V600E
return Substitution(
variant,
transcript,
aa_mutation_start_offset=aa_mutation_start_offset,
aa_ref=aa_ref,
aa_alt=aa_alt)
else:
# multiple amino acids were substituted e.g. p.VQQ39FF
return ComplexSubstitution(
variant,
transcript,
aa_mutation_start_offset=aa_mutation_start_offset,
aa_ref=aa_ref,
aa_alt=aa_alt) | python | def predict_in_frame_coding_effect(
variant,
transcript,
trimmed_cdna_ref,
trimmed_cdna_alt,
sequence_from_start_codon,
cds_offset):
"""Coding effect of an in-frame nucleotide change
Parameters
----------
variant : Variant
transcript : Transcript
trimmed_cdna_ref : str
Reference nucleotides from the coding sequence of the transcript
trimmed_cdna_alt : str
Nucleotides to insert in place of the reference nucleotides
sequence_from_start_codon : Bio.Seq or str
Transcript sequence from the CDS start codon (including the 3' UTR).
This sequence includes the 3' UTR since a mutation may delete the stop
codon and we'll have to translate past the normal end of the CDS to
determine the new protein sequence.
cds_offset : int
Index of first ref nucleotide, starting from 0 = beginning of coding
sequence. If variant is a pure insertion (no ref nucleotides) then this
argument indicates the offset *after* which to insert the alt
nucleotides.
"""
ref_codon_start_offset, ref_codon_end_offset, mutant_codons = get_codons(
variant=variant,
trimmed_cdna_ref=trimmed_cdna_ref,
trimmed_cdna_alt=trimmed_cdna_alt,
sequence_from_start_codon=sequence_from_start_codon,
cds_offset=cds_offset)
mutation_affects_start_codon = (ref_codon_start_offset == 0)
if mutation_affects_start_codon and mutant_codons[:3] not in START_CODONS:
# if we changed a start codon to something else then
# we no longer know where the protein begins (or even in
# what frame).
# TODO: use the Kozak consensus sequence or a predictive model
# to identify the most likely start site
return StartLoss(
variant=variant,
transcript=transcript)
# rely on Ensembl's annotation of the protein sequence since we can't
# easily predict whether the starting nucleotide is a methionine
# (most common) or leucine
aa_ref = transcript.protein_sequence[ref_codon_start_offset:ref_codon_end_offset]
reference_protein_length = len(transcript.protein_sequence)
aa_alt, mutant_stop_codon_index, using_three_prime_utr = \
translate_in_frame_mutation(
transcript=transcript,
ref_codon_start_offset=ref_codon_start_offset,
ref_codon_end_offset=ref_codon_end_offset,
mutant_codons=mutant_codons)
mutant_codons_contain_stop = mutant_stop_codon_index != -1
# trim shared subsequences at the start and end of reference
# and mutated amino acid sequences
aa_ref, aa_alt, shared_prefix, shared_suffix = \
trim_shared_flanking_strings(
aa_ref,
aa_alt)
n_aa_ref = len(aa_ref)
n_aa_alt = len(aa_alt)
n_aa_shared = len(shared_prefix)
is_insertion = (ref_codon_start_offset == ref_codon_end_offset)
# index of first amino acid which is different from the reference
aa_mutation_start_offset = (
ref_codon_start_offset + n_aa_shared + is_insertion)
if mutant_codons_contain_stop:
mutant_stop_codon_index += n_aa_shared
if mutation_affects_start_codon and (aa_ref == aa_alt):
# Substitution between start codons gets special treatment since,
# though superficially synonymous, this could still potentially
# cause a start loss / change in reading frame and might be worth
# closer scrutiny
return AlternateStartCodon(
variant=variant,
transcript=transcript,
ref_codon=transcript.sequence[:3],
alt_codon=mutant_codons[:3])
n_ref_amino_acids_after_mutated_site = (
reference_protein_length - aa_mutation_start_offset - 1)
if mutant_codons_contain_stop and (
n_aa_alt <= n_ref_amino_acids_after_mutated_site):
# if the new coding sequence contains a stop codon, then this is a
# PrematureStop mutation if it decreases the length of the protein
return PrematureStop(
variant=variant,
transcript=transcript,
aa_mutation_start_offset=aa_mutation_start_offset,
aa_ref=aa_ref,
aa_alt=aa_alt)
if (aa_mutation_start_offset > reference_protein_length) or (
n_aa_ref == n_aa_alt == 0):
# if inserted nucleotides go after original stop codon or if nothing
# is changed in the amino acid sequence then this is a Silent variant
return Silent(
variant=variant,
transcript=transcript,
aa_pos=aa_mutation_start_offset,
aa_ref=shared_prefix + shared_suffix)
elif using_three_prime_utr:
# if non-silent mutation is at the end of the protein then
# should be a stop-loss
return StopLoss(
variant,
transcript,
aa_ref=aa_ref,
aa_alt=aa_alt)
elif n_aa_alt == 0:
return Deletion(
variant,
transcript,
aa_mutation_start_offset=aa_mutation_start_offset,
aa_ref=aa_ref)
elif n_aa_ref == 0:
return Insertion(
variant,
transcript,
aa_mutation_start_offset=aa_mutation_start_offset,
aa_alt=aa_alt)
elif n_aa_ref == n_aa_alt == 1:
# simple substitution e.g. p.V600E
return Substitution(
variant,
transcript,
aa_mutation_start_offset=aa_mutation_start_offset,
aa_ref=aa_ref,
aa_alt=aa_alt)
else:
# multiple amino acids were substituted e.g. p.VQQ39FF
return ComplexSubstitution(
variant,
transcript,
aa_mutation_start_offset=aa_mutation_start_offset,
aa_ref=aa_ref,
aa_alt=aa_alt) | [
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] | Coding effect of an in-frame nucleotide change
Parameters
----------
variant : Variant
transcript : Transcript
trimmed_cdna_ref : str
Reference nucleotides from the coding sequence of the transcript
trimmed_cdna_alt : str
Nucleotides to insert in place of the reference nucleotides
sequence_from_start_codon : Bio.Seq or str
Transcript sequence from the CDS start codon (including the 3' UTR).
This sequence includes the 3' UTR since a mutation may delete the stop
codon and we'll have to translate past the normal end of the CDS to
determine the new protein sequence.
cds_offset : int
Index of first ref nucleotide, starting from 0 = beginning of coding
sequence. If variant is a pure insertion (no ref nucleotides) then this
argument indicates the offset *after* which to insert the alt
nucleotides. | [
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"change"
] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/effect_prediction_coding_in_frame.py#L110-L267 | train | Predicts the coding effect of an in - frame nucleotide change in - frame nucleotide change in - frame 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) + chr(2555 - 2444) + chr(0b110011) + chr(0b110110 + 0o1) + '\065', 0b1000), nzTpIcepk0o8(chr(0b100 + 0o54) + chr(0b1101101 + 0o2) + chr(49) + chr(0b101000 + 0o10) + chr(890 - 836), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x32' + '\x34' + chr(0b110011), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(0b110010) + chr(55), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110101 + 0o0) + chr(601 - 549), 3159 - 3151), nzTpIcepk0o8(chr(48) + chr(5226 - 5115) + chr(208 - 159) + '\064', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b101010 + 0o105) + chr(0b110011) + chr(0b110000) + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x32' + '\x37' + chr(0b110011), ord("\x08")), nzTpIcepk0o8(chr(1324 - 1276) + '\157' + chr(0b1011 + 0o50) + chr(0b10010 + 0o41) + '\063', 2009 - 2001), nzTpIcepk0o8(chr(1887 - 1839) + chr(10321 - 10210) + '\x32' + chr(2203 - 2153) + chr(579 - 525), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(995 - 946) + chr(0b1111 + 0o50) + chr(0b1 + 0o64), 0o10), nzTpIcepk0o8(chr(1496 - 1448) + chr(3497 - 3386) + chr(0b101010 + 0o11) + chr(48) + chr(0b110101), 46152 - 46144), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110010) + chr(0b100111 + 0o14) + chr(51), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(3383 - 3272) + chr(0b100101 + 0o21) + chr(0b100101 + 0o13), ord("\x08")), nzTpIcepk0o8(chr(0b11101 + 0o23) + chr(111) + chr(2342 - 2292), 0o10), nzTpIcepk0o8(chr(48) + chr(3244 - 3133) + chr(656 - 604) + '\062', 0b1000), nzTpIcepk0o8(chr(1864 - 1816) + chr(7083 - 6972) + '\063' + chr(52) + chr(53), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110011) + chr(0b101100 + 0o7) + chr(0b110000), 0o10), nzTpIcepk0o8(chr(48) + chr(9594 - 9483) + '\x32' + '\x31' + chr(50), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(845 - 790) + chr(326 - 274), 0b1000), nzTpIcepk0o8(chr(1229 - 1181) + chr(111) + chr(0b1 + 0o61) + chr(0b110001) + chr(49), 0o10), nzTpIcepk0o8('\x30' + chr(5060 - 4949) + chr(1172 - 1121) + chr(0b100010 + 0o20) + '\060', 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(49) + '\064' + '\x36', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(4666 - 4555) + chr(0b10111 + 0o34) + chr(2192 - 2138) + '\065', 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110011) + chr(55) + '\066', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(49) + chr(0b110110) + chr(568 - 518), 21305 - 21297), nzTpIcepk0o8(chr(0b100111 + 0o11) + chr(0b1101111) + chr(0b11111 + 0o22) + chr(49) + chr(48), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110011) + chr(1688 - 1638) + chr(52), 0b1000), nzTpIcepk0o8(chr(2270 - 2222) + chr(0b0 + 0o157) + chr(0b11001 + 0o32) + chr(0b110100) + chr(0b110111), 42470 - 42462), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(325 - 276) + '\x33' + '\x30', 0b1000), nzTpIcepk0o8(chr(0b100100 + 0o14) + chr(0b1101010 + 0o5) + chr(51) + '\061' + '\x30', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110100) + chr(55), 0o10), nzTpIcepk0o8(chr(0b10 + 0o56) + chr(0b111111 + 0o60) + chr(0b101 + 0o56) + '\x31' + chr(55), 0o10), nzTpIcepk0o8(chr(875 - 827) + chr(0b1101111) + '\063' + '\x31' + '\x30', 8), nzTpIcepk0o8('\060' + chr(0b11 + 0o154) + chr(50) + chr(51), 0b1000), nzTpIcepk0o8(chr(2186 - 2138) + '\157' + chr(2407 - 2356) + chr(1798 - 1746) + chr(0b110000), 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(1271 - 1222) + '\x37' + chr(0b100 + 0o55), ord("\x08")), nzTpIcepk0o8(chr(0b111 + 0o51) + '\157' + '\x31' + chr(0b110111) + chr(0b110000), 59131 - 59123), nzTpIcepk0o8(chr(48) + chr(0b100000 + 0o117) + chr(0b110001) + chr(0b11010 + 0o34), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b11 + 0o56) + '\x34' + chr(0b110001), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110101) + '\x30', 23756 - 23748)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xd3'), '\x64' + chr(0b100010 + 0o103) + chr(99) + chr(8720 - 8609) + chr(100) + chr(0b11000 + 0o115))(chr(0b1110101) + '\164' + '\x66' + chr(0b101101) + chr(0b101101 + 0o13)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def pO9RAWVEr_Fw(ZXJSPKxkIyZK, lnOu7fTAiCZI, cduq82jeGeab, lIDGpzyU3VyV, _2B_8srBhfQc, ObtvnJg0h2SR):
(yAcVglMCOnSW, ldyQQqthZOTP, c6suuBZR9Vka) = gg3MRF0sZgLZ(variant=ZXJSPKxkIyZK, trimmed_cdna_ref=cduq82jeGeab, trimmed_cdna_alt=lIDGpzyU3VyV, sequence_from_start_codon=_2B_8srBhfQc, cds_offset=ObtvnJg0h2SR)
alU8_k22SWc7 = yAcVglMCOnSW == nzTpIcepk0o8(chr(2181 - 2133) + chr(8100 - 7989) + chr(0b110000), 0o10)
if alU8_k22SWc7 and c6suuBZR9Vka[:nzTpIcepk0o8('\060' + chr(9690 - 9579) + '\x33', 0b1000)] not in Gp7kmOYS7p1n:
return ryOXnawBJKw_(variant=ZXJSPKxkIyZK, transcript=lnOu7fTAiCZI)
k1f0SIIbhI0T = lnOu7fTAiCZI.protein_sequence[yAcVglMCOnSW:ldyQQqthZOTP]
vQWEcadQ2BcX = ftfygxgFas5X(lnOu7fTAiCZI.protein_sequence)
(BpvTUApuD5xv, zOXVoUlAhKEk, fwKEeyAhA92H) = scNKhF2jAprz(transcript=lnOu7fTAiCZI, ref_codon_start_offset=yAcVglMCOnSW, ref_codon_end_offset=ldyQQqthZOTP, mutant_codons=c6suuBZR9Vka)
TQzOjumZmi_R = zOXVoUlAhKEk != -nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b10110 + 0o33), ord("\x08"))
(k1f0SIIbhI0T, BpvTUApuD5xv, ms4y_Eqzk1bG, bTBk2kXkZgci) = Ajs8ZJ4OfLbv(k1f0SIIbhI0T, BpvTUApuD5xv)
SE6GKhY6yv9S = ftfygxgFas5X(k1f0SIIbhI0T)
v6aOJwiUFF8O = ftfygxgFas5X(BpvTUApuD5xv)
OGrCtDRGVyK7 = ftfygxgFas5X(ms4y_Eqzk1bG)
cKvwmgqx2X4j = yAcVglMCOnSW == ldyQQqthZOTP
BOuEkH_otp5Z = yAcVglMCOnSW + OGrCtDRGVyK7 + cKvwmgqx2X4j
if TQzOjumZmi_R:
zOXVoUlAhKEk += OGrCtDRGVyK7
if alU8_k22SWc7 and k1f0SIIbhI0T == BpvTUApuD5xv:
return B0ZoA8AaBtdD(variant=ZXJSPKxkIyZK, transcript=lnOu7fTAiCZI, ref_codon=roI3spqORKae(lnOu7fTAiCZI, roI3spqORKae(ES5oEprVxulp(b"\xbc'\xe5rC<\xac\xcc\xe8\xa2>\xf6"), chr(100) + '\x65' + chr(0b1100011) + chr(0b1001101 + 0o42) + chr(0b110101 + 0o57) + '\145')(chr(0b1110101) + '\x74' + chr(102) + chr(1581 - 1536) + chr(56)))[:nzTpIcepk0o8('\x30' + chr(5847 - 5736) + chr(0b110011), 8)], alt_codon=c6suuBZR9Vka[:nzTpIcepk0o8(chr(2039 - 1991) + '\157' + chr(0b110011), 8)])
XPcSTUKKA9Y4 = vQWEcadQ2BcX - BOuEkH_otp5Z - nzTpIcepk0o8(chr(0b1110 + 0o42) + '\x6f' + chr(1986 - 1937), 8)
if TQzOjumZmi_R and v6aOJwiUFF8O <= XPcSTUKKA9Y4:
return ZPPQtrES7t5w(variant=ZXJSPKxkIyZK, transcript=lnOu7fTAiCZI, aa_mutation_start_offset=BOuEkH_otp5Z, aa_ref=k1f0SIIbhI0T, aa_alt=BpvTUApuD5xv)
if BOuEkH_otp5Z > vQWEcadQ2BcX or SE6GKhY6yv9S == v6aOJwiUFF8O == nzTpIcepk0o8('\060' + '\157' + chr(0b110000), 8):
return Yb0g_iGWKvE9(variant=ZXJSPKxkIyZK, transcript=lnOu7fTAiCZI, aa_pos=BOuEkH_otp5Z, aa_ref=ms4y_Eqzk1bG + bTBk2kXkZgci)
elif fwKEeyAhA92H:
return U9AaVOS6emP_(ZXJSPKxkIyZK, lnOu7fTAiCZI, aa_ref=k1f0SIIbhI0T, aa_alt=BpvTUApuD5xv)
elif v6aOJwiUFF8O == nzTpIcepk0o8(chr(1581 - 1533) + chr(2728 - 2617) + chr(48), 8):
return VaDIREwCvcuY(ZXJSPKxkIyZK, lnOu7fTAiCZI, aa_mutation_start_offset=BOuEkH_otp5Z, aa_ref=k1f0SIIbhI0T)
elif SE6GKhY6yv9S == nzTpIcepk0o8('\x30' + chr(5188 - 5077) + chr(576 - 528), 8):
return M0qanuV2vfpl(ZXJSPKxkIyZK, lnOu7fTAiCZI, aa_mutation_start_offset=BOuEkH_otp5Z, aa_alt=BpvTUApuD5xv)
elif SE6GKhY6yv9S == v6aOJwiUFF8O == nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x31', 8):
return ouDM9pKKuXnM(ZXJSPKxkIyZK, lnOu7fTAiCZI, aa_mutation_start_offset=BOuEkH_otp5Z, aa_ref=k1f0SIIbhI0T, aa_alt=BpvTUApuD5xv)
else:
return mVgauQJI_8ZP(ZXJSPKxkIyZK, lnOu7fTAiCZI, aa_mutation_start_offset=BOuEkH_otp5Z, aa_ref=k1f0SIIbhI0T, aa_alt=BpvTUApuD5xv) |
openvax/varcode | varcode/cli/variant_args.py | add_variant_args | def add_variant_args(arg_parser):
"""
Extends an ArgumentParser instance with the following commandline arguments:
--vcf
--genome
--maf
--variant
--json-variants
"""
variant_arg_group = arg_parser.add_argument_group(
title="Variants",
description="Genomic variant files")
variant_arg_group.add_argument(
"--vcf",
default=[],
action="append",
help="Genomic variants in VCF format")
variant_arg_group.add_argument(
"--maf",
default=[],
action="append",
help="Genomic variants in TCGA's MAF format",)
variant_arg_group.add_argument(
"--variant",
default=[],
action="append",
nargs=4,
metavar=("CHR", "POS", "REF", "ALT"),
help=(
"Individual variant as 4 arguments giving chromsome, position, ref,"
" and alt. Example: chr1 3848 C G. Use '.' to indicate empty alleles"
" for insertions or deletions."))
variant_arg_group.add_argument(
"--genome",
type=str,
help=(
"What reference assembly your variant coordinates are using. "
"Examples: 'hg19', 'GRCh38', or 'mm9'. "
"This argument is ignored for MAF files, since each row includes "
"the reference. "
"For VCF files, this is used if specified, and otherwise is guessed from "
"the header. For variants specfied on the commandline with --variant, "
"this option is required."))
variant_arg_group.add_argument(
"--download-reference-genome-data",
action="store_true",
default=False,
help=(
("Automatically download genome reference data required for "
"annotation using PyEnsembl. Otherwise you must first run "
"'pyensembl install' for the release/species corresponding "
"to the genome used in your VCF.")))
variant_arg_group.add_argument(
"--json-variants",
default=[],
action="append",
help="Path to Varcode.VariantCollection object serialized as a JSON file.")
return variant_arg_group | python | def add_variant_args(arg_parser):
"""
Extends an ArgumentParser instance with the following commandline arguments:
--vcf
--genome
--maf
--variant
--json-variants
"""
variant_arg_group = arg_parser.add_argument_group(
title="Variants",
description="Genomic variant files")
variant_arg_group.add_argument(
"--vcf",
default=[],
action="append",
help="Genomic variants in VCF format")
variant_arg_group.add_argument(
"--maf",
default=[],
action="append",
help="Genomic variants in TCGA's MAF format",)
variant_arg_group.add_argument(
"--variant",
default=[],
action="append",
nargs=4,
metavar=("CHR", "POS", "REF", "ALT"),
help=(
"Individual variant as 4 arguments giving chromsome, position, ref,"
" and alt. Example: chr1 3848 C G. Use '.' to indicate empty alleles"
" for insertions or deletions."))
variant_arg_group.add_argument(
"--genome",
type=str,
help=(
"What reference assembly your variant coordinates are using. "
"Examples: 'hg19', 'GRCh38', or 'mm9'. "
"This argument is ignored for MAF files, since each row includes "
"the reference. "
"For VCF files, this is used if specified, and otherwise is guessed from "
"the header. For variants specfied on the commandline with --variant, "
"this option is required."))
variant_arg_group.add_argument(
"--download-reference-genome-data",
action="store_true",
default=False,
help=(
("Automatically download genome reference data required for "
"annotation using PyEnsembl. Otherwise you must first run "
"'pyensembl install' for the release/species corresponding "
"to the genome used in your VCF.")))
variant_arg_group.add_argument(
"--json-variants",
default=[],
action="append",
help="Path to Varcode.VariantCollection object serialized as a JSON file.")
return variant_arg_group | [
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",",
"metavar",
"=",
"(",
"\"CHR\"",
",",
"\"POS\"",
",",
"\"REF\"",
",",
"\"ALT\"",
")",
",",
"help",
"=",
"(",
"\"Individual variant as 4 arguments giving chromsome, position, ref,\"",
"\" and alt. Example: chr1 3848 C G. Use '.' to indicate empty alleles\"",
"\" for insertions or deletions.\"",
")",
")",
"variant_arg_group",
".",
"add_argument",
"(",
"\"--genome\"",
",",
"type",
"=",
"str",
",",
"help",
"=",
"(",
"\"What reference assembly your variant coordinates are using. \"",
"\"Examples: 'hg19', 'GRCh38', or 'mm9'. \"",
"\"This argument is ignored for MAF files, since each row includes \"",
"\"the reference. \"",
"\"For VCF files, this is used if specified, and otherwise is guessed from \"",
"\"the header. For variants specfied on the commandline with --variant, \"",
"\"this option is required.\"",
")",
")",
"variant_arg_group",
".",
"add_argument",
"(",
"\"--download-reference-genome-data\"",
",",
"action",
"=",
"\"store_true\"",
",",
"default",
"=",
"False",
",",
"help",
"=",
"(",
"(",
"\"Automatically download genome reference data required for \"",
"\"annotation using PyEnsembl. Otherwise you must first run \"",
"\"'pyensembl install' for the release/species corresponding \"",
"\"to the genome used in your VCF.\"",
")",
")",
")",
"variant_arg_group",
".",
"add_argument",
"(",
"\"--json-variants\"",
",",
"default",
"=",
"[",
"]",
",",
"action",
"=",
"\"append\"",
",",
"help",
"=",
"\"Path to Varcode.VariantCollection object serialized as a JSON file.\"",
")",
"return",
"variant_arg_group"
] | Extends an ArgumentParser instance with the following commandline arguments:
--vcf
--genome
--maf
--variant
--json-variants | [
"Extends",
"an",
"ArgumentParser",
"instance",
"with",
"the",
"following",
"commandline",
"arguments",
":",
"--",
"vcf",
"--",
"genome",
"--",
"maf",
"--",
"variant",
"--",
"json",
"-",
"variants"
] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/cli/variant_args.py#L26-L90 | train | Adds the commandline arguments for the variant command line. | 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(0b110010) + '\065' + '\065', 0o10), nzTpIcepk0o8(chr(1361 - 1313) + chr(111) + chr(49) + chr(0b100101 + 0o16) + '\064', 0b1000), nzTpIcepk0o8(chr(0b100110 + 0o12) + chr(0b1101111) + chr(0b0 + 0o61) + chr(0b110010), 33838 - 33830), nzTpIcepk0o8(chr(0b100100 + 0o14) + chr(1245 - 1134) + chr(0b110010) + chr(0b1111 + 0o47) + chr(0b1111 + 0o50), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(2076 - 2027) + '\x34' + chr(1914 - 1862), 0o10), nzTpIcepk0o8('\060' + chr(111) + '\x33' + '\065' + chr(0b100001 + 0o20), ord("\x08")), nzTpIcepk0o8(chr(0b1000 + 0o50) + chr(0b1101111) + '\062' + '\064' + chr(54), 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + '\066' + chr(0b110011), 0o10), nzTpIcepk0o8(chr(999 - 951) + chr(111) + chr(0b10 + 0o60) + '\x31' + chr(51), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1001001 + 0o46) + chr(0b100100 + 0o17) + chr(0b100110 + 0o16) + chr(374 - 321), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b11100 + 0o32) + chr(1434 - 1383), 8), nzTpIcepk0o8(chr(260 - 212) + '\157' + chr(0b10101 + 0o35) + '\x30' + chr(0b10 + 0o57), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(51) + chr(50) + '\x31', 52116 - 52108), nzTpIcepk0o8(chr(1903 - 1855) + '\157' + chr(1532 - 1482) + chr(0b11110 + 0o27) + chr(51), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(1422 - 1372) + '\061' + '\x31', ord("\x08")), nzTpIcepk0o8(chr(2022 - 1974) + chr(0b1001000 + 0o47) + '\x32' + chr(50) + chr(48), 0o10), nzTpIcepk0o8(chr(1953 - 1905) + chr(12184 - 12073) + '\061' + chr(55) + chr(1051 - 996), 51543 - 51535), nzTpIcepk0o8(chr(0b1001 + 0o47) + chr(9386 - 9275) + chr(50) + chr(0b110001) + '\067', 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(52) + chr(0b110011), 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(1085 - 1036) + '\x33' + '\x31', ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + chr(0b101001 + 0o12) + '\x30' + '\x31', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(394 - 345) + chr(0b110100) + chr(0b10110 + 0o41), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(11927 - 11816) + '\x31' + chr(51) + '\x32', 0b1000), nzTpIcepk0o8('\060' + chr(2727 - 2616) + chr(2473 - 2422) + '\066' + '\x33', 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(2389 - 2338) + chr(51) + '\x37', 35045 - 35037), nzTpIcepk0o8(chr(0b10001 + 0o37) + '\157' + '\063' + '\061' + chr(0b10001 + 0o43), ord("\x08")), nzTpIcepk0o8(chr(0b1001 + 0o47) + chr(0b1 + 0o156) + chr(0b110011) + chr(1065 - 1010) + '\x36', 45001 - 44993), nzTpIcepk0o8(chr(0b10001 + 0o37) + '\157' + chr(0b1010 + 0o51) + '\066' + chr(1349 - 1296), 0o10), nzTpIcepk0o8(chr(48) + chr(246 - 135) + chr(0b10101 + 0o41) + '\067', 487 - 479), nzTpIcepk0o8('\x30' + '\157' + chr(0b11001 + 0o31) + chr(0b110001) + '\063', 8), nzTpIcepk0o8('\060' + chr(111) + chr(50) + '\x36' + '\x36', ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(51) + chr(797 - 743), 1664 - 1656), nzTpIcepk0o8(chr(0b110000) + chr(8441 - 8330) + '\x33' + chr(54) + '\x36', 39388 - 39380), nzTpIcepk0o8('\x30' + '\x6f' + chr(51) + chr(1612 - 1562), 0b1000), nzTpIcepk0o8(chr(2007 - 1959) + '\157' + '\x32' + chr(0b110010), 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(49) + chr(842 - 789), 12606 - 12598), nzTpIcepk0o8(chr(575 - 527) + '\x6f' + '\x35' + chr(0b10010 + 0o36), 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(0b100111 + 0o14) + '\062' + chr(1673 - 1625), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b101100 + 0o7) + chr(0b100100 + 0o20), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1010000 + 0o37) + '\x33' + chr(0b110001), 24758 - 24750)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + '\x6f' + '\x35' + '\x30', 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x83'), '\x64' + '\x65' + '\x63' + chr(0b100011 + 0o114) + chr(0b1100100) + chr(101))(chr(0b1110101) + chr(0b1110100) + chr(0b1100110) + chr(1978 - 1933) + chr(0b10111 + 0o41)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def FdDtFvpp73Iu(bCPkA5flNgHN):
XjosxPK5hJZk = bCPkA5flNgHN.add_argument_group(title=roI3spqORKae(ES5oEprVxulp(b'\xfb=x\xde\x05\x87\xd2@'), '\144' + chr(0b1100101) + chr(3442 - 3343) + chr(0b1000111 + 0o50) + chr(0b1100100) + chr(0b1100101))(chr(0b1110101) + chr(0b1110100) + chr(0b1101 + 0o131) + chr(0b101101) + chr(1435 - 1379)), description=roI3spqORKae(ES5oEprVxulp(b'\xea9d\xd8\t\x80\xc5\x13\xfd\x84A\xe8\xb0\xc5\xfd\xb0\x19\xe6O<\xb2'), '\x64' + chr(0b1100101) + chr(0b1010100 + 0o17) + chr(0b1101111) + chr(0b1010111 + 0o15) + chr(101))('\165' + chr(116) + chr(0b1100110) + chr(45) + chr(1252 - 1196)))
roI3spqORKae(XjosxPK5hJZk, roI3spqORKae(ES5oEprVxulp(b'\xcc8n\xe8\x05\x9b\xc1F\xe6\x80]\xf5'), '\x64' + chr(101) + chr(99) + chr(0b1001010 + 0o45) + chr(3450 - 3350) + chr(0b110000 + 0o65))('\165' + chr(0b1110100) + chr(0b1001010 + 0o34) + chr(1539 - 1494) + chr(1155 - 1099)))(roI3spqORKae(ES5oEprVxulp(b'\x80q|\xd4\x02'), chr(0b10011 + 0o121) + '\x65' + chr(0b1100011) + chr(111) + chr(0b101001 + 0o73) + '\145')('\165' + chr(116) + chr(102) + chr(1680 - 1635) + chr(0b100101 + 0o23)), default=[], action=roI3spqORKae(ES5oEprVxulp(b'\xcc,z\xd2\n\x8d'), chr(8714 - 8614) + '\x65' + '\x63' + '\x6f' + chr(0b110110 + 0o56) + chr(0b1100010 + 0o3))(chr(13252 - 13135) + chr(116) + '\x66' + '\055' + chr(0b111000)), help=roI3spqORKae(ES5oEprVxulp(b'\xea9d\xd8\t\x80\xc5\x13\xfd\x84A\xe8\xb0\xc5\xfd\xe3_\xe6My\x97$\x1c\xd3\xb9\xa3\x8c\x98V\xff'), chr(0b11110 + 0o106) + chr(0b1001110 + 0o27) + chr(0b111000 + 0o53) + '\157' + chr(0b10011 + 0o121) + chr(0b1001000 + 0o35))('\165' + '\x74' + '\146' + chr(1031 - 986) + chr(1704 - 1648)))
roI3spqORKae(XjosxPK5hJZk, roI3spqORKae(ES5oEprVxulp(b'\xcc8n\xe8\x05\x9b\xc1F\xe6\x80]\xf5'), chr(0b1011010 + 0o12) + chr(1218 - 1117) + chr(4626 - 4527) + '\x6f' + chr(0b1011011 + 0o11) + chr(0b1001001 + 0o34))('\x75' + chr(0b111011 + 0o71) + chr(9357 - 9255) + '\055' + '\070'))(roI3spqORKae(ES5oEprVxulp(b'\x80qg\xd6\x02'), chr(100) + chr(0b1100101) + chr(0b1100011) + chr(111) + chr(0b1100100) + '\145')('\x75' + chr(12957 - 12841) + '\x66' + chr(246 - 201) + chr(616 - 560)), default=[], action=roI3spqORKae(ES5oEprVxulp(b'\xcc,z\xd2\n\x8d'), chr(4466 - 4366) + chr(101) + '\143' + '\157' + chr(0b1100100) + chr(0b1100101))(chr(0b1101001 + 0o14) + '\x74' + chr(7694 - 7592) + chr(45) + chr(56)), help=roI3spqORKae(ES5oEprVxulp(b'\xea9d\xd8\t\x80\xc5\x13\xfd\x84A\xe8\xb0\xc5\xfd\xe3_\xe6My\x95$\x1d\xb2\xf8\xbf\xde\xb8v\xcd\x96x\x99h\x7fl\\'), chr(0b1001011 + 0o31) + chr(0b1001111 + 0o26) + '\x63' + '\x6f' + chr(7210 - 7110) + chr(2776 - 2675))('\x75' + chr(0b1100101 + 0o17) + '\x66' + chr(0b11110 + 0o17) + chr(0b110000 + 0o10)))
roI3spqORKae(XjosxPK5hJZk, roI3spqORKae(ES5oEprVxulp(b'\xcc8n\xe8\x05\x9b\xc1F\xe6\x80]\xf5'), chr(100) + chr(101) + chr(3862 - 3763) + chr(0b100110 + 0o111) + '\144' + chr(1389 - 1288))(chr(117) + chr(0b1100010 + 0o22) + chr(10245 - 10143) + chr(45) + '\070'))(roI3spqORKae(ES5oEprVxulp(b'\x80q|\xd6\x16\x80\xc7]\xff'), chr(0b1100100) + chr(9025 - 8924) + chr(3514 - 3415) + chr(8892 - 8781) + chr(0b1100100) + chr(101))('\x75' + '\164' + '\146' + chr(0b101101) + '\x38'), default=[], action=roI3spqORKae(ES5oEprVxulp(b'\xcc,z\xd2\n\x8d'), chr(0b1100100) + chr(0b1100101) + chr(99) + chr(0b1101111) + chr(100) + chr(0b1100101))('\165' + chr(0b10011 + 0o141) + chr(3326 - 3224) + chr(313 - 268) + chr(1728 - 1672)), nargs=nzTpIcepk0o8(chr(48) + '\x6f' + '\x34', 0o10), metavar=(roI3spqORKae(ES5oEprVxulp(b'\xee\x14X'), chr(0b111 + 0o135) + chr(6079 - 5978) + chr(5653 - 5554) + chr(111) + chr(0b10001 + 0o123) + chr(4161 - 4060))(chr(0b1110101) + chr(0b101011 + 0o111) + chr(9727 - 9625) + '\x2d' + chr(2063 - 2007)), roI3spqORKae(ES5oEprVxulp(b'\xfd\x13Y'), '\144' + chr(0b10100 + 0o121) + chr(99) + chr(0b1101111) + '\x64' + chr(0b1100101))(chr(0b1100001 + 0o24) + '\164' + chr(102) + chr(0b101101) + chr(0b11100 + 0o34)), roI3spqORKae(ES5oEprVxulp(b'\xff\x19L'), '\144' + chr(101) + chr(0b110011 + 0o60) + '\157' + chr(0b1100100) + '\x65')(chr(0b1110101) + chr(116) + '\x66' + chr(0b101101) + '\x38'), roI3spqORKae(ES5oEprVxulp(b'\xec\x10^'), '\144' + chr(0b1100101) + '\x63' + chr(111) + '\144' + chr(1491 - 1390))(chr(2745 - 2628) + chr(0b100111 + 0o115) + chr(0b1010100 + 0o22) + chr(0b101101) + '\070')), help=roI3spqORKae(ES5oEprVxulp(b'\xe42n\xde\x12\x80\xc2F\xea\x89\x13\xf7\xb0\xd9\xe0\xf1\x11\xfb\x038\xb2Gn\xd3\xbe\xbe\x99\x80Z\xee\xd8j\x85:ud^\xb9r~\x8d?b\xc5\x0b\x84\xd5\\\xe6\x80\x1f\xa1\xa1\xc4\xfa\xf9\x0b\xe6L7\xedG(\x96\xb9\xe0\xde\x94Y\xef\x96\x7f\x9an<-m\xa8}t\xdd0o\x8dD\x8a\xceA\xba\xc5\x00\xb9\xe5\x93\xa9\xd3_\xc8\ry\x94\x14?\xd3\xf8\xe2\xd9\xd5C\xe4\x96w\x98~{nI\xa4y9\xc81z\xc3\x1d\xc9\xc7_\xe7\x80_\xe4\xa2\x8b\xef\xff\r\xafJ7\xb2\x02(\x87\xb6\xa3\x90\x86\x17\xe4\xc4>\x92\x7f~h\\\xb9sw\xder'), chr(2636 - 2536) + chr(0b100111 + 0o76) + '\143' + chr(0b100100 + 0o113) + chr(0b1100100) + '\145')(chr(0b1101 + 0o150) + '\164' + chr(2447 - 2345) + chr(0b101101) + chr(0b111000)))
roI3spqORKae(XjosxPK5hJZk, roI3spqORKae(ES5oEprVxulp(b'\xcc8n\xe8\x05\x9b\xc1F\xe6\x80]\xf5'), chr(3768 - 3668) + '\x65' + chr(0b1010110 + 0o15) + '\157' + chr(100) + '\x65')(chr(117) + chr(0b1110100) + chr(9763 - 9661) + chr(0b100010 + 0o13) + chr(0b111000)))(roI3spqORKae(ES5oEprVxulp(b'\x80qm\xd2\n\x86\xcbV'), '\x64' + chr(0b1100101) + chr(9530 - 9431) + chr(111) + '\x64' + '\x65')(chr(6006 - 5889) + chr(6374 - 6258) + chr(0b111011 + 0o53) + chr(1880 - 1835) + '\x38'), type=N9zlRy29S1SS, help=roI3spqORKae(ES5oEprVxulp(b'\xfa4k\xc3D\x9b\xc3U\xee\x97V\xef\xb2\xce\xa9\xf1\x0c\xfcF4\xa3\x0b#\xd3\xa6\xa3\x8b\x87\x17\xfd\xd7l\x9f{|y\x08\xb3sv\xdf8c\xd9\x05\x9d\xc3@\xab\x84A\xe4\xf1\xde\xfa\xf9\x11\xe8\ry\x84\x1f;\x9e\xaf\xa0\x9b\x86\r\xab\x91v\x91++*\x04\xf0;^\xff\x1fb\x84\\\xce\x8a\x13\xe4\x97\x13\xa6\xbc\xc6\xb0\xb7Q\xafw1\xa8\x14z\x92\xad\xab\x8b\x98R\xe5\xc2>\x9fi2dO\xbesk\xc88*\xd1\x0b\x9b\x86~\xca\xa3\x13\xe7\xb8\xc7\xec\xe3S\xafP0\xaf\x04?\xd3\xba\xad\x9d\x9d\x17\xf9\xd9i\xd6s|nD\xa5x|\xde|~\xdf\x01\xc9\xd4V\xed\x80A\xe4\xbf\xc8\xec\xbe_\xc9L+\xe11\x19\xb5\xff\xaa\x97\x99R\xf8\x9a>\x82r{~\x08\xb9o9\xd8/o\xd3D\x80\xc0\x13\xf8\x95V\xe2\xb8\xcd\xe0\xf5\x1b\xa3\x038\xaf\x03z\x9c\xab\xa4\x9b\x87@\xe2\xc5{\xd6sa-O\xa5yj\xde9n\x97\x02\x9b\xc9^\xab\x91[\xe4\xf1\xc3\xec\xf1\x1b\xeaQw\xe1!5\x81\xff\xba\x9f\x87^\xea\xd8j\x85:a}M\xb3zp\xc88*\xd8\n\xc9\xd2[\xee\xc5P\xee\xbc\xc6\xe8\xfe\x1b\xe3J7\xa4G-\x9a\xab\xa4\xde\xd8\x1a\xfd\xd7l\x9f{|y\x04\xf0hq\xc4/*\xd8\x14\x9d\xcf\\\xe5\xc5Z\xf2\xf1\xd9\xec\xe1\n\xe6Q<\xa5I'), chr(5571 - 5471) + '\x65' + chr(0b1100011) + '\157' + chr(6945 - 6845) + chr(101))('\x75' + chr(0b1110100) + '\146' + chr(0b101 + 0o50) + '\x38'))
roI3spqORKae(XjosxPK5hJZk, roI3spqORKae(ES5oEprVxulp(b'\xcc8n\xe8\x05\x9b\xc1F\xe6\x80]\xf5'), chr(100) + chr(6477 - 6376) + chr(0b1100011) + chr(0b11011 + 0o124) + chr(5479 - 5379) + '\145')(chr(117) + '\164' + '\146' + chr(0b1010 + 0o43) + '\070'))(roI3spqORKae(ES5oEprVxulp(b'\x80qn\xd8\x13\x87\xca\\\xea\x81\x1e\xf3\xb4\xcd\xec\xe2\x1a\xe1@<\xec\x00?\x9d\xb0\xa1\x9b\xd8S\xea\xc2\x7f'), chr(100) + '\x65' + chr(99) + chr(0b10111 + 0o130) + '\x64' + chr(4264 - 4163))('\x75' + '\164' + '\146' + chr(606 - 561) + chr(0b11100 + 0o34)), action=roI3spqORKae(ES5oEprVxulp(b'\xde(e\xc5\x01\xb6\xd2A\xfe\x80'), chr(0b1100100) + '\x65' + '\143' + '\x6f' + '\144' + chr(101))(chr(117) + chr(116) + chr(7619 - 7517) + '\055' + '\070'), default=nzTpIcepk0o8('\x30' + '\157' + '\x30', 0b1000), help=roI3spqORKae(ES5oEprVxulp(b'\xec)~\xd8\t\x88\xd2Z\xe8\x84_\xed\xa8\x8b\xed\xff\x08\xe1O6\xa0\x03z\x94\xba\xa2\x91\x98R\xab\xc4{\x90\x7f`hF\xb3y9\xc9=~\xd6D\x9b\xc3B\xfe\x8cA\xe4\xb5\x8b\xef\xff\r\xafB7\xaf\x08.\x92\xab\xa5\x91\x9b\x17\xfe\xc5w\x98}2]Q\x95rj\xc81h\xdbJ\xc9\xe9G\xe3\x80A\xf6\xb8\xd8\xec\xb0\x06\xe0Vy\xac\x12)\x87\xff\xaa\x97\x87D\xff\x96l\x83t2*X\xa9yw\xde9g\xd5\x08\xc9\xcf]\xf8\x91R\xed\xbd\x8c\xa9\xf6\x10\xfd\x03-\xa9\x02z\x81\xba\xa0\x9b\x94D\xee\x99m\x86\x7fqdM\xa3<z\xc2.x\xd2\x17\x99\xc9]\xef\x8c]\xe6\xf1\xdf\xe6\xb0\x0b\xe7Fy\xa6\x024\x9c\xb2\xa9\xde\x80D\xee\xd2>\x9ft2tG\xa5n9\xfb\x1fL\x99'), chr(1635 - 1535) + chr(5739 - 5638) + '\143' + chr(0b1101111) + chr(100) + chr(0b1100101))(chr(117) + '\164' + chr(0b1100110) + chr(0b100011 + 0o12) + chr(56)))
roI3spqORKae(XjosxPK5hJZk, roI3spqORKae(ES5oEprVxulp(b'\xcc8n\xe8\x05\x9b\xc1F\xe6\x80]\xf5'), chr(0b1010110 + 0o16) + chr(0b1100101) + '\x63' + chr(0b1011100 + 0o23) + chr(100) + '\145')('\165' + chr(0b1101101 + 0o7) + '\146' + chr(58 - 13) + '\070'))(roI3spqORKae(ES5oEprVxulp(b'\x80q`\xc4\x0b\x87\x8bE\xea\x97Z\xe0\xbf\xdf\xfa'), chr(100) + chr(101) + chr(0b1100011) + '\157' + chr(9180 - 9080) + '\x65')(chr(0b1001111 + 0o46) + '\x74' + '\x66' + '\055' + chr(0b111000)), default=[], action=roI3spqORKae(ES5oEprVxulp(b'\xcc,z\xd2\n\x8d'), chr(367 - 267) + '\145' + chr(0b1100011) + '\x6f' + chr(0b110001 + 0o63) + '\145')('\165' + chr(116) + '\x66' + chr(1264 - 1219) + '\070'), help=roI3spqORKae(ES5oEprVxulp(b'\xfd=~\xdfD\x9d\xc9\x13\xdd\x84A\xe2\xbe\xcf\xec\xbe)\xeeQ0\xa0\t.\xb0\xb0\xa0\x92\x90T\xff\xdfq\x98:}oB\xb5\x7fm\x8d/o\xc5\r\x88\xcaZ\xf1\x80W\xa1\xb0\xd8\xa9\xf1_\xc5p\x16\x8fG<\x9a\xb3\xa9\xd0'), chr(0b1001101 + 0o27) + chr(101) + '\143' + '\157' + chr(7685 - 7585) + chr(9667 - 9566))('\165' + chr(116) + chr(0b1100110) + chr(1557 - 1512) + '\070'))
return XjosxPK5hJZk |
openvax/varcode | varcode/effects/mutate.py | insert_before | def insert_before(sequence, offset, new_residues):
"""Mutate the given sequence by inserting the string `new_residues` before
`offset`.
Parameters
----------
sequence : sequence
String of amino acids or DNA bases
offset : int
Base 0 offset from start of sequence, after which we should insert
`new_residues`.
new_residues : sequence
"""
assert 0 < offset <= len(sequence), \
"Invalid position %d for sequence of length %d" % (
offset, len(sequence))
prefix = sequence[:offset]
suffix = sequence[offset:]
return prefix + new_residues + suffix | python | def insert_before(sequence, offset, new_residues):
"""Mutate the given sequence by inserting the string `new_residues` before
`offset`.
Parameters
----------
sequence : sequence
String of amino acids or DNA bases
offset : int
Base 0 offset from start of sequence, after which we should insert
`new_residues`.
new_residues : sequence
"""
assert 0 < offset <= len(sequence), \
"Invalid position %d for sequence of length %d" % (
offset, len(sequence))
prefix = sequence[:offset]
suffix = sequence[offset:]
return prefix + new_residues + suffix | [
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String of amino acids or DNA bases
offset : int
Base 0 offset from start of sequence, after which we should insert
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ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8('\060' + '\157' + chr(0b110010) + chr(0b110101) + '\x32', ord("\x08")), nzTpIcepk0o8(chr(0b11111 + 0o21) + '\157' + chr(49) + '\x30' + chr(0b110110), 0o10), nzTpIcepk0o8(chr(48) + '\157' + '\061' + chr(52) + chr(0b110011 + 0o0), 0o10), nzTpIcepk0o8(chr(0b100001 + 0o17) + chr(0b1101111) + chr(0b110110) + '\065', 0o10), nzTpIcepk0o8('\060' + '\157' + chr(0b10010 + 0o42) + '\067', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b1010 + 0o50) + chr(0b1001 + 0o52) + chr(2224 - 2175), 0o10), nzTpIcepk0o8(chr(969 - 921) + chr(0b11111 + 0o120) + chr(49) + chr(0b100101 + 0o20) + chr(48), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110001) + '\063' + chr(0b101100 + 0o12), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(50) + chr(50) + '\060', ord("\x08")), nzTpIcepk0o8(chr(0b101001 + 0o7) + '\157' + chr(0b101001 + 0o10) + '\065', ord("\x08")), nzTpIcepk0o8('\x30' + chr(2339 - 2228) + chr(0b10110 + 0o35) + chr(0b1100 + 0o44) + chr(0b101110 + 0o4), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(991 - 942) + chr(2310 - 2257) + '\x36', 0b1000), nzTpIcepk0o8(chr(0b11111 + 0o21) + chr(0b1011000 + 0o27) + '\062' + chr(50), 0o10), nzTpIcepk0o8(chr(0b100001 + 0o17) + chr(0b1101111) + chr(0b110110) + chr(0b110010), 30879 - 30871), nzTpIcepk0o8(chr(48) + chr(7087 - 6976) + '\062' + '\x30' + chr(49), 0o10), nzTpIcepk0o8(chr(996 - 948) + chr(111) + chr(0b110110) + chr(0b110000), 0b1000), nzTpIcepk0o8('\060' + chr(0b110111 + 0o70) + '\062' + '\x31' + '\060', 65110 - 65102), nzTpIcepk0o8('\060' + '\x6f' + chr(49) + '\061' + chr(0b110110), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(49) + '\x33' + '\x35', 0b1000), nzTpIcepk0o8('\x30' + chr(2889 - 2778) + '\x31' + chr(0b101110 + 0o5) + chr(52), 56565 - 56557), nzTpIcepk0o8('\x30' + chr(8506 - 8395) + chr(0b10110 + 0o35) + chr(1519 - 1466) + chr(50), 20461 - 20453), nzTpIcepk0o8('\x30' + '\x6f' + chr(1520 - 1470) + chr(2361 - 2310), ord("\x08")), nzTpIcepk0o8(chr(0b10110 + 0o32) + chr(0b101100 + 0o103) + chr(51) + '\x36' + '\x33', ord("\x08")), nzTpIcepk0o8(chr(1086 - 1038) + chr(10677 - 10566) + chr(0b110011 + 0o1) + '\x36', ord("\x08")), nzTpIcepk0o8(chr(1006 - 958) + chr(1428 - 1317) + chr(1027 - 976) + chr(0b10001 + 0o40), 0b1000), nzTpIcepk0o8(chr(1001 - 953) + '\157' + chr(0b110011) + '\065', 0b1000), nzTpIcepk0o8('\x30' + chr(0b1000010 + 0o55) + chr(49) + chr(0b11111 + 0o22) + chr(544 - 493), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b0 + 0o62) + chr(48) + chr(52), 0o10), nzTpIcepk0o8(chr(48) + '\157' + '\x31' + chr(0b110001) + chr(346 - 296), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1000 + 0o147) + chr(373 - 322) + chr(0b110111), 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(494 - 443) + chr(2455 - 2401) + '\062', 24041 - 24033), nzTpIcepk0o8(chr(0b10100 + 0o34) + '\157' + '\x32' + chr(0b110100) + chr(0b101001 + 0o14), 58101 - 58093), nzTpIcepk0o8('\x30' + chr(0b11 + 0o154) + '\062' + chr(0b110101) + '\x37', 33278 - 33270), nzTpIcepk0o8(chr(48) + chr(5089 - 4978) + chr(2010 - 1961) + chr(0b101001 + 0o16) + chr(49), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1000110 + 0o51) + chr(0b110011) + chr(0b111 + 0o57) + chr(0b110111), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(172 - 120), 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(286 - 237) + chr(2226 - 2176) + '\x36', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x32' + chr(0b110010) + chr(544 - 491), 32302 - 32294), nzTpIcepk0o8(chr(0b11 + 0o55) + chr(3008 - 2897) + '\x33' + '\062' + '\x35', 35056 - 35048), nzTpIcepk0o8(chr(48) + '\x6f' + chr(53) + chr(0b110101), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + '\x6f' + chr(53) + chr(2003 - 1955), 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x84'), chr(100) + chr(0b1010110 + 0o17) + chr(0b1100011) + '\157' + chr(0b0 + 0o144) + chr(101))(chr(117) + chr(116) + chr(102) + chr(0b11010 + 0o23) + chr(389 - 333)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def IKKUjvYHqetj(AaFeo0lw34C3, GuX46MBAOnaQ, waKLMCBmTkiL):
assert nzTpIcepk0o8('\x30' + chr(4368 - 4257) + '\060', ord("\x08")) < GuX46MBAOnaQ <= ftfygxgFas5X(AaFeo0lw34C3), roI3spqORKae(ES5oEprVxulp(b'\xe3(\x15TK\xf0\x0c~\xe0b\xb1\x07f[\xee^\xa8k9|\x8c|\x81\x06jx:\xf1/q\x91\xc0\x8f\x16\x91$:\xf0\xbbJ\xde.C\x10C'), chr(7098 - 6998) + chr(0b110011 + 0o62) + chr(0b10000 + 0o123) + chr(0b1101111) + chr(0b1100100) + chr(101))(chr(0b1100101 + 0o20) + chr(116) + chr(0b101101 + 0o71) + '\055' + '\070') % (GuX46MBAOnaQ, ftfygxgFas5X(AaFeo0lw34C3))
ZJwZgaHE72Po = AaFeo0lw34C3[:GuX46MBAOnaQ]
biRCFepsLie5 = AaFeo0lw34C3[GuX46MBAOnaQ:]
return ZJwZgaHE72Po + waKLMCBmTkiL + biRCFepsLie5 |
openvax/varcode | varcode/effects/mutate.py | insert_after | def insert_after(sequence, offset, new_residues):
"""Mutate the given sequence by inserting the string `new_residues` after
`offset`.
Parameters
----------
sequence : sequence
String of amino acids or DNA bases
offset : int
Base 0 offset from start of sequence, after which we should insert
`new_residues`.
new_residues : sequence
"""
assert 0 <= offset < len(sequence), \
"Invalid position %d for sequence of length %d" % (
offset, len(sequence))
prefix = sequence[:offset + 1]
suffix = sequence[offset + 1:]
return prefix + new_residues + suffix | python | def insert_after(sequence, offset, new_residues):
"""Mutate the given sequence by inserting the string `new_residues` after
`offset`.
Parameters
----------
sequence : sequence
String of amino acids or DNA bases
offset : int
Base 0 offset from start of sequence, after which we should insert
`new_residues`.
new_residues : sequence
"""
assert 0 <= offset < len(sequence), \
"Invalid position %d for sequence of length %d" % (
offset, len(sequence))
prefix = sequence[:offset + 1]
suffix = sequence[offset + 1:]
return prefix + new_residues + suffix | [
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sequence : sequence
String of amino acids or DNA bases
offset : int
Base 0 offset from start of sequence, after which we should insert
`new_residues`.
new_residues : sequence | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/mutate.py#L40-L60 | train | Mutate the given sequence by inserting new_residues after offset. | 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(12042 - 11931) + '\067' + '\x34', 64875 - 64867), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110001) + chr(55) + chr(49), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110010) + chr(0b1100 + 0o51) + '\063', ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + '\061' + chr(0b101101 + 0o6) + chr(2274 - 2220), 10495 - 10487), nzTpIcepk0o8(chr(48) + chr(0b10101 + 0o132) + chr(0b110011) + chr(1548 - 1499) + '\066', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(49) + chr(0b110111) + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(0b110 + 0o52) + chr(0b101001 + 0o106) + '\062' + chr(55) + chr(0b110101), 23604 - 23596), nzTpIcepk0o8('\060' + chr(11031 - 10920) + '\x31' + chr(0b101111 + 0o10) + chr(2352 - 2303), 8), nzTpIcepk0o8(chr(0b11010 + 0o26) + '\x6f' + chr(0b110001) + chr(1677 - 1626), 0o10), nzTpIcepk0o8(chr(0b101010 + 0o6) + chr(7161 - 7050) + chr(0b10011 + 0o36) + chr(53) + chr(1750 - 1699), 61583 - 61575), nzTpIcepk0o8('\060' + '\157' + chr(54) + '\x34', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110001) + '\x35' + '\065', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(974 - 924) + chr(52) + chr(0b110101), 16229 - 16221), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110001) + chr(50) + chr(2261 - 2208), 0b1000), nzTpIcepk0o8('\x30' + '\157' + '\063' + chr(0b110110) + '\x34', 0o10), nzTpIcepk0o8(chr(1669 - 1621) + chr(5749 - 5638) + '\062' + chr(990 - 940) + '\x37', 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(456 - 405) + '\064' + '\x35', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b101010 + 0o11) + '\x33' + chr(0b110100), 0o10), nzTpIcepk0o8(chr(0b110 + 0o52) + '\x6f' + chr(54) + chr(326 - 271), 0o10), nzTpIcepk0o8(chr(0b1100 + 0o44) + chr(111) + chr(0b110010) + '\x34' + chr(0b100000 + 0o20), 0b1000), nzTpIcepk0o8(chr(1843 - 1795) + '\157' + chr(1043 - 994) + chr(0b1010 + 0o46) + chr(54), ord("\x08")), nzTpIcepk0o8(chr(1194 - 1146) + '\x6f' + '\x33' + '\065' + chr(1104 - 1050), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b100001 + 0o20) + '\x30' + chr(0b10 + 0o60), ord("\x08")), nzTpIcepk0o8(chr(0b100111 + 0o11) + chr(0b1101111) + chr(0b1111 + 0o43) + '\067', 0b1000), nzTpIcepk0o8(chr(1138 - 1090) + chr(3827 - 3716) + chr(49) + chr(1934 - 1886) + chr(0b101100 + 0o11), 56037 - 56029), nzTpIcepk0o8(chr(48) + chr(11111 - 11000) + chr(2378 - 2326) + chr(1397 - 1348), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x32' + '\x36' + chr(54), ord("\x08")), nzTpIcepk0o8(chr(0b101110 + 0o2) + chr(6549 - 6438) + '\x31' + '\x31' + '\067', 0b1000), nzTpIcepk0o8('\060' + chr(0b10101 + 0o132) + chr(51 - 2) + chr(778 - 730) + chr(0b110011), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(51) + chr(1415 - 1364) + '\060', 7805 - 7797), nzTpIcepk0o8('\x30' + chr(1317 - 1206) + chr(49) + '\063', 8), nzTpIcepk0o8('\x30' + '\157' + chr(1882 - 1832) + chr(0b101100 + 0o12) + chr(2202 - 2148), 8), nzTpIcepk0o8(chr(0b110000) + chr(0b101000 + 0o107) + '\061' + '\064', 4184 - 4176), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(61 - 10) + chr(49) + chr(0b110000), 0o10), nzTpIcepk0o8(chr(0b110000 + 0o0) + chr(0b1101111) + chr(0b110001) + chr(0b110111) + chr(0b110111), 8), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110011) + chr(0b110001) + chr(0b110001), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b110100 + 0o73) + chr(1484 - 1434) + '\061' + chr(52), 0o10), nzTpIcepk0o8(chr(0b100 + 0o54) + '\x6f' + chr(0b110010) + chr(0b110101) + chr(52), 57 - 49), nzTpIcepk0o8(chr(48) + chr(111) + '\x31' + '\060' + '\x37', 20012 - 20004), nzTpIcepk0o8(chr(0b10100 + 0o34) + chr(0b1001101 + 0o42) + '\063' + '\064', 1481 - 1473)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b100010 + 0o16) + '\x6f' + '\x35' + chr(48), 49152 - 49144)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x12'), chr(0b100110 + 0o76) + chr(101) + chr(454 - 355) + chr(0b1000010 + 0o55) + '\x64' + chr(5976 - 5875))('\165' + chr(11290 - 11174) + '\x66' + chr(0b101101) + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def xmv7b9CZti7i(AaFeo0lw34C3, GuX46MBAOnaQ, waKLMCBmTkiL):
assert nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b11111 + 0o21), 0o10) <= GuX46MBAOnaQ < ftfygxgFas5X(AaFeo0lw34C3), roI3spqORKae(ES5oEprVxulp(b'u\x17\xdd?\xa2\x16\xd9Y{\x04G\x04\xd1<\x9b\xf9\xc5\xf9S\x80 \x81076D\xc7:&\xb6h\xd3,\xa7\x19\xe9\xe0\xc9){H\x11\x8b{\xaa'), '\x64' + '\x65' + '\143' + '\x6f' + '\x64' + chr(9374 - 9273))(chr(863 - 746) + '\x74' + chr(102) + '\x2d' + chr(0b111000)) % (GuX46MBAOnaQ, ftfygxgFas5X(AaFeo0lw34C3))
ZJwZgaHE72Po = AaFeo0lw34C3[:GuX46MBAOnaQ + nzTpIcepk0o8(chr(48) + chr(0b1100011 + 0o14) + chr(0b110001), ord("\x08"))]
biRCFepsLie5 = AaFeo0lw34C3[GuX46MBAOnaQ + nzTpIcepk0o8(chr(48) + chr(0b11111 + 0o120) + chr(49), 8):]
return ZJwZgaHE72Po + waKLMCBmTkiL + biRCFepsLie5 |
openvax/varcode | varcode/effects/mutate.py | substitute | def substitute(sequence, offset, ref, alt):
"""Mutate a sequence by substituting given `alt` at instead of `ref` at the
given `position`.
Parameters
----------
sequence : sequence
String of amino acids or DNA bases
offset : int
Base 0 offset from start of `sequence`
ref : sequence or str
What do we expect to find at the position?
alt : sequence or str
Alternate sequence to insert
"""
n_ref = len(ref)
sequence_ref = sequence[offset:offset + n_ref]
assert str(sequence_ref) == str(ref), \
"Reference %s at offset %d != expected reference %s" % \
(sequence_ref, offset, ref)
prefix = sequence[:offset]
suffix = sequence[offset + n_ref:]
return prefix + alt + suffix | python | def substitute(sequence, offset, ref, alt):
"""Mutate a sequence by substituting given `alt` at instead of `ref` at the
given `position`.
Parameters
----------
sequence : sequence
String of amino acids or DNA bases
offset : int
Base 0 offset from start of `sequence`
ref : sequence or str
What do we expect to find at the position?
alt : sequence or str
Alternate sequence to insert
"""
n_ref = len(ref)
sequence_ref = sequence[offset:offset + n_ref]
assert str(sequence_ref) == str(ref), \
"Reference %s at offset %d != expected reference %s" % \
(sequence_ref, offset, ref)
prefix = sequence[:offset]
suffix = sequence[offset + n_ref:]
return prefix + alt + suffix | [
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sequence : sequence
String of amino acids or DNA bases
offset : int
Base 0 offset from start of `sequence`
ref : sequence or str
What do we expect to find at the position?
alt : sequence or str
Alternate sequence to insert | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/mutate.py#L62-L87 | train | Mutate a sequence by substituting given alt at instead of ref at the given position. | 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(0b110100), 12070 - 12062), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(1392 - 1344) + chr(111) + '\061' + chr(48), ord("\x08")), nzTpIcepk0o8('\060' + chr(7834 - 7723) + '\063' + '\060' + '\064', 0o10), nzTpIcepk0o8(chr(0b1111 + 0o41) + '\x6f' + chr(0b100000 + 0o21) + '\061' + chr(55), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b11011 + 0o124) + chr(50) + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b0 + 0o63) + chr(0b110100) + '\064', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x32' + '\x34', 21388 - 21380), nzTpIcepk0o8(chr(678 - 630) + '\x6f' + chr(2195 - 2145) + '\060' + chr(0b1011 + 0o50), 3778 - 3770), nzTpIcepk0o8(chr(687 - 639) + chr(0b1101111) + chr(2349 - 2300) + '\x34' + chr(0b101100 + 0o6), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(50) + chr(0b110110) + chr(0b101110 + 0o6), 53937 - 53929), nzTpIcepk0o8(chr(1643 - 1595) + chr(0b1101111) + chr(976 - 926) + '\x30' + '\060', 1908 - 1900), nzTpIcepk0o8(chr(0b110000) + chr(11640 - 11529) + chr(1670 - 1620) + chr(49) + chr(0b110001 + 0o2), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110101) + chr(49), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110001) + chr(277 - 229) + '\x37', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(55) + chr(0b101 + 0o55), 0o10), nzTpIcepk0o8(chr(0b101100 + 0o4) + '\157' + chr(2499 - 2447), 8), nzTpIcepk0o8('\x30' + chr(111) + chr(1118 - 1067) + chr(49) + '\x32', 18575 - 18567), nzTpIcepk0o8(chr(1412 - 1364) + chr(0b1101111) + chr(0b11 + 0o57) + '\064' + '\x30', 0b1000), nzTpIcepk0o8('\060' + chr(8255 - 8144) + '\062' + chr(0b10100 + 0o41), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(55) + '\x32', 8), nzTpIcepk0o8(chr(0b101100 + 0o4) + '\157' + '\061' + '\064' + '\066', 0b1000), nzTpIcepk0o8('\060' + chr(3032 - 2921) + chr(49) + chr(0b100000 + 0o24) + '\067', 60676 - 60668), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(49) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(2504 - 2393) + chr(0b110101) + chr(0b11001 + 0o34), 0o10), nzTpIcepk0o8(chr(0b10 + 0o56) + chr(111) + chr(1881 - 1830) + chr(521 - 466) + '\066', 0o10), nzTpIcepk0o8('\060' + '\x6f' + '\x32' + chr(0b1110 + 0o43) + chr(0b101011 + 0o14), 35850 - 35842), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\061' + '\x33' + '\061', 50338 - 50330), nzTpIcepk0o8(chr(180 - 132) + chr(111) + chr(0b100110 + 0o15) + '\061', 35433 - 35425), nzTpIcepk0o8('\x30' + '\157' + chr(0b110011) + chr(51) + chr(49), 0o10), nzTpIcepk0o8(chr(472 - 424) + '\157' + chr(2086 - 2037) + '\064' + chr(49), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\062' + chr(55), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110001) + '\x33' + chr(52), 36531 - 36523), nzTpIcepk0o8('\x30' + chr(0b1011111 + 0o20) + chr(0b0 + 0o61), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(826 - 776) + chr(0b101010 + 0o15) + '\x30', 0o10), nzTpIcepk0o8(chr(2206 - 2158) + chr(0b1101111) + '\x31' + chr(0b10000 + 0o41) + chr(0b1000 + 0o50), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(1733 - 1682) + chr(0b100111 + 0o17) + chr(1125 - 1070), 0b1000), nzTpIcepk0o8(chr(0b101010 + 0o6) + chr(111) + '\061' + chr(804 - 753) + chr(0b110000), 0o10), nzTpIcepk0o8('\060' + '\x6f' + '\067' + chr(0b110101), 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(50) + '\x37' + chr(0b110 + 0o52), 8)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x35' + '\x30', 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'*'), chr(0b1100100) + chr(0b1100101) + chr(3934 - 3835) + chr(0b1101111) + chr(3655 - 3555) + '\x65')('\x75' + chr(5252 - 5136) + '\x66' + '\x2d' + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def fDy17HzkiUYE(AaFeo0lw34C3, GuX46MBAOnaQ, CmNScfxJ1Uih, YVIVvpvk_rzo):
H0vRGyprMf_l = ftfygxgFas5X(CmNScfxJ1Uih)
aM0U6S2swQbk = AaFeo0lw34C3[GuX46MBAOnaQ:GuX46MBAOnaQ + H0vRGyprMf_l]
assert N9zlRy29S1SS(aM0U6S2swQbk) == N9zlRy29S1SS(CmNScfxJ1Uih), roI3spqORKae(ES5oEprVxulp(b'Vfn\xa1=w\x8aw\xe6B\x91\xf3\xabH3\x1ak\xac\xc6f_\x12G)I\xde\xaed9\xbc\x19g9b\xcc-\x93xO\xddbfz\xa1!q\x814\xa6\x11'), '\144' + chr(0b110110 + 0o57) + '\x63' + chr(0b101101 + 0o102) + '\x64' + chr(0b1100101))(chr(403 - 286) + chr(0b11001 + 0o133) + chr(0b1100110) + chr(45) + chr(0b111000)) % (aM0U6S2swQbk, GuX46MBAOnaQ, CmNScfxJ1Uih)
ZJwZgaHE72Po = AaFeo0lw34C3[:GuX46MBAOnaQ]
biRCFepsLie5 = AaFeo0lw34C3[GuX46MBAOnaQ + H0vRGyprMf_l:]
return ZJwZgaHE72Po + YVIVvpvk_rzo + biRCFepsLie5 |
openvax/varcode | varcode/reference.py | _most_recent_assembly | def _most_recent_assembly(assembly_names):
"""
Given list of (in this case, matched) assemblies, identify the most recent
("recency" here is determined by sorting based on the numeric element of the assembly name)
"""
match_recency = [
int(re.search('\d+', assembly_name).group())
for assembly_name in assembly_names
]
most_recent = [
x for (y, x) in sorted(zip(match_recency, assembly_names), reverse=True)][0]
return most_recent | python | def _most_recent_assembly(assembly_names):
"""
Given list of (in this case, matched) assemblies, identify the most recent
("recency" here is determined by sorting based on the numeric element of the assembly name)
"""
match_recency = [
int(re.search('\d+', assembly_name).group())
for assembly_name in assembly_names
]
most_recent = [
x for (y, x) in sorted(zip(match_recency, assembly_names), reverse=True)][0]
return most_recent | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/reference.py#L45-L56 | train | Given a list of assemblies identify the most recent one | 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(3115 - 3004) + chr(902 - 851) + chr(0b110000 + 0o0), 40689 - 40681), nzTpIcepk0o8(chr(0b101 + 0o53) + chr(0b1001 + 0o146) + chr(0b10011 + 0o40) + '\063' + '\x30', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x37' + '\061', 16049 - 16041), nzTpIcepk0o8(chr(48) + chr(0b110001 + 0o76) + chr(0b0 + 0o63) + chr(0b1101 + 0o43) + '\066', 46685 - 46677), nzTpIcepk0o8(chr(2246 - 2198) + '\157' + chr(351 - 300), ord("\x08")), nzTpIcepk0o8(chr(948 - 900) + '\157' + chr(0b10100 + 0o37) + chr(0b11101 + 0o24) + chr(54), 0b1000), nzTpIcepk0o8(chr(1715 - 1667) + '\157' + chr(54) + chr(52), 8859 - 8851), nzTpIcepk0o8(chr(0b101010 + 0o6) + '\x6f' + chr(0b10110 + 0o35) + chr(52) + chr(1115 - 1065), 44747 - 44739), nzTpIcepk0o8(chr(0b100011 + 0o15) + chr(0b1101111) + '\063' + '\x31' + chr(48), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + '\064' + '\x35', 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(0b1111 + 0o42) + chr(48) + chr(0b10 + 0o65), 4632 - 4624), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(1064 - 1014) + '\x33' + chr(2045 - 1997), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\061' + '\063' + '\x32', 36216 - 36208), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b1000 + 0o51) + chr(0b110010 + 0o3) + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(0b101101 + 0o3) + '\157' + '\061' + '\060' + '\063', 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(0b110001) + chr(53) + '\067', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b100011 + 0o114) + '\063' + chr(50) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(50) + '\x33' + '\x31', 21685 - 21677), nzTpIcepk0o8(chr(0b110000) + chr(4887 - 4776) + chr(0b11000 + 0o33), 8), nzTpIcepk0o8(chr(0b110000) + chr(7141 - 7030) + chr(0b110010) + '\x36' + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(2083 - 2035) + chr(111) + '\061' + '\x33' + '\064', ord("\x08")), nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(0b1100101 + 0o12) + chr(1102 - 1054), 0o10), nzTpIcepk0o8('\060' + chr(5642 - 5531) + chr(0b100000 + 0o23) + chr(0b110010) + chr(1475 - 1427), 0b1000), nzTpIcepk0o8(chr(48) + chr(9371 - 9260) + chr(50) + chr(0b110100) + chr(542 - 491), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + '\063' + '\x37' + chr(48), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(1946 - 1896) + '\x30' + chr(941 - 889), 0o10), nzTpIcepk0o8(chr(1863 - 1815) + chr(1043 - 932) + chr(0b100010 + 0o20) + chr(0b110100) + chr(52), 57422 - 57414), nzTpIcepk0o8(chr(0b10011 + 0o35) + chr(0b1101111) + '\x32' + '\060' + '\060', 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(0b111 + 0o52) + chr(0b110000) + chr(0b110000), 0o10), nzTpIcepk0o8(chr(1853 - 1805) + chr(583 - 472) + '\062' + chr(0b101101 + 0o12) + '\x33', 0o10), nzTpIcepk0o8('\x30' + chr(0b111001 + 0o66) + chr(0b101110 + 0o5) + '\x35' + chr(495 - 446), 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110001) + chr(54) + chr(50), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(10768 - 10657) + '\061' + '\061' + chr(52), 28046 - 28038), nzTpIcepk0o8('\x30' + chr(111) + chr(49), 58821 - 58813), nzTpIcepk0o8(chr(770 - 722) + '\157' + chr(49) + chr(54) + chr(53), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x32' + chr(0b110 + 0o55) + chr(54), 45532 - 45524), nzTpIcepk0o8(chr(0b110000) + chr(0b101010 + 0o105) + chr(1907 - 1857) + chr(0b110 + 0o55) + '\x37', 33833 - 33825), nzTpIcepk0o8('\060' + '\157' + chr(0b10001 + 0o41) + chr(0b110110) + chr(0b110000), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(2751 - 2640) + chr(0b110010 + 0o0) + chr(1901 - 1847) + chr(54), 59501 - 59493), nzTpIcepk0o8(chr(2253 - 2205) + chr(0b1101111) + chr(0b10000 + 0o44) + '\x32', 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(507 - 459) + chr(5884 - 5773) + chr(0b110010 + 0o3) + '\060', ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'6'), chr(3320 - 3220) + '\145' + chr(7430 - 7331) + '\157' + '\x64' + chr(101))('\165' + chr(116) + chr(0b1100110) + '\x2d' + chr(0b110110 + 0o2)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def yGzmHabYckoP(QnRGBdRxmt66):
rkH8Qfr1ENyf = [nzTpIcepk0o8(aoTc4YA2bs2R.search(roI3spqORKae(ES5oEprVxulp(b'D\xbc\x12'), '\144' + chr(0b1100101) + chr(4112 - 4013) + chr(111) + chr(0b10011 + 0o121) + chr(0b1100101))('\x75' + '\x74' + '\146' + chr(1848 - 1803) + chr(56)), RrkXweFCNuih).F9lJ8RbIonqb()) for RrkXweFCNuih in QnRGBdRxmt66]
vsRa3pZslVc6 = [bI5jsQ9OkQtj for (Fi3yzxctM1zW, bI5jsQ9OkQtj) in V3OlOVg98A85(TxMFWa_Xzviv(rkH8Qfr1ENyf, QnRGBdRxmt66), reverse=nzTpIcepk0o8('\060' + chr(11293 - 11182) + chr(702 - 653), 8))][nzTpIcepk0o8('\060' + '\157' + '\060', 8)]
return vsRa3pZslVc6 |
openvax/varcode | varcode/reference.py | infer_reference_name | def infer_reference_name(reference_name_or_path):
"""
Given a string containing a reference name (such as a path to
that reference's FASTA file), return its canonical name
as used by Ensembl.
"""
# identify all cases where reference name or path matches candidate aliases
reference_file_name = os.path.basename(reference_name_or_path)
matches = {'file_name': list(), 'full_path': list()}
for assembly_name in reference_alias_dict.keys():
candidate_list = [assembly_name] + reference_alias_dict[assembly_name]
for candidate in candidate_list:
if candidate.lower() in reference_file_name.lower():
matches['file_name'].append(assembly_name)
elif candidate.lower() in reference_name_or_path.lower():
matches['full_path'].append(assembly_name)
# remove duplicate matches (happens due to overlapping aliases)
matches['file_name'] = list(set(matches['file_name']))
matches['full_path'] = list(set(matches['full_path']))
# given set of existing matches, choose one to return
# (first select based on file_name, then full path. If multiples, use most recent)
if len(matches['file_name']) == 1:
match = matches['file_name'][0]
elif len(matches['file_name']) > 1:
# separate logic for >1 vs 1 to give informative warning
match = _most_recent_assembly(matches['file_name'])
warn(
('More than one reference ({}) matches path in header ({}); '
'the most recent one ({}) was used.').format(
','.join(matches['file_name']), reference_file_name, match))
elif len(matches['full_path']) >= 1:
# combine full-path logic since warning is the same
match = _most_recent_assembly(matches['full_path'])
warn((
'Reference could not be matched against filename ({}); '
'using best match against full path ({}).').format(
reference_name_or_path, match))
else:
raise ValueError(
"Failed to infer genome assembly name for %s" % reference_name_or_path)
return match | python | def infer_reference_name(reference_name_or_path):
"""
Given a string containing a reference name (such as a path to
that reference's FASTA file), return its canonical name
as used by Ensembl.
"""
# identify all cases where reference name or path matches candidate aliases
reference_file_name = os.path.basename(reference_name_or_path)
matches = {'file_name': list(), 'full_path': list()}
for assembly_name in reference_alias_dict.keys():
candidate_list = [assembly_name] + reference_alias_dict[assembly_name]
for candidate in candidate_list:
if candidate.lower() in reference_file_name.lower():
matches['file_name'].append(assembly_name)
elif candidate.lower() in reference_name_or_path.lower():
matches['full_path'].append(assembly_name)
# remove duplicate matches (happens due to overlapping aliases)
matches['file_name'] = list(set(matches['file_name']))
matches['full_path'] = list(set(matches['full_path']))
# given set of existing matches, choose one to return
# (first select based on file_name, then full path. If multiples, use most recent)
if len(matches['file_name']) == 1:
match = matches['file_name'][0]
elif len(matches['file_name']) > 1:
# separate logic for >1 vs 1 to give informative warning
match = _most_recent_assembly(matches['file_name'])
warn(
('More than one reference ({}) matches path in header ({}); '
'the most recent one ({}) was used.').format(
','.join(matches['file_name']), reference_file_name, match))
elif len(matches['full_path']) >= 1:
# combine full-path logic since warning is the same
match = _most_recent_assembly(matches['full_path'])
warn((
'Reference could not be matched against filename ({}); '
'using best match against full path ({}).').format(
reference_name_or_path, match))
else:
raise ValueError(
"Failed to infer genome assembly name for %s" % reference_name_or_path)
return match | [
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"."
] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/reference.py#L59-L99 | train | Infer a canonical name from a string containing a reference name or 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(chr(0b110000) + '\157' + '\x33' + chr(53) + chr(0b11110 + 0o26), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x32' + chr(51) + '\x31', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(2522 - 2411) + chr(0b110001) + chr(0b110100) + chr(0b1011 + 0o51), 0o10), nzTpIcepk0o8(chr(48) + chr(1338 - 1227) + chr(0b110010) + chr(0b110100) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1001000 + 0o47) + chr(0b100011 + 0o17) + chr(50) + chr(2299 - 2249), 0b1000), nzTpIcepk0o8(chr(48) + chr(2003 - 1892) + '\065' + '\x35', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x31' + chr(2133 - 2082), 0o10), nzTpIcepk0o8(chr(1004 - 956) + '\157' + chr(0b110010) + '\x36' + chr(0b110111), 0o10), nzTpIcepk0o8(chr(0b11110 + 0o22) + '\157' + chr(263 - 212) + chr(55) + chr(1769 - 1717), 0b1000), nzTpIcepk0o8('\060' + chr(2742 - 2631) + '\x32' + '\064', 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(2023 - 1973) + chr(0b110011) + chr(52), 59005 - 58997), nzTpIcepk0o8(chr(0b11000 + 0o30) + '\157' + chr(0b101110 + 0o3) + chr(54) + '\063', 0b1000), nzTpIcepk0o8('\060' + chr(0b111010 + 0o65) + '\x33' + '\063' + chr(2380 - 2326), 32646 - 32638), nzTpIcepk0o8(chr(2105 - 2057) + '\157' + chr(0b110001) + '\x37', 0o10), nzTpIcepk0o8(chr(0b10 + 0o56) + chr(8559 - 8448) + chr(1204 - 1155) + chr(53) + '\x35', ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110001) + chr(0b110000) + '\063', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b100101 + 0o112) + chr(247 - 197) + '\x33' + chr(2308 - 2258), 4865 - 4857), nzTpIcepk0o8('\060' + chr(0b1000111 + 0o50) + '\x32' + chr(52) + chr(0b100001 + 0o21), 28602 - 28594), nzTpIcepk0o8('\060' + '\x6f' + '\x31' + chr(0b110111) + '\060', 0b1000), nzTpIcepk0o8('\060' + '\157' + '\062' + chr(0b11100 + 0o26) + chr(0b110010), 8), nzTpIcepk0o8('\060' + '\157' + chr(51) + '\x31' + chr(48), 0b1000), nzTpIcepk0o8(chr(0b100001 + 0o17) + chr(0b111000 + 0o67) + '\062' + chr(1804 - 1750) + '\x34', 52743 - 52735), nzTpIcepk0o8(chr(48) + '\157' + chr(0b111 + 0o52) + chr(0b110101) + chr(2845 - 2790), 4057 - 4049), nzTpIcepk0o8('\x30' + chr(1764 - 1653) + '\x33' + '\065', 0o10), nzTpIcepk0o8('\060' + '\157' + chr(50) + chr(52) + '\x31', ord("\x08")), nzTpIcepk0o8(chr(379 - 331) + chr(7638 - 7527) + chr(1072 - 1022) + '\065' + chr(846 - 794), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110011) + '\062' + '\x35', 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(2216 - 2167) + chr(609 - 557) + chr(0b10111 + 0o32), 34446 - 34438), nzTpIcepk0o8(chr(276 - 228) + chr(9242 - 9131) + chr(0b11010 + 0o30) + chr(0b110001 + 0o1) + '\067', 0b1000), nzTpIcepk0o8(chr(872 - 824) + '\x6f' + '\062' + '\062' + chr(0b110010), 8), nzTpIcepk0o8(chr(0b11111 + 0o21) + '\x6f' + chr(50) + '\062' + chr(0b10010 + 0o44), 60134 - 60126), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110001) + chr(135 - 87) + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(316 - 268) + '\x6f' + chr(0b110010) + chr(556 - 501) + chr(0b11011 + 0o34), 0b1000), nzTpIcepk0o8('\060' + '\157' + '\062' + chr(0b110011) + chr(0b110110), 53230 - 53222), nzTpIcepk0o8(chr(105 - 57) + '\157' + chr(51) + '\x35' + chr(0b110001), 0o10), nzTpIcepk0o8(chr(322 - 274) + chr(9223 - 9112) + chr(50) + chr(55) + chr(0b100001 + 0o17), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + '\x32' + chr(50) + chr(1438 - 1386), 37344 - 37336), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(1440 - 1390) + '\065' + '\x34', 8), nzTpIcepk0o8(chr(0b1000 + 0o50) + chr(0b1101111) + chr(531 - 482) + chr(604 - 556) + chr(53), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(0b11101 + 0o24) + chr(0b110111) + chr(0b0 + 0o64), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + chr(0b1010100 + 0o33) + chr(53) + chr(1269 - 1221), 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xc2'), chr(0b1011001 + 0o13) + chr(101) + chr(0b1100011) + '\157' + chr(6254 - 6154) + '\145')(chr(0b1110101) + chr(4877 - 4761) + '\x66' + chr(0b11100 + 0o21) + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def PBu2WjSw42ln(Az48BIxFQgN6):
C7IJ9n1M8oYo = aHUqKstZLeS6.path.pLvIyXSV7qW5(Az48BIxFQgN6)
ONopK8INb53O = {roI3spqORKae(ES5oEprVxulp(b'\x8a\xf0\x08\xc6\xcdCj\xda\x99'), chr(100) + chr(9604 - 9503) + chr(99) + '\157' + '\x64' + '\x65')(chr(3495 - 3378) + '\164' + '\x66' + chr(45) + '\x38'): H4NoA26ON7iG(), roI3spqORKae(ES5oEprVxulp(b'\x8a\xec\x08\xcf\xcd]j\xc3\x94'), chr(0b1100100) + '\145' + '\143' + chr(1497 - 1386) + chr(0b1001 + 0o133) + '\145')(chr(0b1110101) + '\164' + chr(0b1100110) + chr(45) + chr(2616 - 2560)): H4NoA26ON7iG()}
for RrkXweFCNuih in roI3spqORKae(SzvkPT8iBpGA, roI3spqORKae(ES5oEprVxulp(b'\x87\xfc\x1d\xd0'), chr(100) + chr(1755 - 1654) + chr(99) + chr(111) + chr(6704 - 6604) + chr(101))(chr(8063 - 7946) + '\164' + '\146' + chr(0b100110 + 0o7) + chr(0b111000)))():
a_ppiQQNPWZ2 = [RrkXweFCNuih] + SzvkPT8iBpGA[RrkXweFCNuih]
for IOfBQ_wyRXMv in a_ppiQQNPWZ2:
if roI3spqORKae(IOfBQ_wyRXMv, roI3spqORKae(ES5oEprVxulp(b'\xb4\xf7\\\xe6\xdczF\xed\x98]\xce\x07'), chr(0b1010011 + 0o21) + chr(101) + chr(0b0 + 0o143) + chr(111) + '\x64' + '\x65')(chr(117) + chr(530 - 414) + '\x66' + '\055' + chr(56)))() in roI3spqORKae(C7IJ9n1M8oYo, roI3spqORKae(ES5oEprVxulp(b'\xb4\xf7\\\xe6\xdczF\xed\x98]\xce\x07'), chr(3322 - 3222) + '\x65' + chr(0b1100011) + chr(0b1001101 + 0o42) + chr(0b110010 + 0o62) + '\x65')(chr(8599 - 8482) + chr(1113 - 997) + chr(9955 - 9853) + chr(1337 - 1292) + chr(56)))():
roI3spqORKae(ONopK8INb53O[roI3spqORKae(ES5oEprVxulp(b'\x8a\xf0\x08\xc6\xcdCj\xda\x99'), '\144' + chr(0b110010 + 0o63) + chr(0b1100011) + chr(0b1101111) + '\144' + chr(0b0 + 0o145))(chr(0b1001110 + 0o47) + chr(0b101011 + 0o111) + chr(0b110100 + 0o62) + chr(71 - 26) + chr(929 - 873))], roI3spqORKae(ES5oEprVxulp(b'\xa4\xcd7\x97\xeaJL\xd8\x96{\xc9F'), chr(1789 - 1689) + chr(0b1001101 + 0o30) + '\x63' + chr(0b110100 + 0o73) + '\x64' + chr(0b1100101))(chr(0b1110101) + chr(0b1110100) + '\146' + chr(0b101101) + chr(0b1 + 0o67)))(RrkXweFCNuih)
elif roI3spqORKae(IOfBQ_wyRXMv, roI3spqORKae(ES5oEprVxulp(b'\xb4\xf7\\\xe6\xdczF\xed\x98]\xce\x07'), chr(7507 - 7407) + chr(7584 - 7483) + chr(0b1100011) + '\157' + '\x64' + chr(0b100001 + 0o104))('\165' + chr(0b111011 + 0o71) + '\146' + chr(0b1101 + 0o40) + chr(2539 - 2483)))() in roI3spqORKae(Az48BIxFQgN6, roI3spqORKae(ES5oEprVxulp(b'\xb4\xf7\\\xe6\xdczF\xed\x98]\xce\x07'), '\144' + '\x65' + chr(2083 - 1984) + chr(0b1101111) + '\x64' + chr(0b1001000 + 0o35))(chr(0b1110101) + chr(0b1110100) + '\146' + chr(45) + chr(0b100 + 0o64)))():
roI3spqORKae(ONopK8INb53O[roI3spqORKae(ES5oEprVxulp(b'\x8a\xec\x08\xcf\xcd]j\xc3\x94'), chr(3323 - 3223) + chr(8730 - 8629) + chr(99) + '\157' + chr(0b10001 + 0o123) + '\x65')(chr(117) + chr(0b100101 + 0o117) + chr(9272 - 9170) + '\x2d' + chr(0b110100 + 0o4))], roI3spqORKae(ES5oEprVxulp(b'\xa4\xcd7\x97\xeaJL\xd8\x96{\xc9F'), chr(0b1100100) + chr(4654 - 4553) + chr(99) + chr(111) + '\x64' + chr(0b1100101))(chr(10285 - 10168) + chr(116) + chr(0b101110 + 0o70) + chr(1099 - 1054) + chr(0b111000)))(RrkXweFCNuih)
ONopK8INb53O[roI3spqORKae(ES5oEprVxulp(b'\x8a\xf0\x08\xc6\xcdCj\xda\x99'), '\144' + chr(0b1100101) + chr(0b1100011) + chr(0b100110 + 0o111) + chr(0b1001110 + 0o26) + '\x65')('\x75' + '\164' + chr(102) + chr(0b101101) + chr(1655 - 1599))] = H4NoA26ON7iG(Bvi71nNyvlqO(ONopK8INb53O[roI3spqORKae(ES5oEprVxulp(b'\x8a\xf0\x08\xc6\xcdCj\xda\x99'), '\x64' + chr(9553 - 9452) + '\143' + chr(0b1101111) + '\144' + chr(0b1100101))(chr(2860 - 2743) + '\x74' + '\x66' + chr(132 - 87) + chr(0b111000))]))
ONopK8INb53O[roI3spqORKae(ES5oEprVxulp(b'\x8a\xec\x08\xcf\xcd]j\xc3\x94'), chr(100) + chr(0b1000000 + 0o45) + chr(0b1100011) + '\157' + chr(0b1100100) + chr(0b100011 + 0o102))('\x75' + '\x74' + '\146' + '\055' + chr(0b0 + 0o70))] = H4NoA26ON7iG(Bvi71nNyvlqO(ONopK8INb53O[roI3spqORKae(ES5oEprVxulp(b'\x8a\xec\x08\xcf\xcd]j\xc3\x94'), chr(0b1100100) + chr(5524 - 5423) + chr(0b1100011) + chr(0b1000011 + 0o54) + chr(1543 - 1443) + chr(101))(chr(1265 - 1148) + chr(0b1110100) + '\146' + '\x2d' + chr(56))]))
if ftfygxgFas5X(ONopK8INb53O[roI3spqORKae(ES5oEprVxulp(b'\x8a\xf0\x08\xc6\xcdCj\xda\x99'), chr(0b1100100) + chr(0b1100101) + chr(99) + chr(111) + chr(0b10111 + 0o115) + chr(101))(chr(117) + chr(116) + chr(0b1001 + 0o135) + chr(0b100000 + 0o15) + chr(0b111000))]) == nzTpIcepk0o8(chr(48) + '\x6f' + chr(49), ord("\x08")):
hk9OijmiC_zA = ONopK8INb53O[roI3spqORKae(ES5oEprVxulp(b'\x8a\xf0\x08\xc6\xcdCj\xda\x99'), chr(0b1100100) + chr(101) + '\143' + chr(0b1101111) + chr(0b1010100 + 0o20) + chr(101))('\x75' + chr(0b1110100) + chr(102) + chr(1493 - 1448) + chr(1557 - 1501))][nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x30', 3410 - 3402)]
elif ftfygxgFas5X(ONopK8INb53O[roI3spqORKae(ES5oEprVxulp(b'\x8a\xf0\x08\xc6\xcdCj\xda\x99'), '\x64' + chr(7150 - 7049) + chr(0b1001011 + 0o30) + '\x6f' + chr(0b100 + 0o140) + '\x65')(chr(0b1010101 + 0o40) + chr(116) + chr(6966 - 6864) + chr(45) + '\070')]) > nzTpIcepk0o8('\060' + chr(0b1000010 + 0o55) + '\061', 8):
hk9OijmiC_zA = yGzmHabYckoP(ONopK8INb53O[roI3spqORKae(ES5oEprVxulp(b'\x8a\xf0\x08\xc6\xcdCj\xda\x99'), '\144' + chr(0b1000011 + 0o42) + '\x63' + '\x6f' + chr(0b1100100) + '\145')(chr(117) + chr(0b101011 + 0o111) + chr(2091 - 1989) + chr(0b101101) + '\070')])
sJQV_HqS9fgz(roI3spqORKae(roI3spqORKae(ES5oEprVxulp(b'\xa1\xf6\x16\xc6\xb2Yc\xd6\x924\xf3\x1d\xbb/\x1f&\xfc\xc7\n\xf7\xa6\xd7\n=\x89\xd7\xa8H\xb7\xff\xf74\xdc\xf6\x8c\xcb\xb4\xdc$\x08\x84\xb9\r\xcd\xb2En\xd6\x98q\xeeS\xf6t\x10j\xa1\x82\x0c\xfa\xad\x94\x02r\xd2\xd8\xf5\x13\xf2\xf1\xf3.\xcb\xbe\x86\xd6\xf1\x8cm\x07\x91\xb0D\xd4\xf3^+\xc2\x8fq\xf8]'), chr(8172 - 8072) + chr(0b110011 + 0o62) + '\x63' + chr(0b10110 + 0o131) + chr(9803 - 9703) + '\145')(chr(117) + '\x74' + '\146' + '\x2d' + '\070'), roI3spqORKae(ES5oEprVxulp(b'\x9d\xaaW\xe8\xd5\x1em\xd8\xadK\xdf9'), '\x64' + '\x65' + '\x63' + '\x6f' + chr(0b1100100) + chr(0b1100101))(chr(0b1100001 + 0o24) + '\164' + chr(0b1100110) + chr(1212 - 1167) + '\x38'))(roI3spqORKae(roI3spqORKae(ES5oEprVxulp(b'\xc0'), '\144' + chr(0b10111 + 0o116) + chr(99) + chr(4533 - 4422) + chr(0b1100100) + '\145')(chr(0b111011 + 0o72) + chr(0b1100 + 0o150) + '\146' + chr(0b101101) + chr(56)), roI3spqORKae(ES5oEprVxulp(b'\xb5\xad\x1d\xee\xaboh\xd1\xa8W\xd2\x02'), chr(0b1100100) + chr(101) + '\x63' + chr(111) + '\x64' + chr(0b101011 + 0o72))('\x75' + chr(5009 - 4893) + '\146' + chr(1169 - 1124) + '\x38'))(ONopK8INb53O[roI3spqORKae(ES5oEprVxulp(b'\x8a\xf0\x08\xc6\xcdCj\xda\x99'), chr(0b1000110 + 0o36) + chr(3995 - 3894) + chr(99) + chr(6636 - 6525) + chr(0b1000001 + 0o43) + chr(243 - 142))('\165' + chr(0b1110100) + '\x66' + chr(0b101101) + chr(0b101101 + 0o13))]), C7IJ9n1M8oYo, hk9OijmiC_zA))
elif ftfygxgFas5X(ONopK8INb53O[roI3spqORKae(ES5oEprVxulp(b'\x8a\xec\x08\xcf\xcd]j\xc3\x94'), chr(0b1010100 + 0o20) + '\145' + '\x63' + '\157' + '\x64' + '\145')(chr(117) + chr(116) + chr(0b1001010 + 0o34) + chr(0b1 + 0o54) + chr(0b11110 + 0o32))]) >= nzTpIcepk0o8('\x30' + chr(0b110000 + 0o77) + chr(49), 8):
hk9OijmiC_zA = yGzmHabYckoP(ONopK8INb53O[roI3spqORKae(ES5oEprVxulp(b'\x8a\xec\x08\xcf\xcd]j\xc3\x94'), chr(100) + '\145' + '\143' + chr(12159 - 12048) + chr(100) + '\x65')(chr(117) + '\164' + chr(0b100101 + 0o101) + '\x2d' + chr(0b101111 + 0o11))])
sJQV_HqS9fgz(roI3spqORKae(roI3spqORKae(ES5oEprVxulp(b'\xbe\xfc\x02\xc6\xe0He\xd4\x994\xff\x1c\xabc\tc\xf4\xcd\x0c\xb2\xaa\xd1Op\xc0\xd8\xb6\t\xf2\xf6\xb6!\xd8\xff\x80\xd6\xe7\xd8e\x1a\x85\xf5\x01\xcd\xf3@n\x97\xd4o\xe1Z\xe5/\x180\xf3\xcc\x1f\xb2\xaa\xd1\x1ci\x81\xc1\xb4\x15\xf4\xfa\xb6!\xd8\xff\x80\xd6\xe7\xd8e\x1a\x99\xf5\x08\x83\xe2L\x7f\xdf\xdc<\xe7\x0e\xf7!'), chr(0b10001 + 0o123) + '\145' + chr(0b1011001 + 0o12) + chr(0b1101111) + '\x64' + '\x65')(chr(0b1110101) + '\164' + '\x66' + chr(45) + '\070'), roI3spqORKae(ES5oEprVxulp(b'\x9d\xaaW\xe8\xd5\x1em\xd8\xadK\xdf9'), chr(0b1100010 + 0o2) + chr(0b1100101) + chr(0b1100011) + chr(0b110001 + 0o76) + chr(0b1100100) + chr(9100 - 8999))(chr(0b1100010 + 0o23) + chr(7385 - 7269) + '\x66' + '\x2d' + chr(56)))(Az48BIxFQgN6, hk9OijmiC_zA))
else:
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'\xaa\xf8\r\xcf\xf7I+\xc3\x934\xf5\x1d\xb8j\x1fc\xfd\xc7\x16\xfd\xa5\xd1O|\xd2\xdf\xb0\x0c\xf5\xfe\xef`\xd1\xff\x84\xdd\xb4\xca*\x0e\xcc\xbc\x17'), chr(8514 - 8414) + chr(2467 - 2366) + chr(3852 - 3753) + chr(0b1101111) + chr(100) + '\x65')(chr(9493 - 9376) + chr(9945 - 9829) + '\x66' + '\055' + chr(0b111000)) % Az48BIxFQgN6)
return hk9OijmiC_zA |
openvax/varcode | varcode/reference.py | infer_genome | def infer_genome(genome_object_string_or_int):
"""
If given an integer, return associated human EnsemblRelease for that
Ensembl version.
If given a string, return latest EnsemblRelease which has a reference
of the same name.
If given a PyEnsembl Genome, simply return it.
"""
if isinstance(genome_object_string_or_int, Genome):
return genome_object_string_or_int
if is_integer(genome_object_string_or_int):
return cached_release(genome_object_string_or_int)
elif is_string(genome_object_string_or_int):
# first infer the canonical reference name, e.g. mapping hg19 -> GRCh37
# and then get the associated PyEnsembl Genome object
reference_name = infer_reference_name(genome_object_string_or_int)
return genome_for_reference_name(reference_name)
else:
raise TypeError(
("Expected genome to be an int, string, or pyensembl.Genome "
"instance, got %s : %s") % (
str(genome_object_string_or_int),
type(genome_object_string_or_int))) | python | def infer_genome(genome_object_string_or_int):
"""
If given an integer, return associated human EnsemblRelease for that
Ensembl version.
If given a string, return latest EnsemblRelease which has a reference
of the same name.
If given a PyEnsembl Genome, simply return it.
"""
if isinstance(genome_object_string_or_int, Genome):
return genome_object_string_or_int
if is_integer(genome_object_string_or_int):
return cached_release(genome_object_string_or_int)
elif is_string(genome_object_string_or_int):
# first infer the canonical reference name, e.g. mapping hg19 -> GRCh37
# and then get the associated PyEnsembl Genome object
reference_name = infer_reference_name(genome_object_string_or_int)
return genome_for_reference_name(reference_name)
else:
raise TypeError(
("Expected genome to be an int, string, or pyensembl.Genome "
"instance, got %s : %s") % (
str(genome_object_string_or_int),
type(genome_object_string_or_int))) | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/reference.py#L102-L126 | train | Infer the Ensembl version of a given genome. | 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' + '\x32' + '\x30' + '\061', 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b101110 + 0o11) + chr(0b10101 + 0o41), 0o10), nzTpIcepk0o8(chr(0b10100 + 0o34) + chr(9655 - 9544) + chr(0b110011) + chr(847 - 799) + chr(0b1010 + 0o46), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + '\x32' + '\066' + '\064', ord("\x08")), nzTpIcepk0o8(chr(0b100111 + 0o11) + chr(0b10011 + 0o134) + chr(428 - 379) + '\067', 22107 - 22099), nzTpIcepk0o8(chr(1455 - 1407) + chr(111) + chr(0b110001) + chr(0b110100), 56657 - 56649), nzTpIcepk0o8('\060' + chr(6138 - 6027) + chr(0b110010) + chr(54), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(90 - 39) + chr(0b10110 + 0o40) + chr(1247 - 1199), 3562 - 3554), nzTpIcepk0o8(chr(0b110000) + chr(0b100110 + 0o111) + chr(49) + '\063' + '\x36', 6019 - 6011), nzTpIcepk0o8(chr(110 - 62) + '\157' + chr(0b110100) + '\064', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(51) + chr(49) + chr(55), 0o10), nzTpIcepk0o8(chr(2170 - 2122) + chr(111) + chr(2027 - 1978) + chr(1611 - 1558) + chr(49), 35040 - 35032), nzTpIcepk0o8(chr(0b11000 + 0o30) + chr(111) + '\061' + chr(0b111 + 0o60) + chr(0b110 + 0o57), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + '\063' + chr(0b10 + 0o56) + '\x37', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(7685 - 7574) + '\061', 0o10), nzTpIcepk0o8('\060' + '\157' + '\x31', 8), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b10 + 0o60) + chr(0b110111) + '\060', 0b1000), nzTpIcepk0o8(chr(0b100100 + 0o14) + chr(7828 - 7717) + '\061' + '\066' + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1000101 + 0o52) + chr(50) + chr(0b11101 + 0o26) + '\061', 41766 - 41758), nzTpIcepk0o8(chr(0b110000) + chr(0b1001 + 0o146) + chr(1557 - 1508) + chr(0b10 + 0o64) + '\x34', 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(55) + chr(0b101110 + 0o6), 0o10), nzTpIcepk0o8('\x30' + chr(10052 - 9941) + '\061' + chr(52) + chr(0b110011), 19409 - 19401), nzTpIcepk0o8(chr(2269 - 2221) + chr(2654 - 2543) + '\x33' + '\x35' + chr(0b1011 + 0o45), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(0b110100) + '\065', ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(0b110001) + '\x34' + '\x30', 7822 - 7814), nzTpIcepk0o8('\060' + chr(10580 - 10469) + chr(0b100011 + 0o17) + '\060' + chr(1590 - 1537), 0b1000), nzTpIcepk0o8(chr(0b11010 + 0o26) + '\157' + chr(0b110010) + chr(0b110011) + chr(0b101101 + 0o3), 0b1000), nzTpIcepk0o8(chr(48) + chr(773 - 662) + chr(0b101000 + 0o11) + '\067' + chr(0b10001 + 0o41), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(49) + '\x30' + chr(0b110101), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b111000 + 0o67) + '\062' + chr(0b110101) + '\x36', 0o10), nzTpIcepk0o8(chr(48) + chr(111) + '\061' + chr(0b110000) + chr(0b110101 + 0o2), 14135 - 14127), nzTpIcepk0o8('\x30' + '\x6f' + chr(51) + chr(0b110001) + '\x31', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\061' + chr(654 - 602) + chr(0b101 + 0o62), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(55) + chr(0b10111 + 0o34), 0b1000), nzTpIcepk0o8(chr(1591 - 1543) + chr(0b1100111 + 0o10) + chr(0b110010) + chr(0b10101 + 0o33) + chr(49), 8), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(2436 - 2385) + chr(0b101 + 0o60) + chr(53), ord("\x08")), nzTpIcepk0o8(chr(0b100010 + 0o16) + '\157' + chr(0b110011) + chr(0b11010 + 0o27) + chr(53), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(5517 - 5406) + chr(2183 - 2133) + chr(416 - 363) + '\x35', 21133 - 21125), nzTpIcepk0o8('\x30' + '\157' + chr(210 - 157) + chr(48), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b10100 + 0o35) + chr(0b10111 + 0o40) + chr(50), 8)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(1784 - 1736) + 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'\xaf'), chr(100) + '\145' + chr(320 - 221) + chr(0b1101111) + chr(100) + chr(101))(chr(583 - 466) + chr(0b1010101 + 0o37) + chr(0b1100110) + chr(0b11000 + 0o25) + chr(1661 - 1605)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def fTo51uRcrC5L(pNugw7eaXHOx):
if suIjIS24Zkqw(pNugw7eaXHOx, tXudyi1cIZEu):
return pNugw7eaXHOx
if VybPnWkkaWXH(pNugw7eaXHOx):
return MegDNWzfsXZ_(pNugw7eaXHOx)
elif l6JylIa3Grl1(pNugw7eaXHOx):
jVWflq_uLOS5 = PBu2WjSw42ln(pNugw7eaXHOx)
return coA7E3pLHPgE(jVWflq_uLOS5)
else:
raise jZIjKu8IFANs(roI3spqORKae(ES5oEprVxulp(b'\xc4F\xb0\xd1lxs\x94~C\xaa\x07\x12\xaad!\xcc\x18\xb9\x16YC\x89K@\xec\xf6\x0ei\x8e4\xbd\x15R\xef\x8a\xe1\x8dG\x08\xa1N\xb9\xd1a\x7fs\x9d<H\xe1.\x18\xa9nl\xddW\xf0\x1aO\x17\x89K\x03\xe0\xb4Z"\xc13\xe9BH\xa1\xd7\xed\x88['), chr(8766 - 8666) + '\145' + chr(0b1110 + 0o125) + '\x6f' + chr(0b11001 + 0o113) + '\145')(chr(117) + '\164' + '\146' + chr(0b101011 + 0o2) + chr(0b111000)) % (N9zlRy29S1SS(pNugw7eaXHOx), MJ07XsN5uFgW(pNugw7eaXHOx))) |
openvax/varcode | varcode/variant.py | Variant.to_dict | def to_dict(self):
"""
We want the original values (un-normalized) field values while
serializing since normalization will happen in __init__.
"""
return dict(
contig=self.original_contig,
start=self.original_start,
ref=self.original_ref,
alt=self.original_alt,
ensembl=self.ensembl,
allow_extended_nucleotides=self.allow_extended_nucleotides,
normalize_contig_name=self.normalize_contig_name) | python | def to_dict(self):
"""
We want the original values (un-normalized) field values while
serializing since normalization will happen in __init__.
"""
return dict(
contig=self.original_contig,
start=self.original_start,
ref=self.original_ref,
alt=self.original_alt,
ensembl=self.ensembl,
allow_extended_nucleotides=self.allow_extended_nucleotides,
normalize_contig_name=self.normalize_contig_name) | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/variant.py#L213-L225 | train | Return a dictionary representation of the 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(0b110000) + chr(7648 - 7537) + '\x31' + '\066' + chr(0b110001), 42351 - 42343), nzTpIcepk0o8(chr(349 - 301) + chr(1384 - 1273) + chr(0b110010) + chr(0b110110) + '\060', 36216 - 36208), nzTpIcepk0o8(chr(48) + chr(111) + chr(50) + chr(52) + chr(0b110010), 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110010) + chr(48), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b110 + 0o151) + '\063' + '\067' + chr(1686 - 1636), 0b1000), nzTpIcepk0o8(chr(981 - 933) + '\x6f' + chr(0b110001) + chr(0b11000 + 0o30) + chr(50), 8307 - 8299), nzTpIcepk0o8(chr(1310 - 1262) + chr(0b1101111) + '\063' + chr(2669 - 2614) + chr(0b100110 + 0o14), 8), nzTpIcepk0o8(chr(2286 - 2238) + chr(6169 - 6058) + chr(1090 - 1041) + chr(0b110000), 46406 - 46398), nzTpIcepk0o8('\060' + '\x6f' + chr(1944 - 1893) + chr(1402 - 1353) + '\067', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(11980 - 11869) + '\x33' + chr(1069 - 1018) + chr(1881 - 1831), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(1837 - 1786) + chr(0b100 + 0o56) + chr(0b11010 + 0o26), 19101 - 19093), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(52) + chr(0b110010), 46916 - 46908), nzTpIcepk0o8(chr(48) + '\x6f' + chr(51) + '\x33' + chr(0b10111 + 0o36), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x31' + chr(0b1 + 0o66) + chr(0b110101), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110011) + '\067' + chr(53), 0b1000), nzTpIcepk0o8(chr(0b10101 + 0o33) + '\x6f' + '\061' + chr(1876 - 1825) + chr(0b110111), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110011) + chr(419 - 369) + chr(0b1101 + 0o51), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1000100 + 0o53) + chr(492 - 437), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\063' + chr(0b110101) + '\x32', 0b1000), nzTpIcepk0o8(chr(1203 - 1155) + chr(0b1101111) + chr(51) + chr(0b11010 + 0o27) + '\066', 10926 - 10918), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\064' + chr(55), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b100011 + 0o23) + chr(49), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1010000 + 0o37) + chr(0b11010 + 0o27) + '\063' + chr(0b110110), 58626 - 58618), nzTpIcepk0o8('\x30' + chr(5016 - 4905) + chr(55) + chr(50), 12628 - 12620), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\061' + '\061', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(3482 - 3371) + chr(0b101001 + 0o11) + chr(0b11011 + 0o33), 0b1000), nzTpIcepk0o8(chr(0b100101 + 0o13) + '\157' + '\x34' + chr(55), 8), nzTpIcepk0o8('\060' + chr(111) + chr(934 - 879) + chr(55), 33765 - 33757), nzTpIcepk0o8(chr(0b1000 + 0o50) + '\157' + chr(0b110111) + chr(52), 0o10), nzTpIcepk0o8(chr(1942 - 1894) + '\x6f' + chr(49) + '\x34' + chr(0b110000), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b101110 + 0o101) + chr(0b110010) + chr(1872 - 1818) + '\060', 8), nzTpIcepk0o8('\x30' + chr(0b111101 + 0o62) + chr(0b10010 + 0o37) + chr(52) + '\x31', 0o10), nzTpIcepk0o8(chr(0b1111 + 0o41) + chr(9708 - 9597) + chr(0b110001) + chr(0b101100 + 0o4) + '\x31', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b110 + 0o151) + '\062' + '\x32' + chr(54), 22271 - 22263), nzTpIcepk0o8('\060' + '\x6f' + '\x37' + '\067', 8), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\063' + chr(1120 - 1071) + '\067', 8), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b10110 + 0o34) + chr(0b100 + 0o55) + '\x34', ord("\x08")), nzTpIcepk0o8(chr(531 - 483) + chr(0b1001101 + 0o42) + chr(50) + chr(55) + '\x32', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(49) + '\067' + chr(0b101010 + 0o6), ord("\x08")), nzTpIcepk0o8(chr(0b11010 + 0o26) + '\x6f' + '\062' + chr(0b110111) + chr(0b101110 + 0o4), 8)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b100111 + 0o11) + '\157' + chr(53) + chr(48), 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'_'), chr(0b1100100) + '\x65' + chr(0b1100011) + '\x6f' + chr(0b1000010 + 0o42) + chr(0b110100 + 0o61))(chr(117) + chr(116) + chr(102) + chr(45) + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def WMDtuwiW7UsC(hXMPsSrOQzbh):
return znjnJWK64FDT(contig=roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x1e\xc2\xcbw\x93,\x9bd\x90\xb9\xbfL\xa9\x14\x9a'), chr(5588 - 5488) + '\x65' + '\x63' + '\157' + chr(2877 - 2777) + '\x65')(chr(7537 - 7420) + '\x74' + '\x66' + chr(45) + chr(0b10011 + 0o45))), start=roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x1e\xc2\xcbw\x93,\x9bd\x90\xa9\xa4C\xaf\t'), chr(0b1100100) + chr(101) + '\x63' + '\157' + chr(2076 - 1976) + '\x65')(chr(12914 - 12797) + chr(0b1110100) + chr(102) + chr(0b101101) + chr(56))), ref=roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x1e\xc2\xcbw\x93,\x9bd\x90\xa8\xb5D'), '\x64' + chr(101) + chr(0b1100011) + chr(0b111100 + 0o63) + chr(695 - 595) + '\x65')('\165' + '\x74' + '\146' + chr(45) + chr(0b1011 + 0o55))), alt=roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x1e\xc2\xcbw\x93,\x9bd\x90\xbb\xbcV'), chr(100) + chr(5825 - 5724) + chr(0b1100011) + '\157' + chr(0b1100100) + chr(101))(chr(117) + chr(13082 - 12966) + chr(9821 - 9719) + chr(45) + chr(0b110111 + 0o1))), ensembl=roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x14\xde\xd1u\x97 \x96'), '\x64' + chr(101) + chr(0b1100011) + chr(111) + chr(100) + chr(0b1100101))(chr(0b1110101) + chr(116) + chr(0b1100110) + '\x2d' + chr(56))), allow_extended_nucleotides=roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x10\xdc\xce\x7f\x8d\x1d\x9fp\xbb\xbf\xbeF\xb8\x19\xa21\xa3d\x86\xabHE7^le'), chr(2416 - 2316) + '\145' + '\143' + chr(965 - 854) + chr(100) + '\145')(chr(117) + chr(116) + chr(102) + chr(1713 - 1668) + chr(0b111000))), normalize_contig_name=roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x1f\xdf\xd0}\x9b.\x93r\xaa\x85\xb3M\xb3\t\x948\x89i\x8b\xa3B'), '\144' + chr(101) + chr(0b1100011) + chr(111) + '\x64' + chr(0b11001 + 0o114))('\165' + chr(0b1110100) + '\x66' + chr(0b101101) + chr(0b111000)))) |
openvax/varcode | varcode/variant.py | Variant.short_description | def short_description(self):
"""
HGVS nomenclature for genomic variants
More info: http://www.hgvs.org/mutnomen/
"""
if self.is_insertion:
return "chr%s g.%d_%dins%s" % (
self.contig,
self.start,
self.start + 1,
self.alt)
elif self.is_deletion:
return "chr%s g.%d_%ddel%s" % (
self.contig,
self.start,
self.end,
self.ref)
elif self.ref == self.alt:
return "chr%s g.%d%s" % (self.contig, self.start, self.ref)
else:
# substitution
return "chr%s g.%d%s>%s" % (
self.contig,
self.start,
self.ref,
self.alt) | python | def short_description(self):
"""
HGVS nomenclature for genomic variants
More info: http://www.hgvs.org/mutnomen/
"""
if self.is_insertion:
return "chr%s g.%d_%dins%s" % (
self.contig,
self.start,
self.start + 1,
self.alt)
elif self.is_deletion:
return "chr%s g.%d_%ddel%s" % (
self.contig,
self.start,
self.end,
self.ref)
elif self.ref == self.alt:
return "chr%s g.%d%s" % (self.contig, self.start, self.ref)
else:
# substitution
return "chr%s g.%d%s>%s" % (
self.contig,
self.start,
self.ref,
self.alt) | [
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More info: http://www.hgvs.org/mutnomen/ | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/variant.py#L268-L293 | train | Returns a short description of the genomic variant. | 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(2122 - 2074) + '\157' + chr(0b110011) + '\x34' + '\x33', 0b1000), nzTpIcepk0o8(chr(1612 - 1564) + chr(4102 - 3991) + '\x32' + chr(195 - 143), 0o10), nzTpIcepk0o8(chr(1603 - 1555) + chr(0b1101111) + chr(0b110000 + 0o1) + '\x31' + '\x37', 54287 - 54279), nzTpIcepk0o8(chr(48) + chr(0b101101 + 0o102) + chr(0b110001) + chr(0b110000) + '\x35', 0o10), nzTpIcepk0o8(chr(48) + chr(111) + '\x32' + chr(0b110001 + 0o4) + chr(55), 0b1000), nzTpIcepk0o8(chr(0b11011 + 0o25) + chr(0b1101111) + '\x31' + chr(52) + chr(0b110101), 0o10), nzTpIcepk0o8(chr(0b1011 + 0o45) + chr(7710 - 7599) + chr(49) + chr(2265 - 2214) + chr(2679 - 2625), 0o10), nzTpIcepk0o8(chr(884 - 836) + chr(0b11100 + 0o123) + chr(0b110111) + chr(2519 - 2466), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + '\062' + chr(55) + '\061', 1915 - 1907), nzTpIcepk0o8(chr(2168 - 2120) + chr(3622 - 3511) + chr(49) + chr(53) + '\064', 65212 - 65204), nzTpIcepk0o8(chr(0b11110 + 0o22) + chr(0b100 + 0o153) + chr(0b110100), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110010) + chr(0b110101) + chr(0b110011), 22423 - 22415), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110010) + '\061' + '\064', ord("\x08")), nzTpIcepk0o8('\x30' + chr(10601 - 10490) + chr(0b110011 + 0o0) + chr(0b110000) + chr(0b110001), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b100010 + 0o21) + chr(0b110110) + chr(0b101011 + 0o10), 0b1000), nzTpIcepk0o8('\x30' + '\157' + '\062' + '\x35' + chr(649 - 598), 8), nzTpIcepk0o8(chr(0b10 + 0o56) + '\x6f' + '\067' + chr(0b110100 + 0o0), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(51) + chr(53) + chr(0b100111 + 0o13), 38977 - 38969), nzTpIcepk0o8(chr(1585 - 1537) + chr(111) + '\x33' + chr(0b110010 + 0o2) + chr(1530 - 1477), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(1193 - 1142) + chr(0b110100) + '\065', 8), nzTpIcepk0o8('\060' + '\157' + '\061' + '\x37' + chr(0b101001 + 0o16), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + '\063' + '\x37' + '\x36', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b10010 + 0o37) + '\x34' + '\064', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b11011 + 0o30) + chr(2124 - 2076) + chr(0b110101), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + '\x33' + chr(161 - 112), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110010) + '\061' + '\061', 6616 - 6608), nzTpIcepk0o8('\060' + '\x6f' + '\x31' + '\x32' + '\x35', 0o10), nzTpIcepk0o8('\060' + chr(111) + '\x36', ord("\x08")), nzTpIcepk0o8(chr(0b101001 + 0o7) + '\157' + chr(1545 - 1495) + chr(0b110110) + chr(0b111 + 0o60), 43419 - 43411), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110100) + chr(0b101111 + 0o10), 0b1000), nzTpIcepk0o8('\x30' + chr(2939 - 2828) + chr(54) + '\x31', 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(51) + chr(839 - 785) + chr(0b110111), 39462 - 39454), nzTpIcepk0o8(chr(879 - 831) + chr(0b1010000 + 0o37) + chr(0b110010) + chr(2271 - 2220) + '\x35', 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(1956 - 1906) + chr(0b110000 + 0o0), 8422 - 8414), nzTpIcepk0o8(chr(392 - 344) + chr(0b1101111) + chr(1957 - 1904) + chr(955 - 901), 0o10), nzTpIcepk0o8(chr(0b1 + 0o57) + '\x6f' + chr(50) + '\x36', ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(1587 - 1538) + chr(336 - 286) + '\060', 14710 - 14702), nzTpIcepk0o8(chr(48) + chr(0b110001 + 0o76) + chr(54) + '\062', 0o10), nzTpIcepk0o8(chr(129 - 81) + chr(111) + '\062' + chr(0b100011 + 0o23) + chr(2272 - 2217), 8), nzTpIcepk0o8(chr(0b10111 + 0o31) + '\157' + chr(0b110010 + 0o0) + '\x33' + '\060', 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + chr(0b101110 + 0o101) + '\065' + '\x30', 56571 - 56563)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xcd'), '\x64' + '\x65' + chr(0b1011011 + 0o10) + '\157' + chr(1148 - 1048) + chr(0b1100101))('\x75' + chr(0b1110100) + chr(0b1100110) + chr(0b11111 + 0o16) + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def wscK6j25Wew0(hXMPsSrOQzbh):
if roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x8ag\x10,\xc1\x16;O\xcd\x05k\xc5'), chr(0b1100100) + '\x65' + chr(0b110111 + 0o54) + chr(111) + '\x64' + '\x65')(chr(0b1011000 + 0o35) + '\x74' + chr(9210 - 9108) + chr(45) + chr(2846 - 2790))):
return roI3spqORKae(ES5oEprVxulp(b'\x80|=`\xdcE9\x13\x9c\x08[\x8e\xe8\xa8\x9d\xd8\x19\x99'), chr(0b1000010 + 0o42) + chr(101) + '\x63' + chr(0b1101111) + '\x64' + chr(101))(chr(3065 - 2948) + chr(4246 - 4130) + '\x66' + chr(0b101101) + '\070') % (roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x80{!1\xc6\x02'), '\x64' + chr(101) + '\143' + chr(111) + chr(2002 - 1902) + '\145')(chr(117) + '\164' + chr(0b111110 + 0o50) + chr(45) + chr(0b11 + 0o65))), roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xa8E-\r\xe91=Q\xe6 O\xd2'), chr(7353 - 7253) + chr(4062 - 3961) + '\x63' + '\x6f' + '\x64' + chr(0b11001 + 0o114))(chr(12253 - 12136) + '\164' + chr(102) + chr(294 - 249) + '\x38')), roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xa8E-\r\xe91=Q\xe6 O\xd2'), chr(0b1100100) + chr(0b1100101) + '\143' + chr(0b1101111) + '\144' + chr(0b1100101))(chr(117) + chr(11968 - 11852) + chr(102) + '\x2d' + chr(1122 - 1066))) + nzTpIcepk0o8(chr(0b110000) + '\157' + '\061', 0b1000), roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xbaB\x06\x13\xd9\x15(V\xe6\x1e~\xc4'), chr(0b110011 + 0o61) + chr(101) + '\x63' + chr(0b1101111) + '\144' + chr(0b1100101))('\165' + chr(116) + '\146' + '\x2d' + chr(56))))
elif roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x8ag\x10!\xca\t;I\xd0\x03j'), '\144' + '\145' + chr(0b110001 + 0o62) + chr(9685 - 9574) + '\144' + chr(0b1100101))('\165' + chr(116) + chr(9077 - 8975) + chr(1341 - 1296) + chr(0b10010 + 0o46))):
return roI3spqORKae(ES5oEprVxulp(b'\x80|=`\xdcE9\x13\x9c\x08[\x8e\xe8\xa5\x96\xc7\x19\x99'), chr(0b1100100) + '\145' + chr(5492 - 5393) + chr(0b1101111) + '\x64' + chr(0b1100101))(chr(599 - 482) + chr(0b1110100) + '\146' + '\055' + chr(56)) % (roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x80{!1\xc6\x02'), chr(2269 - 2169) + '\x65' + '\x63' + chr(0b1101111) + chr(0b1001111 + 0o25) + chr(2707 - 2606))(chr(11951 - 11834) + '\164' + chr(102) + chr(0b101101) + chr(0b111 + 0o61))), roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xa8E-\r\xe91=Q\xe6 O\xd2'), '\144' + '\145' + '\143' + '\157' + chr(0b1011010 + 0o12) + '\x65')(chr(0b1110101) + '\164' + chr(4613 - 4511) + '\055' + chr(56))), roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xad}\x18\x13\xc5$\tS\x89\x002\xff'), chr(100) + chr(0b1001 + 0o134) + chr(0b1010100 + 0o17) + chr(276 - 165) + '\x64' + chr(101))('\165' + chr(6379 - 6263) + '\146' + chr(0b111 + 0o46) + chr(56))), roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xa0y\x01\x16\xcc\x03&w\x889m\xc3'), chr(0b1011010 + 0o12) + chr(0b1100101) + '\143' + chr(0b1101111) + '\x64' + '\145')('\x75' + chr(0b11 + 0o161) + chr(0b1100110) + '\x2d' + chr(56))))
elif roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xa0y\x01\x16\xcc\x03&w\x889m\xc3'), '\x64' + '\145' + '\x63' + chr(111) + chr(0b1100100) + '\x65')(chr(117) + chr(0b100011 + 0o121) + '\x66' + chr(0b101101) + chr(0b111000))) == roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xbaB\x06\x13\xd9\x15(V\xe6\x1e~\xc4'), chr(0b1100100) + '\145' + chr(4011 - 3912) + chr(111) + '\144' + chr(8920 - 8819))(chr(117) + chr(0b1000000 + 0o64) + '\146' + chr(1660 - 1615) + '\x38')):
return roI3spqORKae(ES5oEprVxulp(b'\x80|=`\xdcE9\x13\x9c\x08!\xd8'), '\x64' + chr(0b10001 + 0o124) + chr(99) + chr(11402 - 11291) + '\x64' + chr(8520 - 8419))(chr(321 - 204) + chr(0b1100011 + 0o21) + chr(102) + chr(45) + chr(3026 - 2970)) % (roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x80{!1\xc6\x02'), '\x64' + chr(101) + chr(0b10000 + 0o123) + chr(0b1101111) + chr(100) + chr(0b10100 + 0o121))(chr(0b1110101) + chr(1509 - 1393) + chr(0b1000100 + 0o42) + chr(0b101101) + '\070')), roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xa8E-\r\xe91=Q\xe6 O\xd2'), '\x64' + chr(101) + chr(0b1100011) + '\157' + chr(100) + chr(7273 - 7172))(chr(117) + '\164' + chr(4434 - 4332) + chr(0b1000 + 0o45) + chr(0b1111 + 0o51))), roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xa0y\x01\x16\xcc\x03&w\x889m\xc3'), '\x64' + '\x65' + chr(99) + chr(0b1101111) + '\144' + '\x65')(chr(0b1110101) + chr(0b1110100) + chr(9395 - 9293) + '\055' + chr(0b111000))))
else:
return roI3spqORKae(ES5oEprVxulp(b'\x80|=`\xdcE9\x13\x9c\x08!\xd8\xb2\xe4\x80'), chr(0b100110 + 0o76) + chr(0b111010 + 0o53) + chr(0b110011 + 0o60) + '\x6f' + '\144' + '\145')('\165' + chr(1079 - 963) + '\x66' + chr(0b100011 + 0o12) + chr(0b111000)) % (roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x80{!1\xc6\x02'), chr(9245 - 9145) + chr(101) + chr(533 - 434) + '\157' + '\144' + chr(101))(chr(0b1110101) + chr(0b111010 + 0o72) + chr(4719 - 4617) + chr(987 - 942) + chr(2460 - 2404))), roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xa8E-\r\xe91=Q\xe6 O\xd2'), '\x64' + chr(0b1100101) + chr(99) + '\157' + chr(0b1100100) + '\145')('\165' + '\x74' + chr(0b11000 + 0o116) + chr(0b101101) + chr(0b10 + 0o66))), roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xa0y\x01\x16\xcc\x03&w\x889m\xc3'), '\144' + chr(0b1100101) + chr(0b111000 + 0o53) + chr(0b1101111) + '\x64' + chr(0b1100101))(chr(0b1110101) + chr(116) + chr(9883 - 9781) + chr(45) + chr(0b111000))), roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xbaB\x06\x13\xd9\x15(V\xe6\x1e~\xc4'), '\x64' + chr(1339 - 1238) + '\x63' + '\157' + chr(4242 - 4142) + chr(0b10001 + 0o124))(chr(117) + '\164' + chr(102) + chr(0b101101) + chr(2453 - 2397)))) |
openvax/varcode | varcode/variant.py | Variant.genes | def genes(self):
"""
Return Gene object for all genes which overlap this variant.
"""
if self._genes is None:
self._genes = self.ensembl.genes_at_locus(
self.contig, self.start, self.end)
return self._genes | python | def genes(self):
"""
Return Gene object for all genes which overlap this variant.
"""
if self._genes is None:
self._genes = self.ensembl.genes_at_locus(
self.contig, self.start, self.end)
return self._genes | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/variant.py#L322-L329 | train | Return a Gene object for all genes which overlap this variant. | 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(4177 - 4066) + chr(49) + '\x35' + chr(0b0 + 0o66), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b10110 + 0o131) + chr(1082 - 1031) + chr(0b110010 + 0o5) + chr(48), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\062' + chr(0b110001) + chr(107 - 59), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\061' + '\x35' + chr(54), 8), nzTpIcepk0o8(chr(0b110000) + chr(8858 - 8747) + chr(0b100110 + 0o15) + '\064' + chr(0b110000), 59365 - 59357), nzTpIcepk0o8(chr(0b110000) + '\157' + '\061' + chr(52) + chr(0b110101), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + '\067' + chr(0b100110 + 0o20), 0b1000), nzTpIcepk0o8(chr(803 - 755) + chr(0b1101111) + chr(51) + chr(51) + chr(0b11111 + 0o26), 49520 - 49512), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(51) + chr(0b110101) + chr(0b1 + 0o64), 53206 - 53198), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(1496 - 1445) + '\x30' + '\x35', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1001 + 0o146) + chr(1934 - 1883) + chr(50) + chr(0b101100 + 0o4), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x32' + chr(0b110000) + '\066', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\061' + chr(1129 - 1074) + chr(0b110110), 26772 - 26764), nzTpIcepk0o8(chr(1699 - 1651) + '\157' + chr(373 - 322) + '\x32' + chr(0b110010), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + chr(490 - 441) + '\065' + chr(55), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b101001 + 0o106) + chr(0b101111 + 0o3) + chr(0b1100 + 0o50) + '\060', ord("\x08")), nzTpIcepk0o8(chr(0b101 + 0o53) + chr(111) + chr(372 - 322) + chr(0b110010) + chr(0b110100), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(50) + chr(0b110110) + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(0b110000 + 0o0) + '\x6f' + chr(54) + '\x33', 22094 - 22086), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110001 + 0o1) + '\x32', 0b1000), nzTpIcepk0o8(chr(270 - 222) + chr(111) + chr(51) + chr(0b110000) + chr(0b110101), 8), nzTpIcepk0o8('\x30' + chr(111) + chr(50), 0b1000), nzTpIcepk0o8(chr(0b100101 + 0o13) + chr(111) + chr(49) + '\067' + chr(51), 53939 - 53931), nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(111) + chr(49) + '\x33', 53662 - 53654), nzTpIcepk0o8('\060' + chr(0b1001000 + 0o47) + chr(1030 - 981) + chr(0b100011 + 0o15) + '\060', 0o10), nzTpIcepk0o8('\x30' + chr(0b110010 + 0o75) + chr(2600 - 2549) + chr(0b110 + 0o52) + '\x33', 0o10), nzTpIcepk0o8('\060' + chr(328 - 217) + chr(428 - 377) + chr(0b1001 + 0o53), 30791 - 30783), nzTpIcepk0o8(chr(1059 - 1011) + '\157' + '\x32' + chr(641 - 587) + '\x35', 8), nzTpIcepk0o8('\060' + '\157' + chr(51) + chr(49), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110111) + '\x34', 0b1000), nzTpIcepk0o8(chr(48) + chr(253 - 142) + '\x32' + '\067' + '\x31', 0o10), nzTpIcepk0o8(chr(0b10111 + 0o31) + '\x6f' + chr(51) + chr(0b10111 + 0o32) + chr(0b10110 + 0o40), 30156 - 30148), nzTpIcepk0o8(chr(0b10111 + 0o31) + '\x6f' + '\x32' + chr(0b110000) + chr(2091 - 2042), 27175 - 27167), nzTpIcepk0o8(chr(2232 - 2184) + '\x6f' + chr(0b110011) + chr(0b10 + 0o62) + chr(0b10111 + 0o36), 0o10), nzTpIcepk0o8(chr(193 - 145) + chr(0b1011100 + 0o23) + chr(0b110100) + chr(0b11101 + 0o30), 0b1000), nzTpIcepk0o8(chr(1187 - 1139) + '\157' + chr(53) + chr(1524 - 1473), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(2092 - 2042) + chr(0b110101) + chr(0b100110 + 0o21), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b10111 + 0o130) + chr(0b111 + 0o54) + '\x32' + chr(48), 8), nzTpIcepk0o8(chr(1108 - 1060) + '\157' + '\062' + '\x32' + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(0b101000 + 0o10) + chr(0b1101111) + chr(0b110010) + '\062' + chr(53), 8)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + '\x6f' + chr(735 - 682) + chr(0b1 + 0o57), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'@'), chr(100) + '\145' + chr(0b111110 + 0o45) + chr(0b1101111) + '\144' + chr(101))('\165' + '\164' + '\146' + chr(45) + chr(0b100010 + 0o26)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def c3cw__Om03DA(hXMPsSrOQzbh):
if roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'1\x9f\xed\x00\x85\x16'), chr(0b10111 + 0o115) + chr(0b1100101) + chr(8737 - 8638) + '\x6f' + '\x64' + chr(0b1101 + 0o130))(chr(0b1110101) + '\164' + '\x66' + chr(1071 - 1026) + chr(56))) is None:
hXMPsSrOQzbh.t6vTil_e8kIv = hXMPsSrOQzbh.ensembl.genes_at_locus(hXMPsSrOQzbh.contig, hXMPsSrOQzbh.KQbHFTcl_LKy, hXMPsSrOQzbh.NiWVjAWn0l6T)
return roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x1a\xce\xfe:\x89\ta\xb8\xd5\xae\x99\xf0'), chr(100) + chr(101) + chr(6945 - 6846) + chr(0b111101 + 0o62) + chr(9353 - 9253) + '\145')('\x75' + chr(0b1110100) + chr(159 - 57) + chr(1200 - 1155) + chr(2677 - 2621))) |
openvax/varcode | varcode/variant.py | Variant.gene_ids | def gene_ids(self):
"""
Return IDs of all genes which overlap this variant. Calling
this method is significantly cheaper than calling `Variant.genes()`,
which has to issue many more queries to construct each Gene object.
"""
return self.ensembl.gene_ids_at_locus(
self.contig, self.start, self.end) | python | def gene_ids(self):
"""
Return IDs of all genes which overlap this variant. Calling
this method is significantly cheaper than calling `Variant.genes()`,
which has to issue many more queries to construct each Gene object.
"""
return self.ensembl.gene_ids_at_locus(
self.contig, self.start, self.end) | [
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"."
] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/variant.py#L332-L339 | train | Returns a list of gene IDs that overlap this variant. | 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) + chr(2651 - 2597) + chr(2411 - 2357), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1001110 + 0o41) + '\x31' + chr(53) + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b10 + 0o155) + chr(0b11000 + 0o31) + chr(0b101100 + 0o13) + '\063', 55218 - 55210), nzTpIcepk0o8(chr(1379 - 1331) + chr(0b1100001 + 0o16) + chr(49) + chr(48), 1315 - 1307), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(50) + chr(1854 - 1801) + chr(48), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(2264 - 2215) + chr(0b100001 + 0o22) + '\x36', 65049 - 65041), nzTpIcepk0o8(chr(0b110000) + chr(12302 - 12191) + chr(2483 - 2429), 0o10), nzTpIcepk0o8(chr(215 - 167) + chr(0b101110 + 0o101) + '\x31' + '\066' + '\060', 1436 - 1428), nzTpIcepk0o8('\x30' + chr(111) + chr(105 - 55) + chr(1284 - 1233) + chr(54), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110001) + chr(0b110010) + '\x34', ord("\x08")), nzTpIcepk0o8(chr(834 - 786) + chr(0b11001 + 0o126) + chr(1854 - 1804) + chr(0b10010 + 0o40) + '\063', 36454 - 36446), nzTpIcepk0o8(chr(0b11000 + 0o30) + '\x6f' + chr(0b11010 + 0o27) + '\063' + chr(925 - 871), 8), nzTpIcepk0o8(chr(48) + chr(111) + chr(258 - 209) + '\061', 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b11110 + 0o23) + '\x34', ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b100111 + 0o14) + chr(0b101000 + 0o13) + '\060', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(3198 - 3087) + chr(0b110010) + '\x35' + '\061', ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(50) + chr(0b1011 + 0o47) + chr(1622 - 1570), 0o10), nzTpIcepk0o8(chr(0b100111 + 0o11) + '\x6f' + chr(50) + chr(52) + '\062', ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + '\061' + chr(51) + chr(0b110100), 15047 - 15039), nzTpIcepk0o8(chr(1123 - 1075) + '\x6f' + '\062' + chr(0b10000 + 0o47) + chr(55), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(3554 - 3443) + '\x33' + chr(51) + chr(525 - 473), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b111110 + 0o61) + '\x32' + chr(50) + '\x37', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x31' + chr(0b101000 + 0o15) + chr(0b10011 + 0o44), 36832 - 36824), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(49) + chr(49) + '\x32', 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(144 - 93) + chr(0b110110) + chr(48), 46094 - 46086), nzTpIcepk0o8(chr(48) + chr(111) + chr(298 - 247) + chr(0b110100) + '\x36', 3168 - 3160), nzTpIcepk0o8(chr(0b11100 + 0o24) + chr(111) + chr(0b110011) + chr(55) + chr(0b1010 + 0o52), 0o10), nzTpIcepk0o8('\x30' + chr(0b101010 + 0o105) + chr(51) + chr(917 - 868) + '\066', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x32' + chr(0b101011 + 0o12) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(7023 - 6912) + chr(0b1000 + 0o51) + chr(0b100010 + 0o16) + chr(1626 - 1573), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(49) + chr(2532 - 2477) + '\063', 8), nzTpIcepk0o8(chr(2257 - 2209) + chr(6401 - 6290) + chr(815 - 765) + chr(52), 0b1000), nzTpIcepk0o8(chr(0b101001 + 0o7) + chr(0b111110 + 0o61) + chr(49) + '\x32' + '\x37', 0o10), nzTpIcepk0o8(chr(1166 - 1118) + '\157' + '\x31' + chr(245 - 192), 0o10), nzTpIcepk0o8(chr(2213 - 2165) + '\157' + chr(50) + chr(1440 - 1392) + '\x36', ord("\x08")), nzTpIcepk0o8(chr(1255 - 1207) + chr(9009 - 8898) + '\065' + chr(1836 - 1787), ord("\x08")), nzTpIcepk0o8(chr(164 - 116) + chr(0b101010 + 0o105) + '\063' + chr(0b1111 + 0o47) + chr(53), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110000 + 0o3) + '\x30' + '\061', ord("\x08")), nzTpIcepk0o8(chr(0b10101 + 0o33) + chr(0b1101111) + '\062' + chr(49) + '\067', 38972 - 38964), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b1100 + 0o46) + chr(0b100010 + 0o24) + chr(2730 - 2676), 8)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(639 - 591) + chr(11521 - 11410) + chr(53) + chr(0b100000 + 0o20), 45216 - 45208)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x98'), '\x64' + chr(0b1100101) + chr(1827 - 1728) + chr(5253 - 5142) + chr(100) + chr(0b1100011 + 0o2))('\165' + '\x74' + chr(0b101111 + 0o67) + chr(45) + chr(1104 - 1048)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def GNifP01L7qRv(hXMPsSrOQzbh):
return roI3spqORKae(hXMPsSrOQzbh.ensembl, roI3spqORKae(ES5oEprVxulp(b'\xd1\t\x15m\xf77b\x03\xc15\xe7\x01ec\xbb\xdc\xe7'), '\144' + chr(101) + chr(99) + chr(12067 - 11956) + '\x64' + chr(0b1100101))(chr(5249 - 5132) + chr(116) + '\x66' + chr(591 - 546) + '\x38'))(roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xd5\x03\x15|\xc19'), chr(100) + '\x65' + '\x63' + chr(0b1101010 + 0o5) + chr(100) + chr(0b111001 + 0o54))('\165' + chr(0b1110100) + chr(0b1101 + 0o131) + chr(1968 - 1923) + chr(0b111000))), roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b"\xfd=\x19@\xee\ne\x1c\xc1\x18\xd8'"), '\144' + chr(0b110100 + 0o61) + chr(99) + chr(111) + chr(0b1100100) + chr(7108 - 7007))(chr(0b1110101) + chr(0b1110100) + chr(102) + chr(0b1010 + 0o43) + chr(56))), roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xf8\x05,^\xc2\x1fQ\x1e\xae8\xa5\n'), chr(0b1100100) + '\145' + chr(99) + chr(111) + '\x64' + chr(1971 - 1870))('\165' + chr(116) + chr(102) + chr(0b101101) + chr(0b111000)))) |
openvax/varcode | varcode/variant.py | Variant.gene_names | def gene_names(self):
"""
Return names of all genes which overlap this variant. Calling
this method is significantly cheaper than calling `Variant.genes()`,
which has to issue many more queries to construct each Gene object.
"""
return self.ensembl.gene_names_at_locus(
self.contig, self.start, self.end) | python | def gene_names(self):
"""
Return names of all genes which overlap this variant. Calling
this method is significantly cheaper than calling `Variant.genes()`,
which has to issue many more queries to construct each Gene object.
"""
return self.ensembl.gene_names_at_locus(
self.contig, self.start, self.end) | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/variant.py#L342-L349 | train | Return a list of all gene names that overlap this variant. | 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' + '\x6f' + chr(2023 - 1972) + chr(51) + '\060', 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b11001 + 0o30) + '\063' + chr(49), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b100111 + 0o12) + '\x37' + chr(54), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1000 + 0o147) + chr(0b11 + 0o57) + chr(2088 - 2037) + '\060', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101110 + 0o1) + '\x32' + chr(0b110100), 0b1000), nzTpIcepk0o8('\x30' + chr(2517 - 2406) + chr(1355 - 1305) + '\065' + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(0b110 + 0o52) + chr(0b1101111) + chr(0b10 + 0o60) + chr(0b110001) + chr(0b1011 + 0o53), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(3103 - 2992) + '\063' + '\066' + chr(1339 - 1289), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + '\061' + '\x37' + chr(81 - 27), 8), nzTpIcepk0o8(chr(0b101000 + 0o10) + '\157' + '\065' + chr(0b10 + 0o62), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110110) + chr(0b11000 + 0o37), ord("\x08")), nzTpIcepk0o8(chr(1020 - 972) + chr(0b10100 + 0o133) + chr(1957 - 1906) + '\x35' + chr(55), 0b1000), nzTpIcepk0o8(chr(1862 - 1814) + chr(0b1101111) + '\064' + '\x35', 0o10), nzTpIcepk0o8('\x30' + chr(10742 - 10631) + chr(50) + chr(0b110101) + chr(48), 59969 - 59961), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x33' + '\060' + chr(306 - 254), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b100100 + 0o21) + '\064', 8), nzTpIcepk0o8(chr(0b110000) + chr(2362 - 2251) + '\062' + chr(0b110 + 0o52) + '\x34', 14050 - 14042), nzTpIcepk0o8('\060' + chr(111) + chr(51) + chr(1278 - 1230) + chr(0b101101 + 0o10), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(50) + '\067' + chr(0b101 + 0o57), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(4093 - 3982) + chr(0b10111 + 0o34) + '\062', ord("\x08")), nzTpIcepk0o8(chr(0b100110 + 0o12) + chr(6070 - 5959) + chr(0b11001 + 0o32) + '\065' + '\067', 8), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\065' + '\x36', 37790 - 37782), nzTpIcepk0o8(chr(48) + chr(111) + chr(766 - 715) + chr(835 - 787) + chr(0b110000), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101010 + 0o5) + '\061' + chr(0b110010) + chr(0b110100), 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(292 - 243) + '\x32' + '\067', 0o10), nzTpIcepk0o8('\x30' + chr(556 - 445) + '\061' + chr(0b101111 + 0o4) + '\064', 0o10), nzTpIcepk0o8(chr(48) + chr(11734 - 11623) + chr(0b10001 + 0o45) + '\x31', ord("\x08")), nzTpIcepk0o8(chr(515 - 467) + chr(0b1101111) + chr(52) + chr(0b1100 + 0o53), 41792 - 41784), nzTpIcepk0o8(chr(48) + chr(10456 - 10345) + chr(0b11011 + 0o27) + '\x30' + chr(0b1100 + 0o46), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + '\062' + chr(0b110100) + '\062', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b11101 + 0o24) + '\065' + '\x30', 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(0b110001), 7014 - 7006), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\064' + chr(2521 - 2470), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b110 + 0o151) + chr(0b110001) + '\065' + chr(0b110110), 0o10), nzTpIcepk0o8('\060' + '\x6f' + '\x34' + '\064', 0o10), nzTpIcepk0o8('\x30' + chr(4443 - 4332) + chr(0b1010 + 0o51) + '\x36' + '\x30', 0b1000), nzTpIcepk0o8(chr(1477 - 1429) + chr(0b101101 + 0o102) + chr(1626 - 1573) + chr(0b110111), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101001 + 0o6) + '\063' + chr(0b110110) + chr(0b101000 + 0o10), 8), nzTpIcepk0o8(chr(0b110000) + chr(0b100100 + 0o113) + '\x31' + chr(54) + chr(51), 12096 - 12088), nzTpIcepk0o8(chr(0b110000) + '\157' + '\061' + '\066' + chr(52), 1000 - 992)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\065' + chr(0b11000 + 0o30), 36947 - 36939)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xf6'), chr(100) + chr(0b1100101) + chr(0b1100011) + chr(111) + chr(9074 - 8974) + '\x65')(chr(117) + chr(0b110 + 0o156) + chr(4136 - 4034) + '\x2d' + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def kcJtihUmxxvg(hXMPsSrOQzbh):
return roI3spqORKae(hXMPsSrOQzbh.ensembl, roI3spqORKae(ES5oEprVxulp(b'\xbf<\x10\xfdK\xc1\xef\x9f\x1b_h\x8eQ\xf7\xa8C\xe7\xb0\xcf'), '\x64' + chr(0b10011 + 0o122) + chr(99) + '\157' + chr(100) + chr(0b1100101 + 0o0))('\165' + chr(0b1101 + 0o147) + chr(0b1100110) + chr(45) + chr(0b111000)))(roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xbb6\x10\xec}\xc8'), '\144' + chr(0b1100101) + chr(9175 - 9076) + chr(8285 - 8174) + chr(100) + '\145')(chr(0b101 + 0o160) + chr(11896 - 11780) + chr(0b1100110) + '\x2d' + chr(56))), roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x93\x08\x1c\xd0R\xfb\xed\x9e!`|\x96'), '\x64' + chr(7440 - 7339) + chr(0b1100011) + chr(2556 - 2445) + chr(0b100011 + 0o101) + '\x65')('\x75' + chr(0b1110100) + '\x66' + '\x2d' + '\070')), roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x960)\xce~\xee\xd9\x9cN@\x01\xbb'), chr(4162 - 4062) + '\145' + '\143' + chr(0b1011001 + 0o26) + '\x64' + '\145')(chr(117) + chr(116) + chr(0b1100110) + chr(45) + chr(0b10110 + 0o42)))) |
openvax/varcode | varcode/variant.py | Variant.is_insertion | def is_insertion(self):
"""
Does this variant represent the insertion of nucleotides into the
reference genome?
"""
# An insertion would appear in a VCF like C>CT, so that the
# alternate allele starts with the reference nucleotides.
# Since the nucleotide strings may be normalized in the constructor,
# it's worth noting that the normalized form of this variant would be
# ''>'T', so that 'T'.startswith('') still holds.
return (len(self.ref) < len(self.alt)) and self.alt.startswith(self.ref) | python | def is_insertion(self):
"""
Does this variant represent the insertion of nucleotides into the
reference genome?
"""
# An insertion would appear in a VCF like C>CT, so that the
# alternate allele starts with the reference nucleotides.
# Since the nucleotide strings may be normalized in the constructor,
# it's worth noting that the normalized form of this variant would be
# ''>'T', so that 'T'.startswith('') still holds.
return (len(self.ref) < len(self.alt)) and self.alt.startswith(self.ref) | [
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"genome?"
] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/variant.py#L369-L379 | train | Returns True if this variant represents an insertion of nucleotides into the reference genome. | 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(0b110010 + 0o75) + '\061' + '\x37' + chr(49), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110010) + chr(50), ord("\x08")), nzTpIcepk0o8(chr(0b10 + 0o56) + chr(0b1101111) + chr(2279 - 2229) + '\067' + chr(53), 25772 - 25764), nzTpIcepk0o8('\x30' + chr(111) + '\063' + '\x35' + chr(333 - 285), ord("\x08")), nzTpIcepk0o8(chr(0b101110 + 0o2) + '\157' + chr(51) + chr(55) + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(0b100 + 0o54) + '\157' + '\062' + chr(2338 - 2283) + '\066', ord("\x08")), nzTpIcepk0o8(chr(0b1011 + 0o45) + chr(111) + chr(0b1011 + 0o50) + '\063' + chr(2110 - 2058), ord("\x08")), nzTpIcepk0o8(chr(214 - 166) + '\x6f' + '\062' + chr(2542 - 2487), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(2409 - 2359) + chr(49) + '\x35', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1011101 + 0o22) + chr(52) + chr(0b1011 + 0o46), 0o10), nzTpIcepk0o8(chr(0b10000 + 0o40) + chr(111) + chr(0b110001) + chr(50) + '\x35', ord("\x08")), nzTpIcepk0o8(chr(1921 - 1873) + chr(1508 - 1397) + chr(0b110001) + chr(0b101 + 0o57) + '\061', 0b1000), nzTpIcepk0o8('\x30' + chr(6777 - 6666) + chr(51) + '\x37' + chr(0b110 + 0o52), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b110110 + 0o71) + chr(50) + '\064' + chr(50), 0b1000), nzTpIcepk0o8('\060' + chr(5725 - 5614) + chr(0b101000 + 0o12) + chr(611 - 561), 8), nzTpIcepk0o8(chr(770 - 722) + chr(111) + chr(0b110010) + chr(2509 - 2458) + '\060', 29173 - 29165), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110001) + '\x32' + chr(1995 - 1946), 30540 - 30532), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(1124 - 1074) + chr(0b110000) + '\062', ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(0b101101 + 0o11) + '\067', ord("\x08")), nzTpIcepk0o8('\x30' + chr(2777 - 2666) + chr(679 - 625) + chr(0b1110 + 0o46), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(0b110010) + '\066' + '\060', 38032 - 38024), nzTpIcepk0o8(chr(0b110000) + chr(9252 - 9141) + chr(2261 - 2210) + '\066' + '\064', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x33' + chr(55) + chr(0b110100), 8), nzTpIcepk0o8(chr(0b10000 + 0o40) + chr(10416 - 10305) + '\x37' + chr(54), 0b1000), nzTpIcepk0o8(chr(2155 - 2107) + '\157' + chr(49) + chr(0b110011) + '\x33', 0o10), nzTpIcepk0o8('\x30' + chr(0b1101000 + 0o7) + '\066' + chr(320 - 272), 59417 - 59409), nzTpIcepk0o8('\060' + '\157' + '\063' + chr(0b110010) + chr(364 - 311), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x31' + '\x34' + '\066', 0o10), nzTpIcepk0o8(chr(0b10110 + 0o32) + '\x6f' + chr(0b110001) + chr(0b1011 + 0o50), 59133 - 59125), nzTpIcepk0o8(chr(1072 - 1024) + '\157' + '\x32' + chr(1212 - 1161) + '\066', 0o10), nzTpIcepk0o8(chr(48) + '\157' + '\x31' + '\065' + chr(51), 60645 - 60637), nzTpIcepk0o8('\x30' + '\157' + chr(0b11 + 0o57) + '\064' + '\063', ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(49) + '\063' + chr(54), 0o10), nzTpIcepk0o8('\060' + chr(0b10011 + 0o134) + chr(0b101101 + 0o6) + chr(2272 - 2218) + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(2065 - 2017) + chr(0b1101111) + '\x34' + chr(0b110001), 8), nzTpIcepk0o8(chr(0b10001 + 0o37) + chr(111) + chr(50) + chr(0b11111 + 0o21) + chr(49), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\061' + chr(0b110101) + chr(0b10 + 0o64), 0b1000), nzTpIcepk0o8(chr(1552 - 1504) + chr(111) + '\062' + '\x36' + chr(51), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(0b10001 + 0o42) + '\060' + chr(721 - 671), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(50) + chr(0b100100 + 0o22) + chr(0b110100), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(0b11011 + 0o124) + '\x35' + chr(989 - 941), 16398 - 16390)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'W'), chr(0b1011101 + 0o7) + chr(101) + chr(99) + '\157' + chr(0b1100011 + 0o1) + chr(0b1100101))(chr(0b1110 + 0o147) + chr(0b110101 + 0o77) + chr(0b1100110) + '\x2d' + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def cKvwmgqx2X4j(hXMPsSrOQzbh):
return ftfygxgFas5X(roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b':\x7f\xf3\xbb\x9f\xd8\xa4]\xbct<\t'), chr(100) + '\145' + chr(0b1100011) + '\x6f' + '\144' + chr(101))(chr(117) + '\x74' + chr(102) + chr(0b101101) + '\070'))) < ftfygxgFas5X(roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b' D\xf4\xbe\x8a\xce\xaa|\xd2S/\x0e'), '\144' + chr(0b1100101) + chr(0b1100011) + '\x6f' + chr(0b1011111 + 0o5) + chr(101))(chr(4880 - 4763) + '\164' + chr(0b1000011 + 0o43) + chr(45) + chr(0b100001 + 0o27)))) and roI3spqORKae(hXMPsSrOQzbh.alt, roI3spqORKae(ES5oEprVxulp(b'\nf\xdc\x9a\x88\xcd\xab~\xf9I'), chr(100) + chr(101) + chr(3635 - 3536) + chr(909 - 798) + chr(0b100011 + 0o101) + chr(0b101000 + 0o75))(chr(10207 - 10090) + chr(0b1110100) + chr(0b1100110) + chr(0b1111 + 0o36) + chr(2144 - 2088)))(roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b':\x7f\xf3\xbb\x9f\xd8\xa4]\xbct<\t'), chr(0b10001 + 0o123) + chr(0b1100000 + 0o5) + '\x63' + '\x6f' + '\x64' + '\x65')(chr(3873 - 3756) + '\x74' + chr(102) + '\055' + chr(348 - 292)))) |
openvax/varcode | varcode/variant.py | Variant.is_deletion | def is_deletion(self):
"""
Does this variant represent the deletion of nucleotides from the
reference genome?
"""
# A deletion would appear in a VCF like CT>C, so that the
# reference allele starts with the alternate nucleotides.
# This is true even in the normalized case, where the alternate
# nucleotides are an empty string.
return (len(self.ref) > len(self.alt)) and self.ref.startswith(self.alt) | python | def is_deletion(self):
"""
Does this variant represent the deletion of nucleotides from the
reference genome?
"""
# A deletion would appear in a VCF like CT>C, so that the
# reference allele starts with the alternate nucleotides.
# This is true even in the normalized case, where the alternate
# nucleotides are an empty string.
return (len(self.ref) > len(self.alt)) and self.ref.startswith(self.alt) | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/variant.py#L382-L391 | train | Is this variant represent the deletion of nucleotides from the reference genome? | 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' + '\062' + chr(49) + chr(52), ord("\x08")), nzTpIcepk0o8('\x30' + chr(10444 - 10333) + chr(49) + chr(0b110110) + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(0b11111 + 0o21) + chr(10471 - 10360) + chr(0b11111 + 0o23) + chr(0b11001 + 0o33) + chr(0b110001), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b100110 + 0o111) + chr(50) + chr(0b110111) + '\067', ord("\x08")), nzTpIcepk0o8('\060' + chr(9107 - 8996) + '\x33' + '\062' + '\060', 60682 - 60674), nzTpIcepk0o8(chr(48) + chr(4710 - 4599) + '\x31' + chr(0b11011 + 0o25), 33758 - 33750), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x32' + chr(0b11001 + 0o32) + chr(0b11111 + 0o30), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\062' + '\x30' + chr(226 - 171), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + '\062' + chr(2551 - 2499) + chr(2543 - 2492), 0b1000), nzTpIcepk0o8(chr(0b1011 + 0o45) + '\x6f' + chr(50) + chr(615 - 565) + '\x36', 0b1000), nzTpIcepk0o8(chr(0b11010 + 0o26) + '\x6f' + '\062' + chr(0b100111 + 0o20) + '\060', 0b1000), nzTpIcepk0o8('\060' + chr(0b1101110 + 0o1) + '\x31' + chr(51) + chr(0b110101 + 0o1), 5688 - 5680), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(1434 - 1383) + '\061' + chr(0b110001), 31326 - 31318), nzTpIcepk0o8(chr(48) + chr(111) + '\x31' + chr(1907 - 1853) + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(48) + chr(10379 - 10268) + '\x31' + chr(48), 8), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(333 - 278) + '\065', 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(0b1101 + 0o45) + '\066' + chr(0b110011), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101001 + 0o6) + chr(0b1111 + 0o43) + chr(0b110000) + chr(0b110111), 8), nzTpIcepk0o8(chr(785 - 737) + chr(0b110000 + 0o77) + '\x35' + '\x36', ord("\x08")), nzTpIcepk0o8('\060' + '\157' + '\062' + '\062', ord("\x08")), nzTpIcepk0o8('\060' + chr(2730 - 2619) + chr(50) + chr(139 - 84) + '\064', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b100010 + 0o115) + chr(0b110011) + chr(0b110111) + chr(55), 0o10), nzTpIcepk0o8(chr(0b1001 + 0o47) + '\157' + '\062' + chr(54) + '\x37', 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(1203 - 1150), ord("\x08")), nzTpIcepk0o8('\060' + chr(6656 - 6545) + chr(49) + chr(1186 - 1132) + chr(0b110111), 14548 - 14540), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(50) + chr(52) + chr(0b10101 + 0o35), 0b1000), nzTpIcepk0o8('\060' + chr(0b110110 + 0o71) + chr(2356 - 2306) + chr(51) + chr(751 - 697), 0b1000), nzTpIcepk0o8(chr(988 - 940) + '\x6f' + '\063' + chr(0b110101) + chr(49), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110110) + chr(0b110110), 0b1000), nzTpIcepk0o8(chr(301 - 253) + '\157' + chr(54), 31386 - 31378), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110010) + chr(0b110001) + chr(0b110000), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(143 - 93) + '\060', 0b1000), nzTpIcepk0o8('\x30' + chr(12306 - 12195) + chr(509 - 458) + '\x34' + chr(0b10110 + 0o37), 25063 - 25055), nzTpIcepk0o8('\x30' + chr(0b11 + 0o154) + chr(1475 - 1423) + '\x31', 47301 - 47293), nzTpIcepk0o8('\x30' + chr(5203 - 5092) + chr(417 - 368) + chr(0b1110 + 0o42) + chr(1568 - 1514), 0b1000), nzTpIcepk0o8(chr(0b1001 + 0o47) + chr(0b101100 + 0o103) + chr(289 - 238) + chr(0b110110) + chr(0b110110), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110011) + '\x36' + chr(1608 - 1553), ord("\x08")), nzTpIcepk0o8(chr(1474 - 1426) + chr(0b1001 + 0o146) + chr(0b110011) + chr(0b110000) + '\x35', 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(0b10111 + 0o32) + chr(54) + '\065', 8), nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(0b111001 + 0o66) + '\061' + '\063' + chr(51), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(1106 - 1058) + '\x6f' + '\065' + '\060', ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xa2'), chr(0b1100010 + 0o2) + chr(1053 - 952) + '\143' + chr(0b1101111) + chr(2663 - 2563) + chr(101))(chr(0b1100000 + 0o25) + '\164' + '\146' + chr(45) + chr(1393 - 1337)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def cy8cYFKcZ_8P(hXMPsSrOQzbh):
return ftfygxgFas5X(roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xcf\x18\xef\xec\xb3n\xe7\xcd\x92\xc3\xd16'), chr(0b111 + 0o135) + chr(101) + chr(99) + chr(3953 - 3842) + chr(8519 - 8419) + '\145')(chr(0b1111 + 0o146) + chr(10067 - 9951) + chr(102) + chr(45) + '\070'))) > ftfygxgFas5X(roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xd5#\xe8\xe9\xa6x\xe9\xec\xfc\xe4\xc21'), chr(0b1100100) + '\145' + '\x63' + chr(0b1101111) + chr(0b1100100) + chr(0b1100101))('\x75' + '\x74' + '\x66' + '\055' + chr(2974 - 2918)))) and roI3spqORKae(hXMPsSrOQzbh.ref, roI3spqORKae(ES5oEprVxulp(b'\xff\x01\xc0\xcd\xa4{\xe8\xee\xd7\xfe'), chr(9652 - 9552) + chr(101) + '\x63' + chr(7059 - 6948) + '\144' + chr(878 - 777))(chr(8020 - 7903) + chr(850 - 734) + chr(5693 - 5591) + chr(663 - 618) + chr(0b111000)))(roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xd5#\xe8\xe9\xa6x\xe9\xec\xfc\xe4\xc21'), chr(0b1100100) + chr(0b100101 + 0o100) + chr(0b1100011) + chr(0b1101111) + '\x64' + chr(0b1100101))('\x75' + '\x74' + '\x66' + chr(896 - 851) + '\070'))) |
openvax/varcode | varcode/variant.py | Variant.is_snv | def is_snv(self):
"""Is the variant a single nucleotide variant"""
return (len(self.ref) == len(self.alt) == 1) and (self.ref != self.alt) | python | def is_snv(self):
"""Is the variant a single nucleotide variant"""
return (len(self.ref) == len(self.alt) == 1) and (self.ref != self.alt) | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/variant.py#L399-L401 | train | Is the variant a single nucleotide variant | 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(273 - 162) + '\062' + '\x32' + chr(54), 0o10), nzTpIcepk0o8('\060' + chr(8634 - 8523) + '\x31' + '\x35' + chr(0b11111 + 0o24), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110110 + 0o1) + chr(53), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(9698 - 9587) + '\063' + chr(704 - 653) + chr(1013 - 959), 31130 - 31122), nzTpIcepk0o8(chr(1925 - 1877) + chr(0b1101111) + '\x37' + chr(2359 - 2309), ord("\x08")), nzTpIcepk0o8(chr(0b101101 + 0o3) + chr(0b100 + 0o153) + '\066' + chr(0b110011), 0o10), nzTpIcepk0o8(chr(0b1000 + 0o50) + chr(10474 - 10363) + chr(0b110011) + '\x33', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110010) + chr(51), 0o10), nzTpIcepk0o8('\x30' + chr(1286 - 1175) + chr(318 - 269) + chr(0b100000 + 0o23) + '\060', 31900 - 31892), nzTpIcepk0o8(chr(159 - 111) + chr(0b1101111) + chr(0b1110 + 0o45) + chr(0b110011) + chr(0b110001 + 0o6), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(1730 - 1680) + chr(0b110010), 0o10), nzTpIcepk0o8('\060' + '\x6f' + '\x31' + chr(0b1110 + 0o42) + chr(1289 - 1240), 0b1000), nzTpIcepk0o8(chr(1718 - 1670) + chr(7846 - 7735) + chr(49) + chr(55) + chr(49), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + '\x31' + chr(541 - 492) + chr(0b110100), 0o10), nzTpIcepk0o8('\x30' + chr(0b1011101 + 0o22) + '\x31' + '\x32' + '\060', ord("\x08")), nzTpIcepk0o8(chr(0b101011 + 0o5) + chr(3743 - 3632) + chr(0b110110 + 0o0) + chr(0b110001), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(235 - 186) + chr(50), 0o10), nzTpIcepk0o8(chr(139 - 91) + chr(0b1100101 + 0o12) + chr(0b101100 + 0o5) + chr(0b10001 + 0o44) + chr(239 - 189), 0o10), nzTpIcepk0o8(chr(0b101000 + 0o10) + '\x6f' + chr(0b100010 + 0o21) + chr(138 - 84) + chr(1078 - 1025), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(51) + chr(48) + chr(158 - 108), 0b1000), nzTpIcepk0o8(chr(990 - 942) + '\x6f' + chr(49) + chr(0b100110 + 0o17), 0b1000), nzTpIcepk0o8('\x30' + chr(3137 - 3026) + chr(0b110001) + '\x34' + '\066', ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + '\x33' + chr(1052 - 997) + chr(48), 11847 - 11839), nzTpIcepk0o8('\060' + '\157' + chr(0b110001 + 0o2) + chr(48) + chr(0b110101), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + '\061' + '\x33' + '\x31', 18122 - 18114), nzTpIcepk0o8(chr(48) + '\x6f' + '\060', 0b1000), nzTpIcepk0o8(chr(377 - 329) + '\157' + chr(499 - 450) + '\064' + '\x35', 0b1000), nzTpIcepk0o8(chr(48) + chr(10636 - 10525) + chr(1318 - 1267) + '\067' + chr(1694 - 1644), 43769 - 43761), nzTpIcepk0o8(chr(48) + chr(5734 - 5623) + chr(0b110001) + chr(0b10111 + 0o33) + '\x36', 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x31' + '\x30' + chr(48), 58798 - 58790), nzTpIcepk0o8('\060' + chr(1330 - 1219) + chr(0b100010 + 0o23) + chr(0b110001), 0o10), nzTpIcepk0o8(chr(1703 - 1655) + chr(4616 - 4505) + '\063' + chr(0b110000) + '\066', ord("\x08")), nzTpIcepk0o8('\x30' + chr(469 - 358) + chr(51) + chr(49) + chr(0b1001 + 0o56), ord("\x08")), nzTpIcepk0o8(chr(2028 - 1980) + chr(0b1101111) + chr(0b10110 + 0o37) + '\063', 723 - 715), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(51) + '\x33' + chr(51), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + '\x33' + chr(0b11111 + 0o22) + chr(53), 37990 - 37982), nzTpIcepk0o8('\060' + chr(111) + chr(2466 - 2416) + chr(0b110001) + chr(52), 14972 - 14964), nzTpIcepk0o8('\x30' + chr(3366 - 3255) + '\x31' + chr(0b100 + 0o56) + chr(0b11111 + 0o22), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(0b11011 + 0o27) + chr(437 - 389) + chr(0b100111 + 0o15), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(1676 - 1626) + '\063' + chr(51), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b10100 + 0o34) + chr(0b1101111) + chr(0b110101) + '\060', ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xb8'), chr(100) + '\145' + chr(99) + chr(2617 - 2506) + chr(0b1100100) + chr(0b1001100 + 0o31))('\x75' + chr(0b1110100) + '\146' + chr(0b11000 + 0o25) + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def ekiqOCxbRQjU(hXMPsSrOQzbh):
return ftfygxgFas5X(roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xd5\x06s\x8dYUcYi\x8a{)'), chr(0b1100100) + chr(2240 - 2139) + chr(99) + chr(0b1101111 + 0o0) + chr(3639 - 3539) + '\x65')('\165' + chr(0b1110100) + chr(0b101011 + 0o73) + '\055' + '\x38'))) == ftfygxgFas5X(roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xcf=t\x88LCmx\x07\xadh.'), '\144' + chr(0b1100101) + chr(99) + chr(0b110110 + 0o71) + chr(8478 - 8378) + chr(2911 - 2810))('\x75' + chr(116) + chr(0b1100110) + chr(45) + chr(0b110110 + 0o2)))) == nzTpIcepk0o8('\x30' + '\x6f' + chr(0b1010 + 0o47), ord("\x08")) and roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xd5\x06s\x8dYUcYi\x8a{)'), chr(1952 - 1852) + chr(101) + chr(99) + '\x6f' + chr(100) + chr(101))('\x75' + '\x74' + chr(1890 - 1788) + '\055' + chr(0b111000))) != roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xcf=t\x88LCmx\x07\xadh.'), chr(0b1100100) + chr(5971 - 5870) + chr(0b1100011) + chr(0b110111 + 0o70) + chr(100) + chr(673 - 572))(chr(0b1110101) + '\164' + chr(0b1100110) + '\055' + chr(56))) |
openvax/varcode | varcode/variant.py | Variant.is_transition | def is_transition(self):
"""Is this variant and pyrimidine to pyrimidine change or purine to purine change"""
return self.is_snv and is_purine(self.ref) == is_purine(self.alt) | python | def is_transition(self):
"""Is this variant and pyrimidine to pyrimidine change or purine to purine change"""
return self.is_snv and is_purine(self.ref) == is_purine(self.alt) | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/variant.py#L404-L406 | train | Is this variant and pyrimidine to pyrimidine change? | 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(0b0 + 0o61) + chr(0b1110 + 0o42) + chr(802 - 753), 30997 - 30989), nzTpIcepk0o8('\060' + '\x6f' + chr(0b11 + 0o56) + chr(55) + chr(0b1100 + 0o53), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1000000 + 0o57) + '\062' + chr(0b110001) + chr(80 - 30), 16918 - 16910), nzTpIcepk0o8(chr(903 - 855) + '\x6f' + '\063' + chr(0b110001 + 0o6) + chr(53), 14109 - 14101), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b100111 + 0o13) + chr(2487 - 2433) + '\060', 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(50) + '\x30' + '\060', 64870 - 64862), nzTpIcepk0o8('\x30' + chr(7640 - 7529) + '\061' + chr(339 - 291) + '\x31', 8), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b10111 + 0o34) + chr(0b110100) + chr(0b110101), 0o10), nzTpIcepk0o8(chr(0b1101 + 0o43) + chr(5258 - 5147) + '\x33' + chr(54) + chr(55), ord("\x08")), nzTpIcepk0o8(chr(368 - 320) + '\x6f' + chr(0b110010) + chr(0b10111 + 0o37) + '\x32', 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(2277 - 2228) + '\x30' + chr(53), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(0b11 + 0o57) + chr(0b110111) + '\067', 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110011) + '\x33' + chr(51), 61798 - 61790), nzTpIcepk0o8(chr(131 - 83) + '\157' + chr(49) + '\064' + '\061', 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(54) + chr(0b101110 + 0o6), 58104 - 58096), nzTpIcepk0o8('\x30' + chr(0b111101 + 0o62) + '\063' + chr(52), 0o10), nzTpIcepk0o8(chr(0b101110 + 0o2) + chr(624 - 513) + chr(0b110011 + 0o0) + chr(0b110110), 22019 - 22011), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b101101 + 0o4) + '\x34' + chr(1321 - 1271), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b100010 + 0o20) + '\x31' + '\061', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(614 - 564) + chr(2658 - 2604) + '\x30', 8), nzTpIcepk0o8(chr(0b100011 + 0o15) + chr(3770 - 3659) + '\061' + chr(0b110110) + chr(1985 - 1936), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\061' + '\x32', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b100110 + 0o111) + chr(835 - 784) + chr(1247 - 1199) + '\066', 30032 - 30024), nzTpIcepk0o8('\060' + chr(4456 - 4345) + chr(0b100000 + 0o22) + chr(48) + chr(0b110000), 8), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(50) + chr(0b100111 + 0o12) + chr(0b1011 + 0o45), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x31' + chr(0b110101) + '\x35', 44283 - 44275), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110011) + chr(0b110101), 26222 - 26214), nzTpIcepk0o8('\x30' + chr(0b1010110 + 0o31) + '\063' + '\x33', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b100110 + 0o17) + chr(1539 - 1491), 430 - 422), nzTpIcepk0o8(chr(0b100010 + 0o16) + '\x6f' + chr(0b110010) + '\x36' + chr(2028 - 1978), 8), nzTpIcepk0o8(chr(0b100011 + 0o15) + chr(111) + '\062' + '\061' + '\x36', 8021 - 8013), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\065' + chr(0b110011), 54998 - 54990), nzTpIcepk0o8(chr(0b10000 + 0o40) + chr(111) + chr(0b100 + 0o57) + chr(50) + chr(0b11001 + 0o34), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110011) + chr(0b110101) + chr(0b10110 + 0o41), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1011110 + 0o21) + chr(0b101111 + 0o3) + '\x37' + chr(0b1001 + 0o52), 33741 - 33733), nzTpIcepk0o8(chr(568 - 520) + chr(111) + chr(0b111 + 0o53) + chr(0b110111) + '\x33', 8), nzTpIcepk0o8(chr(1946 - 1898) + chr(11753 - 11642) + chr(0b1001 + 0o50) + chr(0b110010) + chr(0b10100 + 0o36), ord("\x08")), nzTpIcepk0o8(chr(0b101 + 0o53) + chr(8612 - 8501) + '\x37' + chr(1803 - 1755), 24317 - 24309), nzTpIcepk0o8(chr(0b100111 + 0o11) + '\157' + '\061' + '\065' + chr(0b10000 + 0o40), 16278 - 16270), nzTpIcepk0o8('\x30' + chr(0b1000011 + 0o54) + chr(382 - 332) + chr(0b110110) + chr(0b110000), 8)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + chr(0b1101111) + '\x35' + chr(0b110000), 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'o'), chr(100) + '\x65' + '\x63' + chr(0b1101111) + '\x64' + chr(0b1100101))('\x75' + chr(0b10001 + 0o143) + '\x66' + chr(45) + chr(545 - 489)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def oXBI5ffk7WoK(hXMPsSrOQzbh):
return roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'(\x0c\xd5\x8e\xde\xf6'), chr(0b1010111 + 0o15) + chr(6967 - 6866) + chr(0b1100011) + '\157' + '\x64' + chr(101))(chr(117) + chr(116) + chr(1275 - 1173) + chr(45) + chr(0b111000))) and bYsCaM7zwsek(roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x02\x12\xc4\xae\xd3\xe69\xaf\xc6\xe7,\xd7'), '\144' + '\x65' + '\143' + '\x6f' + chr(0b1 + 0o143) + chr(101))(chr(117) + chr(0b1110100) + chr(8376 - 8274) + '\055' + chr(252 - 196)))) == bYsCaM7zwsek(roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x18)\xc3\xab\xc6\xf07\x8e\xa8\xc0?\xd0'), chr(0b11011 + 0o111) + chr(5975 - 5874) + '\x63' + '\x6f' + chr(0b1100100) + chr(0b110000 + 0o65))(chr(117) + '\164' + chr(0b11011 + 0o113) + '\x2d' + '\070'))) |
openvax/varcode | varcode/variant.py | Variant.is_transversion | def is_transversion(self):
"""Is this variant a pyrimidine to purine change or vice versa"""
return self.is_snv and is_purine(self.ref) != is_purine(self.alt) | python | def is_transversion(self):
"""Is this variant a pyrimidine to purine change or vice versa"""
return self.is_snv and is_purine(self.ref) != is_purine(self.alt) | [
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"versa"
] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/variant.py#L409-L411 | train | Is this variant a pyrimidine to purine change vice versa? | 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(0b10000 + 0o40) + '\157' + chr(0b101 + 0o54) + '\x33' + chr(50), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\061' + chr(50), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\062' + chr(0b110100) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(49) + '\062', 8), nzTpIcepk0o8(chr(1374 - 1326) + chr(490 - 379) + chr(0b1111 + 0o47) + chr(0b110101), 40330 - 40322), nzTpIcepk0o8('\060' + '\x6f' + chr(0b10 + 0o64) + '\067', 13246 - 13238), nzTpIcepk0o8(chr(0b110000) + chr(0b1001 + 0o146) + '\063' + '\x36', 41819 - 41811), nzTpIcepk0o8('\060' + '\x6f' + chr(54), 0o10), nzTpIcepk0o8(chr(48) + chr(6723 - 6612) + '\061' + '\x33' + chr(0b110000 + 0o6), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b10111 + 0o32) + chr(0b10011 + 0o37) + chr(55), 13996 - 13988), nzTpIcepk0o8(chr(0b0 + 0o60) + '\x6f' + chr(0b1010 + 0o50) + chr(0b110001) + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(904 - 855) + chr(0b1100 + 0o47) + '\066', 8), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(318 - 265) + chr(0b110000), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b10 + 0o155) + chr(50) + chr(0b11010 + 0o30) + '\x36', 0b1000), nzTpIcepk0o8(chr(704 - 656) + '\157' + chr(51) + '\064' + chr(0b100000 + 0o22), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(50) + '\x32' + '\x32', 0o10), nzTpIcepk0o8('\060' + chr(0b110010 + 0o75) + '\x33' + '\x31' + chr(0b110001), 0o10), nzTpIcepk0o8(chr(0b1100 + 0o44) + chr(0b111100 + 0o63) + chr(0b1000 + 0o53) + '\x36' + '\x30', ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b1100 + 0o47) + chr(49) + chr(0b110011), 0o10), nzTpIcepk0o8(chr(0b100111 + 0o11) + '\157' + chr(0b1110 + 0o43) + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + '\062' + chr(53) + chr(0b101110 + 0o2), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b110111 + 0o70) + chr(0b110011) + chr(1241 - 1189) + chr(48), 0o10), nzTpIcepk0o8('\x30' + chr(0b111100 + 0o63) + chr(0b10011 + 0o36) + chr(1898 - 1847) + '\063', 0b1000), nzTpIcepk0o8(chr(548 - 500) + chr(9295 - 9184) + chr(0b100100 + 0o15) + chr(54) + chr(54), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x33' + chr(324 - 272) + chr(0b110001), 0o10), nzTpIcepk0o8(chr(1694 - 1646) + chr(858 - 747) + chr(811 - 760) + '\x30' + chr(0b110011), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(50) + '\066', 0o10), nzTpIcepk0o8(chr(0b1011 + 0o45) + chr(0b1101111) + '\x33' + '\063' + '\063', 25564 - 25556), nzTpIcepk0o8(chr(2047 - 1999) + chr(111) + '\x31' + chr(2111 - 2061) + '\066', 45876 - 45868), nzTpIcepk0o8(chr(48) + chr(0b1100100 + 0o13) + '\063' + '\x30' + chr(0b110110), 0o10), nzTpIcepk0o8(chr(1910 - 1862) + '\157' + '\067' + chr(0b110100), 0b1000), nzTpIcepk0o8('\060' + chr(12256 - 12145) + chr(0b10011 + 0o40) + '\065' + chr(2666 - 2614), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(52), 10843 - 10835), nzTpIcepk0o8('\060' + '\x6f' + chr(0b101101 + 0o5) + '\065' + chr(0b11000 + 0o30), 8), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110011) + chr(0b110001) + chr(54), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110101) + '\x31', 59578 - 59570), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110011) + chr(1064 - 1009), 663 - 655), nzTpIcepk0o8(chr(0b11100 + 0o24) + chr(0b10 + 0o155) + chr(0b110001) + chr(0b110010) + chr(0b110001 + 0o6), 8), nzTpIcepk0o8(chr(0b11000 + 0o30) + chr(0b1101111) + chr(0b110011) + chr(1532 - 1478) + chr(51), 0o10), nzTpIcepk0o8(chr(737 - 689) + chr(0b1101111) + chr(0b100 + 0o56) + '\x32' + '\x35', 48395 - 48387)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b101010 + 0o6) + '\x6f' + chr(1624 - 1571) + chr(773 - 725), 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b't'), '\144' + chr(3726 - 3625) + '\143' + '\157' + chr(0b1000011 + 0o41) + chr(0b110001 + 0o64))(chr(117) + chr(116) + chr(102) + chr(0b101101) + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def lehe_5hnrO_q(hXMPsSrOQzbh):
return roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'3y\xfcy[A'), chr(6197 - 6097) + chr(101) + chr(0b1100011) + chr(5935 - 5824) + '\144' + chr(9545 - 9444))(chr(117) + chr(116) + '\146' + '\x2d' + chr(0b111000))) and bYsCaM7zwsek(roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x19g\xedYVQfLo\x02\xe26'), chr(0b1100100) + chr(0b1100101) + chr(0b1100011) + '\x6f' + chr(0b0 + 0o144) + '\x65')('\165' + chr(116) + '\146' + chr(0b10110 + 0o27) + '\x38'))) != bYsCaM7zwsek(roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x03\\\xea\\CGhm\x01%\xf11'), '\144' + chr(0b11111 + 0o106) + chr(99) + chr(0b100100 + 0o113) + '\x64' + chr(0b1100101))(chr(4159 - 4042) + chr(0b1110100) + chr(0b1100110) + '\x2d' + chr(2192 - 2136)))) |
openvax/varcode | varcode/effects/effect_helpers.py | variant_overlaps_interval | def variant_overlaps_interval(
variant_start,
n_ref_bases,
interval_start,
interval_end):
"""
Does a variant overlap a given interval on the same chromosome?
Parameters
----------
variant_start : int
Inclusive base-1 position of variant's starting location
(or location before an insertion)
n_ref_bases : int
Number of reference bases affect by variant (used to compute
end coordinate or determine whether variant is an insertion)
interval_start : int
Interval's inclusive base-1 start position
interval_end : int
Interval's inclusive base-1 end position
"""
if n_ref_bases == 0:
# insertions only overlap intervals which start before and
# end after the insertion point, they must be fully contained
# by the other interval
return interval_start <= variant_start and interval_end >= variant_start
variant_end = variant_start + n_ref_bases
"""
if self._changes_exonic_splice_site(
strand_ref,
strand_alt,)
"""
# overlap means other interval starts before this variant ends
# and the interval ends after this variant starts
return interval_start <= variant_end and interval_end >= variant_start | python | def variant_overlaps_interval(
variant_start,
n_ref_bases,
interval_start,
interval_end):
"""
Does a variant overlap a given interval on the same chromosome?
Parameters
----------
variant_start : int
Inclusive base-1 position of variant's starting location
(or location before an insertion)
n_ref_bases : int
Number of reference bases affect by variant (used to compute
end coordinate or determine whether variant is an insertion)
interval_start : int
Interval's inclusive base-1 start position
interval_end : int
Interval's inclusive base-1 end position
"""
if n_ref_bases == 0:
# insertions only overlap intervals which start before and
# end after the insertion point, they must be fully contained
# by the other interval
return interval_start <= variant_start and interval_end >= variant_start
variant_end = variant_start + n_ref_bases
"""
if self._changes_exonic_splice_site(
strand_ref,
strand_alt,)
"""
# overlap means other interval starts before this variant ends
# and the interval ends after this variant starts
return interval_start <= variant_end and interval_end >= variant_start | [
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variant_start : int
Inclusive base-1 position of variant's starting location
(or location before an insertion)
n_ref_bases : int
Number of reference bases affect by variant (used to compute
end coordinate or determine whether variant is an insertion)
interval_start : int
Interval's inclusive base-1 start position
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Interval's inclusive base-1 end position | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/effect_helpers.py#L23-L61 | train | Returns True if the given interval of a given variant is contained within the given base - 1 interval. | 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(8100 - 7989) + '\x32' + '\063' + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b10001 + 0o136) + chr(0b110000 + 0o4) + chr(54), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1100010 + 0o15) + chr(1153 - 1102) + chr(51) + chr(0b110001), 28400 - 28392), nzTpIcepk0o8('\x30' + chr(111) + '\x30', 9142 - 9134), nzTpIcepk0o8('\x30' + '\x6f' + chr(50) + chr(55) + chr(0b110010), 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(0b1100 + 0o46) + chr(0b100000 + 0o25) + '\066', 62946 - 62938), nzTpIcepk0o8(chr(1137 - 1089) + '\157' + chr(0b110011), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + '\x32' + chr(0b110000), 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(1825 - 1776) + '\060' + '\x32', 0b1000), nzTpIcepk0o8(chr(1467 - 1419) + chr(9669 - 9558) + '\x33' + '\060' + chr(0b110110), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b10010 + 0o135) + chr(49) + chr(0b101100 + 0o11) + chr(0b110101), 0o10), nzTpIcepk0o8(chr(1854 - 1806) + chr(3777 - 3666) + chr(0b110110) + '\x36', 0o10), nzTpIcepk0o8('\x30' + chr(111) + '\x35' + chr(1571 - 1523), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(3147 - 3036) + chr(0b110011) + chr(48) + '\066', 8), nzTpIcepk0o8(chr(0b110000) + chr(6681 - 6570) + chr(930 - 880) + chr(0b100100 + 0o21), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1001010 + 0o45) + chr(53) + '\064', 0b1000), nzTpIcepk0o8(chr(0b11000 + 0o30) + chr(111) + chr(720 - 670) + chr(0b110011) + chr(52), 36574 - 36566), nzTpIcepk0o8(chr(1055 - 1007) + chr(9021 - 8910) + chr(0b101 + 0o56) + '\x33' + chr(2226 - 2175), 35985 - 35977), nzTpIcepk0o8(chr(0b110000) + chr(0b1101101 + 0o2) + chr(51) + chr(0b110000) + chr(0b11110 + 0o31), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(55) + chr(48), 32269 - 32261), nzTpIcepk0o8('\060' + chr(111) + chr(0b100011 + 0o17) + chr(0b1101 + 0o50) + chr(0b101 + 0o60), 0o10), nzTpIcepk0o8(chr(0b10011 + 0o35) + '\157' + chr(484 - 435) + '\x31' + '\x30', 0o10), nzTpIcepk0o8(chr(1481 - 1433) + '\x6f' + chr(0b110001 + 0o0) + chr(0b111 + 0o57) + chr(48), ord("\x08")), nzTpIcepk0o8(chr(0b100011 + 0o15) + '\157' + chr(0b11100 + 0o27) + chr(0b110010) + '\x37', 0o10), nzTpIcepk0o8(chr(0b10110 + 0o32) + chr(111) + chr(0b110011) + chr(49) + chr(0b100001 + 0o26), ord("\x08")), nzTpIcepk0o8(chr(0b110 + 0o52) + chr(0b1010010 + 0o35) + '\061' + chr(0b10 + 0o62) + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(0b100000 + 0o21) + chr(51) + chr(2219 - 2170), 0b1000), nzTpIcepk0o8('\x30' + chr(8699 - 8588) + chr(0b110011) + chr(51) + '\062', 0o10), nzTpIcepk0o8(chr(0b10010 + 0o36) + chr(5296 - 5185) + '\x32' + chr(2190 - 2136) + chr(0b110100), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110010) + '\063' + chr(0b110110), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(51) + chr(0b110010) + '\062', 0o10), nzTpIcepk0o8(chr(0b11101 + 0o23) + chr(0b1001111 + 0o40) + chr(0b110010) + chr(1148 - 1097) + chr(2140 - 2090), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(1841 - 1788) + chr(0b1001 + 0o47), 8), nzTpIcepk0o8('\x30' + chr(0b1101011 + 0o4) + '\x36' + '\x30', 0o10), nzTpIcepk0o8('\060' + chr(111) + '\062' + chr(394 - 341) + '\x35', 8), nzTpIcepk0o8(chr(0b110000) + chr(0b110010 + 0o75) + chr(0b110010) + chr(0b110010) + chr(1987 - 1935), ord("\x08")), nzTpIcepk0o8('\x30' + chr(8282 - 8171) + chr(115 - 66) + chr(54), 0o10), nzTpIcepk0o8('\060' + chr(10798 - 10687) + chr(0b100 + 0o55) + '\x33' + '\x37', 0o10), nzTpIcepk0o8(chr(0b101101 + 0o3) + chr(111) + chr(51) + chr(0b0 + 0o63) + chr(0b110110), 6811 - 6803), nzTpIcepk0o8('\060' + chr(9238 - 9127) + chr(0b11 + 0o60) + chr(0b101110 + 0o4) + '\x35', 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b10110 + 0o32) + chr(0b111101 + 0o62) + chr(525 - 472) + '\x30', 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xb1'), '\144' + chr(0b1000101 + 0o40) + chr(0b1000000 + 0o43) + chr(0b1100101 + 0o12) + chr(0b1001110 + 0o26) + chr(0b100 + 0o141))('\x75' + chr(0b101110 + 0o106) + chr(0b1100110) + '\055' + chr(591 - 535)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def EhFLzadzq9Mc(fvOw4SZvhoGW, gcOdJ8X5uoo4, Q2fEodRHzPLg, gK1XqSrjqaxP):
if gcOdJ8X5uoo4 == nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110000), 8):
return Q2fEodRHzPLg <= fvOw4SZvhoGW and gK1XqSrjqaxP >= fvOw4SZvhoGW
QjYr_nlhPhpd = fvOw4SZvhoGW + gcOdJ8X5uoo4
return Q2fEodRHzPLg <= QjYr_nlhPhpd and gK1XqSrjqaxP >= fvOw4SZvhoGW |
openvax/varcode | varcode/effects/effect_helpers.py | changes_exonic_splice_site | def changes_exonic_splice_site(
transcript_offset,
transcript,
transcript_ref,
transcript_alt,
exon_start_offset,
exon_end_offset,
exon_number):
"""Does the given exonic mutation of a particular transcript change a
splice site?
Parameters
----------
transcript_offset : int
Offset from start of transcript of first reference nucleotide
(or the last nucleotide before an insertion)
transcript : pyensembl.Transcript
transcript_ref : str
Reference nucleotides
transcript_alt : alt
Alternate nucleotides
exon_start_offset : int
Start offset of exon relative to beginning of transcript
exon_end_offset : int
End offset of exon relative to beginning of transcript
exon_number : int
Which exon in the order they form the transcript
"""
# first we're going to make sure the variant doesn't disrupt the
# splicing sequences we got from Divina et. al's
# Ab initio prediction of mutation-induced cryptic
# splice-site activation and exon skipping
# (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2947103/)
#
# 5' splice site: MAG|GURAGU consensus
# M is A or C; R is purine; | is the exon-intron boundary
#
# 3' splice site: YAG|R
#
if exon_number > 1 and transcript_offset == exon_start_offset:
# if this is any exon past the first, check to see if it lost
# the purine on its left side
#
# the 3' splice site sequence has just a single purine on
# the exon side
if len(transcript_ref) > 0 and transcript_ref[0] in PURINE_NUCLEOTIDES:
if len(transcript_alt) > 0:
if transcript_alt[0] not in PURINE_NUCLEOTIDES:
return True
else:
# if the mutation is a deletion, are there ref nucleotides
# afterward?
offset_after_deletion = transcript_offset + len(transcript_ref)
if len(transcript.sequence) > offset_after_deletion:
next_base = transcript.sequence[offset_after_deletion]
if next_base not in PURINE_NUCLEOTIDES:
return True
if exon_number < len(transcript.exons):
# if the mutation affects an exon whose right end gets spliced
# to a next exon, check if the variant alters the exon side of
# 5' consensus splicing sequence
#
# splicing sequence:
# MAG|GURAGU
# M is A or C; R is purine; | is the exon-intron boundary
#
# TODO: check for overlap of two intervals instead of just
# seeing if the mutation starts inside the exonic splice site
if variant_overlaps_interval(
variant_start=transcript_offset,
n_ref_bases=len(transcript_ref),
interval_start=exon_end_offset - 2,
interval_end=exon_end_offset):
end_of_reference_exon = transcript.sequence[
exon_end_offset - 2:exon_end_offset + 1]
if matches_exon_end_pattern(end_of_reference_exon):
# if the last three nucleotides conform to the consensus
# sequence then treat any deviation as an ExonicSpliceSite
# mutation
end_of_variant_exon = end_of_reference_exon
if matches_exon_end_pattern(end_of_variant_exon):
# end of exon matches splicing signal, check if it still
# does after the mutation
return True | python | def changes_exonic_splice_site(
transcript_offset,
transcript,
transcript_ref,
transcript_alt,
exon_start_offset,
exon_end_offset,
exon_number):
"""Does the given exonic mutation of a particular transcript change a
splice site?
Parameters
----------
transcript_offset : int
Offset from start of transcript of first reference nucleotide
(or the last nucleotide before an insertion)
transcript : pyensembl.Transcript
transcript_ref : str
Reference nucleotides
transcript_alt : alt
Alternate nucleotides
exon_start_offset : int
Start offset of exon relative to beginning of transcript
exon_end_offset : int
End offset of exon relative to beginning of transcript
exon_number : int
Which exon in the order they form the transcript
"""
# first we're going to make sure the variant doesn't disrupt the
# splicing sequences we got from Divina et. al's
# Ab initio prediction of mutation-induced cryptic
# splice-site activation and exon skipping
# (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2947103/)
#
# 5' splice site: MAG|GURAGU consensus
# M is A or C; R is purine; | is the exon-intron boundary
#
# 3' splice site: YAG|R
#
if exon_number > 1 and transcript_offset == exon_start_offset:
# if this is any exon past the first, check to see if it lost
# the purine on its left side
#
# the 3' splice site sequence has just a single purine on
# the exon side
if len(transcript_ref) > 0 and transcript_ref[0] in PURINE_NUCLEOTIDES:
if len(transcript_alt) > 0:
if transcript_alt[0] not in PURINE_NUCLEOTIDES:
return True
else:
# if the mutation is a deletion, are there ref nucleotides
# afterward?
offset_after_deletion = transcript_offset + len(transcript_ref)
if len(transcript.sequence) > offset_after_deletion:
next_base = transcript.sequence[offset_after_deletion]
if next_base not in PURINE_NUCLEOTIDES:
return True
if exon_number < len(transcript.exons):
# if the mutation affects an exon whose right end gets spliced
# to a next exon, check if the variant alters the exon side of
# 5' consensus splicing sequence
#
# splicing sequence:
# MAG|GURAGU
# M is A or C; R is purine; | is the exon-intron boundary
#
# TODO: check for overlap of two intervals instead of just
# seeing if the mutation starts inside the exonic splice site
if variant_overlaps_interval(
variant_start=transcript_offset,
n_ref_bases=len(transcript_ref),
interval_start=exon_end_offset - 2,
interval_end=exon_end_offset):
end_of_reference_exon = transcript.sequence[
exon_end_offset - 2:exon_end_offset + 1]
if matches_exon_end_pattern(end_of_reference_exon):
# if the last three nucleotides conform to the consensus
# sequence then treat any deviation as an ExonicSpliceSite
# mutation
end_of_variant_exon = end_of_reference_exon
if matches_exon_end_pattern(end_of_variant_exon):
# end of exon matches splicing signal, check if it still
# does after the mutation
return True | [
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splice site?
Parameters
----------
transcript_offset : int
Offset from start of transcript of first reference nucleotide
(or the last nucleotide before an insertion)
transcript : pyensembl.Transcript
transcript_ref : str
Reference nucleotides
transcript_alt : alt
Alternate nucleotides
exon_start_offset : int
Start offset of exon relative to beginning of transcript
exon_end_offset : int
End offset of exon relative to beginning of transcript
exon_number : int
Which exon in the order they form the transcript | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/effect_helpers.py#L72-L163 | train | Does the given exonic mutation of a particular transcript change a specific splice site? | 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(0b101000 + 0o10) + chr(0b1010101 + 0o32) + chr(50) + '\065' + chr(48), 664 - 656), nzTpIcepk0o8(chr(1986 - 1938) + chr(111) + '\x31' + '\x35' + chr(451 - 403), 15541 - 15533), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(54) + chr(0b111 + 0o52), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + '\062' + '\x34', ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110001) + '\x30' + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + '\x31' + chr(0b110000 + 0o5) + chr(0b100100 + 0o20), 59431 - 59423), nzTpIcepk0o8('\x30' + chr(6737 - 6626) + chr(0b11000 + 0o31) + '\062' + '\063', 10879 - 10871), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x31' + '\x33' + chr(1794 - 1743), 57556 - 57548), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b100 + 0o57) + '\x34' + chr(2093 - 2039), 10421 - 10413), nzTpIcepk0o8(chr(2241 - 2193) + '\157' + chr(0b10 + 0o60) + '\060' + chr(0b110000), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b10000 + 0o43) + chr(1548 - 1499) + chr(54), ord("\x08")), nzTpIcepk0o8('\x30' + chr(7293 - 7182) + chr(0b1111 + 0o42) + chr(49) + chr(49), 10762 - 10754), nzTpIcepk0o8('\060' + '\x6f' + chr(1376 - 1327) + chr(0b11100 + 0o27) + '\067', 49742 - 49734), nzTpIcepk0o8(chr(0b11101 + 0o23) + chr(0b11100 + 0o123) + '\063' + chr(0b110110) + chr(1162 - 1109), 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(0b1010 + 0o47) + '\065' + chr(2300 - 2252), 8), nzTpIcepk0o8(chr(2068 - 2020) + chr(0b1101111) + '\x32' + '\067' + chr(2311 - 2261), 0b1000), nzTpIcepk0o8('\x30' + chr(10805 - 10694) + chr(0b100 + 0o61), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(50) + chr(51) + chr(1308 - 1256), 40712 - 40704), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b100111 + 0o14) + '\x32', 0b1000), nzTpIcepk0o8(chr(0b101011 + 0o5) + '\157' + chr(55), 0b1000), nzTpIcepk0o8(chr(0b101011 + 0o5) + chr(111) + chr(266 - 215) + chr(0b110000) + '\063', 0o10), nzTpIcepk0o8(chr(428 - 380) + '\157' + '\062' + chr(0b110100) + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(0b1000 + 0o50) + chr(0b110101 + 0o72) + chr(50) + chr(54) + chr(0b110000 + 0o6), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110010) + chr(0b1111 + 0o41) + chr(0b110000), 8), nzTpIcepk0o8('\060' + '\x6f' + chr(53) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1000 + 0o147) + chr(0b110001) + '\065' + '\x36', ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(51) + chr(702 - 654) + '\x32', 43471 - 43463), nzTpIcepk0o8(chr(2055 - 2007) + chr(4020 - 3909) + chr(0b110010) + chr(50) + '\x32', 38994 - 38986), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x33' + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110001) + chr(0b110001) + chr(51), ord("\x08")), nzTpIcepk0o8(chr(1246 - 1198) + chr(111) + chr(0b110010) + chr(210 - 161) + '\x37', 15435 - 15427), nzTpIcepk0o8(chr(1477 - 1429) + chr(10284 - 10173) + chr(88 - 39) + chr(49) + chr(52), ord("\x08")), nzTpIcepk0o8(chr(0b111 + 0o51) + '\157' + chr(0b110001) + chr(0b101 + 0o53) + '\067', 34789 - 34781), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110100) + chr(0b11 + 0o61), 36695 - 36687), nzTpIcepk0o8('\x30' + chr(111) + '\063' + '\063' + chr(52), 15 - 7), nzTpIcepk0o8('\060' + '\x6f' + chr(50) + '\x35' + chr(55), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1001011 + 0o44) + '\x31' + chr(51) + chr(0b101011 + 0o7), ord("\x08")), nzTpIcepk0o8(chr(215 - 167) + chr(0b1101111) + chr(51) + chr(139 - 84) + chr(55), 14126 - 14118), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(1180 - 1131) + chr(0b101000 + 0o12) + '\060', 1690 - 1682), nzTpIcepk0o8(chr(0b101001 + 0o7) + chr(0b0 + 0o157) + '\063' + chr(0b1010 + 0o46) + chr(0b110000), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b11111 + 0o26) + chr(659 - 611), ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x86'), chr(0b1100100) + chr(0b1100101) + chr(99) + chr(0b110111 + 0o70) + chr(0b1001110 + 0o26) + chr(0b10110 + 0o117))(chr(12349 - 12232) + chr(7058 - 6942) + '\146' + chr(45) + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def a1OBqqzQuYvL(yoXAYvufKlQI, lnOu7fTAiCZI, furNo6W52D9L, PTc0kKuqGalX, LmmN5lXqrrTe, B2izCwRBt5Gv, VaBlaQ94SGbZ):
if VaBlaQ94SGbZ > nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110001), 0b1000) and yoXAYvufKlQI == LmmN5lXqrrTe:
if ftfygxgFas5X(furNo6W52D9L) > nzTpIcepk0o8('\060' + chr(0b1101111) + chr(1077 - 1029), 0o10) and furNo6W52D9L[nzTpIcepk0o8('\x30' + '\x6f' + chr(0b10110 + 0o32), 8)] in VEwIbROOWHXN:
if ftfygxgFas5X(PTc0kKuqGalX) > nzTpIcepk0o8(chr(1627 - 1579) + chr(0b101011 + 0o104) + chr(0b11101 + 0o23), 8):
if PTc0kKuqGalX[nzTpIcepk0o8('\x30' + chr(535 - 424) + '\060', 8)] not in VEwIbROOWHXN:
return nzTpIcepk0o8(chr(48) + chr(0b1010110 + 0o31) + '\x31', 8)
else:
cmEbPtgemnC8 = yoXAYvufKlQI + ftfygxgFas5X(furNo6W52D9L)
if ftfygxgFas5X(roI3spqORKae(lnOu7fTAiCZI, roI3spqORKae(ES5oEprVxulp(b'\xe9\twq+\\?,\xd5\xb4\x8dz'), chr(0b1001101 + 0o27) + chr(101) + chr(0b1100011) + chr(111) + chr(0b100110 + 0o76) + chr(0b1100101))('\165' + '\x74' + '\x66' + chr(0b101011 + 0o2) + chr(0b10000 + 0o50)))) > cmEbPtgemnC8:
H9CoxnM0xp2k = lnOu7fTAiCZI.AaFeo0lw34C3[cmEbPtgemnC8]
if H9CoxnM0xp2k not in VEwIbROOWHXN:
return nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b101011 + 0o6), 8)
if VaBlaQ94SGbZ < ftfygxgFas5X(roI3spqORKae(lnOu7fTAiCZI, roI3spqORKae(ES5oEprVxulp(b'\xcd\x10^z7'), '\x64' + chr(6947 - 6846) + chr(6028 - 5929) + '\x6f' + chr(3968 - 3868) + chr(101))(chr(0b1110101) + chr(0b1001000 + 0o54) + chr(5225 - 5123) + '\x2d' + chr(0b111000)))):
if EhFLzadzq9Mc(variant_start=yoXAYvufKlQI, n_ref_bases=ftfygxgFas5X(furNo6W52D9L), interval_start=B2izCwRBt5Gv - nzTpIcepk0o8('\060' + chr(0b1101111) + chr(225 - 175), 0o10), interval_end=B2izCwRBt5Gv):
HqHKfxiRNYR0 = lnOu7fTAiCZI.AaFeo0lw34C3[B2izCwRBt5Gv - nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110010), 8):B2izCwRBt5Gv + nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b100100 + 0o15), 8)]
if s5dOSrL1Uzz7(HqHKfxiRNYR0):
BSkgt7mvuYlt = HqHKfxiRNYR0
if s5dOSrL1Uzz7(BSkgt7mvuYlt):
return nzTpIcepk0o8(chr(48) + chr(111) + '\x31', 8) |
openvax/varcode | varcode/nucleotides.py | is_purine | def is_purine(nucleotide, allow_extended_nucleotides=False):
"""Is the nucleotide a purine"""
if not allow_extended_nucleotides and nucleotide not in STANDARD_NUCLEOTIDES:
raise ValueError(
"{} is a non-standard nucleotide, neither purine or pyrimidine".format(nucleotide))
return nucleotide in PURINE_NUCLEOTIDES | python | def is_purine(nucleotide, allow_extended_nucleotides=False):
"""Is the nucleotide a purine"""
if not allow_extended_nucleotides and nucleotide not in STANDARD_NUCLEOTIDES:
raise ValueError(
"{} is a non-standard nucleotide, neither purine or pyrimidine".format(nucleotide))
return nucleotide in PURINE_NUCLEOTIDES | [
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"a",
"purine"
] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/nucleotides.py#L55-L60 | train | Is the nucleotide a purine | 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) + '\157' + chr(0b110011) + '\063' + '\060', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1001001 + 0o46) + chr(0b1000 + 0o51) + chr(2332 - 2281) + chr(899 - 847), ord("\x08")), nzTpIcepk0o8('\x30' + chr(10859 - 10748) + chr(55) + chr(2286 - 2238), 41643 - 41635), nzTpIcepk0o8('\060' + '\157' + chr(2385 - 2333) + '\065', 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b1110 + 0o44) + chr(53) + '\065', 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + '\063' + chr(0b10101 + 0o34) + chr(0b101001 + 0o16), 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(0b110011) + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + '\067' + chr(0b10011 + 0o37), 0o10), nzTpIcepk0o8(chr(0b100000 + 0o20) + chr(0b101010 + 0o105) + '\063' + '\x37', 0b1000), nzTpIcepk0o8('\060' + '\x6f' + '\061' + chr(0b110011) + chr(0b11001 + 0o34), ord("\x08")), nzTpIcepk0o8(chr(0b10111 + 0o31) + chr(0b100111 + 0o110) + chr(0b10 + 0o57) + chr(50) + '\060', ord("\x08")), nzTpIcepk0o8(chr(0b11 + 0o55) + chr(0b1010110 + 0o31) + chr(2229 - 2178) + chr(2311 - 2262) + chr(0b101111 + 0o3), ord("\x08")), nzTpIcepk0o8(chr(1352 - 1304) + chr(2769 - 2658) + chr(50) + chr(0b0 + 0o65) + chr(564 - 516), 6120 - 6112), nzTpIcepk0o8(chr(48) + chr(0b1101011 + 0o4) + '\x32' + chr(0b10000 + 0o41), 19619 - 19611), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x34' + '\064', 0o10), nzTpIcepk0o8('\060' + chr(1209 - 1098) + chr(49) + '\067' + chr(54), 56238 - 56230), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(50) + chr(0b110010) + chr(1413 - 1362), 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(51) + chr(1827 - 1776) + '\065', 0o10), nzTpIcepk0o8(chr(1513 - 1465) + '\157' + '\x32' + chr(52) + chr(51), 47040 - 47032), nzTpIcepk0o8(chr(0b10000 + 0o40) + chr(0b1101111) + chr(51) + '\063' + chr(0b110001), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(1813 - 1702) + '\062' + chr(50) + '\066', ord("\x08")), nzTpIcepk0o8(chr(0b10111 + 0o31) + chr(9183 - 9072) + chr(0b110000 + 0o3) + '\061' + chr(0b10011 + 0o41), ord("\x08")), nzTpIcepk0o8(chr(1808 - 1760) + '\157' + '\x32' + '\062' + '\x31', 0o10), nzTpIcepk0o8('\x30' + chr(0b0 + 0o157) + '\x36' + chr(0b110101), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b100100 + 0o17) + chr(0b101 + 0o60) + chr(0b110110), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b100110 + 0o15) + chr(1131 - 1077) + chr(0b101010 + 0o13), 0b1000), nzTpIcepk0o8(chr(0b101000 + 0o10) + chr(0b1101111) + chr(50) + chr(0b110110) + '\x31', 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(221 - 170) + chr(557 - 506), 2801 - 2793), nzTpIcepk0o8('\x30' + '\157' + '\x31' + chr(0b101000 + 0o10) + chr(1293 - 1242), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(358 - 247) + chr(0b10110 + 0o34) + chr(0b101000 + 0o14) + chr(0b100100 + 0o22), ord("\x08")), nzTpIcepk0o8(chr(389 - 341) + chr(0b1101111) + '\062' + chr(0b110111) + chr(0b1111 + 0o47), 9681 - 9673), nzTpIcepk0o8(chr(0b10111 + 0o31) + chr(6674 - 6563) + chr(0b110110) + chr(53), 8), nzTpIcepk0o8(chr(48) + chr(7100 - 6989) + chr(51) + chr(54) + chr(48), 0b1000), nzTpIcepk0o8(chr(0b100001 + 0o17) + '\x6f' + chr(0b110010), 600 - 592), nzTpIcepk0o8(chr(1245 - 1197) + chr(0b1101100 + 0o3) + '\x32' + chr(53) + '\x37', ord("\x08")), nzTpIcepk0o8(chr(1628 - 1580) + '\x6f' + '\x32' + chr(49) + chr(54), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(49) + chr(0b110000) + chr(50), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1011111 + 0o20) + chr(0b110011) + chr(0b110101) + chr(231 - 180), 0b1000), nzTpIcepk0o8(chr(0b101011 + 0o5) + '\x6f' + chr(0b110011) + chr(0b10011 + 0o35) + chr(0b110000), 23585 - 23577), nzTpIcepk0o8('\060' + '\157' + chr(64 - 9) + '\x37', 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(53) + chr(1804 - 1756), 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xf6'), '\x64' + chr(0b1100101) + chr(0b101101 + 0o66) + chr(0b1101111) + chr(0b1100100) + chr(101))(chr(0b1 + 0o164) + chr(0b1110100) + '\146' + chr(0b101 + 0o50) + chr(0b100001 + 0o27)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def bYsCaM7zwsek(UAjDTXM97W9J, h_UgyRy_oE5P=nzTpIcepk0o8('\060' + chr(0b1101111) + '\060', 0b1000)):
if not h_UgyRy_oE5P and UAjDTXM97W9J not in az4yUYHXwe4T:
raise WbNHlDKpyPtQ(roI3spqORKae(roI3spqORKae(ES5oEprVxulp(b'\xa3!\x18L\xde\xefy\x1aq2>\xe7\xdbeE\x10\xf7\xbc\xd1\xbd\xb6\xa2\xe4V\x82\x90\xdeo*\xc2\xdb\x19\xd0l\xca\xe76\x83\xa5M\xf8,MW\xc4\xa1}\x1ap/p\xba\xd1cM\x13\xfa\xb9\xca\xb7\xf3'), chr(0b110111 + 0o55) + chr(2595 - 2494) + chr(99) + '\x6f' + '\144' + '\145')(chr(8492 - 8375) + chr(116) + '\x66' + chr(45) + chr(2003 - 1947)), roI3spqORKae(ES5oEprVxulp(b'\xa9o\x0bn\xea\xfc~UN\x02\x13\x80'), chr(0b1100100 + 0o0) + '\x65' + chr(0b11110 + 0o105) + chr(0b1000001 + 0o56) + chr(3813 - 3713) + '\x65')('\x75' + '\x74' + '\146' + chr(0b11011 + 0o22) + chr(846 - 790)))(UAjDTXM97W9J))
return UAjDTXM97W9J in VEwIbROOWHXN |
openvax/varcode | varcode/nucleotides.py | normalize_nucleotide_string | def normalize_nucleotide_string(
nucleotides,
allow_extended_nucleotides=False,
empty_chars=".-",
treat_nan_as_empty=True):
"""
Normalizes a nucleotide string by converting various ways of encoding empty
strings into "", making all letters upper case, and checking to make sure
all letters in the string are actually nucleotides.
Parameters
----------
nucleotides : str
Sequence of nucleotides, e.g. "ACCTG"
extended_nucleotides : bool
Allow non-canonical nucleotide characters like 'X' for unknown base
empty_chars : str
Characters which encode empty strings, such as "." used in VCF format
or "-" used in MAF format
treat_nan_as_empty : bool
Some MAF files represent deletions/insertions with NaN ref/alt values
"""
if nucleotides in empty_chars:
return ""
elif treat_nan_as_empty and isinstance(nucleotides, float) and np.isnan(nucleotides):
return ""
require_string(nucleotides, name="nucleotide string")
nucleotides = nucleotides.upper()
if allow_extended_nucleotides:
valid_nucleotides = EXTENDED_NUCLEOTIDES
else:
valid_nucleotides = STANDARD_NUCLEOTIDES
if not set(nucleotides) <= valid_nucleotides:
raise ValueError(
"Invalid character(s) in nucleotide string: %s" % (
",".join(set(nucleotides) - valid_nucleotides),))
return nucleotides | python | def normalize_nucleotide_string(
nucleotides,
allow_extended_nucleotides=False,
empty_chars=".-",
treat_nan_as_empty=True):
"""
Normalizes a nucleotide string by converting various ways of encoding empty
strings into "", making all letters upper case, and checking to make sure
all letters in the string are actually nucleotides.
Parameters
----------
nucleotides : str
Sequence of nucleotides, e.g. "ACCTG"
extended_nucleotides : bool
Allow non-canonical nucleotide characters like 'X' for unknown base
empty_chars : str
Characters which encode empty strings, such as "." used in VCF format
or "-" used in MAF format
treat_nan_as_empty : bool
Some MAF files represent deletions/insertions with NaN ref/alt values
"""
if nucleotides in empty_chars:
return ""
elif treat_nan_as_empty and isinstance(nucleotides, float) and np.isnan(nucleotides):
return ""
require_string(nucleotides, name="nucleotide string")
nucleotides = nucleotides.upper()
if allow_extended_nucleotides:
valid_nucleotides = EXTENDED_NUCLEOTIDES
else:
valid_nucleotides = STANDARD_NUCLEOTIDES
if not set(nucleotides) <= valid_nucleotides:
raise ValueError(
"Invalid character(s) in nucleotide string: %s" % (
",".join(set(nucleotides) - valid_nucleotides),))
return nucleotides | [
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strings into "", making all letters upper case, and checking to make sure
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nucleotides : str
Sequence of nucleotides, e.g. "ACCTG"
extended_nucleotides : bool
Allow non-canonical nucleotide characters like 'X' for unknown base
empty_chars : str
Characters which encode empty strings, such as "." used in VCF format
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treat_nan_as_empty : bool
Some MAF files represent deletions/insertions with NaN ref/alt values | [
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"nucleotides",
"."
] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/nucleotides.py#L67-L111 | train | Normalizes a nucleotide string by converting all letters upper case checking to make sure all letters in the string are actually nucleotides. | 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(0b111001 + 0o66) + chr(0b110011) + chr(50) + '\065', 0o10), nzTpIcepk0o8(chr(0b0 + 0o60) + chr(111) + chr(53) + '\x34', 0o10), nzTpIcepk0o8(chr(0b101100 + 0o4) + '\157' + chr(0b110001) + '\x33' + '\x34', 0o10), nzTpIcepk0o8(chr(0b1101 + 0o43) + '\x6f' + chr(0b101111 + 0o2) + '\x30', 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + '\061' + '\x34' + chr(0b110001), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + '\x31' + chr(1091 - 1042), 9805 - 9797), nzTpIcepk0o8('\060' + '\x6f' + '\063' + chr(561 - 508) + '\x37', 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(0b110001) + '\x33' + '\x34', 8), nzTpIcepk0o8('\060' + '\x6f' + '\x32' + chr(0b110010) + chr(0b101011 + 0o10), 16373 - 16365), nzTpIcepk0o8(chr(0b110000) + chr(0b1101001 + 0o6) + '\062' + chr(0b110000) + chr(51), 0b1000), nzTpIcepk0o8('\060' + chr(111) + '\x36' + chr(0b100010 + 0o21), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b10001 + 0o40) + '\065' + chr(0b1011 + 0o45), ord("\x08")), nzTpIcepk0o8(chr(0b1111 + 0o41) + '\157' + chr(0b10010 + 0o37) + chr(54) + '\061', ord("\x08")), nzTpIcepk0o8('\x30' + chr(11230 - 11119) + '\x34' + '\061', 0o10), nzTpIcepk0o8(chr(48) + chr(0b101111 + 0o100) + chr(0b11100 + 0o26) + chr(0b1110 + 0o47) + chr(748 - 695), ord("\x08")), nzTpIcepk0o8(chr(0b10100 + 0o34) + chr(111) + chr(0b110101) + chr(50), 22294 - 22286), nzTpIcepk0o8(chr(1181 - 1133) + chr(111) + '\x33' + chr(0b110 + 0o60) + chr(2795 - 2741), 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110010) + chr(52), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b100010 + 0o20) + '\x32' + chr(48), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(2087 - 2033) + '\062', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b11000 + 0o127) + chr(0b110011) + chr(0b10000 + 0o40) + chr(546 - 491), 42732 - 42724), nzTpIcepk0o8(chr(48) + chr(111) + chr(1914 - 1864) + chr(0b110001) + chr(1529 - 1480), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(1426 - 1315) + '\063' + '\066' + chr(0b110001), 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(51) + chr(55) + chr(2611 - 2559), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(1916 - 1862) + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(1089 - 1041) + chr(10794 - 10683) + '\x35' + '\063', ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + '\x35' + chr(2062 - 2014), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(1464 - 1414) + '\x33' + chr(2318 - 2264), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(0b110010) + chr(0b110111) + chr(216 - 166), 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(165 - 116) + '\x35' + '\062', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x31' + '\x31', 8), nzTpIcepk0o8(chr(0b1000 + 0o50) + '\157' + chr(0b110011) + chr(642 - 589) + '\060', 7830 - 7822), nzTpIcepk0o8('\060' + '\157' + '\062' + '\x32', 0b1000), nzTpIcepk0o8(chr(2015 - 1967) + chr(10155 - 10044) + chr(1963 - 1914) + '\x34' + chr(0b11011 + 0o27), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110011 + 0o1), 17885 - 17877), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(49) + '\060' + '\x33', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b100100 + 0o22) + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(0b10001 + 0o37) + chr(0b101100 + 0o103) + chr(51) + chr(0b100101 + 0o22) + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(656 - 608) + chr(0b1011010 + 0o25) + chr(0b110011) + chr(0b110010) + '\x36', 42523 - 42515), nzTpIcepk0o8(chr(1395 - 1347) + '\x6f' + chr(51) + '\065' + '\x31', 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(0b101110 + 0o101) + chr(53) + chr(48), 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xfb'), chr(100) + chr(6608 - 6507) + chr(0b1100011) + chr(3022 - 2911) + chr(100) + chr(0b1000110 + 0o37))(chr(117) + chr(12962 - 12846) + chr(102) + chr(1438 - 1393) + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def E7SQrg7dltQF(b4hLEor0h9Oj, h_UgyRy_oE5P=nzTpIcepk0o8('\060' + chr(0b1100101 + 0o12) + '\060', 24359 - 24351), ieKdi5SNYgmr=roI3spqORKae(ES5oEprVxulp(b'\xfb\x01'), chr(100) + chr(1485 - 1384) + '\x63' + chr(0b1101111) + '\144' + chr(9664 - 9563))(chr(0b110110 + 0o77) + '\x74' + '\x66' + chr(0b101101) + '\x38'), hjWjVw7Z1_yW=nzTpIcepk0o8('\x30' + chr(111) + '\061', 0o10)):
if b4hLEor0h9Oj in ieKdi5SNYgmr:
return roI3spqORKae(ES5oEprVxulp(b''), '\144' + chr(0b1100101) + '\x63' + chr(0b1001111 + 0o40) + chr(100) + '\145')('\165' + '\164' + '\146' + chr(1093 - 1048) + '\070')
elif hjWjVw7Z1_yW and suIjIS24Zkqw(b4hLEor0h9Oj, jLW6pRf2DSRk) and roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'\xa2\x1d-85~\x9b\x1d\xc7\xd2\x050'), chr(6717 - 6617) + chr(1585 - 1484) + chr(99) + chr(11736 - 11625) + chr(0b1100100) + chr(101))(chr(0b111110 + 0o67) + '\x74' + '\x66' + chr(538 - 493) + '\x38'))(b4hLEor0h9Oj):
return roI3spqORKae(ES5oEprVxulp(b''), chr(1744 - 1644) + '\145' + chr(0b1100011) + '\x6f' + chr(0b110001 + 0o63) + chr(0b1010000 + 0o25))(chr(117) + '\x74' + chr(291 - 189) + chr(0b101101) + '\x38')
znPfuRrJRNOF(b4hLEor0h9Oj, name=roI3spqORKae(ES5oEprVxulp(b'\xbbY?d\x04f\x9b5\xf7\xe6\x13\x1b\x05S\xc4D\x91'), chr(100) + chr(0b1100010 + 0o3) + chr(99) + '\157' + chr(2434 - 2334) + chr(101))('\x75' + chr(116) + chr(0b1100110) + chr(0b101101) + chr(2166 - 2110)))
b4hLEor0h9Oj = b4hLEor0h9Oj.iq1mNMefb1Zd()
if h_UgyRy_oE5P:
ht6VyzVEjnLU = hvXM5BVHzDvy
else:
ht6VyzVEjnLU = az4yUYHXwe4T
if not Bvi71nNyvlqO(b4hLEor0h9Oj) <= ht6VyzVEjnLU:
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'\x9cB*i\r`\x8b|\xf0\xebR\x1a\x10B\xd9O\x84<\xe3\x1b\xe7\xe0\x9f\xdc[^K\xf2\xdf\x05}\x81v\x07$0C\x8d\xbf\x87\xb2\x16|-\x12'), chr(0b1100100) + chr(3228 - 3127) + chr(661 - 562) + chr(111) + chr(0b10001 + 0o123) + chr(2293 - 2192))(chr(0b1001110 + 0o47) + '\164' + chr(102) + '\055' + chr(0b10010 + 0o46)) % (roI3spqORKae(roI3spqORKae(ES5oEprVxulp(b'\xf9'), chr(3183 - 3083) + '\x65' + chr(99) + chr(111) + chr(0b1100100) + chr(5973 - 5872))(chr(0b1000101 + 0o60) + chr(6547 - 6431) + chr(0b1001001 + 0o35) + chr(1481 - 1436) + '\x38'), roI3spqORKae(ES5oEprVxulp(b'\x8c\x18%EXK\x8c:\xc7\xc0}\x19'), chr(0b1100100) + chr(6400 - 6299) + chr(5694 - 5595) + '\x6f' + '\x64' + chr(1086 - 985))(chr(117) + '\164' + chr(0b1010101 + 0o21) + chr(0b1110 + 0o37) + '\x38'))(Bvi71nNyvlqO(b4hLEor0h9Oj) - ht6VyzVEjnLU),))
return b4hLEor0h9Oj |
openvax/varcode | varcode/vcf.py | load_vcf | def load_vcf(
path,
genome=None,
reference_vcf_key="reference",
only_passing=True,
allow_extended_nucleotides=False,
include_info=True,
chunk_size=10 ** 5,
max_variants=None,
sort_key=variant_ascending_position_sort_key,
distinct=True):
"""
Load reference name and Variant objects from the given VCF filename.
Currently only local files are supported by this function (no http). If you
call this on an HTTP URL, it will fall back to `load_vcf`.
Parameters
----------
path : str
Path to VCF (*.vcf) or compressed VCF (*.vcf.gz).
genome : {pyensembl.Genome, reference name, Ensembl version int}, optional
Optionally pass in a PyEnsembl Genome object, name of reference, or
PyEnsembl release version to specify the reference associated with a
VCF (otherwise infer reference from VCF using reference_vcf_key)
reference_vcf_key : str, optional
Name of metadata field which contains path to reference FASTA
file (default = 'reference')
only_passing : boolean, optional
If true, any entries whose FILTER field is not one of "." or "PASS" is
dropped.
allow_extended_nucleotides : boolean, default False
Allow characters other that A,C,T,G in the ref and alt strings.
include_info : boolean, default True
Whether to parse the INFO and per-sample columns. If you don't need
these, set to False for faster parsing.
chunk_size: int, optional
Number of records to load in memory at once.
max_variants : int, optional
If specified, return only the first max_variants variants.
sort_key : fn
Function which maps each element to a sorting criterion.
Set to None to not to sort the variants.
distinct : boolean, default True
Don't keep repeated variants
"""
require_string(path, "Path or URL to VCF")
parsed_path = parse_url_or_path(path)
if parsed_path.scheme and parsed_path.scheme.lower() != "file":
# pandas.read_table nominally supports HTTP, but it tends to crash on
# large files and does not support gzip. Switching to the python-based
# implementation of read_table (with engine="python") helps with some
# issues but introduces a new set of problems (e.g. the dtype parameter
# is not accepted). For these reasons, we're currently not attempting
# to load VCFs over HTTP with pandas directly, and instead download it
# to a temporary file and open that.
(filename, headers) = urllib.request.urlretrieve(path)
try:
# The downloaded file has no file extension, which confuses pyvcf
# for gziped files in Python 3. We rename it to have the correct
# file extension.
new_filename = "%s.%s" % (
filename, parsed_path.path.split(".")[-1])
os.rename(filename, new_filename)
filename = new_filename
return load_vcf(
filename,
genome=genome,
reference_vcf_key=reference_vcf_key,
only_passing=only_passing,
allow_extended_nucleotides=allow_extended_nucleotides,
include_info=include_info,
chunk_size=chunk_size,
max_variants=max_variants,
sort_key=sort_key,
distinct=distinct)
finally:
logger.info("Removing temporary file: %s", filename)
os.unlink(filename)
# Loading a local file.
# The file will be opened twice: first to parse the header with pyvcf, then
# by pandas to read the data.
# PyVCF reads the metadata immediately and stops at the first line with
# data. We can close the file after that.
handle = PyVCFReaderFromPathOrURL(path)
handle.close()
genome = infer_genome_from_vcf(
genome,
handle.vcf_reader,
reference_vcf_key)
df_iterator = read_vcf_into_dataframe(
path,
include_info=include_info,
sample_names=handle.vcf_reader.samples if include_info else None,
chunk_size=chunk_size)
if include_info:
def sample_info_parser(unparsed_sample_info_strings, format_string):
"""
Given a format string like "GT:AD:ADP:DP:FS"
and a list of sample info strings where each entry is like
"0/1:3,22:T=3,G=22:25:33", return a dict that maps:
sample name -> field name -> value. Uses pyvcf to parse the fields.
"""
return pyvcf_calls_to_sample_info_list(
handle.vcf_reader._parse_samples(
unparsed_sample_info_strings, format_string, None))
else:
sample_info_parser = None
return dataframes_to_variant_collection(
df_iterator,
source_path=path,
info_parser=handle.vcf_reader._parse_info if include_info else None,
only_passing=only_passing,
max_variants=max_variants,
sample_names=handle.vcf_reader.samples if include_info else None,
sample_info_parser=sample_info_parser,
variant_kwargs={
'ensembl': genome,
'allow_extended_nucleotides': allow_extended_nucleotides},
variant_collection_kwargs={
'sort_key': sort_key,
'distinct': distinct}) | python | def load_vcf(
path,
genome=None,
reference_vcf_key="reference",
only_passing=True,
allow_extended_nucleotides=False,
include_info=True,
chunk_size=10 ** 5,
max_variants=None,
sort_key=variant_ascending_position_sort_key,
distinct=True):
"""
Load reference name and Variant objects from the given VCF filename.
Currently only local files are supported by this function (no http). If you
call this on an HTTP URL, it will fall back to `load_vcf`.
Parameters
----------
path : str
Path to VCF (*.vcf) or compressed VCF (*.vcf.gz).
genome : {pyensembl.Genome, reference name, Ensembl version int}, optional
Optionally pass in a PyEnsembl Genome object, name of reference, or
PyEnsembl release version to specify the reference associated with a
VCF (otherwise infer reference from VCF using reference_vcf_key)
reference_vcf_key : str, optional
Name of metadata field which contains path to reference FASTA
file (default = 'reference')
only_passing : boolean, optional
If true, any entries whose FILTER field is not one of "." or "PASS" is
dropped.
allow_extended_nucleotides : boolean, default False
Allow characters other that A,C,T,G in the ref and alt strings.
include_info : boolean, default True
Whether to parse the INFO and per-sample columns. If you don't need
these, set to False for faster parsing.
chunk_size: int, optional
Number of records to load in memory at once.
max_variants : int, optional
If specified, return only the first max_variants variants.
sort_key : fn
Function which maps each element to a sorting criterion.
Set to None to not to sort the variants.
distinct : boolean, default True
Don't keep repeated variants
"""
require_string(path, "Path or URL to VCF")
parsed_path = parse_url_or_path(path)
if parsed_path.scheme and parsed_path.scheme.lower() != "file":
# pandas.read_table nominally supports HTTP, but it tends to crash on
# large files and does not support gzip. Switching to the python-based
# implementation of read_table (with engine="python") helps with some
# issues but introduces a new set of problems (e.g. the dtype parameter
# is not accepted). For these reasons, we're currently not attempting
# to load VCFs over HTTP with pandas directly, and instead download it
# to a temporary file and open that.
(filename, headers) = urllib.request.urlretrieve(path)
try:
# The downloaded file has no file extension, which confuses pyvcf
# for gziped files in Python 3. We rename it to have the correct
# file extension.
new_filename = "%s.%s" % (
filename, parsed_path.path.split(".")[-1])
os.rename(filename, new_filename)
filename = new_filename
return load_vcf(
filename,
genome=genome,
reference_vcf_key=reference_vcf_key,
only_passing=only_passing,
allow_extended_nucleotides=allow_extended_nucleotides,
include_info=include_info,
chunk_size=chunk_size,
max_variants=max_variants,
sort_key=sort_key,
distinct=distinct)
finally:
logger.info("Removing temporary file: %s", filename)
os.unlink(filename)
# Loading a local file.
# The file will be opened twice: first to parse the header with pyvcf, then
# by pandas to read the data.
# PyVCF reads the metadata immediately and stops at the first line with
# data. We can close the file after that.
handle = PyVCFReaderFromPathOrURL(path)
handle.close()
genome = infer_genome_from_vcf(
genome,
handle.vcf_reader,
reference_vcf_key)
df_iterator = read_vcf_into_dataframe(
path,
include_info=include_info,
sample_names=handle.vcf_reader.samples if include_info else None,
chunk_size=chunk_size)
if include_info:
def sample_info_parser(unparsed_sample_info_strings, format_string):
"""
Given a format string like "GT:AD:ADP:DP:FS"
and a list of sample info strings where each entry is like
"0/1:3,22:T=3,G=22:25:33", return a dict that maps:
sample name -> field name -> value. Uses pyvcf to parse the fields.
"""
return pyvcf_calls_to_sample_info_list(
handle.vcf_reader._parse_samples(
unparsed_sample_info_strings, format_string, None))
else:
sample_info_parser = None
return dataframes_to_variant_collection(
df_iterator,
source_path=path,
info_parser=handle.vcf_reader._parse_info if include_info else None,
only_passing=only_passing,
max_variants=max_variants,
sample_names=handle.vcf_reader.samples if include_info else None,
sample_info_parser=sample_info_parser,
variant_kwargs={
'ensembl': genome,
'allow_extended_nucleotides': allow_extended_nucleotides},
variant_collection_kwargs={
'sort_key': sort_key,
'distinct': distinct}) | [
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] | Load reference name and Variant objects from the given VCF filename.
Currently only local files are supported by this function (no http). If you
call this on an HTTP URL, it will fall back to `load_vcf`.
Parameters
----------
path : str
Path to VCF (*.vcf) or compressed VCF (*.vcf.gz).
genome : {pyensembl.Genome, reference name, Ensembl version int}, optional
Optionally pass in a PyEnsembl Genome object, name of reference, or
PyEnsembl release version to specify the reference associated with a
VCF (otherwise infer reference from VCF using reference_vcf_key)
reference_vcf_key : str, optional
Name of metadata field which contains path to reference FASTA
file (default = 'reference')
only_passing : boolean, optional
If true, any entries whose FILTER field is not one of "." or "PASS" is
dropped.
allow_extended_nucleotides : boolean, default False
Allow characters other that A,C,T,G in the ref and alt strings.
include_info : boolean, default True
Whether to parse the INFO and per-sample columns. If you don't need
these, set to False for faster parsing.
chunk_size: int, optional
Number of records to load in memory at once.
max_variants : int, optional
If specified, return only the first max_variants variants.
sort_key : fn
Function which maps each element to a sorting criterion.
Set to None to not to sort the variants.
distinct : boolean, default True
Don't keep repeated variants | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/vcf.py#L37-L176 | train | Load a VCF file into memory. | 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(0b110011) + chr(49) + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110010) + '\064' + '\060', 0b1000), nzTpIcepk0o8(chr(0b101000 + 0o10) + '\157' + chr(0b1101 + 0o45) + '\x34', 0o10), nzTpIcepk0o8(chr(0b1111 + 0o41) + chr(0b1111 + 0o140) + chr(718 - 668) + '\x31' + '\062', 0o10), nzTpIcepk0o8('\x30' + chr(11813 - 11702) + chr(1704 - 1655) + chr(52) + '\x36', ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + chr(49) + '\064' + chr(51), 19751 - 19743), nzTpIcepk0o8(chr(1196 - 1148) + chr(0b1101111) + chr(51) + '\x36' + chr(0b110011), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110010) + chr(0b110010 + 0o2) + chr(0b110110), 21625 - 21617), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(2359 - 2309) + '\x37', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\062' + chr(0b110000 + 0o3) + chr(54), 0o10), nzTpIcepk0o8('\060' + chr(0b1101100 + 0o3) + '\062' + chr(48) + chr(134 - 80), 28646 - 28638), nzTpIcepk0o8(chr(0b10101 + 0o33) + chr(111) + chr(0b110010) + chr(77 - 29), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(53) + '\060', 0o10), nzTpIcepk0o8(chr(0b1010 + 0o46) + '\x6f' + '\063' + '\x33', 17073 - 17065), nzTpIcepk0o8(chr(517 - 469) + chr(4502 - 4391) + chr(51) + chr(53) + chr(49), 10801 - 10793), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110011) + chr(53) + '\x34', ord("\x08")), nzTpIcepk0o8(chr(1985 - 1937) + chr(11896 - 11785) + chr(2319 - 2270) + chr(0b110010), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(3437 - 3326) + '\x32' + chr(55) + '\x33', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101 + 0o142) + '\x34' + chr(544 - 491), 0b1000), nzTpIcepk0o8(chr(1556 - 1508) + chr(111) + '\063' + '\x33' + '\x33', 22903 - 22895), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110001) + '\x31' + chr(2648 - 2596), 0b1000), nzTpIcepk0o8(chr(1775 - 1727) + chr(0b11001 + 0o126) + '\x32' + chr(2485 - 2432) + chr(0b10100 + 0o40), 0o10), nzTpIcepk0o8(chr(0b100110 + 0o12) + chr(6326 - 6215) + chr(0b11011 + 0o33) + chr(901 - 850), 5571 - 5563), nzTpIcepk0o8('\x30' + '\157' + chr(1719 - 1670) + '\x32' + chr(0b1101 + 0o45), 61236 - 61228), nzTpIcepk0o8(chr(48) + chr(0b1001011 + 0o44) + '\061' + chr(701 - 646) + chr(50), 0b1000), nzTpIcepk0o8(chr(0b111 + 0o51) + chr(0b1101111) + chr(50) + chr(1662 - 1608) + '\062', 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(50) + '\064' + chr(1510 - 1455), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110110) + chr(2216 - 2166), 0o10), nzTpIcepk0o8(chr(1308 - 1260) + chr(132 - 21) + chr(0b110010 + 0o1) + chr(1112 - 1063) + '\061', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(9366 - 9255) + chr(0b110011) + chr(0b10100 + 0o40) + chr(49), 0o10), nzTpIcepk0o8(chr(0b1101 + 0o43) + chr(0b1000011 + 0o54) + chr(0b101100 + 0o6) + chr(54) + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(466 - 415) + chr(0b100100 + 0o21) + chr(53), 10178 - 10170), nzTpIcepk0o8(chr(254 - 206) + chr(0b1101111) + '\063' + chr(0b110010) + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b100111 + 0o110) + chr(1894 - 1845) + chr(1187 - 1137) + '\060', ord("\x08")), nzTpIcepk0o8(chr(0b11111 + 0o21) + '\157' + '\062' + '\x37' + '\x31', 0o10), nzTpIcepk0o8('\060' + '\157' + chr(50) + chr(0b110111) + '\066', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(2114 - 2063) + chr(0b110010) + chr(48), 8), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110001) + chr(221 - 173) + chr(0b110010), 47966 - 47958), nzTpIcepk0o8('\x30' + chr(111) + '\x31' + chr(0b1001 + 0o51) + chr(2692 - 2639), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\062' + chr(263 - 212) + '\065', 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + '\157' + chr(53) + chr(891 - 843), 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xe1'), chr(0b1100100) + chr(0b1100101) + chr(7175 - 7076) + chr(3515 - 3404) + '\144' + chr(101))('\x75' + chr(0b1100000 + 0o24) + '\146' + chr(0b101101) + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def xBF0Co8C06I1(_pSYqrosNb95, sBpYBMNzXOlv=None, vIiRQl2siAim=roI3spqORKae(ES5oEprVxulp(b'\xbd\xc5r\xef\x14\x06\x9d\xc5r'), chr(0b1100100) + chr(0b11001 + 0o114) + '\143' + chr(111) + chr(2064 - 1964) + chr(0b110 + 0o137))(chr(5518 - 5401) + chr(0b1110100) + chr(0b10001 + 0o125) + chr(45) + chr(56)), Bvv1N65tH2pI=nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110001), 0b1000), h_UgyRy_oE5P=nzTpIcepk0o8('\060' + chr(0b1101111) + '\060', ord("\x08")), sLgKHMPDbfhR=nzTpIcepk0o8('\060' + chr(111) + chr(0b110001), 8), CyjJOdV7xEsi=nzTpIcepk0o8('\060' + '\x6f' + '\061' + chr(0b1 + 0o61), 8) ** nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110101), ord("\x08")), TsUqs1HTOUNo=None, Kyzd6JCYDN1s=McLi3ofCchY7, VrgGMdABDVy2=nzTpIcepk0o8(chr(48) + '\x6f' + '\061', 8)):
znPfuRrJRNOF(_pSYqrosNb95, roI3spqORKae(ES5oEprVxulp(b'\x9f\xc1`\xe2F\x0c\x81\x86B\xcc\xca0\\t\xc9\xbaI\xfd'), '\x64' + chr(101) + chr(7376 - 7277) + chr(0b1101111) + '\144' + chr(101))(chr(0b1110101) + chr(0b1110100) + chr(0b1000010 + 0o44) + '\055' + chr(1417 - 1361)))
u_eZo_f9F0ni = vSgXMKm9j9A2(_pSYqrosNb95)
if roI3spqORKae(u_eZo_f9F0ni, roI3spqORKae(ES5oEprVxulp(b'\xa0\xd4c\xec(\x1b\x96\xdcD\xf7\xf0s'), '\x64' + '\x65' + chr(1205 - 1106) + chr(111) + '\144' + chr(7108 - 7007))(chr(4643 - 4526) + chr(1372 - 1256) + '\x66' + chr(45) + '\x38')) and roI3spqORKae(u_eZo_f9F0ni.scheme, roI3spqORKae(ES5oEprVxulp(b'\x97\xce,\xcf(4\xbe\xfcs\xd7\xd4d'), chr(9296 - 9196) + chr(2214 - 2113) + chr(3335 - 3236) + chr(5805 - 5694) + chr(100) + chr(0b1100101))(chr(0b1010100 + 0o41) + '\x74' + chr(0b11110 + 0o110) + '\x2d' + '\070'))() != roI3spqORKae(ES5oEprVxulp(b'\xa9\xc9x\xef'), chr(100) + '\x65' + chr(0b1100011) + chr(0b1001111 + 0o40) + chr(2365 - 2265) + '\145')('\165' + chr(0b1110100) + chr(0b1100110) + chr(0b1000 + 0o45) + chr(56)):
(FxZHtXEolYsL, UyworZfslHjc) = O7cVixZ4g0oW.request.urlretrieve(_pSYqrosNb95)
try:
LgC3k4L1QGTj = roI3spqORKae(ES5oEprVxulp(b'\xea\xd3:\xaf\x15'), chr(4409 - 4309) + chr(101) + chr(0b1100 + 0o127) + chr(8974 - 8863) + chr(0b10 + 0o142) + '\145')(chr(0b1110101) + '\164' + '\x66' + chr(45) + chr(0b111000)) % (FxZHtXEolYsL, u_eZo_f9F0ni.path.LfRrQOxuDvnC(roI3spqORKae(ES5oEprVxulp(b'\xe1'), chr(0b1100100) + '\145' + chr(0b1100011) + chr(0b10111 + 0o130) + chr(100) + chr(0b1100101))(chr(0b1110101) + '\x74' + '\146' + chr(0b11011 + 0o22) + '\x38'))[-nzTpIcepk0o8('\x30' + '\x6f' + chr(0b11110 + 0o23), 8)])
roI3spqORKae(aHUqKstZLeS6, roI3spqORKae(ES5oEprVxulp(b'\xbd\xc5z\xeb\x0b\x06'), '\144' + chr(101) + '\x63' + '\157' + chr(0b110101 + 0o57) + chr(101))(chr(0b101101 + 0o110) + chr(12872 - 12756) + chr(434 - 332) + chr(0b101101) + chr(56)))(FxZHtXEolYsL, LgC3k4L1QGTj)
FxZHtXEolYsL = LgC3k4L1QGTj
return xBF0Co8C06I1(FxZHtXEolYsL, genome=sBpYBMNzXOlv, reference_vcf_key=vIiRQl2siAim, only_passing=Bvv1N65tH2pI, allow_extended_nucleotides=h_UgyRy_oE5P, include_info=sLgKHMPDbfhR, chunk_size=CyjJOdV7xEsi, max_variants=TsUqs1HTOUNo, sort_key=Kyzd6JCYDN1s, distinct=VrgGMdABDVy2)
finally:
roI3spqORKae(iKLp4UdyhCfx, roI3spqORKae(ES5oEprVxulp(b'\xa6\xd8Z\xf2_/\x84\xf9&\xf9\xf4_'), '\x64' + chr(101) + chr(0b1110 + 0o125) + chr(0b1101111) + '\x64' + chr(0b1010111 + 0o16))(chr(117) + '\164' + '\146' + '\055' + chr(56)))(roI3spqORKae(ES5oEprVxulp(b'\x9d\xc5y\xe5\x10\n\x9d\xc17\xea\xe3}Xt\x9b\x8dx\xc2\x05\xbd%\xc0VhZ\x97\xd4'), chr(100) + chr(0b1100101) + chr(99) + chr(111) + chr(0b1000100 + 0o40) + '\x65')(chr(0b1110101) + '\x74' + '\x66' + chr(1150 - 1105) + chr(56)), FxZHtXEolYsL)
roI3spqORKae(aHUqKstZLeS6, roI3spqORKae(ES5oEprVxulp(b'\xba\xcex\xe3\x08\x08'), chr(0b1100100) + chr(0b1100101) + '\143' + chr(10779 - 10668) + chr(7974 - 7874) + chr(101))('\165' + chr(0b1101010 + 0o12) + chr(0b1100110) + '\x2d' + '\x38'))(FxZHtXEolYsL)
ecbIicWlHedY = eiJyMm8tGQqG(_pSYqrosNb95)
roI3spqORKae(ecbIicWlHedY, roI3spqORKae(ES5oEprVxulp(b'\x95\xc5e\xbd%\x00\x95\x9fB\xfa\xbez'), '\144' + chr(0b1100101) + chr(99) + chr(111) + '\144' + chr(1418 - 1317))(chr(0b1110101) + '\x74' + chr(0b1100110) + chr(45) + chr(2230 - 2174)))()
sBpYBMNzXOlv = v2USfLJrt7yV(sBpYBMNzXOlv, ecbIicWlHedY.vcf_reader, vIiRQl2siAim)
gDxjRH8_uONb = yNoFyFaVTZ6f(_pSYqrosNb95, include_info=sLgKHMPDbfhR, sample_names=ecbIicWlHedY.vcf_reader.samples if sLgKHMPDbfhR else None, chunk_size=CyjJOdV7xEsi)
if sLgKHMPDbfhR:
def MNj_1ygyIrtn(qIASQ1PkBVUA, BE3NiaWjZKGq):
return iMFM2Bubdu6n(roI3spqORKae(ecbIicWlHedY.vcf_reader, roI3spqORKae(ES5oEprVxulp(b'\x90\xd0u\xf8\x15\x06\xac\xd5v\xf3\xf6|Mh'), chr(6681 - 6581) + chr(0b1100101) + chr(0b1100011) + chr(0b101 + 0o152) + chr(0b1001011 + 0o31) + chr(101))(chr(9657 - 9540) + chr(0b1110100) + chr(6421 - 6319) + '\x2d' + chr(0b111000)))(qIASQ1PkBVUA, BE3NiaWjZKGq, None))
else:
MNj_1ygyIrtn = None
return HFwXsnYQ0Io6(gDxjRH8_uONb, source_path=_pSYqrosNb95, info_parser=roI3spqORKae(ecbIicWlHedY.vcf_reader, roI3spqORKae(ES5oEprVxulp(b'\x90\xd0u\xf8\x15\x06\xac\xcfy\xf8\xe9'), chr(0b101000 + 0o74) + chr(8539 - 8438) + chr(1453 - 1354) + chr(0b1101011 + 0o4) + chr(100) + chr(0b1100101))('\x75' + chr(0b100111 + 0o115) + '\146' + '\055' + chr(0b10010 + 0o46))) if sLgKHMPDbfhR else None, only_passing=Bvv1N65tH2pI, max_variants=TsUqs1HTOUNo, sample_names=roI3spqORKae(ecbIicWlHedY.vcf_reader, roI3spqORKae(ES5oEprVxulp(b'\xbc\xc1y\xfa\n\x06\x80'), chr(0b1100100) + chr(0b111011 + 0o52) + chr(99) + chr(4457 - 4346) + '\144' + chr(930 - 829))('\x75' + '\x74' + '\146' + chr(45) + chr(0b10110 + 0o42))) if sLgKHMPDbfhR else None, sample_info_parser=MNj_1ygyIrtn, variant_kwargs={roI3spqORKae(ES5oEprVxulp(b'\xaa\xceg\xef\x0b\x01\x9f'), '\144' + chr(101) + chr(99) + '\x6f' + '\x64' + chr(101))('\165' + chr(12251 - 12135) + chr(0b1100110) + '\055' + '\x38'): sBpYBMNzXOlv, roI3spqORKae(ES5oEprVxulp(b'\xae\xccx\xe5\x11<\x96\xdec\xfb\xe8tM\x7f\xb6\x82\x7f\xd8I\xbe#\xd8Z6\x1f\xc1'), chr(100) + chr(1407 - 1306) + chr(3430 - 3331) + chr(111) + '\x64' + '\145')(chr(117) + chr(10290 - 10174) + chr(0b1100110) + chr(0b1100 + 0o41) + '\x38'): h_UgyRy_oE5P}, variant_collection_kwargs={roI3spqORKae(ES5oEprVxulp(b'\xbc\xcff\xfe9\x08\x96\xdf'), chr(0b1100100) + chr(0b1100101) + chr(99) + chr(0b1001111 + 0o40) + chr(100) + chr(101))('\165' + chr(116) + chr(8152 - 8050) + chr(45) + chr(0b100001 + 0o27)): Kyzd6JCYDN1s, roI3spqORKae(ES5oEprVxulp(b'\xab\xc9g\xfe\x0f\r\x90\xd2'), chr(0b1100100) + '\145' + chr(99) + chr(0b1010 + 0o145) + chr(0b1001101 + 0o27) + chr(101))(chr(4721 - 4604) + chr(0b1011101 + 0o27) + chr(0b101011 + 0o73) + chr(0b100111 + 0o6) + '\070'): VrgGMdABDVy2}) |
openvax/varcode | varcode/vcf.py | pyvcf_calls_to_sample_info_list | def pyvcf_calls_to_sample_info_list(calls):
"""
Given pyvcf.model._Call instances, return a dict mapping each sample
name to its per-sample info:
sample name -> field -> value
"""
return OrderedDict(
(call.sample, call.data._asdict()) for call in calls) | python | def pyvcf_calls_to_sample_info_list(calls):
"""
Given pyvcf.model._Call instances, return a dict mapping each sample
name to its per-sample info:
sample name -> field -> value
"""
return OrderedDict(
(call.sample, call.data._asdict()) for call in calls) | [
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ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8('\x30' + chr(111) + chr(1536 - 1486) + '\067' + chr(0b110001), 0b1000), nzTpIcepk0o8('\x30' + chr(0b111000 + 0o67) + chr(1595 - 1546) + chr(1720 - 1667) + '\x33', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b100100 + 0o16) + chr(1122 - 1069), ord("\x08")), nzTpIcepk0o8(chr(770 - 722) + chr(9674 - 9563) + '\x31' + chr(0b0 + 0o66) + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101101 + 0o2) + '\x31' + chr(400 - 351) + '\066', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1011010 + 0o25) + chr(0b110111) + chr(52), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x33', 0b1000), nzTpIcepk0o8(chr(1518 - 1470) + chr(111) + chr(49) + chr(0b110000) + chr(0b100011 + 0o15), ord("\x08")), nzTpIcepk0o8('\060' + chr(8472 - 8361) + chr(0b100110 + 0o14) + '\062' + chr(0b110001), 11733 - 11725), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\063' + chr(0b101 + 0o61) + chr(50), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\062' + chr(0b11100 + 0o25) + chr(423 - 375), 13725 - 13717), nzTpIcepk0o8('\060' + chr(0b11100 + 0o123) + '\061' + chr(196 - 145) + chr(0b110010), 0o10), nzTpIcepk0o8(chr(103 - 55) + chr(0b1101111) + '\066' + chr(0b110001), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + '\x31' + '\x34' + chr(0b11 + 0o64), 0o10), nzTpIcepk0o8('\060' + chr(0b110001 + 0o76) + chr(50) + '\067' + chr(1379 - 1330), 8), nzTpIcepk0o8('\x30' + chr(9671 - 9560) + '\061' + '\x36' + '\x33', 52708 - 52700), nzTpIcepk0o8(chr(1968 - 1920) + chr(0b1101111) + chr(2541 - 2487) + chr(751 - 699), 60211 - 60203), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(1334 - 1283) + '\062' + chr(1114 - 1060), 19861 - 19853), nzTpIcepk0o8(chr(1074 - 1026) + chr(0b1101111) + chr(0b110 + 0o54) + chr(0b101110 + 0o2) + '\065', 54639 - 54631), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110010) + chr(1714 - 1663) + chr(0b10100 + 0o37), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(8023 - 7912) + '\062' + '\063' + chr(0b11110 + 0o30), ord("\x08")), nzTpIcepk0o8(chr(91 - 43) + chr(111) + '\x33' + chr(55) + chr(0b110100), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + '\064' + chr(0b110001 + 0o3), 0b1000), nzTpIcepk0o8(chr(0b100101 + 0o13) + '\x6f' + chr(0b110011) + '\063' + chr(48), ord("\x08")), nzTpIcepk0o8(chr(943 - 895) + chr(0b1101111) + chr(1439 - 1387) + chr(0b110111), 64005 - 63997), nzTpIcepk0o8(chr(0b110000) + chr(0b10011 + 0o134) + '\x31' + chr(54) + chr(0b100000 + 0o23), 8), nzTpIcepk0o8(chr(1482 - 1434) + chr(0b10001 + 0o136) + chr(51) + '\065' + chr(1108 - 1057), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x33' + chr(0b11110 + 0o31) + '\x35', 0o10), nzTpIcepk0o8(chr(0b10000 + 0o40) + '\157' + chr(50) + chr(2291 - 2242) + '\x35', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b1001 + 0o51) + chr(0b10101 + 0o37) + chr(471 - 419), 0o10), nzTpIcepk0o8(chr(0b11 + 0o55) + '\x6f' + chr(461 - 412) + '\065' + chr(51), 8), nzTpIcepk0o8('\x30' + '\x6f' + '\065' + chr(0b1100 + 0o52), 0b1000), nzTpIcepk0o8('\060' + chr(111) + '\x31' + chr(0b110110) + '\x37', 8), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x32' + chr(2598 - 2547), 0b1000), nzTpIcepk0o8('\060' + chr(10819 - 10708) + chr(463 - 413) + '\x34' + '\x35', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + '\062' + '\x35' + '\x34', 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(93 - 44) + '\065' + '\x30', 0o10), nzTpIcepk0o8(chr(339 - 291) + chr(0b1101111) + chr(0b10100 + 0o36) + chr(327 - 275) + chr(0b110101), 8), nzTpIcepk0o8('\x30' + chr(0b1100000 + 0o17) + chr(51) + chr(2251 - 2199) + '\x35', 55982 - 55974), nzTpIcepk0o8('\x30' + chr(111) + '\x33' + chr(2543 - 2489) + '\x31', 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + chr(0b101111 + 0o100) + chr(0b10001 + 0o44) + chr(0b110000), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x97'), chr(100) + chr(0b100010 + 0o103) + chr(2222 - 2123) + chr(111) + chr(100) + chr(7175 - 7074))(chr(0b1100000 + 0o25) + chr(116) + '\146' + '\055' + chr(1262 - 1206)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def iMFM2Bubdu6n(a0PQMDyaTVKH):
return Ov4KLivfl4p6(((roI3spqORKae(c76Yf40Q6MeM, roI3spqORKae(ES5oEprVxulp(b'\xce:\\E\x1eDD\x02\xc8\xbf\xcd2'), chr(0b1100100) + '\x65' + '\x63' + '\x6f' + chr(0b1100100) + '\x65')(chr(11484 - 11367) + chr(7434 - 7318) + '\146' + chr(0b101101) + chr(0b11 + 0o65))), roI3spqORKae(c76Yf40Q6MeM.data, roI3spqORKae(ES5oEprVxulp(b"\xe6\nf\x13'_w"), chr(100) + '\145' + '\x63' + '\157' + '\x64' + chr(0b1100101))(chr(0b1110101) + chr(0b1001110 + 0o46) + chr(0b1100110) + chr(1862 - 1817) + chr(0b111000)))()) for c76Yf40Q6MeM in a0PQMDyaTVKH)) |
openvax/varcode | varcode/vcf.py | dataframes_to_variant_collection | def dataframes_to_variant_collection(
dataframes,
source_path,
info_parser=None,
only_passing=True,
max_variants=None,
sample_names=None,
sample_info_parser=None,
variant_kwargs={},
variant_collection_kwargs={}):
"""
Load a VariantCollection from an iterable of pandas dataframes.
This takes an iterable of dataframes instead of a single dataframe to avoid
having to load huge dataframes at once into memory. If you have a single
dataframe, just pass it in a single-element list.
Parameters
----------
dataframes
Iterable of dataframes (e.g. a generator). Expected columns are:
["CHROM", "POS", "ID", "REF", "ALT", "QUAL", "FILTER"]
and 'INFO' if `info_parser` is not Null. Columns must be in this
order.
source_path : str
Path of VCF file from which DataFrame chunks were generated.
info_parser : string -> object, optional
Callable to parse INFO strings.
only_passing : boolean, optional
If true, any entries whose FILTER field is not one of "." or "PASS" is
dropped.
max_variants : int, optional
If specified, return only the first max_variants variants.
sample_names : list of strings, optional
Sample names. The final columns of the dataframe should match these.
If specified, the per-sample info columns will be parsed. You must
also specify sample_info_parser.
sample_info_parser : string list * string -> dict, optional
Callable to parse per-sample info columns.
variant_kwargs : dict, optional
Additional keyword paramters to pass to Variant.__init__
variant_collection_kwargs : dict, optional
Additional keyword parameters to pass to VariantCollection.__init__.
"""
expected_columns = (
["CHROM", "POS", "ID", "REF", "ALT", "QUAL", "FILTER"] +
(["INFO"] if info_parser else []))
if info_parser and sample_names:
if sample_info_parser is None:
raise TypeError(
"Must specify sample_info_parser if specifying sample_names")
expected_columns.append("FORMAT")
expected_columns.extend(sample_names)
variants = []
metadata = {}
try:
for chunk in dataframes:
assert chunk.columns.tolist() == expected_columns,\
"dataframe columns (%s) do not match expected columns (%s)" % (
chunk.columns, expected_columns)
for tpl in chunk.itertuples():
(i, chrom, pos, id_, ref, alts, qual, flter) = tpl[:8]
if flter == ".":
flter = None
elif flter == "PASS":
flter = []
elif only_passing:
continue
else:
flter = flter.split(';')
if id_ == ".":
id_ = None
qual = float(qual) if qual != "." else None
alt_num = 0
info = sample_info = None
for alt in alts.split(","):
if alt != ".":
if info_parser is not None and info is None:
info = info_parser(tpl[8]) # INFO column
if sample_names:
# Sample name -> field -> value dict.
sample_info = sample_info_parser(
list(tpl[10:]), # sample info columns
tpl[9], # FORMAT column
)
variant = Variant(
chrom,
int(pos), # want a Python int not numpy.int64
ref,
alt,
**variant_kwargs)
variants.append(variant)
metadata[variant] = {
'id': id_,
'qual': qual,
'filter': flter,
'info': info,
'sample_info': sample_info,
'alt_allele_index': alt_num,
}
if max_variants and len(variants) > max_variants:
raise StopIteration
alt_num += 1
except StopIteration:
pass
return VariantCollection(
variants=variants,
source_to_metadata_dict={source_path: metadata},
**variant_collection_kwargs) | python | def dataframes_to_variant_collection(
dataframes,
source_path,
info_parser=None,
only_passing=True,
max_variants=None,
sample_names=None,
sample_info_parser=None,
variant_kwargs={},
variant_collection_kwargs={}):
"""
Load a VariantCollection from an iterable of pandas dataframes.
This takes an iterable of dataframes instead of a single dataframe to avoid
having to load huge dataframes at once into memory. If you have a single
dataframe, just pass it in a single-element list.
Parameters
----------
dataframes
Iterable of dataframes (e.g. a generator). Expected columns are:
["CHROM", "POS", "ID", "REF", "ALT", "QUAL", "FILTER"]
and 'INFO' if `info_parser` is not Null. Columns must be in this
order.
source_path : str
Path of VCF file from which DataFrame chunks were generated.
info_parser : string -> object, optional
Callable to parse INFO strings.
only_passing : boolean, optional
If true, any entries whose FILTER field is not one of "." or "PASS" is
dropped.
max_variants : int, optional
If specified, return only the first max_variants variants.
sample_names : list of strings, optional
Sample names. The final columns of the dataframe should match these.
If specified, the per-sample info columns will be parsed. You must
also specify sample_info_parser.
sample_info_parser : string list * string -> dict, optional
Callable to parse per-sample info columns.
variant_kwargs : dict, optional
Additional keyword paramters to pass to Variant.__init__
variant_collection_kwargs : dict, optional
Additional keyword parameters to pass to VariantCollection.__init__.
"""
expected_columns = (
["CHROM", "POS", "ID", "REF", "ALT", "QUAL", "FILTER"] +
(["INFO"] if info_parser else []))
if info_parser and sample_names:
if sample_info_parser is None:
raise TypeError(
"Must specify sample_info_parser if specifying sample_names")
expected_columns.append("FORMAT")
expected_columns.extend(sample_names)
variants = []
metadata = {}
try:
for chunk in dataframes:
assert chunk.columns.tolist() == expected_columns,\
"dataframe columns (%s) do not match expected columns (%s)" % (
chunk.columns, expected_columns)
for tpl in chunk.itertuples():
(i, chrom, pos, id_, ref, alts, qual, flter) = tpl[:8]
if flter == ".":
flter = None
elif flter == "PASS":
flter = []
elif only_passing:
continue
else:
flter = flter.split(';')
if id_ == ".":
id_ = None
qual = float(qual) if qual != "." else None
alt_num = 0
info = sample_info = None
for alt in alts.split(","):
if alt != ".":
if info_parser is not None and info is None:
info = info_parser(tpl[8]) # INFO column
if sample_names:
# Sample name -> field -> value dict.
sample_info = sample_info_parser(
list(tpl[10:]), # sample info columns
tpl[9], # FORMAT column
)
variant = Variant(
chrom,
int(pos), # want a Python int not numpy.int64
ref,
alt,
**variant_kwargs)
variants.append(variant)
metadata[variant] = {
'id': id_,
'qual': qual,
'filter': flter,
'info': info,
'sample_info': sample_info,
'alt_allele_index': alt_num,
}
if max_variants and len(variants) > max_variants:
raise StopIteration
alt_num += 1
except StopIteration:
pass
return VariantCollection(
variants=variants,
source_to_metadata_dict={source_path: metadata},
**variant_collection_kwargs) | [
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"chrom",
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] | Load a VariantCollection from an iterable of pandas dataframes.
This takes an iterable of dataframes instead of a single dataframe to avoid
having to load huge dataframes at once into memory. If you have a single
dataframe, just pass it in a single-element list.
Parameters
----------
dataframes
Iterable of dataframes (e.g. a generator). Expected columns are:
["CHROM", "POS", "ID", "REF", "ALT", "QUAL", "FILTER"]
and 'INFO' if `info_parser` is not Null. Columns must be in this
order.
source_path : str
Path of VCF file from which DataFrame chunks were generated.
info_parser : string -> object, optional
Callable to parse INFO strings.
only_passing : boolean, optional
If true, any entries whose FILTER field is not one of "." or "PASS" is
dropped.
max_variants : int, optional
If specified, return only the first max_variants variants.
sample_names : list of strings, optional
Sample names. The final columns of the dataframe should match these.
If specified, the per-sample info columns will be parsed. You must
also specify sample_info_parser.
sample_info_parser : string list * string -> dict, optional
Callable to parse per-sample info columns.
variant_kwargs : dict, optional
Additional keyword paramters to pass to Variant.__init__
variant_collection_kwargs : dict, optional
Additional keyword parameters to pass to VariantCollection.__init__. | [
"Load",
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"."
] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/vcf.py#L199-L321 | train | Load a VariantCollection from a list of pandas dataframes. | 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) + '\157' + chr(49) + chr(49) + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b101000 + 0o13) + '\x34' + chr(0b100111 + 0o11), 0o10), nzTpIcepk0o8('\060' + chr(0b1101011 + 0o4) + chr(0b101001 + 0o10) + '\x35' + chr(0b110001), 57287 - 57279), nzTpIcepk0o8('\060' + chr(0b11101 + 0o122) + chr(0b110101) + '\x37', 0o10), nzTpIcepk0o8(chr(1233 - 1185) + chr(0b1101111) + '\063' + chr(1151 - 1096) + chr(0b11011 + 0o31), 25106 - 25098), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110011) + '\x34' + chr(52), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + '\x32' + chr(0b110011) + chr(0b11010 + 0o33), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1110 + 0o141) + '\x32' + chr(0b10010 + 0o45) + chr(48), 3497 - 3489), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(50) + chr(51) + chr(0b11111 + 0o24), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(49) + chr(1108 - 1056) + chr(0b110000 + 0o2), 50067 - 50059), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110101) + chr(0b110010), 0b1000), nzTpIcepk0o8(chr(0b100110 + 0o12) + '\157' + '\x33' + chr(0b1101 + 0o45) + chr(0b110000), 0o10), nzTpIcepk0o8(chr(0b11001 + 0o27) + chr(0b1100001 + 0o16) + chr(0b110010) + '\066' + chr(1760 - 1711), 10832 - 10824), nzTpIcepk0o8(chr(48) + chr(3969 - 3858) + chr(1238 - 1187) + '\x31' + chr(50), 0o10), nzTpIcepk0o8(chr(0b11011 + 0o25) + chr(111) + '\x32' + '\065' + chr(0b110101), ord("\x08")), nzTpIcepk0o8('\x30' + chr(2915 - 2804) + chr(0b110011) + chr(1734 - 1684) + '\062', 0o10), nzTpIcepk0o8(chr(48) + chr(551 - 440) + chr(50) + chr(276 - 226) + chr(51), 0b1000), nzTpIcepk0o8('\x30' + chr(7385 - 7274) + chr(55) + chr(49), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(3376 - 3265) + '\x31' + chr(0b11011 + 0o32), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\063' + chr(0b110111) + chr(0b110001), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1000100 + 0o53) + chr(0b11 + 0o60) + chr(0b10011 + 0o43) + chr(0b1101 + 0o45), 48957 - 48949), nzTpIcepk0o8('\x30' + chr(0b101011 + 0o104) + chr(2465 - 2415) + '\066' + chr(0b110 + 0o57), 0o10), nzTpIcepk0o8('\x30' + chr(0b11101 + 0o122) + chr(1587 - 1535), 1012 - 1004), nzTpIcepk0o8('\x30' + chr(0b1101100 + 0o3) + '\062' + chr(0b110011) + chr(703 - 651), 46015 - 46007), nzTpIcepk0o8('\060' + '\157' + '\061' + chr(0b110111) + chr(1457 - 1409), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\063', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(2276 - 2225) + '\x33' + chr(53), 5823 - 5815), nzTpIcepk0o8(chr(0b1011 + 0o45) + chr(0b1101111) + chr(0b110010) + chr(0b111 + 0o56) + chr(1083 - 1033), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101101 + 0o2) + '\x37' + chr(0b10101 + 0o35), 0o10), nzTpIcepk0o8(chr(48) + chr(11051 - 10940) + chr(49) + chr(0b10111 + 0o31) + chr(0b100 + 0o54), 15252 - 15244), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x32' + chr(0b110 + 0o53), 38214 - 38206), nzTpIcepk0o8(chr(387 - 339) + '\x6f' + chr(728 - 674) + '\x30', 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(171 - 122) + '\x32', ord("\x08")), nzTpIcepk0o8('\060' + chr(1884 - 1773) + chr(1749 - 1698) + '\x33' + '\x32', ord("\x08")), nzTpIcepk0o8(chr(1706 - 1658) + chr(2559 - 2448) + '\x33' + chr(0b110100) + chr(0b110010), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(49) + '\x31', 3841 - 3833), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(49) + chr(0b101111 + 0o3) + chr(0b110101), 0o10), nzTpIcepk0o8(chr(2222 - 2174) + chr(10280 - 10169) + '\061' + chr(0b10101 + 0o41) + chr(0b11 + 0o63), ord("\x08")), nzTpIcepk0o8(chr(934 - 886) + '\x6f' + chr(0b110011) + chr(0b110010) + '\060', 8), nzTpIcepk0o8(chr(500 - 452) + '\157' + chr(0b100010 + 0o17) + chr(0b110000) + '\064', 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b100001 + 0o17) + chr(0b1101111) + '\x35' + chr(0b110000), 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'e'), chr(0b1100100) + chr(0b10000 + 0o125) + '\x63' + chr(3827 - 3716) + chr(0b1100100) + '\145')(chr(0b1110101) + '\x74' + chr(2213 - 2111) + '\055' + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def HFwXsnYQ0Io6(EnpLkd2aiqG2, lGm16iRtt3rc, c5Agb1YNZKi6=None, Bvv1N65tH2pI=nzTpIcepk0o8(chr(0b110000) + chr(2717 - 2606) + '\x31', 0b1000), TsUqs1HTOUNo=None, VqvgnKhNIk_w=None, MNj_1ygyIrtn=None, UBP8BijUdZWe={}, ZIaLwr4yKAlM={}):
LjI7yM97tO82 = [roI3spqORKae(ES5oEprVxulp(b'\x08\xa8;`\xb1'), chr(6345 - 6245) + chr(2633 - 2532) + '\x63' + '\157' + '\144' + '\x65')('\165' + chr(0b10011 + 0o141) + chr(2772 - 2670) + chr(1900 - 1855) + '\x38'), roI3spqORKae(ES5oEprVxulp(b'\x1b\xaf:'), '\x64' + chr(8336 - 8235) + chr(99) + chr(111) + '\x64' + chr(0b111110 + 0o47))('\x75' + '\x74' + '\146' + '\x2d' + chr(56)), roI3spqORKae(ES5oEprVxulp(b'\x02\xa4'), chr(0b1100100) + chr(0b1 + 0o144) + chr(0b1100011) + chr(4395 - 4284) + '\144' + '\145')(chr(0b11101 + 0o130) + '\x74' + '\146' + chr(0b101101) + '\x38'), roI3spqORKae(ES5oEprVxulp(b'\x19\xa5/'), '\x64' + chr(6055 - 5954) + chr(0b1100011) + chr(4024 - 3913) + '\144' + chr(0b1100101))('\x75' + '\x74' + '\146' + chr(0b10010 + 0o33) + '\x38'), roI3spqORKae(ES5oEprVxulp(b'\n\xac='), chr(0b1100100) + '\145' + '\143' + chr(0b10000 + 0o137) + '\144' + chr(0b1100101))(chr(117) + '\x74' + chr(6779 - 6677) + chr(919 - 874) + '\070'), roI3spqORKae(ES5oEprVxulp(b'\x1a\xb5(c'), chr(0b1000110 + 0o36) + '\145' + '\x63' + chr(0b1101111) + chr(0b1000 + 0o134) + '\x65')(chr(117) + chr(116) + chr(0b101011 + 0o73) + chr(45) + chr(0b11 + 0o65)), roI3spqORKae(ES5oEprVxulp(b'\r\xa9%{\xb9\xb6'), chr(8541 - 8441) + chr(7902 - 7801) + chr(0b110110 + 0o55) + '\x6f' + '\144' + chr(0b1000000 + 0o45))(chr(117) + chr(0b110101 + 0o77) + chr(9540 - 9438) + chr(550 - 505) + chr(56))] + ([roI3spqORKae(ES5oEprVxulp(b'\x02\xae/`'), chr(0b1100100) + chr(0b11000 + 0o115) + '\x63' + chr(12286 - 12175) + chr(1207 - 1107) + chr(0b1100101))(chr(0b1010 + 0o153) + '\164' + chr(0b1100110) + chr(169 - 124) + chr(56))] if c5Agb1YNZKi6 else [])
if c5Agb1YNZKi6 and VqvgnKhNIk_w:
if MNj_1ygyIrtn is None:
raise jZIjKu8IFANs(roI3spqORKae(ES5oEprVxulp(b"\x06\x95\x1a[\xdc\x97\xed\xdd\xf8\x0bL\xa9\x91\xb9\xcc\xbf\xe3Uh\xa6\x9b\xdbb\xf3's\xbc\xd8I%c\x10c\xbc\xc2z%\x13\xb3--\x99\x00A\x9b\xc4\xee\xd9\xf6\x12F\xb5\xee\xa4\xcc\xbf\xf6J"), chr(577 - 477) + chr(101) + chr(2400 - 2301) + chr(10020 - 9909) + chr(0b11000 + 0o114) + '\145')(chr(1675 - 1558) + '\x74' + chr(0b1011101 + 0o11) + chr(1941 - 1896) + '\x38'))
roI3spqORKae(LjI7yM97tO82, roI3spqORKae(ES5oEprVxulp(b'\x03\xb4:\x1b\x84\x83\xda\xd7\xf1\r\x7f\xe5'), chr(0b110001 + 0o63) + '\145' + chr(0b1100011) + '\157' + chr(0b1001110 + 0o26) + chr(5519 - 5418))(chr(9461 - 9344) + chr(116) + chr(0b1100110) + '\055' + '\070'))(roI3spqORKae(ES5oEprVxulp(b'\r\xaf;b\xbd\xb0'), '\144' + chr(101) + '\143' + chr(0b1101111) + chr(100) + '\145')('\x75' + chr(0b1110100) + '\x66' + chr(0b1110 + 0o37) + chr(56)))
roI3spqORKae(LjI7yM97tO82, roI3spqORKae(ES5oEprVxulp(b'\x1f\xbfZb\x93\x80\xd1\xef\xc4 H\xa1'), '\x64' + '\x65' + chr(99) + '\157' + '\144' + '\145')(chr(10025 - 9908) + chr(116) + chr(0b1100001 + 0o5) + '\x2d' + chr(56)))(VqvgnKhNIk_w)
Loszd1LxpkfW = []
nmf2TsIJJ3IK = {}
try:
for WckxBx1Uqdpm in EnpLkd2aiqG2:
assert roI3spqORKae(WckxBx1Uqdpm.columns, roI3spqORKae(ES5oEprVxulp(b'?\x8f\x05F\x8f\x90'), chr(0b110001 + 0o63) + '\145' + chr(0b1100011) + chr(111) + chr(8290 - 8190) + '\145')('\x75' + chr(11217 - 11101) + chr(0b1100110) + '\x2d' + chr(2950 - 2894)))() == LjI7yM97tO82, roI3spqORKae(ES5oEprVxulp(b'/\x81\x1dN\x9a\x96\xfc\xd5\xfeBI\xbf\xdd\xbf\xc0\xbc\xe0\x19%\xdc\x81\x9c$\xf8\x17#\xb3\xc5N`|Q~\xb9\x8a)0\x0e\xa0!(\x94\x0cK\xdc\x87\xf2\xd4\xee\x0fD\xa3\x91\xe2\x88\xa1\xba'), chr(3662 - 3562) + chr(3293 - 3192) + '\x63' + '\x6f' + '\144' + chr(101))('\x75' + chr(0b100001 + 0o123) + chr(0b1110 + 0o130) + chr(45) + chr(0b111000)) % (roI3spqORKae(WckxBx1Uqdpm, roI3spqORKae(ES5oEprVxulp(b'\x1e\xd3PE\xaf\x8d\xd4\x8d\xaf/F\xa0'), chr(0b1001001 + 0o33) + chr(0b1001001 + 0o34) + chr(0b1100011) + '\x6f' + chr(0b110011 + 0o61) + chr(0b1100010 + 0o3))(chr(9000 - 8883) + chr(0b1011 + 0o151) + '\x66' + chr(0b100010 + 0o13) + chr(0b100100 + 0o24))), LjI7yM97tO82)
for XEE_WbWc84EQ in roI3spqORKae(WckxBx1Uqdpm, roI3spqORKae(ES5oEprVxulp(b'"\x94\x0c]\x88\x91\xed\xd4\xfe\x11'), chr(100) + chr(2713 - 2612) + chr(4304 - 4205) + chr(111) + chr(100) + chr(0b1100101))(chr(0b1110101) + chr(0b11011 + 0o131) + chr(0b1100110) + chr(45) + chr(2089 - 2033)))():
(ZlbFMSG8gCoF, fW0_QlhvSEii, IGIA_fu6MbaO, iGbEKd8wXMMm, CmNScfxJ1Uih, YXFYvuIgpx0K, vMMyG1fTqMo3, G86RVnhQjSDA) = XEE_WbWc84EQ[:nzTpIcepk0o8(chr(0b101000 + 0o10) + chr(0b1101111) + chr(49) + chr(1132 - 1084), 0b1000)]
if G86RVnhQjSDA == roI3spqORKae(ES5oEprVxulp(b'e'), chr(0b1010111 + 0o15) + chr(6635 - 6534) + chr(0b1100011) + chr(111) + chr(100) + chr(0b1100101))(chr(10479 - 10362) + chr(2501 - 2385) + chr(6837 - 6735) + chr(0b1001 + 0o44) + chr(0b111000)):
G86RVnhQjSDA = None
elif G86RVnhQjSDA == roI3spqORKae(ES5oEprVxulp(b'\x1b\xa1:|'), chr(0b1100100) + chr(0b1100101) + chr(8682 - 8583) + chr(3202 - 3091) + chr(2863 - 2763) + chr(0b1100101))(chr(0b1110101) + '\x74' + chr(102) + chr(45) + chr(1822 - 1766)):
G86RVnhQjSDA = []
elif Bvv1N65tH2pI:
continue
else:
G86RVnhQjSDA = G86RVnhQjSDA.LfRrQOxuDvnC(roI3spqORKae(ES5oEprVxulp(b'p'), '\x64' + chr(0b1100101) + chr(99) + '\x6f' + chr(0b110110 + 0o56) + '\145')(chr(234 - 117) + chr(441 - 325) + '\146' + chr(889 - 844) + '\070'))
if iGbEKd8wXMMm == roI3spqORKae(ES5oEprVxulp(b'e'), chr(100) + chr(8957 - 8856) + chr(0b101011 + 0o70) + '\x6f' + chr(100) + '\x65')(chr(0b1100111 + 0o16) + chr(0b110111 + 0o75) + '\146' + chr(322 - 277) + '\x38'):
iGbEKd8wXMMm = None
vMMyG1fTqMo3 = jLW6pRf2DSRk(vMMyG1fTqMo3) if vMMyG1fTqMo3 != roI3spqORKae(ES5oEprVxulp(b'e'), chr(100) + chr(101) + chr(0b10000 + 0o123) + '\157' + '\x64' + '\145')(chr(0b1110101) + '\164' + chr(0b1100110) + '\055' + '\x38') else None
WU6xhEbTGpA3 = nzTpIcepk0o8('\060' + chr(111) + '\060', 0b1000)
ixNx9Lw_1grO = XyzZqDGjMWmz = None
for YVIVvpvk_rzo in roI3spqORKae(YXFYvuIgpx0K, roI3spqORKae(ES5oEprVxulp(b'\x07\x86;]\xad\xab\xe5\xcd\xdf\x14D\x93'), '\144' + chr(0b1001010 + 0o33) + chr(772 - 673) + chr(0b111110 + 0o61) + '\x64' + chr(0b1100101))('\x75' + chr(0b1110100) + chr(0b110100 + 0o62) + chr(45) + chr(3072 - 3016)))(roI3spqORKae(ES5oEprVxulp(b'g'), '\144' + '\145' + chr(3424 - 3325) + '\157' + '\x64' + chr(941 - 840))(chr(117) + '\164' + '\146' + chr(1765 - 1720) + '\070')):
if YVIVvpvk_rzo != roI3spqORKae(ES5oEprVxulp(b'e'), chr(100) + '\145' + chr(0b1100011) + '\x6f' + chr(0b1100100) + chr(4314 - 4213))('\165' + '\x74' + chr(0b11000 + 0o116) + chr(45) + chr(0b111000)):
if c5Agb1YNZKi6 is not None and ixNx9Lw_1grO is None:
ixNx9Lw_1grO = c5Agb1YNZKi6(XEE_WbWc84EQ[nzTpIcepk0o8(chr(0b110000) + chr(0b100101 + 0o112) + chr(49) + chr(0b11 + 0o55), 8)])
if VqvgnKhNIk_w:
XyzZqDGjMWmz = MNj_1ygyIrtn(H4NoA26ON7iG(XEE_WbWc84EQ[nzTpIcepk0o8('\060' + chr(11379 - 11268) + chr(712 - 663) + chr(163 - 113), 8):]), XEE_WbWc84EQ[nzTpIcepk0o8(chr(0b10011 + 0o35) + chr(0b1101111) + chr(49) + '\x31', 8)])
ZXJSPKxkIyZK = Aw3KqnTlyD0Y(fW0_QlhvSEii, nzTpIcepk0o8(IGIA_fu6MbaO), CmNScfxJ1Uih, YVIVvpvk_rzo, **UBP8BijUdZWe)
roI3spqORKae(Loszd1LxpkfW, roI3spqORKae(ES5oEprVxulp(b'\x03\xb4:\x1b\x84\x83\xda\xd7\xf1\r\x7f\xe5'), '\x64' + chr(0b100000 + 0o105) + '\143' + '\157' + chr(100) + chr(0b1100101))('\165' + chr(1193 - 1077) + chr(0b1100110) + '\055' + '\x38'))(ZXJSPKxkIyZK)
nmf2TsIJJ3IK[ZXJSPKxkIyZK] = {roI3spqORKae(ES5oEprVxulp(b'"\x84'), chr(0b1000100 + 0o40) + chr(0b1100101) + chr(99) + '\157' + chr(0b100110 + 0o76) + chr(0b111001 + 0o54))(chr(117) + chr(7326 - 7210) + '\146' + chr(0b11000 + 0o25) + chr(56)): iGbEKd8wXMMm, roI3spqORKae(ES5oEprVxulp(b':\x95\x08C'), chr(9439 - 9339) + '\145' + chr(99) + chr(0b1001110 + 0o41) + chr(0b1011110 + 0o6) + '\145')(chr(117) + chr(3732 - 3616) + chr(0b111001 + 0o55) + chr(1676 - 1631) + chr(56)): vMMyG1fTqMo3, roI3spqORKae(ES5oEprVxulp(b'-\x89\x05[\x99\x96'), chr(0b1100100) + chr(0b1100011 + 0o2) + chr(2681 - 2582) + chr(1952 - 1841) + chr(0b1100100) + '\145')(chr(117) + '\164' + chr(2900 - 2798) + '\x2d' + '\070'): G86RVnhQjSDA, roI3spqORKae(ES5oEprVxulp(b'"\x8e\x0f@'), chr(0b1100100) + chr(8546 - 8445) + chr(4815 - 4716) + '\x6f' + chr(100) + '\145')(chr(0b11100 + 0o131) + chr(6537 - 6421) + '\x66' + chr(0b101101) + chr(56)): ixNx9Lw_1grO, roI3spqORKae(ES5oEprVxulp(b'8\x81\x04_\x90\x81\xc2\xd1\xf5\x04E'), chr(0b111101 + 0o47) + chr(5761 - 5660) + chr(99) + chr(9741 - 9630) + chr(100) + chr(0b100011 + 0o102))(chr(10236 - 10119) + chr(0b1110100) + chr(8280 - 8178) + chr(0b101101) + chr(56)): XyzZqDGjMWmz, roI3spqORKae(ES5oEprVxulp(b'*\x8c\x1dp\x9d\x88\xf1\xdd\xf7\x07u\xb9\xdf\xae\xc8\xaa'), chr(9573 - 9473) + '\x65' + chr(0b1000100 + 0o37) + chr(3431 - 3320) + chr(0b111101 + 0o47) + chr(0b1100101))('\165' + '\x74' + chr(0b1001 + 0o135) + chr(45) + chr(0b101011 + 0o15)): WU6xhEbTGpA3}
if TsUqs1HTOUNo and ftfygxgFas5X(Loszd1LxpkfW) > TsUqs1HTOUNo:
raise ZOdpVDJPWn4I
WU6xhEbTGpA3 += nzTpIcepk0o8(chr(48) + '\x6f' + '\x31', 8)
except ZOdpVDJPWn4I:
pass
return XqoyAjJpppwZ(variants=Loszd1LxpkfW, source_to_metadata_dict={lGm16iRtt3rc: nmf2TsIJJ3IK}, **ZIaLwr4yKAlM) |
openvax/varcode | varcode/vcf.py | read_vcf_into_dataframe | def read_vcf_into_dataframe(
path,
include_info=False,
sample_names=None,
chunk_size=None):
"""
Load the data of a VCF into a pandas dataframe. All headers are ignored.
Parameters
----------
path : str
Path to local file. HTTP and other protocols are not implemented.
include_info : boolean, default False
If true, the INFO field is not parsed, but is included as a string in
the resulting data frame. If false, the INFO field is omitted.
sample_names: string list, optional
Sample names. The final columns of the dataframe should match these.
If specified (and include_info is also specified), the FORMAT and
per-sample info columns will be included in the result dataframe.
chunk_size : int, optional
If buffering is desired, the number of rows per chunk.
Returns
---------
If chunk_size is None (the default), a dataframe with the contents of the
VCF file. Otherwise, an iterable of dataframes, each with chunk_size rows.
"""
vcf_field_types = OrderedDict()
vcf_field_types['CHROM'] = str
vcf_field_types['POS'] = int
vcf_field_types['ID'] = str
vcf_field_types['REF'] = str
vcf_field_types['ALT'] = str
vcf_field_types['QUAL'] = str
vcf_field_types['FILTER'] = str
if include_info:
vcf_field_types['INFO'] = str
if sample_names:
vcf_field_types['FORMAT'] = str
for name in sample_names:
vcf_field_types[name] = str
parsed_path = parse_url_or_path(path)
if not parsed_path.scheme or parsed_path.scheme.lower() == "file":
path = parsed_path.path
else:
raise NotImplementedError("Only local files are supported.")
compression = None
if path.endswith(".gz"):
compression = "gzip"
elif path.endswith(".bz2"):
compression = "bz2"
reader = pandas.read_table(
path,
compression=compression,
comment="#",
chunksize=chunk_size,
dtype=vcf_field_types,
names=list(vcf_field_types),
usecols=range(len(vcf_field_types)))
return reader | python | def read_vcf_into_dataframe(
path,
include_info=False,
sample_names=None,
chunk_size=None):
"""
Load the data of a VCF into a pandas dataframe. All headers are ignored.
Parameters
----------
path : str
Path to local file. HTTP and other protocols are not implemented.
include_info : boolean, default False
If true, the INFO field is not parsed, but is included as a string in
the resulting data frame. If false, the INFO field is omitted.
sample_names: string list, optional
Sample names. The final columns of the dataframe should match these.
If specified (and include_info is also specified), the FORMAT and
per-sample info columns will be included in the result dataframe.
chunk_size : int, optional
If buffering is desired, the number of rows per chunk.
Returns
---------
If chunk_size is None (the default), a dataframe with the contents of the
VCF file. Otherwise, an iterable of dataframes, each with chunk_size rows.
"""
vcf_field_types = OrderedDict()
vcf_field_types['CHROM'] = str
vcf_field_types['POS'] = int
vcf_field_types['ID'] = str
vcf_field_types['REF'] = str
vcf_field_types['ALT'] = str
vcf_field_types['QUAL'] = str
vcf_field_types['FILTER'] = str
if include_info:
vcf_field_types['INFO'] = str
if sample_names:
vcf_field_types['FORMAT'] = str
for name in sample_names:
vcf_field_types[name] = str
parsed_path = parse_url_or_path(path)
if not parsed_path.scheme or parsed_path.scheme.lower() == "file":
path = parsed_path.path
else:
raise NotImplementedError("Only local files are supported.")
compression = None
if path.endswith(".gz"):
compression = "gzip"
elif path.endswith(".bz2"):
compression = "bz2"
reader = pandas.read_table(
path,
compression=compression,
comment="#",
chunksize=chunk_size,
dtype=vcf_field_types,
names=list(vcf_field_types),
usecols=range(len(vcf_field_types)))
return reader | [
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Parameters
----------
path : str
Path to local file. HTTP and other protocols are not implemented.
include_info : boolean, default False
If true, the INFO field is not parsed, but is included as a string in
the resulting data frame. If false, the INFO field is omitted.
sample_names: string list, optional
Sample names. The final columns of the dataframe should match these.
If specified (and include_info is also specified), the FORMAT and
per-sample info columns will be included in the result dataframe.
chunk_size : int, optional
If buffering is desired, the number of rows per chunk.
Returns
---------
If chunk_size is None (the default), a dataframe with the contents of the
VCF file. Otherwise, an iterable of dataframes, each with chunk_size rows. | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/vcf.py#L324-L390 | train | Reads the contents of a VCF file into a pandas dataframe. | 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) + '\157' + chr(508 - 459) + chr(0b110110) + chr(0b110011), 61871 - 61863), nzTpIcepk0o8(chr(48) + '\x6f' + chr(50) + chr(0b110001) + '\x32', 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b10111 + 0o37) + chr(51), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + '\061' + chr(52) + chr(2069 - 2019), 2006 - 1998), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\065' + chr(0b101101 + 0o11), 0b1000), nzTpIcepk0o8('\060' + chr(0b10011 + 0o134) + chr(51) + '\x34' + chr(0b110011), 0o10), nzTpIcepk0o8('\060' + '\x6f' + '\x31' + chr(0b100110 + 0o15) + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\063' + chr(49) + chr(0b110100), 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110011) + chr(0b110110), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + '\x31' + chr(0b110110) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110010) + chr(49) + chr(53), 0b1000), nzTpIcepk0o8(chr(1408 - 1360) + '\157' + chr(1469 - 1418) + chr(0b110000), 0b1000), nzTpIcepk0o8(chr(0b100101 + 0o13) + '\157' + chr(0b101110 + 0o4) + '\x31' + chr(0b110101), 8), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110100 + 0o3) + '\x34', ord("\x08")), nzTpIcepk0o8(chr(0b111 + 0o51) + chr(111) + chr(0b110011) + chr(48) + chr(0b11011 + 0o25), ord("\x08")), nzTpIcepk0o8(chr(1424 - 1376) + '\x6f' + chr(746 - 697) + '\067' + '\061', 0b1000), nzTpIcepk0o8('\x30' + chr(10982 - 10871) + chr(2778 - 2724) + '\064', 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(51) + chr(1177 - 1127) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(0b100101 + 0o13) + '\x6f' + chr(49) + chr(0b110000) + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b11 + 0o57) + chr(49) + chr(2394 - 2342), ord("\x08")), nzTpIcepk0o8('\060' + chr(10176 - 10065) + chr(2365 - 2315) + chr(2047 - 1994), 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110011) + chr(1310 - 1262) + chr(0b110010), 6370 - 6362), nzTpIcepk0o8(chr(48) + chr(0b1 + 0o156) + '\062' + chr(1091 - 1042) + chr(0b110100), 8), nzTpIcepk0o8('\060' + chr(0b1010000 + 0o37) + chr(0b101110 + 0o11) + '\060', ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110010) + '\062' + chr(0b110100), 0o10), nzTpIcepk0o8('\x30' + chr(6713 - 6602) + chr(1283 - 1234) + chr(0b11110 + 0o26) + '\x32', 8), nzTpIcepk0o8('\060' + chr(111) + '\062' + chr(2334 - 2281), 8), nzTpIcepk0o8(chr(0b110000) + chr(5770 - 5659) + chr(0b11000 + 0o31) + '\062' + chr(640 - 587), ord("\x08")), nzTpIcepk0o8(chr(0b10100 + 0o34) + '\x6f' + chr(0b110001) + '\067' + chr(0b110001), 8), nzTpIcepk0o8(chr(0b10010 + 0o36) + chr(111) + chr(0b11111 + 0o22) + '\x36' + '\x34', 8), nzTpIcepk0o8('\x30' + chr(369 - 258) + chr(1359 - 1308) + chr(55), ord("\x08")), nzTpIcepk0o8(chr(1724 - 1676) + chr(0b1101111) + '\x32' + chr(0b110000) + '\065', ord("\x08")), nzTpIcepk0o8(chr(1770 - 1722) + '\157' + chr(0b10110 + 0o34) + chr(0b10001 + 0o40) + chr(0b100010 + 0o20), 8), nzTpIcepk0o8('\x30' + chr(7024 - 6913) + chr(0b11000 + 0o31) + chr(0b110100) + '\064', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(1965 - 1854) + '\x33' + '\065' + '\062', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b111101 + 0o62) + chr(2008 - 1958) + '\065' + chr(0b110001), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1010000 + 0o37) + '\067', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b10100 + 0o133) + chr(394 - 344) + chr(0b110010) + chr(0b100110 + 0o15), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110001) + '\x36' + '\061', 34063 - 34055), nzTpIcepk0o8('\x30' + '\157' + '\x31' + chr(49) + chr(0b110110), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + '\x6f' + '\065' + '\060', 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b']'), '\144' + '\145' + chr(6369 - 6270) + '\x6f' + chr(0b1100100) + chr(0b101 + 0o140))('\165' + chr(0b1110100) + chr(0b1100 + 0o132) + chr(0b101101) + chr(0b100011 + 0o25)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def yNoFyFaVTZ6f(_pSYqrosNb95, sLgKHMPDbfhR=nzTpIcepk0o8(chr(0b110000) + chr(8173 - 8062) + '\060', 0o10), VqvgnKhNIk_w=None, CyjJOdV7xEsi=None):
L61IVXIPRE2a = Ov4KLivfl4p6()
L61IVXIPRE2a[roI3spqORKae(ES5oEprVxulp(b'0\xc2a-c'), chr(0b110101 + 0o57) + chr(1810 - 1709) + '\x63' + chr(0b1101111) + chr(0b1100100 + 0o0) + chr(101))('\x75' + chr(0b110111 + 0o75) + '\146' + chr(0b101101) + '\070')] = N9zlRy29S1SS
L61IVXIPRE2a[roI3spqORKae(ES5oEprVxulp(b'#\xc5`'), '\144' + chr(0b100001 + 0o104) + '\143' + '\x6f' + '\x64' + chr(8989 - 8888))(chr(117) + '\x74' + chr(0b1000110 + 0o40) + chr(0b101101) + chr(0b110101 + 0o3))] = nzTpIcepk0o8
L61IVXIPRE2a[roI3spqORKae(ES5oEprVxulp(b':\xce'), '\144' + chr(0b1100101) + '\143' + '\x6f' + chr(0b111110 + 0o46) + chr(8496 - 8395))(chr(0b1110101) + chr(0b1100 + 0o150) + '\146' + chr(0b10001 + 0o34) + '\x38')] = N9zlRy29S1SS
L61IVXIPRE2a[roI3spqORKae(ES5oEprVxulp(b'!\xcfu'), chr(0b10110 + 0o116) + chr(101) + chr(6434 - 6335) + '\x6f' + chr(0b1100100) + '\145')(chr(0b1000110 + 0o57) + chr(116) + chr(102) + chr(1659 - 1614) + chr(1946 - 1890))] = N9zlRy29S1SS
L61IVXIPRE2a[roI3spqORKae(ES5oEprVxulp(b'2\xc6g'), '\x64' + chr(999 - 898) + '\143' + chr(8021 - 7910) + '\x64' + chr(0b1010010 + 0o23))('\165' + '\x74' + '\146' + '\055' + chr(56))] = N9zlRy29S1SS
L61IVXIPRE2a[roI3spqORKae(ES5oEprVxulp(b'"\xdfr.'), chr(0b1100100) + chr(0b1100101) + chr(0b1100011) + chr(0b1101111) + chr(0b110101 + 0o57) + chr(0b10111 + 0o116))(chr(0b1110101) + chr(0b1110100) + chr(0b1100110) + chr(904 - 859) + chr(0b111000 + 0o0))] = N9zlRy29S1SS
L61IVXIPRE2a[roI3spqORKae(ES5oEprVxulp(b'5\xc3\x7f6k\xb1'), '\x64' + chr(4687 - 4586) + '\143' + chr(111) + chr(100) + chr(101))(chr(0b11010 + 0o133) + '\x74' + '\146' + chr(0b101 + 0o50) + '\x38')] = N9zlRy29S1SS
if sLgKHMPDbfhR:
L61IVXIPRE2a[roI3spqORKae(ES5oEprVxulp(b':\xc4u-'), '\144' + chr(101) + chr(0b101 + 0o136) + chr(111) + '\144' + chr(0b11011 + 0o112))('\x75' + chr(0b1001 + 0o153) + chr(0b1001110 + 0o30) + '\055' + '\070')] = N9zlRy29S1SS
if VqvgnKhNIk_w:
L61IVXIPRE2a[roI3spqORKae(ES5oEprVxulp(b'5\xc5a/o\xb7'), '\x64' + '\x65' + chr(0b100001 + 0o102) + chr(111) + '\144' + chr(0b1100101))('\165' + chr(1666 - 1550) + '\146' + chr(0b101101) + chr(56))] = N9zlRy29S1SS
for SLVB2BPA_mIe in VqvgnKhNIk_w:
L61IVXIPRE2a[SLVB2BPA_mIe] = N9zlRy29S1SS
u_eZo_f9F0ni = vSgXMKm9j9A2(_pSYqrosNb95)
if not roI3spqORKae(u_eZo_f9F0ni, roI3spqORKae(ES5oEprVxulp(b'\x1c\xfeD\x04`\x9b9\xb6M\x1d\xfb{'), chr(100) + '\145' + chr(0b1001010 + 0o31) + '\x6f' + '\144' + chr(2828 - 2727))(chr(0b1110101) + chr(0b1010001 + 0o43) + chr(102) + '\055' + chr(581 - 525))) or roI3spqORKae(u_eZo_f9F0ni.scheme, roI3spqORKae(ES5oEprVxulp(b"+\xe4\x0b'`\xb4\x11\x96z=\xdfl"), '\x64' + chr(0b1100101) + chr(99) + chr(0b1000100 + 0o53) + chr(100) + chr(0b1000110 + 0o37))('\x75' + chr(0b1110100) + '\146' + chr(0b101101) + chr(0b11111 + 0o31)))() == roI3spqORKae(ES5oEprVxulp(b'\x15\xe3_\x07'), chr(0b1100100) + chr(101) + '\143' + chr(111) + '\144' + chr(101))('\x75' + chr(3034 - 2918) + chr(102) + chr(0b11001 + 0o24) + chr(56)):
_pSYqrosNb95 = u_eZo_f9F0ni._pSYqrosNb95
else:
raise Y1otPTwLRJvi(roI3spqORKae(ES5oEprVxulp(b'<\xe4_\x1b\x0e\x8f3\xaf\x7f\x18\xad~\xe4P\xa5\n\x14\xb25\xe95\xb1\xf9H\xe4\rg!\x1c\x101'), chr(100) + '\x65' + chr(99) + chr(11521 - 11410) + chr(100) + chr(6899 - 6798))('\165' + chr(116) + chr(0b10101 + 0o121) + chr(0b10101 + 0o30) + chr(2226 - 2170)))
fMBaJ20ka8As = None
if roI3spqORKae(_pSYqrosNb95, roI3spqORKae(ES5oEprVxulp(b':\xb3U)g\xa0\x1d\x80\x7f\x01\xc7j'), chr(0b1100100) + chr(0b110011 + 0o62) + '\143' + chr(0b1101111) + chr(0b1100100 + 0o0) + '\145')('\x75' + '\x74' + chr(0b1100110) + '\x2d' + chr(56)))(roI3spqORKae(ES5oEprVxulp(b']\xedI'), chr(100) + chr(0b1100101) + chr(0b1100011) + chr(0b1101111) + chr(100) + '\145')(chr(0b100011 + 0o122) + chr(0b1010 + 0o152) + chr(0b101010 + 0o74) + chr(45) + '\x38')):
fMBaJ20ka8As = roI3spqORKae(ES5oEprVxulp(b'\x14\xf0Z\x12'), chr(2788 - 2688) + '\145' + chr(6224 - 6125) + '\157' + '\x64' + '\145')(chr(0b1110101) + '\x74' + chr(0b1100110) + chr(0b101001 + 0o4) + '\070')
elif roI3spqORKae(_pSYqrosNb95, roI3spqORKae(ES5oEprVxulp(b':\xb3U)g\xa0\x1d\x80\x7f\x01\xc7j'), '\x64' + '\x65' + '\143' + '\157' + '\x64' + '\x65')('\x75' + chr(116) + chr(102) + '\055' + chr(0b100010 + 0o26)))(roI3spqORKae(ES5oEprVxulp(b']\xe8IP'), chr(100) + chr(0b1100101) + chr(6665 - 6566) + chr(111) + '\x64' + chr(0b100001 + 0o104))(chr(117) + chr(8182 - 8066) + chr(102) + chr(1288 - 1243) + chr(0b111000))):
fMBaJ20ka8As = roI3spqORKae(ES5oEprVxulp(b'\x11\xf0\x01'), '\x64' + chr(0b1100101) + '\x63' + chr(0b1000000 + 0o57) + chr(0b1100100) + chr(0b1011011 + 0o12))(chr(1246 - 1129) + chr(0b1101111 + 0o5) + chr(609 - 507) + '\055' + chr(0b111000))
kWvgahJQKTiF = DlW31l1chrSA.read_table(_pSYqrosNb95, compression=fMBaJ20ka8As, comment=roI3spqORKae(ES5oEprVxulp(b'P'), chr(0b1100100) + '\145' + chr(3425 - 3326) + chr(0b1101111) + chr(0b111111 + 0o45) + chr(1544 - 1443))(chr(0b101 + 0o160) + chr(6645 - 6529) + chr(0b1100110) + '\x2d' + chr(0b111000)), chunksize=CyjJOdV7xEsi, dtype=L61IVXIPRE2a, names=H4NoA26ON7iG(L61IVXIPRE2a), usecols=bbT2xIe5pzk7(ftfygxgFas5X(L61IVXIPRE2a)))
return kWvgahJQKTiF |
openvax/varcode | varcode/vcf.py | stream_gzip_decompress_lines | def stream_gzip_decompress_lines(stream):
"""
Uncompress a gzip stream into lines of text.
Parameters
----------
Generator of chunks of gzip compressed text.
Returns
-------
Generator of uncompressed lines.
"""
dec = zlib.decompressobj(zlib.MAX_WBITS | 16)
previous = ""
for compressed_chunk in stream:
chunk = dec.decompress(compressed_chunk).decode()
if chunk:
lines = (previous + chunk).split("\n")
previous = lines.pop()
for line in lines:
yield line
yield previous | python | def stream_gzip_decompress_lines(stream):
"""
Uncompress a gzip stream into lines of text.
Parameters
----------
Generator of chunks of gzip compressed text.
Returns
-------
Generator of uncompressed lines.
"""
dec = zlib.decompressobj(zlib.MAX_WBITS | 16)
previous = ""
for compressed_chunk in stream:
chunk = dec.decompress(compressed_chunk).decode()
if chunk:
lines = (previous + chunk).split("\n")
previous = lines.pop()
for line in lines:
yield line
yield previous | [
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Generator of chunks of gzip compressed text.
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Generator of uncompressed lines. | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/vcf.py#L448-L469 | train | Decompress a gzip stream into lines of text. | 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) + '\x33' + '\x35' + chr(1097 - 1047), 24569 - 24561), nzTpIcepk0o8(chr(0b101110 + 0o2) + '\157' + chr(2161 - 2112) + chr(2174 - 2120) + '\061', 0b1000), nzTpIcepk0o8('\060' + chr(0b11001 + 0o126) + chr(51) + chr(0b110011), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(0b100 + 0o56) + '\x37' + '\x37', 28774 - 28766), nzTpIcepk0o8(chr(726 - 678) + chr(111) + '\x32' + '\x33' + chr(0b100 + 0o55), 0o10), nzTpIcepk0o8(chr(0b101101 + 0o3) + '\x6f' + '\061' + '\062' + chr(0b110100), 22946 - 22938), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x35' + chr(0b101001 + 0o10), 0b1000), nzTpIcepk0o8(chr(1216 - 1168) + chr(111) + chr(53) + '\066', ord("\x08")), nzTpIcepk0o8('\060' + chr(1833 - 1722) + chr(0b101000 + 0o12) + chr(0b110101) + chr(50), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(2247 - 2197) + chr(207 - 154) + chr(55), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + '\x33' + chr(0b10001 + 0o43) + '\066', 42703 - 42695), nzTpIcepk0o8(chr(0b1111 + 0o41) + chr(111) + chr(50) + '\066' + chr(321 - 272), 18410 - 18402), nzTpIcepk0o8('\060' + '\157' + chr(51) + chr(1880 - 1829) + chr(0b110101 + 0o0), 0o10), nzTpIcepk0o8(chr(0b11110 + 0o22) + '\157' + '\x31', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(751 - 640) + chr(0b100011 + 0o17) + chr(52) + chr(53), 13787 - 13779), nzTpIcepk0o8(chr(698 - 650) + chr(0b1101111) + '\061' + chr(0b110111) + chr(54), 0o10), nzTpIcepk0o8('\060' + '\x6f' + '\x33' + '\063' + chr(181 - 130), 0b1000), nzTpIcepk0o8(chr(1051 - 1003) + chr(0b1101111) + chr(2379 - 2329) + '\060' + chr(1808 - 1753), 0b1000), nzTpIcepk0o8(chr(48) + chr(3437 - 3326) + chr(0b110001) + chr(1299 - 1244) + chr(0b1000 + 0o50), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(49) + chr(2678 - 2623) + '\x37', 0o10), nzTpIcepk0o8('\060' + '\157' + chr(51) + '\x36' + '\x35', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b101000 + 0o12) + '\061' + '\x35', 4827 - 4819), nzTpIcepk0o8(chr(48) + '\157' + chr(0b10100 + 0o35) + '\x34' + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(11995 - 11884) + '\x32' + '\065' + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x32' + '\x31' + chr(1841 - 1793), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + '\063' + chr(0b110011), 8), nzTpIcepk0o8('\060' + chr(0b11001 + 0o126) + '\x33' + chr(0b1100 + 0o51), 39479 - 39471), nzTpIcepk0o8(chr(0b100 + 0o54) + chr(0b1101111) + chr(0b110001) + chr(52) + chr(51), 32476 - 32468), nzTpIcepk0o8(chr(48) + chr(0b1100110 + 0o11) + chr(1840 - 1791) + '\063' + chr(0b110011), 63440 - 63432), nzTpIcepk0o8(chr(48) + '\x6f' + '\x32' + chr(0b101110 + 0o5) + '\063', 35016 - 35008), nzTpIcepk0o8('\060' + '\x6f' + chr(0b1001 + 0o51) + chr(55) + chr(0b100001 + 0o25), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + chr(0b110010) + chr(50) + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(1012 - 964) + '\157' + '\063' + chr(0b110010) + '\065', 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(0b110011) + chr(0b110001), ord("\x08")), nzTpIcepk0o8(chr(0b1110 + 0o42) + chr(0b1101111) + chr(674 - 621) + '\x32', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(1924 - 1874) + chr(0b100110 + 0o15) + chr(1554 - 1500), 64465 - 64457), nzTpIcepk0o8(chr(1504 - 1456) + chr(9167 - 9056) + '\x32' + chr(54) + chr(0b1000 + 0o50), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1010101 + 0o32) + '\063' + chr(0b110101), 8), nzTpIcepk0o8('\x30' + '\157' + chr(54), 35081 - 35073), nzTpIcepk0o8('\060' + '\x6f' + chr(0b101000 + 0o13) + chr(2262 - 2208) + chr(52), 17875 - 17867)][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + '\157' + '\065' + chr(48), 26437 - 26429)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xc4'), '\x64' + '\145' + chr(0b1100011) + chr(0b1101111) + '\x64' + chr(101))(chr(0b1110101) + '\164' + '\146' + chr(45) + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def I7CZX721l5qw(ztC3O2ZXmsJr):
oD8LLo_zqNZe = uh0lZwgdsVwB.decompressobj(uh0lZwgdsVwB.MAX_WBITS | nzTpIcepk0o8('\060' + chr(6483 - 6372) + '\x32' + chr(0b1101 + 0o43), 0b1000))
aAI4kJZu3Qcx = roI3spqORKae(ES5oEprVxulp(b''), chr(3633 - 3533) + chr(101) + '\143' + '\157' + chr(0b1100100) + '\145')(chr(0b1100000 + 0o25) + '\164' + chr(0b1100101 + 0o1) + chr(0b100101 + 0o10) + '\070')
for MB36uk0Bwhzh in ztC3O2ZXmsJr:
WckxBx1Uqdpm = oD8LLo_zqNZe.decompress(MB36uk0Bwhzh).lfbFsdWlT3MB()
if WckxBx1Uqdpm:
vniSnlI09HNg = (aAI4kJZu3Qcx + WckxBx1Uqdpm).LfRrQOxuDvnC(roI3spqORKae(ES5oEprVxulp(b'\xe0'), chr(0b1100100) + chr(101) + '\x63' + chr(0b1101111) + chr(100) + chr(0b1100001 + 0o4))('\165' + chr(0b1110100) + '\146' + '\x2d' + chr(0b111000)))
aAI4kJZu3Qcx = vniSnlI09HNg.uC_Yoybx7J0I()
for ffiOpFBWGmZU in vniSnlI09HNg:
yield ffiOpFBWGmZU
yield aAI4kJZu3Qcx |
openvax/varcode | varcode/vcf.py | infer_genome_from_vcf | def infer_genome_from_vcf(genome, vcf_reader, reference_vcf_key):
"""
Helper function to make a pyensembl.Genome instance.
"""
if genome:
return infer_genome(genome)
elif reference_vcf_key not in vcf_reader.metadata:
raise ValueError("Unable to infer reference genome for %s" % (
vcf_reader.filename,))
else:
reference_path = vcf_reader.metadata[reference_vcf_key]
return infer_genome(reference_path) | python | def infer_genome_from_vcf(genome, vcf_reader, reference_vcf_key):
"""
Helper function to make a pyensembl.Genome instance.
"""
if genome:
return infer_genome(genome)
elif reference_vcf_key not in vcf_reader.metadata:
raise ValueError("Unable to infer reference genome for %s" % (
vcf_reader.filename,))
else:
reference_path = vcf_reader.metadata[reference_vcf_key]
return infer_genome(reference_path) | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/vcf.py#L472-L483 | train | Helper function to make a pyensembl. Genome instance from a vcf 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('\x30' + chr(0b1101111) + chr(51) + chr(0b110000) + chr(0b110000), 0b1000), nzTpIcepk0o8(chr(0b100 + 0o54) + '\x6f' + chr(51) + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(1330 - 1282) + chr(0b1101111) + chr(0b101000 + 0o14) + '\x30', 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110010) + chr(0b110100) + chr(0b110001 + 0o6), 26278 - 26270), nzTpIcepk0o8(chr(0b110000) + chr(2330 - 2219) + chr(0b110001) + '\062' + '\x34', ord("\x08")), nzTpIcepk0o8(chr(0b100 + 0o54) + '\x6f' + chr(0b11101 + 0o24) + '\064' + '\x37', 18175 - 18167), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b1010 + 0o50) + chr(0b110100), 0o10), nzTpIcepk0o8(chr(154 - 106) + chr(0b1101111) + '\062' + chr(53) + chr(50), 0b1000), nzTpIcepk0o8(chr(0b10110 + 0o32) + '\157' + '\063' + chr(50) + '\062', 40254 - 40246), nzTpIcepk0o8(chr(0b0 + 0o60) + chr(2081 - 1970) + chr(50) + '\x35' + chr(0b11111 + 0o25), 35729 - 35721), nzTpIcepk0o8(chr(0b110000) + '\157' + '\062' + chr(0b1001 + 0o54) + chr(53), ord("\x08")), nzTpIcepk0o8(chr(0b1001 + 0o47) + chr(3476 - 3365) + '\x33' + chr(0b101001 + 0o16) + chr(683 - 635), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(1025 - 972), 0b1000), nzTpIcepk0o8(chr(0b10100 + 0o34) + chr(111) + chr(49) + chr(1315 - 1265), 0o10), nzTpIcepk0o8(chr(0b11000 + 0o30) + '\x6f' + chr(0b110001) + chr(151 - 96) + '\062', 30340 - 30332), nzTpIcepk0o8(chr(2045 - 1997) + chr(0b1101111) + chr(1293 - 1244) + chr(2282 - 2232) + chr(0b110100), 8), nzTpIcepk0o8(chr(1856 - 1808) + '\x6f' + chr(0b11010 + 0o27) + chr(0b110111) + chr(566 - 514), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + '\x32' + '\x32' + '\x30', 0b1000), nzTpIcepk0o8('\060' + chr(111) + '\061' + chr(49) + '\062', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x31' + chr(0b1011 + 0o46), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(606 - 557) + chr(0b110110) + '\065', 2551 - 2543), nzTpIcepk0o8(chr(1340 - 1292) + chr(0b1101111) + '\061' + '\x33' + '\067', 0b1000), nzTpIcepk0o8(chr(0b11001 + 0o27) + chr(5772 - 5661) + chr(0b10011 + 0o36) + chr(55) + chr(0b11001 + 0o32), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(8031 - 7920) + chr(1579 - 1528) + chr(52) + '\x33', 0o10), nzTpIcepk0o8(chr(0b11 + 0o55) + chr(111) + chr(0b100010 + 0o20) + '\060' + chr(1841 - 1786), 0b1000), nzTpIcepk0o8('\x30' + chr(0b11101 + 0o122) + chr(49) + chr(49) + chr(50), 8), nzTpIcepk0o8(chr(48) + '\157' + chr(874 - 825) + chr(1161 - 1110) + '\x36', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(1582 - 1471) + '\063' + chr(50) + '\066', ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(51) + '\061' + '\x32', 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(0b110010) + chr(0b110101) + chr(1747 - 1698), 21223 - 21215), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b100000 + 0o22) + chr(53) + chr(0b101110 + 0o5), 37025 - 37017), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x37' + chr(714 - 659), 47955 - 47947), nzTpIcepk0o8('\x30' + chr(111) + chr(0b10010 + 0o37) + chr(0b110001) + chr(0b110010), 8), nzTpIcepk0o8('\060' + '\157' + chr(0b110011) + '\067' + '\x34', ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110010) + chr(55) + '\x32', 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110010) + chr(1944 - 1890) + chr(48), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110010) + '\060' + chr(0b110001), 0b1000), nzTpIcepk0o8(chr(2276 - 2228) + chr(0b1101111) + chr(50) + chr(0b110110) + '\062', ord("\x08")), nzTpIcepk0o8(chr(1804 - 1756) + chr(0b10100 + 0o133) + '\063' + chr(54) + '\x37', 0o10), nzTpIcepk0o8(chr(0b10 + 0o56) + chr(111) + chr(2357 - 2308) + chr(0b110011) + '\061', 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x35' + chr(0b110000), 29665 - 29657)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xee'), '\144' + '\145' + chr(8415 - 8316) + chr(9742 - 9631) + chr(0b1100100) + '\145')('\x75' + chr(0b1110100) + chr(9979 - 9877) + '\055' + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def v2USfLJrt7yV(sBpYBMNzXOlv, c3JR_5B14GiM, vIiRQl2siAim):
if sBpYBMNzXOlv:
return fTo51uRcrC5L(sBpYBMNzXOlv)
elif vIiRQl2siAim not in roI3spqORKae(c3JR_5B14GiM, roI3spqORKae(ES5oEprVxulp(b'\xaeuF\x95\x00\x14]\xe0\x98\x9f\xe4\xb3'), chr(8135 - 8035) + chr(0b1100101) + chr(99) + '\x6f' + chr(5251 - 5151) + chr(8842 - 8741))(chr(117) + chr(116) + chr(0b1100110) + '\x2d' + '\x38')):
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'\x95vA\xc58\x024\xde\xbd\x8c\xc4\x96co\x08t\x0e\xf5,l\x07:\x15\x80\xe2j9\xb3\xa4\xc6\xc6Zj\x9a\xd5\xc2\xa1\x97\x84'), chr(2660 - 2560) + chr(4460 - 4359) + '\143' + '\x6f' + '\x64' + '\x65')(chr(117) + chr(0b1011001 + 0o33) + '\146' + chr(1241 - 1196) + chr(872 - 816)) % (roI3spqORKae(c3JR_5B14GiM, roI3spqORKae(ES5oEprVxulp(b'\x86`z\xef ?Q\xc5\xbe\xf5\xde\xb4'), '\144' + chr(101) + '\x63' + chr(111) + chr(0b10011 + 0o121) + chr(0b1100101))('\x75' + chr(116) + '\x66' + '\055' + chr(0b1100 + 0o54))),))
else:
HqUq1JK4QpGJ = c3JR_5B14GiM.nmf2TsIJJ3IK[vIiRQl2siAim]
return fTo51uRcrC5L(HqUq1JK4QpGJ) |
openvax/varcode | varcode/effects/effect_prediction_coding_frameshift.py | create_frameshift_effect | def create_frameshift_effect(
mutated_codon_index,
sequence_from_mutated_codon,
variant,
transcript):
"""
Determine frameshift effect within a coding sequence (possibly affecting
either the start or stop codons, or anythign in between)
Parameters
----------
mutated_codon_index : int
Codon offset (starting from 0 = start codon) of first non-reference
amino acid in the variant protein
sequence_from_mutated_codon: Bio.Seq
Sequence of mutated cDNA, starting from first mutated codon, until
the end of the transcript
variant : Variant
transcript : transcript
"""
assert transcript.protein_sequence is not None, \
"Expect transcript %s to have protein sequence" % transcript
original_protein_sequence = transcript.protein_sequence
original_protein_length = len(original_protein_sequence)
mutant_protein_suffix = translate(
nucleotide_sequence=sequence_from_mutated_codon,
first_codon_is_start=False,
to_stop=True,
truncate=True)
if mutated_codon_index == 0:
# TODO: scan through sequence_from_mutated_codon for
# Kozak sequence + start codon to choose the new start
return StartLoss(variant=variant, transcript=transcript)
# the frameshifted sequence may contain some amino acids which are
# the same as the original protein!
_, mutant_protein_suffix, unchanged_amino_acids = trim_shared_prefix(
ref=original_protein_sequence[mutated_codon_index:],
alt=mutant_protein_suffix)
n_unchanged_amino_acids = len(unchanged_amino_acids)
offset_to_first_different_amino_acid = mutated_codon_index + n_unchanged_amino_acids
# miraculously, this frameshift left the protein unchanged,
# most likely by turning one stop codon into another stop codon
if n_unchanged_amino_acids == 0:
aa_ref = ""
else:
aa_ref = original_protein_sequence[-n_unchanged_amino_acids:]
if offset_to_first_different_amino_acid >= original_protein_length:
# frameshift is either extending the protein or leaving it unchanged
if len(mutant_protein_suffix) == 0:
return Silent(
variant=variant,
transcript=transcript,
aa_pos=mutated_codon_index,
aa_ref=aa_ref)
else:
# When all the amino acids are the same as the original, we either
# have the original protein or we've extended it.
# If we've extended it, it means we must have lost our stop codon.
return StopLoss(
variant=variant,
transcript=transcript,
aa_ref=aa_ref,
aa_alt=mutant_protein_suffix)
# original amino acid at the mutated codon before the frameshift occurred
aa_ref = original_protein_sequence[offset_to_first_different_amino_acid]
# TODO: what if all the shifted amino acids were the same and the protein
# ended up the same length? Add a Silent case?
if len(mutant_protein_suffix) == 0:
# if a frameshift doesn't create any new amino acids, then
# it must immediately have hit a stop codon
return FrameShiftTruncation(
variant=variant,
transcript=transcript,
stop_codon_offset=offset_to_first_different_amino_acid)
return FrameShift(
variant=variant,
transcript=transcript,
aa_mutation_start_offset=offset_to_first_different_amino_acid,
shifted_sequence=str(mutant_protein_suffix)) | python | def create_frameshift_effect(
mutated_codon_index,
sequence_from_mutated_codon,
variant,
transcript):
"""
Determine frameshift effect within a coding sequence (possibly affecting
either the start or stop codons, or anythign in between)
Parameters
----------
mutated_codon_index : int
Codon offset (starting from 0 = start codon) of first non-reference
amino acid in the variant protein
sequence_from_mutated_codon: Bio.Seq
Sequence of mutated cDNA, starting from first mutated codon, until
the end of the transcript
variant : Variant
transcript : transcript
"""
assert transcript.protein_sequence is not None, \
"Expect transcript %s to have protein sequence" % transcript
original_protein_sequence = transcript.protein_sequence
original_protein_length = len(original_protein_sequence)
mutant_protein_suffix = translate(
nucleotide_sequence=sequence_from_mutated_codon,
first_codon_is_start=False,
to_stop=True,
truncate=True)
if mutated_codon_index == 0:
# TODO: scan through sequence_from_mutated_codon for
# Kozak sequence + start codon to choose the new start
return StartLoss(variant=variant, transcript=transcript)
# the frameshifted sequence may contain some amino acids which are
# the same as the original protein!
_, mutant_protein_suffix, unchanged_amino_acids = trim_shared_prefix(
ref=original_protein_sequence[mutated_codon_index:],
alt=mutant_protein_suffix)
n_unchanged_amino_acids = len(unchanged_amino_acids)
offset_to_first_different_amino_acid = mutated_codon_index + n_unchanged_amino_acids
# miraculously, this frameshift left the protein unchanged,
# most likely by turning one stop codon into another stop codon
if n_unchanged_amino_acids == 0:
aa_ref = ""
else:
aa_ref = original_protein_sequence[-n_unchanged_amino_acids:]
if offset_to_first_different_amino_acid >= original_protein_length:
# frameshift is either extending the protein or leaving it unchanged
if len(mutant_protein_suffix) == 0:
return Silent(
variant=variant,
transcript=transcript,
aa_pos=mutated_codon_index,
aa_ref=aa_ref)
else:
# When all the amino acids are the same as the original, we either
# have the original protein or we've extended it.
# If we've extended it, it means we must have lost our stop codon.
return StopLoss(
variant=variant,
transcript=transcript,
aa_ref=aa_ref,
aa_alt=mutant_protein_suffix)
# original amino acid at the mutated codon before the frameshift occurred
aa_ref = original_protein_sequence[offset_to_first_different_amino_acid]
# TODO: what if all the shifted amino acids were the same and the protein
# ended up the same length? Add a Silent case?
if len(mutant_protein_suffix) == 0:
# if a frameshift doesn't create any new amino acids, then
# it must immediately have hit a stop codon
return FrameShiftTruncation(
variant=variant,
transcript=transcript,
stop_codon_offset=offset_to_first_different_amino_acid)
return FrameShift(
variant=variant,
transcript=transcript,
aa_mutation_start_offset=offset_to_first_different_amino_acid,
shifted_sequence=str(mutant_protein_suffix)) | [
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"# original amino acid at the mutated codon before the frameshift occurred",
"aa_ref",
"=",
"original_protein_sequence",
"[",
"offset_to_first_different_amino_acid",
"]",
"# TODO: what if all the shifted amino acids were the same and the protein",
"# ended up the same length? Add a Silent case?",
"if",
"len",
"(",
"mutant_protein_suffix",
")",
"==",
"0",
":",
"# if a frameshift doesn't create any new amino acids, then",
"# it must immediately have hit a stop codon",
"return",
"FrameShiftTruncation",
"(",
"variant",
"=",
"variant",
",",
"transcript",
"=",
"transcript",
",",
"stop_codon_offset",
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"offset_to_first_different_amino_acid",
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"FrameShift",
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"transcript",
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"transcript",
",",
"aa_mutation_start_offset",
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"offset_to_first_different_amino_acid",
",",
"shifted_sequence",
"=",
"str",
"(",
"mutant_protein_suffix",
")",
")"
] | Determine frameshift effect within a coding sequence (possibly affecting
either the start or stop codons, or anythign in between)
Parameters
----------
mutated_codon_index : int
Codon offset (starting from 0 = start codon) of first non-reference
amino acid in the variant protein
sequence_from_mutated_codon: Bio.Seq
Sequence of mutated cDNA, starting from first mutated codon, until
the end of the transcript
variant : Variant
transcript : transcript | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/effect_prediction_coding_frameshift.py#L35-L123 | train | Create a new sequence that is part of a frameshift effect within a sequence of mutated codons. | 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(0b110100) + chr(0b110110), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(575 - 526) + chr(0b11011 + 0o25), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1010001 + 0o36) + '\x33' + '\x36' + chr(0b101111 + 0o7), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(2035 - 1984) + '\067' + '\063', 18756 - 18748), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x32' + chr(54) + chr(0b1010 + 0o46), ord("\x08")), nzTpIcepk0o8(chr(2034 - 1986) + chr(111) + chr(0b101010 + 0o7) + '\x31' + chr(50), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(49) + chr(1396 - 1348) + chr(0b10 + 0o61), 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(49) + chr(255 - 200) + chr(647 - 598), 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(49) + chr(1677 - 1623) + chr(0b101 + 0o56), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(0b1101 + 0o46) + '\066' + chr(359 - 307), 0o10), nzTpIcepk0o8(chr(48) + '\157' + '\x32' + '\066' + '\067', 19460 - 19452), nzTpIcepk0o8(chr(48) + '\x6f' + chr(1178 - 1126) + chr(0b110001), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110010) + '\x34' + '\x32', 16993 - 16985), nzTpIcepk0o8(chr(269 - 221) + '\157' + chr(0b110010) + '\060' + chr(0b110000), 0b1000), nzTpIcepk0o8('\060' + chr(0b10000 + 0o137) + '\063' + '\x35' + chr(0b101100 + 0o6), 49793 - 49785), nzTpIcepk0o8('\x30' + '\157' + chr(0b1001 + 0o52) + chr(0b110110) + chr(0b110100), 8), nzTpIcepk0o8(chr(48) + chr(0b1101110 + 0o1) + chr(0b110001) + chr(0b10110 + 0o34) + chr(0b110010), 29704 - 29696), nzTpIcepk0o8(chr(1337 - 1289) + chr(0b1101111) + chr(50) + chr(52) + chr(245 - 191), 23893 - 23885), nzTpIcepk0o8(chr(0b10101 + 0o33) + '\x6f' + '\061' + chr(0b110111) + '\x32', 14483 - 14475), nzTpIcepk0o8(chr(0b100101 + 0o13) + chr(1718 - 1607) + '\x31', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x33' + chr(1944 - 1895) + chr(747 - 695), 0o10), nzTpIcepk0o8('\060' + chr(10293 - 10182) + '\063' + chr(49) + chr(0b11111 + 0o27), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x33' + '\061' + chr(0b101011 + 0o11), 8), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x31' + chr(0b11001 + 0o27) + chr(55), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110010) + chr(0b110010), 43865 - 43857), nzTpIcepk0o8('\x30' + '\157' + '\x32' + chr(0b110000) + chr(2064 - 2013), 0o10), nzTpIcepk0o8(chr(0b10000 + 0o40) + chr(111) + chr(0b101110 + 0o6) + '\x36', 8), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110010) + '\060' + chr(0b110011), 8), nzTpIcepk0o8(chr(48) + '\x6f' + '\061' + chr(51) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(0b1110 + 0o42) + '\x6f' + chr(0b100 + 0o62) + chr(0b110011), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x31' + chr(0b101001 + 0o12) + chr(0b110000 + 0o2), 56362 - 56354), nzTpIcepk0o8(chr(48) + chr(111) + chr(49) + chr(54) + chr(0b110100), 37106 - 37098), nzTpIcepk0o8(chr(0b110000) + chr(10352 - 10241) + chr(1865 - 1811) + '\x30', ord("\x08")), nzTpIcepk0o8(chr(416 - 368) + chr(10783 - 10672) + '\x33' + chr(0b110 + 0o56) + chr(55), ord("\x08")), nzTpIcepk0o8(chr(0b100 + 0o54) + chr(6280 - 6169) + '\x32' + chr(0b10110 + 0o40), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110010) + chr(1404 - 1352) + chr(0b110000), 17707 - 17699), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110011) + '\x32' + '\x32', ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + '\061' + chr(48) + chr(48), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110001) + chr(393 - 338), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(49) + '\x33' + '\062', 8)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(111) + '\x35' + chr(0b110000), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x08'), chr(1676 - 1576) + chr(0b1100101) + '\143' + chr(4668 - 4557) + chr(9653 - 9553) + chr(101))('\x75' + '\164' + chr(0b110011 + 0o63) + '\055' + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def Mb1Cc2hkLG3I(Cr0WI5Kf2xeX, CciUfnQPZMcH, ZXJSPKxkIyZK, lnOu7fTAiCZI):
assert roI3spqORKae(lnOu7fTAiCZI, roI3spqORKae(ES5oEprVxulp(b'Vz\x99\x8f\xd5#-&\x00\x91\xc6T\xc7\xee\x89\x91'), '\144' + '\x65' + chr(0b1100011) + chr(0b1011 + 0o144) + '\x64' + chr(0b1100101))('\165' + chr(116) + chr(102) + '\055' + chr(0b101101 + 0o13))) is not None, roI3spqORKae(ES5oEprVxulp(b'cp\x86\x9e\xd3>c\r\x01\x95\xd9R\xc1\xf2\x83\x84&\x86_r\xec\xba\xa3gz\xe2P\xe6|C(\x1bD\x82\x7f\xce\xf23j+Sm\x98\x98\xd5'), '\x64' + '\x65' + chr(99) + chr(111) + chr(0b1011011 + 0o11) + '\145')('\165' + chr(116) + '\146' + chr(0b1111 + 0o36) + '\070') % lnOu7fTAiCZI
EazUxxz05v7m = lnOu7fTAiCZI.protein_sequence
HCCzhgjUpHly = ftfygxgFas5X(EazUxxz05v7m)
KnNi8WXloXEQ = kvuEMq_gEAUS(nucleotide_sequence=CciUfnQPZMcH, first_codon_is_start=nzTpIcepk0o8('\060' + chr(11429 - 11318) + chr(48), ord("\x08")), to_stop=nzTpIcepk0o8('\x30' + chr(0b1101111) + '\061', 8), truncate=nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(49), 8))
if Cr0WI5Kf2xeX == nzTpIcepk0o8('\060' + chr(0b1101111) + '\060', 8):
return ryOXnawBJKw_(variant=ZXJSPKxkIyZK, transcript=lnOu7fTAiCZI)
(zIqcgNgQ9U6F, KnNi8WXloXEQ, iTUyDBh6IXki) = F1E8Unal0je5(ref=EazUxxz05v7m[Cr0WI5Kf2xeX:], alt=KnNi8WXloXEQ)
h__5Nsfohj0K = ftfygxgFas5X(iTUyDBh6IXki)
otOOmDffYt6E = Cr0WI5Kf2xeX + h__5Nsfohj0K
if h__5Nsfohj0K == nzTpIcepk0o8(chr(0b11000 + 0o30) + chr(10851 - 10740) + chr(0b100001 + 0o17), 8):
k1f0SIIbhI0T = roI3spqORKae(ES5oEprVxulp(b''), chr(1999 - 1899) + '\145' + '\x63' + chr(1786 - 1675) + '\144' + chr(8817 - 8716))(chr(0b1001100 + 0o51) + '\164' + chr(368 - 266) + chr(45) + '\x38')
else:
k1f0SIIbhI0T = EazUxxz05v7m[-h__5Nsfohj0K:]
if otOOmDffYt6E >= HCCzhgjUpHly:
if ftfygxgFas5X(KnNi8WXloXEQ) == nzTpIcepk0o8('\060' + '\157' + chr(1053 - 1005), 8):
return Yb0g_iGWKvE9(variant=ZXJSPKxkIyZK, transcript=lnOu7fTAiCZI, aa_pos=Cr0WI5Kf2xeX, aa_ref=k1f0SIIbhI0T)
else:
return U9AaVOS6emP_(variant=ZXJSPKxkIyZK, transcript=lnOu7fTAiCZI, aa_ref=k1f0SIIbhI0T, aa_alt=KnNi8WXloXEQ)
k1f0SIIbhI0T = EazUxxz05v7m[otOOmDffYt6E]
if ftfygxgFas5X(KnNi8WXloXEQ) == nzTpIcepk0o8(chr(0b110000) + chr(3059 - 2948) + chr(2211 - 2163), 8):
return JhJRHIHorXjg(variant=ZXJSPKxkIyZK, transcript=lnOu7fTAiCZI, stop_codon_offset=otOOmDffYt6E)
return a4ptWdBOVOAz(variant=ZXJSPKxkIyZK, transcript=lnOu7fTAiCZI, aa_mutation_start_offset=otOOmDffYt6E, shifted_sequence=N9zlRy29S1SS(KnNi8WXloXEQ)) |
openvax/varcode | varcode/effects/effect_prediction_coding_frameshift.py | cdna_codon_sequence_after_insertion_frameshift | def cdna_codon_sequence_after_insertion_frameshift(
sequence_from_start_codon,
cds_offset_before_insertion,
inserted_nucleotides):
"""
Returns index of mutated codon and nucleotide sequence starting at the first
mutated codon.
"""
# special logic for insertions
coding_sequence_after_insertion = \
sequence_from_start_codon[cds_offset_before_insertion + 1:]
if cds_offset_before_insertion % 3 == 2:
# insertion happens after last nucleotide in a codon,
# doesn't disrupt the existing codon from cds_offset-2 to cds_offset
mutated_codon_index = cds_offset_before_insertion // 3 + 1
nucleotides_before = ""
elif cds_offset_before_insertion % 3 == 1:
# insertion happens after 2nd nucleotide of a codon
# codon positions:
# 1) cds_offset - 1
# 2) cds_offset
# <----- Insertsion
# 3) cds_offset + 1
mutated_codon_index = cds_offset_before_insertion // 3
# the first codon in the returned sequence will contain two reference
# nucleotides before the insertion
nucleotides_before = sequence_from_start_codon[
cds_offset_before_insertion - 1:cds_offset_before_insertion + 1]
elif cds_offset_before_insertion % 3 == 0:
# insertion happens after 1st nucleotide of a codon
# codon positions:
# 1) cds_offset
# <----- Insertsion
# 2) cds_offset + 1
# 3) cds_offset + 2
mutated_codon_index = cds_offset_before_insertion // 3
# the first codon in the returned sequence will contain one reference
# nucleotide before the insertion
nucleotides_before = sequence_from_start_codon[cds_offset_before_insertion]
sequence_from_mutated_codon = (
nucleotides_before +
inserted_nucleotides +
coding_sequence_after_insertion)
return mutated_codon_index, sequence_from_mutated_codon | python | def cdna_codon_sequence_after_insertion_frameshift(
sequence_from_start_codon,
cds_offset_before_insertion,
inserted_nucleotides):
"""
Returns index of mutated codon and nucleotide sequence starting at the first
mutated codon.
"""
# special logic for insertions
coding_sequence_after_insertion = \
sequence_from_start_codon[cds_offset_before_insertion + 1:]
if cds_offset_before_insertion % 3 == 2:
# insertion happens after last nucleotide in a codon,
# doesn't disrupt the existing codon from cds_offset-2 to cds_offset
mutated_codon_index = cds_offset_before_insertion // 3 + 1
nucleotides_before = ""
elif cds_offset_before_insertion % 3 == 1:
# insertion happens after 2nd nucleotide of a codon
# codon positions:
# 1) cds_offset - 1
# 2) cds_offset
# <----- Insertsion
# 3) cds_offset + 1
mutated_codon_index = cds_offset_before_insertion // 3
# the first codon in the returned sequence will contain two reference
# nucleotides before the insertion
nucleotides_before = sequence_from_start_codon[
cds_offset_before_insertion - 1:cds_offset_before_insertion + 1]
elif cds_offset_before_insertion % 3 == 0:
# insertion happens after 1st nucleotide of a codon
# codon positions:
# 1) cds_offset
# <----- Insertsion
# 2) cds_offset + 1
# 3) cds_offset + 2
mutated_codon_index = cds_offset_before_insertion // 3
# the first codon in the returned sequence will contain one reference
# nucleotide before the insertion
nucleotides_before = sequence_from_start_codon[cds_offset_before_insertion]
sequence_from_mutated_codon = (
nucleotides_before +
inserted_nucleotides +
coding_sequence_after_insertion)
return mutated_codon_index, sequence_from_mutated_codon | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/effect_prediction_coding_frameshift.py#L125-L169 | train | Returns the index of mutated codon and nucleotide sequence after the insertion. | 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(4602 - 4491) + '\x33' + '\061' + '\065', 0o10), nzTpIcepk0o8('\060' + chr(0b1100001 + 0o16) + chr(55) + chr(0b110111), 40315 - 40307), nzTpIcepk0o8(chr(0b110000) + chr(11186 - 11075) + '\061' + chr(1827 - 1774) + chr(0b110101), 0o10), nzTpIcepk0o8('\x30' + chr(111) + '\x32' + chr(0b100000 + 0o25) + chr(0b110110), 32022 - 32014), nzTpIcepk0o8('\x30' + '\x6f' + '\x31' + chr(974 - 920) + chr(48), 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(51) + chr(0b110000) + chr(1775 - 1726), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + '\x31' + '\x36' + chr(1541 - 1492), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(0b1 + 0o60) + chr(0b110101) + chr(53), 8), nzTpIcepk0o8('\x30' + chr(0b11110 + 0o121) + '\061' + chr(0b1001 + 0o51), ord("\x08")), nzTpIcepk0o8(chr(1269 - 1221) + '\x6f' + chr(0b110010) + chr(0b10101 + 0o33) + chr(0b10111 + 0o33), ord("\x08")), nzTpIcepk0o8(chr(2115 - 2067) + '\157' + chr(0b110001) + '\x34' + '\063', 0b1000), nzTpIcepk0o8(chr(2165 - 2117) + chr(0b10011 + 0o134) + chr(0b110001) + chr(0b110100) + chr(0b110110), 0o10), nzTpIcepk0o8(chr(361 - 313) + chr(0b1101111) + chr(859 - 810) + chr(0b101011 + 0o7) + '\061', 55086 - 55078), nzTpIcepk0o8(chr(1765 - 1717) + '\157' + chr(49) + chr(51) + chr(0b1010 + 0o55), 0o10), nzTpIcepk0o8(chr(0b11001 + 0o27) + chr(111) + '\061' + '\x30' + '\060', 30568 - 30560), nzTpIcepk0o8(chr(0b1011 + 0o45) + chr(0b1101111) + chr(49) + chr(0b110001), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + '\064' + chr(0b11110 + 0o24), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + '\x32' + '\061' + chr(0b110000), 0o10), nzTpIcepk0o8('\x30' + chr(0b1100010 + 0o15) + '\063' + '\x31' + chr(373 - 325), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110001) + chr(0b110011) + chr(1910 - 1860), 51348 - 51340), nzTpIcepk0o8('\x30' + chr(0b101 + 0o152) + chr(0b110011) + chr(2186 - 2132) + '\x30', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b101001 + 0o106) + '\x33' + '\x37' + '\065', 44116 - 44108), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110011) + chr(0b110001) + chr(0b110000 + 0o4), 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(0b1100 + 0o47) + '\x34', 0o10), nzTpIcepk0o8(chr(0b101110 + 0o2) + chr(111) + chr(49) + '\066' + chr(0b1100 + 0o45), 8), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110011) + '\x32', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b101100 + 0o103) + chr(0b101001 + 0o10) + chr(49) + chr(50), 0o10), nzTpIcepk0o8(chr(48) + chr(0b100101 + 0o112) + chr(0b110011 + 0o4) + '\x36', 0b1000), nzTpIcepk0o8(chr(1607 - 1559) + '\157' + chr(871 - 820) + chr(0b110111) + '\060', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101011 + 0o4) + chr(0b100001 + 0o21) + chr(1566 - 1513) + chr(51), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(49) + chr(50) + chr(0b110000), 10528 - 10520), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b101110 + 0o3) + chr(0b100 + 0o56) + '\x35', ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + '\x31' + '\x32' + chr(541 - 488), 8), nzTpIcepk0o8(chr(0b110000) + chr(0b11111 + 0o120) + '\x32' + '\060' + '\x30', 50070 - 50062), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x31' + '\064' + chr(51), 8), nzTpIcepk0o8(chr(0b100000 + 0o20) + '\x6f' + '\x33' + '\062' + '\063', 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(0b101010 + 0o7) + chr(53) + '\063', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(11711 - 11600) + chr(0b110001) + chr(0b110000) + '\061', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(1620 - 1569) + chr(0b10100 + 0o36) + chr(2505 - 2452), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1100000 + 0o17) + '\063' + '\x35' + '\064', 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + chr(0b10111 + 0o130) + chr(53) + chr(0b110000), 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xe3'), '\144' + '\x65' + '\143' + '\x6f' + chr(0b1100100) + '\145')(chr(11507 - 11390) + chr(116) + '\x66' + chr(0b10000 + 0o35) + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def kVY9fevafJz5(_2B_8srBhfQc, R7sN1ugeSn6X, N09F2Ib09Rib):
TDYZpl3G3sii = _2B_8srBhfQc[R7sN1ugeSn6X + nzTpIcepk0o8('\060' + chr(111) + chr(49), 39227 - 39219):]
if R7sN1ugeSn6X % nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(51), ord("\x08")) == nzTpIcepk0o8(chr(1123 - 1075) + chr(0b1001100 + 0o43) + chr(50), 0b1000):
Cr0WI5Kf2xeX = R7sN1ugeSn6X // nzTpIcepk0o8(chr(487 - 439) + '\157' + chr(0b101111 + 0o4), 8) + nzTpIcepk0o8('\060' + chr(0b1101111) + '\x31', 8)
CBO3vkT34V0I = roI3spqORKae(ES5oEprVxulp(b''), chr(7815 - 7715) + chr(7861 - 7760) + chr(0b1000110 + 0o35) + chr(0b101100 + 0o103) + chr(1642 - 1542) + chr(0b1100101))(chr(117) + '\x74' + chr(5579 - 5477) + '\055' + '\070')
elif R7sN1ugeSn6X % nzTpIcepk0o8(chr(48) + '\x6f' + '\063', 8) == nzTpIcepk0o8(chr(1960 - 1912) + chr(111) + chr(49), 8):
Cr0WI5Kf2xeX = R7sN1ugeSn6X // nzTpIcepk0o8(chr(0b101000 + 0o10) + '\x6f' + '\063', 8)
CBO3vkT34V0I = _2B_8srBhfQc[R7sN1ugeSn6X - nzTpIcepk0o8(chr(0b110000) + chr(7444 - 7333) + chr(49), 8):R7sN1ugeSn6X + nzTpIcepk0o8('\060' + chr(0b1101111) + chr(49), 8)]
elif R7sN1ugeSn6X % nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x33', 8) == nzTpIcepk0o8(chr(48) + chr(0b111110 + 0o61) + chr(0b0 + 0o60), ord("\x08")):
Cr0WI5Kf2xeX = R7sN1ugeSn6X // nzTpIcepk0o8(chr(790 - 742) + '\157' + chr(0b101010 + 0o11), 8)
CBO3vkT34V0I = _2B_8srBhfQc[R7sN1ugeSn6X]
CciUfnQPZMcH = CBO3vkT34V0I + N09F2Ib09Rib + TDYZpl3G3sii
return (Cr0WI5Kf2xeX, CciUfnQPZMcH) |
openvax/varcode | varcode/effects/effect_prediction_coding_frameshift.py | cdna_codon_sequence_after_deletion_or_substitution_frameshift | def cdna_codon_sequence_after_deletion_or_substitution_frameshift(
sequence_from_start_codon,
cds_offset,
trimmed_cdna_ref,
trimmed_cdna_alt):
"""
Logic for any frameshift which isn't an insertion.
We have insertions as a special case since our base-inclusive
indexing means something different for insertions:
cds_offset = base before insertion
Whereas in this case:
cds_offset = first reference base affected by a variant
Returns index of first modified codon and sequence from that codon
onward.
"""
mutated_codon_index = cds_offset // 3
# get the sequence starting from the first modified codon until the end
# of the transcript.
sequence_after_mutated_codon = \
sequence_from_start_codon[mutated_codon_index * 3:]
# the variant's ref nucleotides should start either 0, 1, or 2 nucleotides
# into `sequence_after_mutated_codon`
offset_into_mutated_codon = cds_offset % 3
sequence_from_mutated_codon = substitute(
sequence=sequence_after_mutated_codon,
offset=offset_into_mutated_codon,
ref=trimmed_cdna_ref,
alt=trimmed_cdna_alt)
return mutated_codon_index, sequence_from_mutated_codon | python | def cdna_codon_sequence_after_deletion_or_substitution_frameshift(
sequence_from_start_codon,
cds_offset,
trimmed_cdna_ref,
trimmed_cdna_alt):
"""
Logic for any frameshift which isn't an insertion.
We have insertions as a special case since our base-inclusive
indexing means something different for insertions:
cds_offset = base before insertion
Whereas in this case:
cds_offset = first reference base affected by a variant
Returns index of first modified codon and sequence from that codon
onward.
"""
mutated_codon_index = cds_offset // 3
# get the sequence starting from the first modified codon until the end
# of the transcript.
sequence_after_mutated_codon = \
sequence_from_start_codon[mutated_codon_index * 3:]
# the variant's ref nucleotides should start either 0, 1, or 2 nucleotides
# into `sequence_after_mutated_codon`
offset_into_mutated_codon = cds_offset % 3
sequence_from_mutated_codon = substitute(
sequence=sequence_after_mutated_codon,
offset=offset_into_mutated_codon,
ref=trimmed_cdna_ref,
alt=trimmed_cdna_alt)
return mutated_codon_index, sequence_from_mutated_codon | [
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cds_offset = base before insertion
Whereas in this case:
cds_offset = first reference base affected by a variant
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/effect_prediction_coding_frameshift.py#L172-L204 | train | This function returns the index of the mutated codon and sequence after the frameshift which is an insertion or substitution. | 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(0b101111 + 0o7) + '\x36', 0o10), nzTpIcepk0o8(chr(0b1100 + 0o44) + chr(111) + chr(0b10010 + 0o37) + chr(0b110001) + chr(1012 - 958), 0o10), nzTpIcepk0o8(chr(0b101 + 0o53) + chr(0b101 + 0o152) + chr(0b11 + 0o60) + chr(53) + chr(2268 - 2213), 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(1614 - 1565) + chr(321 - 268) + chr(49), 0o10), nzTpIcepk0o8(chr(48) + chr(3432 - 3321) + '\x31' + '\065' + '\x33', 29737 - 29729), nzTpIcepk0o8(chr(1488 - 1440) + '\157' + chr(49) + chr(50) + chr(0b110011), 0b1000), nzTpIcepk0o8('\060' + '\157' + '\x33' + chr(0b11111 + 0o24) + chr(0b110010), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(12059 - 11948) + '\x32' + '\x35' + chr(53), 0b1000), nzTpIcepk0o8('\x30' + chr(0b111111 + 0o60) + chr(0b110010) + '\x30' + chr(49), 28595 - 28587), nzTpIcepk0o8('\x30' + chr(111) + chr(49) + '\x35' + chr(677 - 627), ord("\x08")), nzTpIcepk0o8(chr(0b10000 + 0o40) + chr(0b1101111) + chr(0b110110) + chr(52), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b110110 + 0o71) + '\062' + '\x32' + chr(53), 14196 - 14188), nzTpIcepk0o8(chr(1250 - 1202) + chr(7674 - 7563) + chr(0b101011 + 0o10) + '\065' + chr(646 - 592), 0b1000), nzTpIcepk0o8(chr(0b10000 + 0o40) + chr(0b100010 + 0o115) + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(1784 - 1736) + chr(0b11100 + 0o123) + '\061' + '\x30' + chr(735 - 686), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + '\x31' + chr(1135 - 1080) + chr(0b110011), 0b1000), nzTpIcepk0o8('\060' + chr(11534 - 11423) + '\x32' + chr(1270 - 1222), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(51) + chr(2587 - 2536) + '\x34', 61587 - 61579), nzTpIcepk0o8('\060' + chr(859 - 748) + chr(0b11011 + 0o32) + chr(0b11000 + 0o30), 14123 - 14115), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x32' + '\066', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b110011 + 0o74) + '\061' + '\x35' + '\060', 15615 - 15607), nzTpIcepk0o8(chr(48) + chr(0b110001 + 0o76) + chr(49) + chr(0b110110) + chr(54), 37936 - 37928), nzTpIcepk0o8('\060' + chr(111) + chr(49) + chr(0b101010 + 0o14) + '\065', 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b1110 + 0o44) + '\x35' + chr(54), 63029 - 63021), nzTpIcepk0o8('\x30' + chr(846 - 735) + chr(0b110011) + '\066' + chr(54), 28539 - 28531), nzTpIcepk0o8('\060' + '\157' + chr(285 - 231) + chr(0b110011), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + '\x33' + chr(0b110000) + chr(50), 44738 - 44730), nzTpIcepk0o8(chr(1587 - 1539) + chr(111) + chr(49) + '\066', 15651 - 15643), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x33' + chr(0b101111 + 0o5) + '\061', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1011 + 0o144) + '\061' + '\061' + chr(52), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(11701 - 11590) + '\063' + chr(0b110011) + chr(2778 - 2725), ord("\x08")), nzTpIcepk0o8(chr(2231 - 2183) + '\x6f' + chr(0b110001) + chr(0b110101) + '\062', 8), nzTpIcepk0o8(chr(48) + chr(6229 - 6118) + '\067' + '\x34', ord("\x08")), nzTpIcepk0o8(chr(1487 - 1439) + chr(0b1101111) + chr(51) + '\x32' + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(2157 - 2109) + chr(0b110010 + 0o75) + chr(0b1110 + 0o43) + chr(0b110001) + '\062', 46327 - 46319), nzTpIcepk0o8(chr(48) + chr(0b0 + 0o157) + '\063' + chr(50), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(1173 - 1122) + chr(55) + chr(1665 - 1610), 39793 - 39785), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(860 - 810) + chr(52) + chr(49), 0b1000), nzTpIcepk0o8(chr(0b100101 + 0o13) + '\x6f' + chr(0b110000), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x31' + chr(0b110110) + '\066', 8)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + chr(0b1101111) + chr(2707 - 2654) + chr(48), 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x18'), chr(342 - 242) + chr(101) + '\143' + chr(0b10000 + 0o137) + chr(0b111001 + 0o53) + '\x65')('\165' + chr(0b1110100) + '\146' + chr(0b10 + 0o53) + chr(938 - 882)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def aRvFkxfm6DJw(_2B_8srBhfQc, ObtvnJg0h2SR, cduq82jeGeab, lIDGpzyU3VyV):
Cr0WI5Kf2xeX = ObtvnJg0h2SR // nzTpIcepk0o8(chr(0b100100 + 0o14) + chr(4050 - 3939) + chr(2090 - 2039), 17091 - 17083)
N3ZQWCd3P5yZ = _2B_8srBhfQc[Cr0WI5Kf2xeX * nzTpIcepk0o8('\x30' + chr(0b1100100 + 0o13) + '\x33', 8):]
mz3Vc0lVnrYZ = ObtvnJg0h2SR % nzTpIcepk0o8(chr(1867 - 1819) + chr(111) + '\x33', 8)
CciUfnQPZMcH = fDy17HzkiUYE(sequence=N3ZQWCd3P5yZ, offset=mz3Vc0lVnrYZ, ref=cduq82jeGeab, alt=lIDGpzyU3VyV)
return (Cr0WI5Kf2xeX, CciUfnQPZMcH) |
openvax/varcode | varcode/effects/effect_prediction_coding_frameshift.py | predict_frameshift_coding_effect | def predict_frameshift_coding_effect(
variant,
transcript,
trimmed_cdna_ref,
trimmed_cdna_alt,
cds_offset,
sequence_from_start_codon):
"""
Coding effect of a frameshift mutation.
Parameters
----------
variant : Variant
transcript : Transcript
trimmed_cdna_ref : nucleotide sequence
Reference nucleotides in the coding sequence of the given transcript.
trimmed_cdna_alt : nucleotide sequence
Alternate nucleotides introduced by mutation
cds_offset : int
Offset into the CDS of first ref nucleotide. For insertions, this
is the offset of the last ref nucleotide before the insertion.
sequence_from_start_codon : nucleotide sequence
Nucleotides of the coding sequence and 3' UTR
"""
if len(trimmed_cdna_ref) != 0:
mutated_codon_index, sequence_from_mutated_codon = \
cdna_codon_sequence_after_deletion_or_substitution_frameshift(
sequence_from_start_codon=sequence_from_start_codon,
cds_offset=cds_offset,
trimmed_cdna_ref=trimmed_cdna_ref,
trimmed_cdna_alt=trimmed_cdna_alt)
else:
mutated_codon_index, sequence_from_mutated_codon = \
cdna_codon_sequence_after_insertion_frameshift(
sequence_from_start_codon=sequence_from_start_codon,
cds_offset_before_insertion=cds_offset,
inserted_nucleotides=trimmed_cdna_alt)
return create_frameshift_effect(
mutated_codon_index=mutated_codon_index,
sequence_from_mutated_codon=sequence_from_mutated_codon,
variant=variant,
transcript=transcript) | python | def predict_frameshift_coding_effect(
variant,
transcript,
trimmed_cdna_ref,
trimmed_cdna_alt,
cds_offset,
sequence_from_start_codon):
"""
Coding effect of a frameshift mutation.
Parameters
----------
variant : Variant
transcript : Transcript
trimmed_cdna_ref : nucleotide sequence
Reference nucleotides in the coding sequence of the given transcript.
trimmed_cdna_alt : nucleotide sequence
Alternate nucleotides introduced by mutation
cds_offset : int
Offset into the CDS of first ref nucleotide. For insertions, this
is the offset of the last ref nucleotide before the insertion.
sequence_from_start_codon : nucleotide sequence
Nucleotides of the coding sequence and 3' UTR
"""
if len(trimmed_cdna_ref) != 0:
mutated_codon_index, sequence_from_mutated_codon = \
cdna_codon_sequence_after_deletion_or_substitution_frameshift(
sequence_from_start_codon=sequence_from_start_codon,
cds_offset=cds_offset,
trimmed_cdna_ref=trimmed_cdna_ref,
trimmed_cdna_alt=trimmed_cdna_alt)
else:
mutated_codon_index, sequence_from_mutated_codon = \
cdna_codon_sequence_after_insertion_frameshift(
sequence_from_start_codon=sequence_from_start_codon,
cds_offset_before_insertion=cds_offset,
inserted_nucleotides=trimmed_cdna_alt)
return create_frameshift_effect(
mutated_codon_index=mutated_codon_index,
sequence_from_mutated_codon=sequence_from_mutated_codon,
variant=variant,
transcript=transcript) | [
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Parameters
----------
variant : Variant
transcript : Transcript
trimmed_cdna_ref : nucleotide sequence
Reference nucleotides in the coding sequence of the given transcript.
trimmed_cdna_alt : nucleotide sequence
Alternate nucleotides introduced by mutation
cds_offset : int
Offset into the CDS of first ref nucleotide. For insertions, this
is the offset of the last ref nucleotide before the insertion.
sequence_from_start_codon : nucleotide sequence
Nucleotides of the coding sequence and 3' UTR | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/effect_prediction_coding_frameshift.py#L207-L254 | train | Predicts the coding effect of a frameshift mutation. | 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' + '\063' + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b111001 + 0o66) + '\063' + '\064' + chr(768 - 716), 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(0b10001 + 0o42) + chr(2434 - 2380) + '\060', 0o10), nzTpIcepk0o8(chr(48) + chr(5005 - 4894) + '\062' + '\065' + chr(54), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(642 - 592) + chr(0b101111 + 0o3) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(50) + chr(1328 - 1274), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b11100 + 0o26) + chr(53) + chr(0b10100 + 0o43), ord("\x08")), nzTpIcepk0o8(chr(520 - 472) + chr(7445 - 7334) + chr(50) + chr(401 - 353) + chr(0b110000), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(0b1110 + 0o43) + '\x31' + chr(0b110000 + 0o4), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + '\x33' + chr(0b110100) + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(710 - 662) + chr(0b10000 + 0o137) + chr(0b110011) + chr(0b110101) + chr(0b101010 + 0o13), 59882 - 59874), nzTpIcepk0o8('\060' + chr(0b1100000 + 0o17) + '\x32' + chr(52), 24242 - 24234), nzTpIcepk0o8(chr(0b1100 + 0o44) + chr(4690 - 4579) + chr(0b110011) + '\x30' + '\x34', 0o10), nzTpIcepk0o8(chr(0b10 + 0o56) + chr(2735 - 2624) + '\x37' + '\x34', 54856 - 54848), nzTpIcepk0o8(chr(0b1001 + 0o47) + chr(111) + chr(0b101 + 0o55) + chr(0b110100) + chr(55), 14435 - 14427), nzTpIcepk0o8('\060' + '\157' + chr(0b110001) + chr(0b11110 + 0o27) + chr(1203 - 1153), ord("\x08")), nzTpIcepk0o8(chr(1018 - 970) + '\157' + '\x33' + chr(0b110110) + chr(53), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b100011 + 0o17) + chr(49) + chr(54), 0b1000), nzTpIcepk0o8('\060' + chr(111) + '\x32' + '\x30' + chr(50), 0o10), nzTpIcepk0o8(chr(48) + '\157' + '\061' + chr(0b100000 + 0o23) + chr(48), 0b1000), nzTpIcepk0o8(chr(0b11001 + 0o27) + chr(111) + '\x32', ord("\x08")), nzTpIcepk0o8('\x30' + chr(5548 - 5437) + chr(0b10001 + 0o42) + chr(0b11101 + 0o23) + chr(367 - 319), 0o10), nzTpIcepk0o8('\060' + chr(111) + '\x31' + chr(1085 - 1036) + chr(0b110100), 8), nzTpIcepk0o8(chr(48) + chr(111) + chr(1527 - 1477) + chr(53) + chr(0b11 + 0o57), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(0b101011 + 0o10) + chr(0b110111) + '\x32', 0b1000), nzTpIcepk0o8('\060' + '\157' + '\061' + chr(55) + chr(50), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110001) + '\065' + '\x35', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b10010 + 0o41) + chr(0b10101 + 0o36) + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(600 - 552) + '\157' + chr(0b10111 + 0o33) + chr(51), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110001) + chr(1520 - 1469) + '\066', 0b1000), nzTpIcepk0o8(chr(0b101110 + 0o2) + chr(9540 - 9429) + chr(420 - 369) + '\067' + chr(0b11111 + 0o23), 8), nzTpIcepk0o8('\x30' + chr(2412 - 2301) + chr(0b110001) + '\x35', 62773 - 62765), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\063' + chr(0b110111) + '\065', 0b1000), nzTpIcepk0o8(chr(48) + '\157' + '\x36' + '\x30', 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + '\063' + chr(49) + '\067', 0o10), nzTpIcepk0o8(chr(1448 - 1400) + chr(0b111001 + 0o66) + chr(0b1011 + 0o50) + chr(0b1000 + 0o52) + chr(0b110110), 0o10), nzTpIcepk0o8(chr(1517 - 1469) + '\x6f' + chr(0b1110 + 0o44) + chr(0b110110) + '\x35', 10777 - 10769), nzTpIcepk0o8(chr(0b100111 + 0o11) + chr(0b11111 + 0o120) + chr(0b110001) + chr(0b110111) + chr(0b110001), 0o10), nzTpIcepk0o8('\060' + '\x6f' + '\x33' + '\x37' + chr(0b100110 + 0o14), 8), nzTpIcepk0o8('\060' + '\157' + chr(0b10 + 0o60) + chr(691 - 636) + chr(52), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(340 - 292) + '\x6f' + chr(0b110101) + chr(48), 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'3'), chr(0b1000100 + 0o40) + chr(101) + '\143' + chr(0b1101111) + chr(3027 - 2927) + chr(101))(chr(117) + chr(116) + chr(0b1100110) + chr(45) + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def G7TB9qjEagXb(ZXJSPKxkIyZK, lnOu7fTAiCZI, cduq82jeGeab, lIDGpzyU3VyV, ObtvnJg0h2SR, _2B_8srBhfQc):
if ftfygxgFas5X(cduq82jeGeab) != nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x30', ord("\x08")):
(Cr0WI5Kf2xeX, CciUfnQPZMcH) = aRvFkxfm6DJw(sequence_from_start_codon=_2B_8srBhfQc, cds_offset=ObtvnJg0h2SR, trimmed_cdna_ref=cduq82jeGeab, trimmed_cdna_alt=lIDGpzyU3VyV)
else:
(Cr0WI5Kf2xeX, CciUfnQPZMcH) = kVY9fevafJz5(sequence_from_start_codon=_2B_8srBhfQc, cds_offset_before_insertion=ObtvnJg0h2SR, inserted_nucleotides=lIDGpzyU3VyV)
return Mb1Cc2hkLG3I(mutated_codon_index=Cr0WI5Kf2xeX, sequence_from_mutated_codon=CciUfnQPZMcH, variant=ZXJSPKxkIyZK, transcript=lnOu7fTAiCZI) |
openvax/varcode | varcode/effects/effect_prediction_coding.py | predict_variant_coding_effect_on_transcript | def predict_variant_coding_effect_on_transcript(
variant,
transcript,
trimmed_cdna_ref,
trimmed_cdna_alt,
transcript_offset):
"""
Given a minimal cDNA ref/alt nucleotide string pair and an offset into a
given transcript, determine the coding effect of this nucleotide substitution
onto the translated protein.
Parameters
----------
variant : Variant
transcript : Transcript
trimmed_cdna_ref : str
Reference nucleotides we expect to find in the transcript's CDS
trimmed_cdna_alt : str
Alternate nucleotides we're replacing the reference with
transcript_offset : int
Offset into the full transcript sequence of the ref->alt substitution
"""
if not transcript.complete:
raise ValueError(
("Can't annotate coding effect for %s"
" on incomplete transcript %s" % (variant, transcript)))
sequence = transcript.sequence
n_ref = len(trimmed_cdna_ref)
n_alt = len(trimmed_cdna_alt)
# reference nucleotides found on the transcript, if these don't match
# what we were told to expect from the variant then raise an exception
ref_nucleotides_from_transcript = str(
sequence[transcript_offset:transcript_offset + n_ref])
# Make sure that the reference sequence agrees with what we expected
# from the VCF
assert ref_nucleotides_from_transcript == trimmed_cdna_ref, \
"%s: expected ref '%s' at offset %d of %s, transcript has '%s'" % (
variant,
trimmed_cdna_ref,
transcript_offset,
transcript,
ref_nucleotides_from_transcript)
start_codon_offset = transcript.first_start_codon_spliced_offset
stop_codon_offset = transcript.last_stop_codon_spliced_offset
cds_len = stop_codon_offset - start_codon_offset + 1
if cds_len < 3:
raise ValueError(
"Coding sequence for %s is too short: '%s'" % (
transcript,
transcript.sequence[start_codon_offset:stop_codon_offset + 1]))
if n_ref == 0 and transcript.strand == "-":
# By convention, genomic insertions happen *after* their base 1 position on
# a chromosome. On the reverse strand, however, an insertion has to go
# before the nucleotide at some transcript offset.
# Example:
# chromosome sequence:
# TTT|GATCTCGTA|CCC
# transcript on reverse strand:
# CCC|ATGCTCTAG|TTT
# where the CDS is emphasized:
# ATGCTCTAG
# If we have a genomic insertion g.6insATT
# the genomic sequence becomes:
# TTT|GAT_ATT_CTCGTA|CCC
# (insert the "ATT" after the "T" at position 6)
# On the reverse strand this becomes:
# CCC|ATGCTC_TTA_TAG|TTT
# (insert the "ATT" *before* the "T" at position 10)
#
# To preserve the interpretation of the start offset as the base
# before the insertion, need to subtract one
cds_offset = transcript_offset - start_codon_offset - 1
else:
cds_offset = transcript_offset - start_codon_offset
assert cds_offset < cds_len, \
"Expected CDS offset (%d) < |CDS| (%d) for %s on %s" % (
cds_offset, cds_len, variant, transcript)
sequence_from_start_codon = str(sequence[start_codon_offset:])
# is this an in-frame mutations?
if (n_ref - n_alt) % 3 == 0:
return predict_in_frame_coding_effect(
variant=variant,
transcript=transcript,
trimmed_cdna_ref=trimmed_cdna_ref,
trimmed_cdna_alt=trimmed_cdna_alt,
cds_offset=cds_offset,
sequence_from_start_codon=sequence_from_start_codon)
else:
return predict_frameshift_coding_effect(
variant=variant,
transcript=transcript,
trimmed_cdna_ref=trimmed_cdna_ref,
trimmed_cdna_alt=trimmed_cdna_alt,
cds_offset=cds_offset,
sequence_from_start_codon=sequence_from_start_codon) | python | def predict_variant_coding_effect_on_transcript(
variant,
transcript,
trimmed_cdna_ref,
trimmed_cdna_alt,
transcript_offset):
"""
Given a minimal cDNA ref/alt nucleotide string pair and an offset into a
given transcript, determine the coding effect of this nucleotide substitution
onto the translated protein.
Parameters
----------
variant : Variant
transcript : Transcript
trimmed_cdna_ref : str
Reference nucleotides we expect to find in the transcript's CDS
trimmed_cdna_alt : str
Alternate nucleotides we're replacing the reference with
transcript_offset : int
Offset into the full transcript sequence of the ref->alt substitution
"""
if not transcript.complete:
raise ValueError(
("Can't annotate coding effect for %s"
" on incomplete transcript %s" % (variant, transcript)))
sequence = transcript.sequence
n_ref = len(trimmed_cdna_ref)
n_alt = len(trimmed_cdna_alt)
# reference nucleotides found on the transcript, if these don't match
# what we were told to expect from the variant then raise an exception
ref_nucleotides_from_transcript = str(
sequence[transcript_offset:transcript_offset + n_ref])
# Make sure that the reference sequence agrees with what we expected
# from the VCF
assert ref_nucleotides_from_transcript == trimmed_cdna_ref, \
"%s: expected ref '%s' at offset %d of %s, transcript has '%s'" % (
variant,
trimmed_cdna_ref,
transcript_offset,
transcript,
ref_nucleotides_from_transcript)
start_codon_offset = transcript.first_start_codon_spliced_offset
stop_codon_offset = transcript.last_stop_codon_spliced_offset
cds_len = stop_codon_offset - start_codon_offset + 1
if cds_len < 3:
raise ValueError(
"Coding sequence for %s is too short: '%s'" % (
transcript,
transcript.sequence[start_codon_offset:stop_codon_offset + 1]))
if n_ref == 0 and transcript.strand == "-":
# By convention, genomic insertions happen *after* their base 1 position on
# a chromosome. On the reverse strand, however, an insertion has to go
# before the nucleotide at some transcript offset.
# Example:
# chromosome sequence:
# TTT|GATCTCGTA|CCC
# transcript on reverse strand:
# CCC|ATGCTCTAG|TTT
# where the CDS is emphasized:
# ATGCTCTAG
# If we have a genomic insertion g.6insATT
# the genomic sequence becomes:
# TTT|GAT_ATT_CTCGTA|CCC
# (insert the "ATT" after the "T" at position 6)
# On the reverse strand this becomes:
# CCC|ATGCTC_TTA_TAG|TTT
# (insert the "ATT" *before* the "T" at position 10)
#
# To preserve the interpretation of the start offset as the base
# before the insertion, need to subtract one
cds_offset = transcript_offset - start_codon_offset - 1
else:
cds_offset = transcript_offset - start_codon_offset
assert cds_offset < cds_len, \
"Expected CDS offset (%d) < |CDS| (%d) for %s on %s" % (
cds_offset, cds_len, variant, transcript)
sequence_from_start_codon = str(sequence[start_codon_offset:])
# is this an in-frame mutations?
if (n_ref - n_alt) % 3 == 0:
return predict_in_frame_coding_effect(
variant=variant,
transcript=transcript,
trimmed_cdna_ref=trimmed_cdna_ref,
trimmed_cdna_alt=trimmed_cdna_alt,
cds_offset=cds_offset,
sequence_from_start_codon=sequence_from_start_codon)
else:
return predict_frameshift_coding_effect(
variant=variant,
transcript=transcript,
trimmed_cdna_ref=trimmed_cdna_ref,
trimmed_cdna_alt=trimmed_cdna_alt,
cds_offset=cds_offset,
sequence_from_start_codon=sequence_from_start_codon) | [
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"# TTT|GAT_ATT_CTCGTA|CCC",
"# (insert the \"ATT\" after the \"T\" at position 6)",
"# On the reverse strand this becomes:",
"# CCC|ATGCTC_TTA_TAG|TTT",
"# (insert the \"ATT\" *before* the \"T\" at position 10)",
"#",
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] | Given a minimal cDNA ref/alt nucleotide string pair and an offset into a
given transcript, determine the coding effect of this nucleotide substitution
onto the translated protein.
Parameters
----------
variant : Variant
transcript : Transcript
trimmed_cdna_ref : str
Reference nucleotides we expect to find in the transcript's CDS
trimmed_cdna_alt : str
Alternate nucleotides we're replacing the reference with
transcript_offset : int
Offset into the full transcript sequence of the ref->alt substitution | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/effect_prediction_coding.py#L21-L130 | train | Given a minimal cDNA reference nucleotide string pair and an offset into a CDS containing that nucleotide and the original nucleotide of the variant and the original nucleotide of the variant. | 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(49) + chr(0b10100 + 0o34) + chr(0b101010 + 0o7), 0o10), nzTpIcepk0o8(chr(48) + '\157' + '\065' + chr(54), 41179 - 41171), nzTpIcepk0o8('\x30' + chr(9474 - 9363) + chr(810 - 760) + '\062' + chr(2517 - 2464), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b11 + 0o56) + chr(0b110101) + chr(0b110111), 23108 - 23100), nzTpIcepk0o8('\x30' + '\x6f' + chr(749 - 699) + chr(0b10000 + 0o47) + '\x37', 0b1000), nzTpIcepk0o8(chr(193 - 145) + chr(111) + '\061' + chr(0b110111) + chr(0b110000), 39639 - 39631), nzTpIcepk0o8(chr(1107 - 1059) + '\x6f' + chr(325 - 276) + chr(0b110001) + chr(0b100 + 0o61), ord("\x08")), nzTpIcepk0o8(chr(0b1001 + 0o47) + '\157' + chr(0b110010) + '\060' + chr(0b110000), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + '\062' + chr(2638 - 2585) + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(309 - 261) + '\157' + chr(0b110100) + chr(2882 - 2828), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(50) + chr(0b110011) + '\x33', ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + '\x35' + chr(0b100000 + 0o26), 8), nzTpIcepk0o8(chr(0b1101 + 0o43) + chr(0b1000111 + 0o50) + chr(0b11101 + 0o24) + chr(0b110010) + chr(0b110000), 0b1000), nzTpIcepk0o8(chr(0b10 + 0o56) + chr(111) + chr(49) + chr(0b110100) + chr(0b100001 + 0o25), 0b1000), nzTpIcepk0o8(chr(937 - 889) + '\x6f' + '\061' + chr(0b110010) + chr(0b110100), 55307 - 55299), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(2274 - 2225) + chr(556 - 501) + chr(49), 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(51) + chr(55) + chr(0b110010), 44590 - 44582), nzTpIcepk0o8(chr(48) + '\x6f' + chr(50) + chr(0b110111) + chr(2797 - 2744), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(10886 - 10775) + '\x35' + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x31' + '\x30', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(415 - 304) + '\063' + '\x37' + chr(879 - 829), 8), nzTpIcepk0o8(chr(48) + '\157' + chr(0b1010 + 0o47) + '\060' + '\062', ord("\x08")), nzTpIcepk0o8(chr(0b101010 + 0o6) + '\157' + '\x31' + '\062', 0b1000), nzTpIcepk0o8(chr(1766 - 1718) + '\x6f' + '\067' + '\x32', 0b1000), nzTpIcepk0o8(chr(1895 - 1847) + chr(0b1000000 + 0o57) + '\x33' + chr(0b11000 + 0o37), 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(0b10010 + 0o40) + '\x35' + '\x32', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b11011 + 0o30) + chr(0b110 + 0o56) + '\x37', 0o10), nzTpIcepk0o8('\x30' + chr(0b1111 + 0o140) + chr(51) + '\064' + chr(0b110100), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(579 - 530) + chr(0b11011 + 0o34) + chr(440 - 386), 5429 - 5421), nzTpIcepk0o8(chr(0b1000 + 0o50) + chr(0b1101111) + chr(0b101101 + 0o6) + '\x30' + chr(52), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(1608 - 1557) + chr(0b110001) + chr(50), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b100111 + 0o110) + chr(0b11101 + 0o24) + '\063' + chr(0b110001 + 0o2), ord("\x08")), nzTpIcepk0o8(chr(111 - 63) + chr(0b1101111) + chr(2062 - 2011) + chr(0b11 + 0o57) + chr(1007 - 958), ord("\x08")), nzTpIcepk0o8(chr(1169 - 1121) + '\x6f' + '\063' + '\064' + chr(0b101101 + 0o11), 0b1000), nzTpIcepk0o8('\x30' + chr(9025 - 8914) + chr(0b0 + 0o61) + '\067' + '\x33', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(10076 - 9965) + '\064' + chr(52), 0b1000), nzTpIcepk0o8(chr(668 - 620) + chr(0b110011 + 0o74) + chr(1087 - 1036) + chr(0b101000 + 0o12) + '\065', 47801 - 47793), nzTpIcepk0o8('\x30' + '\x6f' + '\063' + '\x33' + chr(1710 - 1656), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110111) + '\060', 50526 - 50518), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110101) + '\x36', 8)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + '\x6f' + '\x35' + '\060', 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'o'), chr(100) + chr(4346 - 4245) + chr(0b1100011) + '\157' + chr(100) + chr(5733 - 5632))(chr(0b10101 + 0o140) + '\x74' + chr(10278 - 10176) + chr(93 - 48) + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def H9dXJ2zwmGvh(ZXJSPKxkIyZK, lnOu7fTAiCZI, cduq82jeGeab, lIDGpzyU3VyV, yoXAYvufKlQI):
if not roI3spqORKae(lnOu7fTAiCZI, roI3spqORKae(ES5oEprVxulp(b'\x15J\xe0:\xea\x14\x18\xeb\xfcv\xe8\x18'), chr(0b1010100 + 0o20) + chr(0b1100101) + '\x63' + chr(0b1101111) + chr(100) + chr(0b1001001 + 0o34))(chr(0b1110101) + chr(0b1110100 + 0o0) + chr(0b1100110) + chr(45) + '\x38')):
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b"\x02O\xfbH\xcbX,\xee\xc5I\xefO$\x03t\x1a\x95\xd9Af\x9dbo\\y\xcf\x84\x90^\xa2\xa5)\xf1\xc3\x08\x04\xba\xb0\x18G/M\xfa\x02\xcf\x14(\xf4\xce\x06\xef\\1\x08'\x1a\x88\xd4X|\xdagy"), '\x64' + '\x65' + '\x63' + chr(111) + '\x64' + '\145')('\x75' + '\164' + '\146' + chr(45) + '\x38') % (ZXJSPKxkIyZK, lnOu7fTAiCZI))
AaFeo0lw34C3 = lnOu7fTAiCZI.AaFeo0lw34C3
H0vRGyprMf_l = ftfygxgFas5X(cduq82jeGeab)
CRM06y2Nk0Uf = ftfygxgFas5X(lIDGpzyU3VyV)
Swhfrai56VHc = N9zlRy29S1SS(AaFeo0lw34C3[yoXAYvufKlQI:yoXAYvufKlQI + H0vRGyprMf_l])
assert Swhfrai56VHc == cduq82jeGeab, roI3spqORKae(ES5oEprVxulp(b'd]\xafO\xda\x00=\xe5\xc8R\xfeJp\x141\x1f\xda\x9a\r{\xddbkN?\xc5\x81\x82\r\xa1\xbe{\xf4\x82[K\xb3\xfe\x1d]m\x0e\xe1\x1d\xde\x16>\xe3\xd9O\xebZp\x0e5\n\xda\x9a\r{\xdd'), chr(0b1100100) + chr(0b1010000 + 0o25) + chr(0b10 + 0o141) + chr(7148 - 7037) + chr(0b1100100) + chr(0b1100101))('\x75' + '\x74' + '\x66' + chr(45) + '\070') % (ZXJSPKxkIyZK, cduq82jeGeab, yoXAYvufKlQI, lnOu7fTAiCZI, Swhfrai56VHc)
_FiIP0p2c06c = lnOu7fTAiCZI.first_start_codon_spliced_offset
tqW8hqim1inh = lnOu7fTAiCZI.last_stop_codon_spliced_offset
It8LMXOHCTSW = tqW8hqim1inh - _FiIP0p2c06c + nzTpIcepk0o8('\x30' + chr(111) + '\x31', 0o10)
if It8LMXOHCTSW < nzTpIcepk0o8(chr(0b110000) + '\157' + '\063', 8629 - 8621):
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'\x02A\xf1\x06\xd1\x1fm\xf3\xceW\xeeK>\x051Y\x9c\xd2Z(\xdf1*Sl\x8a\x93\x8b\x11\xe4\xb93\xbe\x94\x0f\x1e\xf5\xf9\x1d]f'), chr(100) + chr(0b110111 + 0o56) + chr(4371 - 4272) + chr(0b1101101 + 0o2) + chr(0b1010010 + 0o22) + chr(6494 - 6393))(chr(117) + chr(9616 - 9500) + chr(0b1100110) + chr(186 - 141) + chr(0b110100 + 0o4)) % (lnOu7fTAiCZI, roI3spqORKae(lnOu7fTAiCZI, roI3spqORKae(ES5oEprVxulp(b'\x00O\xd3\n\xd0H!\xf7\x98\x12\xd8\x1d'), chr(0b110101 + 0o57) + chr(0b1100101) + chr(0b111011 + 0o50) + '\x6f' + chr(9963 - 9863) + '\x65')(chr(0b1100100 + 0o21) + chr(116) + '\x66' + chr(1642 - 1597) + chr(675 - 619)))[_FiIP0p2c06c:tqW8hqim1inh + nzTpIcepk0o8(chr(0b100000 + 0o20) + chr(0b1101111) + '\061', 8)]))
if H0vRGyprMf_l == nzTpIcepk0o8('\x30' + chr(111) + '\060', ord("\x08")) and roI3spqORKae(lnOu7fTAiCZI, roI3spqORKae(ES5oEprVxulp(b'2a\xe3?\xdb\x08:\xb6\xe1M\xdf\x18'), '\x64' + chr(0b1100101) + '\143' + chr(0b1101111) + '\144' + chr(0b1010001 + 0o24))(chr(0b1010011 + 0o42) + '\x74' + chr(102) + chr(0b10111 + 0o26) + chr(0b110101 + 0o3))) == roI3spqORKae(ES5oEprVxulp(b'l'), '\x64' + chr(0b1100101) + chr(0b110001 + 0o62) + chr(0b11011 + 0o124) + chr(0b101001 + 0o73) + chr(0b1011001 + 0o14))('\x75' + chr(0b1110100) + chr(3385 - 3283) + '\x2d' + '\070'):
ObtvnJg0h2SR = yoXAYvufKlQI - _FiIP0p2c06c - nzTpIcepk0o8(chr(48) + '\157' + chr(0b100110 + 0o13), 8)
else:
ObtvnJg0h2SR = yoXAYvufKlQI - _FiIP0p2c06c
assert ObtvnJg0h2SR < It8LMXOHCTSW, roI3spqORKae(ES5oEprVxulp(b"\x04V\xe5\n\xdc\x0c(\xe4\x8be\xdf}p\t2\x1f\x89\xd8\\(\xd2gn\x13?\x96\xc7\x98=\x80\x99'\xf1\xce^@\xfc\xfe^A3\x0e\xb0\x1c\x9f\x17#\xa0\x8eU"), chr(0b1100100) + chr(0b1100101) + chr(0b100100 + 0o77) + chr(0b1101111) + chr(8880 - 8780) + chr(5923 - 5822))(chr(7608 - 7491) + chr(6980 - 6864) + chr(0b1100110) + '\055' + chr(0b10001 + 0o47)) % (ObtvnJg0h2SR, It8LMXOHCTSW, ZXJSPKxkIyZK, lnOu7fTAiCZI)
_2B_8srBhfQc = N9zlRy29S1SS(AaFeo0lw34C3[_FiIP0p2c06c:])
if (H0vRGyprMf_l - CRM06y2Nk0Uf) % nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110011), 8) == nzTpIcepk0o8(chr(747 - 699) + chr(111) + '\x30', 8):
return pO9RAWVEr_Fw(variant=ZXJSPKxkIyZK, transcript=lnOu7fTAiCZI, trimmed_cdna_ref=cduq82jeGeab, trimmed_cdna_alt=lIDGpzyU3VyV, cds_offset=ObtvnJg0h2SR, sequence_from_start_codon=_2B_8srBhfQc)
else:
return G7TB9qjEagXb(variant=ZXJSPKxkIyZK, transcript=lnOu7fTAiCZI, trimmed_cdna_ref=cduq82jeGeab, trimmed_cdna_alt=lIDGpzyU3VyV, cds_offset=ObtvnJg0h2SR, sequence_from_start_codon=_2B_8srBhfQc) |
openvax/varcode | varcode/effects/effect_prediction.py | predict_variant_effects | def predict_variant_effects(variant, raise_on_error=False):
"""Determine the effects of a variant on any transcripts it overlaps.
Returns an EffectCollection object.
Parameters
----------
variant : Variant
raise_on_error : bool
Raise an exception if we encounter an error while trying to
determine the effect of this variant on a transcript, or simply
log the error and continue.
"""
# if this variant isn't overlapping any genes, return a
# Intergenic effect
# TODO: look for nearby genes and mark those as Upstream and Downstream
# effects
if len(variant.gene_ids) == 0:
effects = [Intergenic(variant)]
else:
# list of all MutationEffects for all genes & transcripts
effects = []
# group transcripts by their gene ID
transcripts_grouped_by_gene = groupby_field(variant.transcripts, 'gene_id')
# want effects in the list grouped by the gene they come from
for gene_id in sorted(variant.gene_ids):
if gene_id not in transcripts_grouped_by_gene:
# intragenic variant overlaps a gene but not any transcripts
gene = variant.ensembl.gene_by_id(gene_id)
effects.append(Intragenic(variant, gene))
else:
# gene ID has transcripts overlapped by this variant
for transcript in transcripts_grouped_by_gene[gene_id]:
if raise_on_error:
effect = predict_variant_effect_on_transcript(
variant=variant,
transcript=transcript)
else:
effect = predict_variant_effect_on_transcript_or_failure(
variant=variant,
transcript=transcript)
effects.append(effect)
return EffectCollection(effects) | python | def predict_variant_effects(variant, raise_on_error=False):
"""Determine the effects of a variant on any transcripts it overlaps.
Returns an EffectCollection object.
Parameters
----------
variant : Variant
raise_on_error : bool
Raise an exception if we encounter an error while trying to
determine the effect of this variant on a transcript, or simply
log the error and continue.
"""
# if this variant isn't overlapping any genes, return a
# Intergenic effect
# TODO: look for nearby genes and mark those as Upstream and Downstream
# effects
if len(variant.gene_ids) == 0:
effects = [Intergenic(variant)]
else:
# list of all MutationEffects for all genes & transcripts
effects = []
# group transcripts by their gene ID
transcripts_grouped_by_gene = groupby_field(variant.transcripts, 'gene_id')
# want effects in the list grouped by the gene they come from
for gene_id in sorted(variant.gene_ids):
if gene_id not in transcripts_grouped_by_gene:
# intragenic variant overlaps a gene but not any transcripts
gene = variant.ensembl.gene_by_id(gene_id)
effects.append(Intragenic(variant, gene))
else:
# gene ID has transcripts overlapped by this variant
for transcript in transcripts_grouped_by_gene[gene_id]:
if raise_on_error:
effect = predict_variant_effect_on_transcript(
variant=variant,
transcript=transcript)
else:
effect = predict_variant_effect_on_transcript_or_failure(
variant=variant,
transcript=transcript)
effects.append(effect)
return EffectCollection(effects) | [
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variant : Variant
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ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8('\x30' + chr(2591 - 2480) + '\062' + '\x34' + chr(150 - 98), 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(0b100111 + 0o14) + '\065' + chr(0b110100), 0o10), nzTpIcepk0o8(chr(48) + chr(3061 - 2950) + chr(0b110010) + '\x37', 59223 - 59215), nzTpIcepk0o8('\060' + chr(111) + chr(0b110111) + '\x34', 63421 - 63413), nzTpIcepk0o8('\x30' + chr(0b111010 + 0o65) + chr(53) + chr(162 - 111), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(50) + chr(0b110000) + chr(0b11001 + 0o32), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\062' + '\066' + chr(0b110100), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b11000 + 0o32) + chr(0b10000 + 0o46) + '\x33', 0o10), nzTpIcepk0o8(chr(0b110000 + 0o0) + chr(0b1101111) + chr(0b110001 + 0o1) + '\x32' + chr(0b11011 + 0o26), 56721 - 56713), nzTpIcepk0o8(chr(48) + '\157' + chr(1665 - 1613) + '\066', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b100101 + 0o16) + chr(0b110001) + chr(0b110011), 51212 - 51204), nzTpIcepk0o8(chr(0b110000) + chr(0b10001 + 0o136) + chr(1118 - 1065) + '\x36', ord("\x08")), nzTpIcepk0o8(chr(0b101101 + 0o3) + chr(6151 - 6040) + '\x32' + chr(2589 - 2536) + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b111101 + 0o62) + chr(1295 - 1245) + chr(0b1 + 0o66) + '\066', ord("\x08")), nzTpIcepk0o8(chr(133 - 85) + chr(111) + chr(0b1 + 0o60) + chr(0b11101 + 0o26) + '\x35', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + '\x35' + chr(0b10111 + 0o40), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(54), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(5735 - 5624) + chr(0b1001 + 0o50) + chr(54) + '\x31', 61268 - 61260), nzTpIcepk0o8('\x30' + chr(9763 - 9652) + '\x37' + '\x34', 8), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b1010 + 0o47) + '\062' + chr(48), 35568 - 35560), nzTpIcepk0o8('\x30' + chr(10908 - 10797) + chr(0b10010 + 0o44) + chr(52), 42321 - 42313), nzTpIcepk0o8(chr(48) + chr(7719 - 7608) + '\062' + chr(0b101100 + 0o4) + chr(0b110111), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110001) + chr(54) + chr(2403 - 2352), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + '\061' + '\x30' + chr(0b100110 + 0o12), 0o10), nzTpIcepk0o8(chr(0b1100 + 0o44) + chr(0b1101111) + chr(2122 - 2071) + chr(54) + chr(2405 - 2352), 0o10), nzTpIcepk0o8(chr(233 - 185) + chr(0b1100000 + 0o17) + chr(54) + chr(107 - 57), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b1001 + 0o55) + '\x36', 34070 - 34062), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x31' + chr(51) + chr(0b101101 + 0o5), ord("\x08")), nzTpIcepk0o8(chr(0b100 + 0o54) + chr(8809 - 8698) + '\062' + '\x36' + '\x36', 32950 - 32942), nzTpIcepk0o8(chr(1672 - 1624) + '\x6f' + chr(49) + '\x37' + '\x37', 60176 - 60168), nzTpIcepk0o8('\x30' + '\157' + chr(0b110011) + chr(1536 - 1488) + chr(0b10111 + 0o32), ord("\x08")), nzTpIcepk0o8(chr(0b101000 + 0o10) + chr(0b1100010 + 0o15) + '\063' + '\x36' + chr(51), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(436 - 387) + chr(51) + '\060', ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110010) + chr(1731 - 1679) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + '\064' + chr(0b110001), 29570 - 29562), nzTpIcepk0o8(chr(1979 - 1931) + chr(0b1101111) + chr(0b110010) + '\063', 14328 - 14320), nzTpIcepk0o8(chr(0b110000) + chr(0b1000000 + 0o57) + chr(1727 - 1673) + '\062', 8), nzTpIcepk0o8(chr(0b10110 + 0o32) + '\157' + chr(0b11110 + 0o24) + chr(0b110011 + 0o3) + chr(0b101111 + 0o6), 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(50) + '\x37' + chr(0b110100), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110000 + 0o1) + chr(53) + '\x37', 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + chr(0b1001101 + 0o42) + chr(0b101110 + 0o7) + '\060', 27842 - 27834)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x8a'), '\144' + chr(0b100000 + 0o105) + chr(0b1010000 + 0o23) + '\x6f' + chr(100) + chr(7591 - 7490))(chr(117) + '\164' + chr(0b1100110) + chr(0b11111 + 0o16) + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def js3WMoIA9424(ZXJSPKxkIyZK, QW8XFQ5ICIcT=nzTpIcepk0o8(chr(1743 - 1695) + chr(0b1001101 + 0o42) + '\x30', 0b1000)):
if ftfygxgFas5X(roI3spqORKae(ZXJSPKxkIyZK, roI3spqORKae(ES5oEprVxulp(b'\xc3\x89yYt\xea\xd0\xc0'), '\x64' + chr(500 - 399) + chr(0b110100 + 0o57) + chr(0b1101111) + '\144' + '\145')(chr(5538 - 5421) + '\164' + chr(165 - 63) + '\x2d' + chr(1915 - 1859)))) == nzTpIcepk0o8('\060' + chr(11835 - 11724) + chr(0b1101 + 0o43), 8):
WShYeokTxOn7 = [kQ2Jnp3kXRww(ZXJSPKxkIyZK)]
else:
WShYeokTxOn7 = []
Qz3Rqzs3G_HA = YQ4TjIVIUY0J(ZXJSPKxkIyZK.transcripts, roI3spqORKae(ES5oEprVxulp(b'\xc3\x89yYt\xea\xd0'), '\144' + chr(3585 - 3484) + '\143' + '\x6f' + chr(0b1011010 + 0o12) + chr(101))(chr(117) + '\164' + chr(0b110101 + 0o61) + '\x2d' + '\070'))
for vrLC5E1ClU9l in V3OlOVg98A85(roI3spqORKae(ZXJSPKxkIyZK, roI3spqORKae(ES5oEprVxulp(b'\xc3\x89yYt\xea\xd0\xc0'), chr(3405 - 3305) + '\145' + chr(99) + chr(0b1101111) + chr(0b110010 + 0o62) + chr(0b1100101 + 0o0))(chr(3198 - 3081) + chr(116) + '\146' + chr(45) + chr(0b111 + 0o61)))):
if vrLC5E1ClU9l not in Qz3Rqzs3G_HA:
_Qb3Sp2ECG81 = ZXJSPKxkIyZK.ensembl.gene_by_id(vrLC5E1ClU9l)
roI3spqORKae(WShYeokTxOn7, roI3spqORKae(ES5oEprVxulp(b'\xec\xb8D\x08S\xe4\xf3\xdc\xfbI\x9e\x1b'), chr(7605 - 7505) + chr(101) + chr(4104 - 4005) + chr(0b1101111) + '\144' + chr(0b11000 + 0o115))(chr(0b11110 + 0o127) + chr(11463 - 11347) + chr(102) + '\055' + chr(0b10111 + 0o41)))(NxMUjCLW8oNh(ZXJSPKxkIyZK, _Qb3Sp2ECG81))
else:
for lnOu7fTAiCZI in Qz3Rqzs3G_HA[vrLC5E1ClU9l]:
if QW8XFQ5ICIcT:
WueclzVPVP7r = FQzfGCbBrZUK(variant=ZXJSPKxkIyZK, transcript=lnOu7fTAiCZI)
else:
WueclzVPVP7r = HVCyl3Ak7Y8b(variant=ZXJSPKxkIyZK, transcript=lnOu7fTAiCZI)
roI3spqORKae(WShYeokTxOn7, roI3spqORKae(ES5oEprVxulp(b'\xec\xb8D\x08S\xe4\xf3\xdc\xfbI\x9e\x1b'), '\x64' + chr(0b1100101) + '\x63' + chr(0b1101111) + chr(0b110101 + 0o57) + chr(101))('\165' + chr(116) + chr(102) + chr(0b101101) + '\x38'))(WueclzVPVP7r)
return aUmLUkPZ7w_n(WShYeokTxOn7) |
openvax/varcode | varcode/effects/effect_prediction.py | predict_variant_effect_on_transcript_or_failure | def predict_variant_effect_on_transcript_or_failure(variant, transcript):
"""
Try predicting the effect of a variant on a particular transcript but
suppress raised exceptions by converting them into `Failure` effect
values.
"""
try:
return predict_variant_effect_on_transcript(
variant=variant,
transcript=transcript)
except (AssertionError, ValueError) as error:
logger.warn(
"Encountered error annotating %s for %s: %s",
variant,
transcript,
error)
return Failure(variant, transcript) | python | def predict_variant_effect_on_transcript_or_failure(variant, transcript):
"""
Try predicting the effect of a variant on a particular transcript but
suppress raised exceptions by converting them into `Failure` effect
values.
"""
try:
return predict_variant_effect_on_transcript(
variant=variant,
transcript=transcript)
except (AssertionError, ValueError) as error:
logger.warn(
"Encountered error annotating %s for %s: %s",
variant,
transcript,
error)
return Failure(variant, transcript) | [
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suppress raised exceptions by converting them into `Failure` effect
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/effect_prediction.py#L95-L111 | train | Predict the effect of a variant on a particular transcript or return a Failure 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(48) + chr(0b1101111) + '\062' + chr(0b110101) + chr(53), 32384 - 32376), nzTpIcepk0o8(chr(0b100100 + 0o14) + '\x6f' + '\x33' + '\066' + '\061', 15336 - 15328), nzTpIcepk0o8('\x30' + chr(0b111001 + 0o66) + '\x33' + chr(0b110001) + chr(51), 0b1000), nzTpIcepk0o8('\x30' + chr(7035 - 6924) + '\x31' + '\065' + chr(122 - 68), ord("\x08")), nzTpIcepk0o8(chr(0b101010 + 0o6) + '\x6f' + chr(0b110010) + '\064' + '\x30', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b100111 + 0o14) + '\x31' + chr(474 - 424), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(0b1111 + 0o44) + '\x30' + '\x30', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b11100 + 0o27) + '\063' + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(11166 - 11055) + chr(0b110001) + '\x30' + chr(0b100111 + 0o15), ord("\x08")), nzTpIcepk0o8(chr(0b101111 + 0o1) + chr(0b1101111) + '\062' + chr(0b110110) + chr(1347 - 1293), 0b1000), nzTpIcepk0o8(chr(0b1001 + 0o47) + chr(111) + chr(88 - 38) + chr(1883 - 1829) + '\060', 0o10), nzTpIcepk0o8(chr(0b0 + 0o60) + chr(4338 - 4227) + '\x34' + chr(0b110111), 58809 - 58801), nzTpIcepk0o8(chr(0b100011 + 0o15) + '\x6f' + '\061' + chr(0b10000 + 0o43) + chr(0b110110), 0o10), nzTpIcepk0o8(chr(154 - 106) + chr(0b1001101 + 0o42) + chr(49) + chr(0b110010) + chr(1828 - 1773), 14896 - 14888), nzTpIcepk0o8(chr(2197 - 2149) + chr(111) + chr(1620 - 1571) + chr(48) + chr(0b1111 + 0o44), 25815 - 25807), nzTpIcepk0o8(chr(492 - 444) + chr(111) + chr(2505 - 2454) + '\x32' + chr(53), 0b1000), nzTpIcepk0o8(chr(48) + chr(3350 - 3239) + chr(1580 - 1530) + chr(54) + '\065', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x32' + chr(0b110000) + '\062', 51035 - 51027), nzTpIcepk0o8('\060' + chr(111) + chr(1834 - 1783) + chr(0b110001 + 0o5) + chr(1511 - 1460), 0o10), nzTpIcepk0o8(chr(373 - 325) + '\x6f' + chr(49) + chr(55) + chr(2969 - 2914), 0o10), nzTpIcepk0o8(chr(1565 - 1517) + chr(111) + chr(0b110011) + chr(55) + '\065', 0b1000), nzTpIcepk0o8(chr(0b100000 + 0o20) + chr(7073 - 6962) + '\x32' + '\063' + chr(0b110110), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(1519 - 1469) + chr(1789 - 1734) + '\x35', 0o10), nzTpIcepk0o8(chr(0b100110 + 0o12) + chr(0b100010 + 0o115) + chr(49) + chr(330 - 282) + chr(0b100001 + 0o24), 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(1106 - 1055) + chr(0b110110) + chr(351 - 302), 8), nzTpIcepk0o8('\060' + chr(6113 - 6002) + chr(0b110001) + '\062', 16178 - 16170), nzTpIcepk0o8(chr(0b100110 + 0o12) + chr(111) + '\x32' + chr(0b110100) + chr(0b110000), 8), nzTpIcepk0o8('\x30' + chr(4163 - 4052) + '\061' + chr(0b100000 + 0o20) + '\063', 8), nzTpIcepk0o8(chr(0b0 + 0o60) + chr(111) + chr(50) + chr(1389 - 1341) + '\x36', 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110011) + '\062' + '\x33', 24144 - 24136), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\061' + chr(0b10100 + 0o34), 0b1000), nzTpIcepk0o8(chr(0b1111 + 0o41) + chr(0b10101 + 0o132) + chr(51) + chr(0b100001 + 0o24) + chr(50), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + '\x33' + chr(77 - 26) + chr(0b100000 + 0o21), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(50) + chr(0b100011 + 0o15) + '\065', ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(51) + '\063', 0o10), nzTpIcepk0o8(chr(48) + '\157' + '\x33' + '\x30' + chr(0b110000), 8), nzTpIcepk0o8(chr(364 - 316) + chr(0b110111 + 0o70) + chr(0b10001 + 0o42) + '\x34' + '\x32', 48644 - 48636), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(51) + chr(0b10011 + 0o43) + chr(1259 - 1208), 8), nzTpIcepk0o8(chr(0b100011 + 0o15) + chr(10296 - 10185) + chr(54) + chr(0b110110), 13838 - 13830), nzTpIcepk0o8('\x30' + chr(4190 - 4079) + '\063' + '\x34' + '\065', 2864 - 2856)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b10101 + 0o33) + chr(1661 - 1550) + chr(2042 - 1989) + chr(48), 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x83'), chr(100) + '\x65' + chr(99) + '\x6f' + chr(0b101 + 0o137) + '\x65')(chr(117) + '\x74' + chr(102) + chr(1407 - 1362) + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def HVCyl3Ak7Y8b(ZXJSPKxkIyZK, lnOu7fTAiCZI):
try:
return FQzfGCbBrZUK(variant=ZXJSPKxkIyZK, transcript=lnOu7fTAiCZI)
except (B3LV8Eo811Ma, WbNHlDKpyPtQ) as qi1wipPVvEKd:
roI3spqORKae(iKLp4UdyhCfx, roI3spqORKae(ES5oEprVxulp(b'\xde\xbb\x9a8\xff\x82\xb1\x8b}\xd0\xd7]'), chr(9082 - 8982) + chr(0b1011000 + 0o15) + chr(0b1100011) + '\157' + '\x64' + chr(0b101100 + 0o71))(chr(0b1110101) + chr(0b1110100) + chr(0b1010011 + 0o23) + chr(0b101001 + 0o4) + '\x38'))(roI3spqORKae(ES5oEprVxulp(b'\xe8\x9f\xa8\x01\xd5\xa4\xb4\xbd6\xd3\xd4\x07;%1\xba\xc7\xa2\x92\x11\x93\xf1\xc9$\x85c\xce$\xa6\xf6{\xca\xbf\xeai\xe0\xc7\x80\x0c\xc5\x88\x82'), chr(100) + chr(4768 - 4667) + chr(0b1100 + 0o127) + '\x6f' + chr(0b1100100) + chr(0b1100001 + 0o4))('\x75' + chr(0b1110100) + chr(0b1100110) + chr(1191 - 1146) + chr(594 - 538)), ZXJSPKxkIyZK, lnOu7fTAiCZI, qi1wipPVvEKd)
return WqTcOGBMJIY7(ZXJSPKxkIyZK, lnOu7fTAiCZI) |
openvax/varcode | varcode/effects/effect_prediction.py | predict_variant_effect_on_transcript | def predict_variant_effect_on_transcript(variant, transcript):
"""Return the transcript effect (such as FrameShift) that results from
applying this genomic variant to a particular transcript.
Parameters
----------
transcript : Transcript
Transcript we're going to apply mutation to.
"""
if transcript.__class__ is not Transcript:
raise TypeError(
"Expected %s : %s to have type Transcript" % (
transcript, type(transcript)))
# check for non-coding transcripts first, since
# every non-coding transcript is "incomplete".
if not transcript.is_protein_coding:
return NoncodingTranscript(variant, transcript)
if not transcript.complete:
return IncompleteTranscript(variant, transcript)
# since we're using inclusive base-1 coordinates,
# checking for overlap requires special logic for insertions
is_insertion = variant.is_insertion
# determine if any exons are deleted, and if not,
# what is the closest exon and how far is this variant
# from that exon (overlapping the exon = 0 distance)
completely_lost_exons = []
# list of which (exon #, Exon) pairs this mutation overlaps
overlapping_exon_numbers_and_exons = []
distance_to_nearest_exon = float("inf")
start_in_exon = False
end_in_exon = False
nearest_exon = None
variant_start = variant.trimmed_base1_start
variant_end = variant.trimmed_base1_end
for i, exon in enumerate(transcript.exons):
if variant_start <= exon.start and variant_end >= exon.end:
completely_lost_exons.append(exon)
if is_insertion and exon.strand == "+" and variant_end == exon.end:
# insertions after an exon don't overlap the exon
distance = 1
elif is_insertion and exon.strand == "-" and variant_start == exon.start:
distance = 1
else:
distance = exon.distance_to_interval(variant_start, variant_end)
if distance == 0:
overlapping_exon_numbers_and_exons.append((i + 1, exon))
# start is contained in current exon
if exon.start <= variant_start <= exon.end:
start_in_exon = True
# end is contained in current exon
if exon.end >= variant_end >= exon.start:
end_in_exon = True
elif distance < distance_to_nearest_exon:
distance_to_nearest_exon = distance
nearest_exon = exon
if len(overlapping_exon_numbers_and_exons) == 0:
intronic_effect_class = choose_intronic_effect_class(
variant=variant,
nearest_exon=nearest_exon,
distance_to_exon=distance_to_nearest_exon)
return intronic_effect_class(
variant=variant,
transcript=transcript,
nearest_exon=nearest_exon,
distance_to_exon=distance_to_nearest_exon)
elif len(completely_lost_exons) > 0 or (
len(overlapping_exon_numbers_and_exons) > 1):
# if spanning multiple exons, or completely deleted an exon
# then consider that an ExonLoss mutation
exons = [exon for (_, exon) in overlapping_exon_numbers_and_exons]
return ExonLoss(variant, transcript, exons)
assert len(overlapping_exon_numbers_and_exons) == 1
exon_number, exon = overlapping_exon_numbers_and_exons[0]
exonic_effect_annotation = exonic_transcript_effect(
variant, exon, exon_number, transcript)
# simple case: both start and end are in the same
if start_in_exon and end_in_exon:
return exonic_effect_annotation
elif isinstance(exonic_effect_annotation, ExonicSpliceSite):
# if mutation bleeds over into intro but even just
# the exonic portion got annotated as an exonic splice site
# then return it
return exonic_effect_annotation
return ExonicSpliceSite(
variant=variant,
transcript=transcript,
exon=exon,
alternate_effect=exonic_effect_annotation) | python | def predict_variant_effect_on_transcript(variant, transcript):
"""Return the transcript effect (such as FrameShift) that results from
applying this genomic variant to a particular transcript.
Parameters
----------
transcript : Transcript
Transcript we're going to apply mutation to.
"""
if transcript.__class__ is not Transcript:
raise TypeError(
"Expected %s : %s to have type Transcript" % (
transcript, type(transcript)))
# check for non-coding transcripts first, since
# every non-coding transcript is "incomplete".
if not transcript.is_protein_coding:
return NoncodingTranscript(variant, transcript)
if not transcript.complete:
return IncompleteTranscript(variant, transcript)
# since we're using inclusive base-1 coordinates,
# checking for overlap requires special logic for insertions
is_insertion = variant.is_insertion
# determine if any exons are deleted, and if not,
# what is the closest exon and how far is this variant
# from that exon (overlapping the exon = 0 distance)
completely_lost_exons = []
# list of which (exon #, Exon) pairs this mutation overlaps
overlapping_exon_numbers_and_exons = []
distance_to_nearest_exon = float("inf")
start_in_exon = False
end_in_exon = False
nearest_exon = None
variant_start = variant.trimmed_base1_start
variant_end = variant.trimmed_base1_end
for i, exon in enumerate(transcript.exons):
if variant_start <= exon.start and variant_end >= exon.end:
completely_lost_exons.append(exon)
if is_insertion and exon.strand == "+" and variant_end == exon.end:
# insertions after an exon don't overlap the exon
distance = 1
elif is_insertion and exon.strand == "-" and variant_start == exon.start:
distance = 1
else:
distance = exon.distance_to_interval(variant_start, variant_end)
if distance == 0:
overlapping_exon_numbers_and_exons.append((i + 1, exon))
# start is contained in current exon
if exon.start <= variant_start <= exon.end:
start_in_exon = True
# end is contained in current exon
if exon.end >= variant_end >= exon.start:
end_in_exon = True
elif distance < distance_to_nearest_exon:
distance_to_nearest_exon = distance
nearest_exon = exon
if len(overlapping_exon_numbers_and_exons) == 0:
intronic_effect_class = choose_intronic_effect_class(
variant=variant,
nearest_exon=nearest_exon,
distance_to_exon=distance_to_nearest_exon)
return intronic_effect_class(
variant=variant,
transcript=transcript,
nearest_exon=nearest_exon,
distance_to_exon=distance_to_nearest_exon)
elif len(completely_lost_exons) > 0 or (
len(overlapping_exon_numbers_and_exons) > 1):
# if spanning multiple exons, or completely deleted an exon
# then consider that an ExonLoss mutation
exons = [exon for (_, exon) in overlapping_exon_numbers_and_exons]
return ExonLoss(variant, transcript, exons)
assert len(overlapping_exon_numbers_and_exons) == 1
exon_number, exon = overlapping_exon_numbers_and_exons[0]
exonic_effect_annotation = exonic_transcript_effect(
variant, exon, exon_number, transcript)
# simple case: both start and end are in the same
if start_in_exon and end_in_exon:
return exonic_effect_annotation
elif isinstance(exonic_effect_annotation, ExonicSpliceSite):
# if mutation bleeds over into intro but even just
# the exonic portion got annotated as an exonic splice site
# then return it
return exonic_effect_annotation
return ExonicSpliceSite(
variant=variant,
transcript=transcript,
exon=exon,
alternate_effect=exonic_effect_annotation) | [
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] | Return the transcript effect (such as FrameShift) that results from
applying this genomic variant to a particular transcript.
Parameters
----------
transcript : Transcript
Transcript we're going to apply mutation to. | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/effect_prediction.py#L114-L220 | train | Predicts the transcript effect that results from applying this variant to a particular transcript. | 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(111) + chr(0b11111 + 0o24) + chr(0b110111) + chr(0b110101), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(0b11010 + 0o31) + '\x32' + chr(0b110110), 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110001) + chr(52) + '\x31', 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + '\063' + chr(53) + chr(0b110100), 19951 - 19943), nzTpIcepk0o8('\x30' + chr(111) + chr(1396 - 1347) + '\067' + chr(0b11100 + 0o31), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(49) + chr(1140 - 1088) + chr(49), 8), nzTpIcepk0o8('\x30' + chr(0b1000101 + 0o52) + '\x31' + chr(0b110101) + chr(0b1100 + 0o44), ord("\x08")), nzTpIcepk0o8(chr(0b1100 + 0o44) + chr(111) + chr(0b110001) + chr(0b1101 + 0o47) + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(0b10100 + 0o34) + '\157' + chr(756 - 706) + chr(0b1100 + 0o45) + chr(401 - 350), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b10110 + 0o131) + chr(0b10111 + 0o32) + chr(0b110001), 0b1000), nzTpIcepk0o8(chr(2096 - 2048) + chr(111) + chr(50) + chr(55) + chr(54), 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(633 - 584) + chr(569 - 517), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1001101 + 0o42) + '\061' + chr(0b110100) + chr(2022 - 1974), ord("\x08")), nzTpIcepk0o8(chr(328 - 280) + chr(111) + chr(0b10111 + 0o32) + chr(0b100 + 0o55) + chr(0b1011 + 0o45), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1011011 + 0o24) + chr(51) + '\x35' + chr(863 - 815), 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(0b111 + 0o54) + chr(0b111 + 0o52) + chr(157 - 108), 0o10), nzTpIcepk0o8(chr(48) + '\157' + '\064' + '\061', ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(1577 - 1528), 0o10), nzTpIcepk0o8(chr(1309 - 1261) + chr(0b11001 + 0o126) + '\x32' + chr(0b110100) + '\063', 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + '\063' + chr(52) + '\x35', 44243 - 44235), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x31' + chr(0b100110 + 0o20) + chr(0b1 + 0o64), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(1426 - 1372) + chr(0b110000), 64901 - 64893), nzTpIcepk0o8(chr(1041 - 993) + '\157' + chr(0b110010) + chr(0b110011) + chr(1969 - 1918), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(9294 - 9183) + chr(55) + chr(1721 - 1666), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + '\x31' + chr(457 - 408), 8), nzTpIcepk0o8(chr(0b10111 + 0o31) + chr(0b10001 + 0o136) + chr(0b110101) + '\062', 10335 - 10327), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110110) + chr(0b101000 + 0o13), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(50) + chr(0b101110 + 0o4) + chr(54), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(0b110011) + '\066', 0b1000), nzTpIcepk0o8(chr(0b100100 + 0o14) + chr(111) + '\x31' + chr(49) + chr(50), 0o10), nzTpIcepk0o8(chr(0b1 + 0o57) + '\x6f' + chr(0b0 + 0o62) + chr(52) + chr(0b100100 + 0o16), 0o10), nzTpIcepk0o8('\060' + chr(111) + '\x32' + chr(0b100011 + 0o22) + '\x36', 53265 - 53257), nzTpIcepk0o8('\x30' + chr(1016 - 905) + chr(169 - 119) + '\x32' + '\061', ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + '\061' + chr(1939 - 1888) + chr(0b101100 + 0o13), 0o10), nzTpIcepk0o8(chr(0b11 + 0o55) + '\x6f' + '\063' + chr(51) + '\067', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(49) + chr(0b10111 + 0o36) + '\066', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1001110 + 0o41) + chr(0b110011) + chr(555 - 503) + chr(100 - 49), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + '\063' + '\062' + '\x32', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b101001 + 0o11) + '\063' + chr(0b110110), ord("\x08")), nzTpIcepk0o8(chr(0b10 + 0o56) + chr(0b1101111) + chr(51) + chr(2078 - 2030), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + chr(4514 - 4403) + chr(0b1111 + 0o46) + chr(0b101110 + 0o2), 29068 - 29060)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xd3'), chr(0b11110 + 0o106) + chr(0b100 + 0o141) + '\x63' + chr(111) + '\x64' + chr(0b1011010 + 0o13))('\x75' + '\x74' + chr(0b1100110) + '\055' + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def FQzfGCbBrZUK(ZXJSPKxkIyZK, lnOu7fTAiCZI):
if roI3spqORKae(lnOu7fTAiCZI, roI3spqORKae(ES5oEprVxulp(b'\x90\xa5U\xd5\t\x039\x03\xddB\xc9M'), chr(0b1100100) + '\x65' + chr(0b1100011) + chr(0b11100 + 0o123) + chr(0b101100 + 0o70) + chr(0b1011001 + 0o14))(chr(117) + chr(116) + '\x66' + chr(45) + chr(0b111000))) is not ErwyXXkkBnKD:
raise jZIjKu8IFANs(roI3spqORKae(ES5oEprVxulp(b'\xb8\xae\x11\x89\x1e\x15\r\x06\xab,\xcd,Zh\xcd\xba\x01u\xcc\xc5\x1dQ\xedZ)^J\xe6{j\xf6\xdc\xf01\xac\r\x91\xbb\xeel'), chr(7145 - 7045) + chr(0b1100101) + chr(7043 - 6944) + '\x6f' + chr(0b1100000 + 0o4) + '\145')(chr(0b1110101) + chr(116) + '\x66' + chr(0b101101) + chr(0b111000)) % (lnOu7fTAiCZI, MJ07XsN5uFgW(lnOu7fTAiCZI)))
if not roI3spqORKae(lnOu7fTAiCZI, roI3spqORKae(ES5oEprVxulp(b'\x94\xa5>\x9c\x0f\x0e\x1c\x07\xe2g\xe1o\x0f,\x81\xa7F'), chr(0b110001 + 0o63) + '\x65' + '\x63' + chr(0b1101111) + chr(0b1011 + 0o131) + chr(101))(chr(0b1010101 + 0o40) + chr(941 - 825) + '\x66' + '\055' + chr(1789 - 1733))):
return Bow6ObNtSu4B(ZXJSPKxkIyZK, lnOu7fTAiCZI)
if not roI3spqORKae(lnOu7fTAiCZI, roI3spqORKae(ES5oEprVxulp(b'\xa9\xb2\x14\xb9(\r=\t\xdcY\xcd:'), '\144' + chr(0b101110 + 0o67) + chr(0b110101 + 0o56) + '\157' + chr(100) + '\x65')(chr(7974 - 7857) + chr(6327 - 6211) + chr(0b1001101 + 0o31) + '\x2d' + '\070')):
return u7rO1epO2KSm(ZXJSPKxkIyZK, lnOu7fTAiCZI)
cKvwmgqx2X4j = ZXJSPKxkIyZK.is_insertion
pynFRsuzOaew = []
qcDW6uhgBFD9 = []
Jf1lrSPcOaw7 = jLW6pRf2DSRk(roI3spqORKae(ES5oEprVxulp(b'\x94\xb8\x07'), chr(0b10100 + 0o120) + '\x65' + chr(5321 - 5222) + chr(0b1101111) + '\144' + chr(505 - 404))(chr(8121 - 8004) + chr(0b1000001 + 0o63) + '\146' + '\055' + chr(0b111000)))
WWv0Z91oE3fA = nzTpIcepk0o8(chr(1111 - 1063) + '\x6f' + '\060', 33102 - 33094)
GhoY8vgFQK7O = nzTpIcepk0o8(chr(0b11010 + 0o26) + chr(111) + chr(920 - 872), 8)
aUBzwlcRfc5C = None
fvOw4SZvhoGW = ZXJSPKxkIyZK.trimmed_base1_start
QjYr_nlhPhpd = ZXJSPKxkIyZK.trimmed_base1_end
for (ZlbFMSG8gCoF, Rxu3AkImGCU1) in _kV_Bomx8PZ4(roI3spqORKae(lnOu7fTAiCZI, roI3spqORKae(ES5oEprVxulp(b'\x98\xae\x0e\x82\x0e'), chr(8607 - 8507) + chr(101) + chr(99) + '\x6f' + '\x64' + chr(0b1100101))(chr(0b1101001 + 0o14) + chr(116) + chr(102) + chr(45) + chr(56)))):
if fvOw4SZvhoGW <= roI3spqORKae(Rxu3AkImGCU1, roI3spqORKae(ES5oEprVxulp(b'\xb6\x87\x03\xa4;5\x0b\x0e\xd4E\xf5u'), chr(100) + '\x65' + chr(9678 - 9579) + '\157' + '\x64' + '\x65')(chr(117) + '\164' + chr(0b1100110) + '\055' + chr(56))) and QjYr_nlhPhpd >= roI3spqORKae(Rxu3AkImGCU1, roI3spqORKae(ES5oEprVxulp(b'\xb3\xbf6\xba\x17 ?\x0c\xbbe\x88X'), chr(0b1100100) + chr(101) + '\143' + chr(111) + chr(0b110100 + 0o60) + '\x65')(chr(0b1110101) + chr(0b1110100) + chr(8305 - 8203) + '\055' + chr(56))):
roI3spqORKae(pynFRsuzOaew, roI3spqORKae(ES5oEprVxulp(b'\xb5\x822\xd8\x05\x06/\r\xe1f\xeb9'), chr(0b1100100) + '\145' + chr(0b101010 + 0o71) + '\157' + chr(0b110010 + 0o62) + chr(0b1000111 + 0o36))('\x75' + chr(6822 - 6706) + chr(102) + chr(1889 - 1844) + '\x38'))(Rxu3AkImGCU1)
if cKvwmgqx2X4j and roI3spqORKae(Rxu3AkImGCU1, roI3spqORKae(ES5oEprVxulp(b'\x8e\x99\x17\xbc\x19\x11\x1fT\xc1b\xfa:'), '\x64' + chr(1106 - 1005) + '\x63' + chr(0b1101111) + '\144' + chr(0b1100101))(chr(0b100010 + 0o123) + chr(0b1110100) + '\x66' + '\x2d' + chr(0b100 + 0o64))) == roI3spqORKae(ES5oEprVxulp(b'\xd6'), chr(0b1100100) + chr(0b1100101) + chr(0b1100011) + chr(0b1000110 + 0o51) + chr(0b11 + 0o141) + chr(0b1010100 + 0o21))(chr(117) + '\164' + chr(0b1011110 + 0o10) + chr(0b100010 + 0o13) + '\x38') and (QjYr_nlhPhpd == roI3spqORKae(Rxu3AkImGCU1, roI3spqORKae(ES5oEprVxulp(b'\xb3\xbf6\xba\x17 ?\x0c\xbbe\x88X'), chr(0b1100000 + 0o4) + chr(0b1100101) + '\143' + '\157' + '\x64' + '\x65')(chr(0b1110101) + chr(116) + chr(0b1100110) + chr(0b101101) + '\070'))):
cWxJ9qIyBuTI = nzTpIcepk0o8(chr(0b110000) + chr(0b1011 + 0o144) + '\x31', 8)
elif cKvwmgqx2X4j and roI3spqORKae(Rxu3AkImGCU1, roI3spqORKae(ES5oEprVxulp(b'\x8e\x99\x17\xbc\x19\x11\x1fT\xc1b\xfa:'), chr(0b1100100) + '\145' + '\143' + chr(9163 - 9052) + '\x64' + '\145')(chr(0b1110101) + chr(116) + chr(0b11011 + 0o113) + '\x2d' + chr(2900 - 2844))) == roI3spqORKae(ES5oEprVxulp(b'\xd0'), '\144' + chr(101) + chr(0b111111 + 0o44) + chr(0b10 + 0o155) + '\144' + '\x65')(chr(12800 - 12683) + chr(0b1001 + 0o153) + chr(102) + '\055' + chr(0b111000)) and (fvOw4SZvhoGW == roI3spqORKae(Rxu3AkImGCU1, roI3spqORKae(ES5oEprVxulp(b'\xb6\x87\x03\xa4;5\x0b\x0e\xd4E\xf5u'), '\144' + chr(0b1100101) + chr(0b1100011) + chr(111) + chr(100) + '\x65')(chr(6089 - 5972) + '\164' + chr(2432 - 2330) + chr(636 - 591) + '\070'))):
cWxJ9qIyBuTI = nzTpIcepk0o8(chr(2072 - 2024) + '\x6f' + chr(0b110001), 8)
else:
cWxJ9qIyBuTI = Rxu3AkImGCU1.distance_to_interval(fvOw4SZvhoGW, QjYr_nlhPhpd)
if cWxJ9qIyBuTI == nzTpIcepk0o8(chr(1291 - 1243) + '\x6f' + '\x30', 8):
roI3spqORKae(qcDW6uhgBFD9, roI3spqORKae(ES5oEprVxulp(b'\xb5\x822\xd8\x05\x06/\r\xe1f\xeb9'), chr(100) + '\x65' + chr(99) + chr(111) + '\144' + chr(101))(chr(117) + chr(0b0 + 0o164) + chr(6532 - 6430) + chr(0b101101) + chr(2685 - 2629)))((ZlbFMSG8gCoF + nzTpIcepk0o8('\x30' + chr(370 - 259) + chr(49), 8), Rxu3AkImGCU1))
if roI3spqORKae(Rxu3AkImGCU1, roI3spqORKae(ES5oEprVxulp(b'\xb6\x87\x03\xa4;5\x0b\x0e\xd4E\xf5u'), chr(0b11011 + 0o111) + '\145' + chr(99) + chr(111) + chr(100) + chr(1247 - 1146))(chr(0b1110100 + 0o1) + chr(116) + '\146' + '\x2d' + '\x38')) <= fvOw4SZvhoGW <= roI3spqORKae(Rxu3AkImGCU1, roI3spqORKae(ES5oEprVxulp(b'\xb3\xbf6\xba\x17 ?\x0c\xbbe\x88X'), chr(1348 - 1248) + chr(101) + '\143' + '\x6f' + '\x64' + chr(101))(chr(0b1110101) + '\164' + chr(102) + chr(1893 - 1848) + '\070')):
WWv0Z91oE3fA = nzTpIcepk0o8(chr(0b11101 + 0o23) + chr(111) + chr(49), 8)
if roI3spqORKae(Rxu3AkImGCU1, roI3spqORKae(ES5oEprVxulp(b'\xb3\xbf6\xba\x17 ?\x0c\xbbe\x88X'), chr(0b1100100) + chr(101) + chr(0b1100011) + '\x6f' + chr(0b1100100) + chr(0b1100101))('\165' + chr(116) + '\146' + chr(45) + chr(56))) >= QjYr_nlhPhpd >= roI3spqORKae(Rxu3AkImGCU1, roI3spqORKae(ES5oEprVxulp(b'\xb6\x87\x03\xa4;5\x0b\x0e\xd4E\xf5u'), '\144' + chr(101) + chr(99) + chr(6776 - 6665) + chr(0b1100100) + chr(0b1001001 + 0o34))(chr(0b110111 + 0o76) + '\x74' + chr(0b10011 + 0o123) + '\055' + chr(0b111000))):
GhoY8vgFQK7O = nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(49), 8)
elif cWxJ9qIyBuTI < Jf1lrSPcOaw7:
Jf1lrSPcOaw7 = cWxJ9qIyBuTI
aUBzwlcRfc5C = Rxu3AkImGCU1
if ftfygxgFas5X(qcDW6uhgBFD9) == nzTpIcepk0o8(chr(0b10100 + 0o34) + chr(0b1101111) + chr(48), 8):
ZeMHQOBcY3ik = nG9zJMmcEs3J(variant=ZXJSPKxkIyZK, nearest_exon=aUBzwlcRfc5C, distance_to_exon=Jf1lrSPcOaw7)
return ZeMHQOBcY3ik(variant=ZXJSPKxkIyZK, transcript=lnOu7fTAiCZI, nearest_exon=aUBzwlcRfc5C, distance_to_exon=Jf1lrSPcOaw7)
elif ftfygxgFas5X(pynFRsuzOaew) > nzTpIcepk0o8('\x30' + chr(9237 - 9126) + '\060', 8) or ftfygxgFas5X(qcDW6uhgBFD9) > nzTpIcepk0o8('\060' + chr(2527 - 2416) + chr(0b110001), 8):
f5WNAkO_0SwS = [Rxu3AkImGCU1 for (zIqcgNgQ9U6F, Rxu3AkImGCU1) in qcDW6uhgBFD9]
return ZE4MrfvVjb6F(ZXJSPKxkIyZK, lnOu7fTAiCZI, f5WNAkO_0SwS)
assert ftfygxgFas5X(qcDW6uhgBFD9) == nzTpIcepk0o8(chr(0b10010 + 0o36) + chr(8707 - 8596) + '\061', 8)
(VaBlaQ94SGbZ, Rxu3AkImGCU1) = qcDW6uhgBFD9[nzTpIcepk0o8(chr(928 - 880) + '\x6f' + chr(48), 8)]
uMmB28MGZfLn = c28iNVDft2OW(ZXJSPKxkIyZK, Rxu3AkImGCU1, VaBlaQ94SGbZ, lnOu7fTAiCZI)
if WWv0Z91oE3fA and GhoY8vgFQK7O:
return uMmB28MGZfLn
elif suIjIS24Zkqw(uMmB28MGZfLn, j1aB_lXmg5Oq):
return uMmB28MGZfLn
return j1aB_lXmg5Oq(variant=ZXJSPKxkIyZK, transcript=lnOu7fTAiCZI, exon=Rxu3AkImGCU1, alternate_effect=uMmB28MGZfLn) |
openvax/varcode | varcode/effects/effect_prediction.py | choose_intronic_effect_class | def choose_intronic_effect_class(
variant,
nearest_exon,
distance_to_exon):
"""
Infer effect of variant which does not overlap any exon of
the given transcript.
"""
assert distance_to_exon > 0, \
"Expected intronic effect to have distance_to_exon > 0, got %d" % (
distance_to_exon,)
if nearest_exon.strand == "+":
# if exon on positive strand
start_before = variant.trimmed_base1_start < nearest_exon.start
start_same = variant.trimmed_base1_start == nearest_exon.start
before_exon = start_before or (variant.is_insertion and start_same)
else:
# if exon on negative strand
end_after = variant.trimmed_base1_end > nearest_exon.end
end_same = variant.trimmed_base1_end == nearest_exon.end
before_exon = end_after or (variant.is_insertion and end_same)
# distance cutoffs based on consensus splice sequences from
# http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2947103/
# 5' splice site: MAG|GURAGU consensus
# M is A or C; R is purine; | is the exon-intron boundary
# 3' splice site: YAG|R
if distance_to_exon <= 2:
if before_exon:
# 2 last nucleotides of intron before exon are the splice
# acceptor site, typically "AG"
return SpliceAcceptor
else:
# 2 first nucleotides of intron after exon are the splice donor
# site, typically "GT"
return SpliceDonor
elif not before_exon and distance_to_exon <= 6:
# variants in nucleotides 3-6 at start of intron aren't as certain
# to cause problems as nucleotides 1-2 but still implicated in
# alternative splicing
return IntronicSpliceSite
elif before_exon and distance_to_exon <= 3:
# nucleotide -3 before exon is part of the 3' splicing
# motif but allows for more degeneracy than the -2, -1 nucleotides
return IntronicSpliceSite
else:
# intronic mutation unrelated to splicing
return Intronic | python | def choose_intronic_effect_class(
variant,
nearest_exon,
distance_to_exon):
"""
Infer effect of variant which does not overlap any exon of
the given transcript.
"""
assert distance_to_exon > 0, \
"Expected intronic effect to have distance_to_exon > 0, got %d" % (
distance_to_exon,)
if nearest_exon.strand == "+":
# if exon on positive strand
start_before = variant.trimmed_base1_start < nearest_exon.start
start_same = variant.trimmed_base1_start == nearest_exon.start
before_exon = start_before or (variant.is_insertion and start_same)
else:
# if exon on negative strand
end_after = variant.trimmed_base1_end > nearest_exon.end
end_same = variant.trimmed_base1_end == nearest_exon.end
before_exon = end_after or (variant.is_insertion and end_same)
# distance cutoffs based on consensus splice sequences from
# http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2947103/
# 5' splice site: MAG|GURAGU consensus
# M is A or C; R is purine; | is the exon-intron boundary
# 3' splice site: YAG|R
if distance_to_exon <= 2:
if before_exon:
# 2 last nucleotides of intron before exon are the splice
# acceptor site, typically "AG"
return SpliceAcceptor
else:
# 2 first nucleotides of intron after exon are the splice donor
# site, typically "GT"
return SpliceDonor
elif not before_exon and distance_to_exon <= 6:
# variants in nucleotides 3-6 at start of intron aren't as certain
# to cause problems as nucleotides 1-2 but still implicated in
# alternative splicing
return IntronicSpliceSite
elif before_exon and distance_to_exon <= 3:
# nucleotide -3 before exon is part of the 3' splicing
# motif but allows for more degeneracy than the -2, -1 nucleotides
return IntronicSpliceSite
else:
# intronic mutation unrelated to splicing
return Intronic | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/effect_prediction.py#L223-L271 | train | Choose the intronic effect class for a given variant. | 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(49) + chr(0b110101) + chr(0b110101), 40744 - 40736), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110001) + chr(0b110000) + '\062', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b0 + 0o157) + chr(0b1100 + 0o47) + chr(2726 - 2672) + chr(0b101000 + 0o10), 0b1000), nzTpIcepk0o8(chr(2278 - 2230) + chr(0b1101000 + 0o7) + '\x33' + chr(0b110101) + chr(706 - 653), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + '\062' + '\x30' + '\x31', 31869 - 31861), nzTpIcepk0o8(chr(552 - 504) + '\157' + '\x31' + '\061' + chr(0b1 + 0o61), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1100001 + 0o16) + chr(50) + chr(0b110000) + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(0b100100 + 0o14) + '\x6f' + chr(0b100100 + 0o15) + chr(2250 - 2202) + chr(53), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(55) + '\067', ord("\x08")), nzTpIcepk0o8(chr(2041 - 1993) + chr(11180 - 11069) + '\x31' + chr(0b110110) + '\062', 0b1000), nzTpIcepk0o8('\x30' + chr(0b101101 + 0o102) + chr(0b11000 + 0o31) + chr(0b110100) + chr(0b101000 + 0o12), 2179 - 2171), nzTpIcepk0o8(chr(0b111 + 0o51) + '\157' + chr(54) + chr(55), 55209 - 55201), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b101010 + 0o10) + chr(0b1011 + 0o45) + chr(52), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1000001 + 0o56) + '\061' + chr(52) + '\x34', 0b1000), nzTpIcepk0o8(chr(0b100101 + 0o13) + chr(0b1101111) + chr(0b110010) + chr(0b110000), 0o10), nzTpIcepk0o8('\x30' + chr(0b1100000 + 0o17) + chr(0b110011) + chr(1605 - 1553) + '\063', 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b1000 + 0o53) + '\064' + chr(1267 - 1218), ord("\x08")), nzTpIcepk0o8(chr(1608 - 1560) + '\x6f' + chr(50) + '\x35' + chr(2442 - 2388), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(710 - 660) + chr(0b110010) + '\x31', 0o10), nzTpIcepk0o8(chr(717 - 669) + '\x6f' + '\062' + '\062' + chr(0b110110), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x31' + chr(0b1011 + 0o50) + '\x37', 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110010) + chr(1445 - 1395), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + '\x33' + '\065' + chr(48), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(49) + chr(48), 58103 - 58095), nzTpIcepk0o8(chr(113 - 65) + '\157' + chr(428 - 377) + chr(0b10100 + 0o40) + chr(0b110010), 0o10), nzTpIcepk0o8('\060' + chr(0b1101011 + 0o4) + chr(0b110010) + '\x33' + chr(0b110001), 0o10), nzTpIcepk0o8(chr(479 - 431) + '\157' + chr(0b110011) + '\065' + chr(50), 0b1000), nzTpIcepk0o8(chr(0b11101 + 0o23) + chr(12070 - 11959) + chr(0b110111) + '\067', 8), nzTpIcepk0o8('\060' + chr(0b1101111) + '\063' + chr(53) + '\x37', ord("\x08")), nzTpIcepk0o8(chr(1560 - 1512) + chr(111) + '\062' + chr(1782 - 1730), 64530 - 64522), nzTpIcepk0o8(chr(0b1111 + 0o41) + chr(111) + chr(50) + chr(0b1010 + 0o46) + chr(0b111 + 0o60), 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(1842 - 1791) + '\x33' + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(1765 - 1717) + chr(111) + chr(2335 - 2285) + '\062' + '\064', 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110010) + chr(51), 0o10), nzTpIcepk0o8(chr(0b10010 + 0o36) + chr(0b101110 + 0o101) + chr(0b100010 + 0o20) + chr(156 - 105) + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(5732 - 5621) + chr(0b110001) + chr(0b110011) + chr(50), 55938 - 55930), nzTpIcepk0o8('\x30' + chr(0b1001011 + 0o44) + '\062' + chr(2103 - 2053) + chr(0b110000), 26113 - 26105), nzTpIcepk0o8('\060' + chr(0b1000001 + 0o56) + chr(0b110100) + chr(0b11000 + 0o31), 0b1000), nzTpIcepk0o8(chr(969 - 921) + '\157' + chr(0b101101 + 0o5) + '\061' + '\x35', 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(2066 - 2015) + chr(383 - 333) + chr(502 - 450), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(1029 - 981) + chr(0b110 + 0o151) + chr(2336 - 2283) + '\x30', ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'C'), chr(0b1001000 + 0o34) + chr(0b1100101) + chr(0b111000 + 0o53) + chr(0b1011111 + 0o20) + chr(0b1100100) + '\145')('\165' + '\164' + chr(0b1100100 + 0o2) + chr(693 - 648) + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def nG9zJMmcEs3J(ZXJSPKxkIyZK, aUBzwlcRfc5C, YjcKHfW57huf):
assert YjcKHfW57huf > nzTpIcepk0o8('\060' + chr(12036 - 11925) + '\x30', 31342 - 31334), roI3spqORKae(ES5oEprVxulp(b'(:\x80\x88\xe2>\xe0!\x1f\x1b\x0cC\xf6\x0b~\x8a\x82\x8e\xf4\xf09w\x8b|\xc2\xed\x85\x1f\x87u\xf1\xba\xb4w\xf4)\xe4@\xe3\xb7\x08\x1d\x84\x82\xde/\xfd*QR\\\x17\xb4H0\x84\x8e\xda\xb1\xb3;'), chr(100) + '\x65' + '\x63' + chr(0b1101111) + chr(0b1100100) + chr(101))('\165' + '\164' + chr(0b0 + 0o146) + '\x2d' + '\070') % (YjcKHfW57huf,)
if roI3spqORKae(aUBzwlcRfc5C, roI3spqORKae(ES5oEprVxulp(b'\x1e\r\x86\xbd\xe5:\xf2su\x19&\x01'), chr(0b110011 + 0o61) + chr(0b1100101) + chr(4904 - 4805) + chr(0b1101111) + chr(0b1000100 + 0o40) + chr(101))(chr(6408 - 6291) + chr(0b1110100) + chr(0b1100110) + chr(45) + chr(0b111000))) == roI3spqORKae(ES5oEprVxulp(b'F'), chr(0b1100100) + chr(6074 - 5973) + chr(0b1100011) + '\157' + chr(0b1100100) + chr(101))('\x75' + chr(0b1110100) + '\146' + chr(0b101101) + '\070'):
WWFgZ_68YI__ = ZXJSPKxkIyZK.trimmed_base1_start < aUBzwlcRfc5C.KQbHFTcl_LKy
BBkf1qhhJUy9 = ZXJSPKxkIyZK.trimmed_base1_start == aUBzwlcRfc5C.KQbHFTcl_LKy
RFhrspODQA6N = WWFgZ_68YI__ or (ZXJSPKxkIyZK.is_insertion and BBkf1qhhJUy9)
else:
xHTDis2hgBIC = ZXJSPKxkIyZK.trimmed_base1_end > aUBzwlcRfc5C.NiWVjAWn0l6T
C8OqTr0IeK7_ = ZXJSPKxkIyZK.trimmed_base1_end == aUBzwlcRfc5C.NiWVjAWn0l6T
RFhrspODQA6N = xHTDis2hgBIC or (ZXJSPKxkIyZK.is_insertion and C8OqTr0IeK7_)
if YjcKHfW57huf <= nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(50), 19236 - 19228):
if RFhrspODQA6N:
return a_E6a4fuOy8W
else:
return VNGD5P7DUHjM
elif not RFhrspODQA6N and YjcKHfW57huf <= nzTpIcepk0o8(chr(48) + chr(0b1000001 + 0o56) + chr(0b110110), 0o10):
return aosLOMOAH_69
elif RFhrspODQA6N and YjcKHfW57huf <= nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110001 + 0o2), 0b1000):
return aosLOMOAH_69
else:
return I35vjuK8PpZu |
openvax/varcode | varcode/effects/effect_prediction.py | exonic_transcript_effect | def exonic_transcript_effect(variant, exon, exon_number, transcript):
"""Effect of this variant on a Transcript, assuming we already know
that this variant overlaps some exon of the transcript.
Parameters
----------
variant : Variant
exon : pyensembl.Exon
Exon which this variant overlaps
exon_number : int
Index (starting from 1) of the given exon in the transcript's
sequence of exons.
transcript : pyensembl.Transcript
"""
genome_ref = variant.trimmed_ref
genome_alt = variant.trimmed_alt
variant_start = variant.trimmed_base1_start
variant_end = variant.trimmed_base1_end
# clip mutation to only affect the current exon
if variant_start < exon.start:
# if mutation starts before current exon then only look
# at nucleotides which overlap the exon
logger.info('Mutation in variant %s starts before exon %s', variant, exon)
assert len(genome_ref) > 0, "Unexpected insertion into intron"
n_skip_start = exon.start - variant_start
genome_ref = genome_ref[n_skip_start:]
genome_alt = genome_alt[n_skip_start:]
genome_start = exon.start
else:
genome_start = variant_start
if variant_end > exon.end:
# if mutation goes past exon end then only look at nucleotides
# which overlap the exon
logger.info('Mutation in variant %s ends after exon %s', variant, exon)
n_skip_end = variant_end - exon.end
genome_ref = genome_ref[:-n_skip_end]
genome_alt = genome_alt[:len(genome_ref)]
genome_end = exon.end
else:
genome_end = variant_end
transcript_offset = interval_offset_on_transcript(
genome_start, genome_end, transcript)
if transcript.on_backward_strand:
cdna_ref = reverse_complement(genome_ref)
cdna_alt = reverse_complement(genome_alt)
else:
cdna_ref = genome_ref
cdna_alt = genome_alt
n_ref = len(cdna_ref)
expected_ref = str(
transcript.sequence[transcript_offset:transcript_offset + n_ref])
if cdna_ref != expected_ref:
raise ValueError(
("Found ref nucleotides '%s' in sequence"
" of %s at offset %d (chromosome positions %d:%d)"
" but variant %s has '%s'") % (
expected_ref,
transcript,
transcript_offset,
genome_start,
genome_end,
variant,
cdna_ref))
utr5_length = min(transcript.start_codon_spliced_offsets)
# does the variant start inside the 5' UTR?
if utr5_length > transcript_offset:
# does the variant end after the 5' UTR, within the coding region?
if utr5_length < transcript_offset + n_ref:
# TODO: we *might* lose the Kozak sequence or the start codon
# but without looking at the modified sequence how can we tell
# for sure that this is a start-loss variant?
return StartLoss(variant, transcript)
else:
# if variant contained within 5' UTR
return FivePrimeUTR(variant, transcript)
utr3_offset = max(transcript.stop_codon_spliced_offsets) + 1
if transcript_offset >= utr3_offset:
return ThreePrimeUTR(variant, transcript)
exon_start_offset = interval_offset_on_transcript(
exon.start, exon.end, transcript)
exon_end_offset = exon_start_offset + len(exon) - 1
# Further below we're going to try to predict exonic splice site
# modifications, which will take this effect_annotation as their
# alternative hypothesis for what happens if splicing doesn't change.
# If the mutation doesn't affect an exonic splice site, then
# we'll just return this effect.
coding_effect_annotation = predict_variant_coding_effect_on_transcript(
variant=variant,
transcript=transcript,
trimmed_cdna_ref=cdna_ref,
trimmed_cdna_alt=cdna_alt,
transcript_offset=transcript_offset)
if changes_exonic_splice_site(
transcript=transcript,
transcript_ref=cdna_ref,
transcript_alt=cdna_alt,
transcript_offset=transcript_offset,
exon_start_offset=exon_start_offset,
exon_end_offset=exon_end_offset,
exon_number=exon_number):
return ExonicSpliceSite(
variant=variant,
transcript=transcript,
exon=exon,
alternate_effect=coding_effect_annotation)
return coding_effect_annotation | python | def exonic_transcript_effect(variant, exon, exon_number, transcript):
"""Effect of this variant on a Transcript, assuming we already know
that this variant overlaps some exon of the transcript.
Parameters
----------
variant : Variant
exon : pyensembl.Exon
Exon which this variant overlaps
exon_number : int
Index (starting from 1) of the given exon in the transcript's
sequence of exons.
transcript : pyensembl.Transcript
"""
genome_ref = variant.trimmed_ref
genome_alt = variant.trimmed_alt
variant_start = variant.trimmed_base1_start
variant_end = variant.trimmed_base1_end
# clip mutation to only affect the current exon
if variant_start < exon.start:
# if mutation starts before current exon then only look
# at nucleotides which overlap the exon
logger.info('Mutation in variant %s starts before exon %s', variant, exon)
assert len(genome_ref) > 0, "Unexpected insertion into intron"
n_skip_start = exon.start - variant_start
genome_ref = genome_ref[n_skip_start:]
genome_alt = genome_alt[n_skip_start:]
genome_start = exon.start
else:
genome_start = variant_start
if variant_end > exon.end:
# if mutation goes past exon end then only look at nucleotides
# which overlap the exon
logger.info('Mutation in variant %s ends after exon %s', variant, exon)
n_skip_end = variant_end - exon.end
genome_ref = genome_ref[:-n_skip_end]
genome_alt = genome_alt[:len(genome_ref)]
genome_end = exon.end
else:
genome_end = variant_end
transcript_offset = interval_offset_on_transcript(
genome_start, genome_end, transcript)
if transcript.on_backward_strand:
cdna_ref = reverse_complement(genome_ref)
cdna_alt = reverse_complement(genome_alt)
else:
cdna_ref = genome_ref
cdna_alt = genome_alt
n_ref = len(cdna_ref)
expected_ref = str(
transcript.sequence[transcript_offset:transcript_offset + n_ref])
if cdna_ref != expected_ref:
raise ValueError(
("Found ref nucleotides '%s' in sequence"
" of %s at offset %d (chromosome positions %d:%d)"
" but variant %s has '%s'") % (
expected_ref,
transcript,
transcript_offset,
genome_start,
genome_end,
variant,
cdna_ref))
utr5_length = min(transcript.start_codon_spliced_offsets)
# does the variant start inside the 5' UTR?
if utr5_length > transcript_offset:
# does the variant end after the 5' UTR, within the coding region?
if utr5_length < transcript_offset + n_ref:
# TODO: we *might* lose the Kozak sequence or the start codon
# but without looking at the modified sequence how can we tell
# for sure that this is a start-loss variant?
return StartLoss(variant, transcript)
else:
# if variant contained within 5' UTR
return FivePrimeUTR(variant, transcript)
utr3_offset = max(transcript.stop_codon_spliced_offsets) + 1
if transcript_offset >= utr3_offset:
return ThreePrimeUTR(variant, transcript)
exon_start_offset = interval_offset_on_transcript(
exon.start, exon.end, transcript)
exon_end_offset = exon_start_offset + len(exon) - 1
# Further below we're going to try to predict exonic splice site
# modifications, which will take this effect_annotation as their
# alternative hypothesis for what happens if splicing doesn't change.
# If the mutation doesn't affect an exonic splice site, then
# we'll just return this effect.
coding_effect_annotation = predict_variant_coding_effect_on_transcript(
variant=variant,
transcript=transcript,
trimmed_cdna_ref=cdna_ref,
trimmed_cdna_alt=cdna_alt,
transcript_offset=transcript_offset)
if changes_exonic_splice_site(
transcript=transcript,
transcript_ref=cdna_ref,
transcript_alt=cdna_alt,
transcript_offset=transcript_offset,
exon_start_offset=exon_start_offset,
exon_end_offset=exon_end_offset,
exon_number=exon_number):
return ExonicSpliceSite(
variant=variant,
transcript=transcript,
exon=exon,
alternate_effect=coding_effect_annotation)
return coding_effect_annotation | [
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] | Effect of this variant on a Transcript, assuming we already know
that this variant overlaps some exon of the transcript.
Parameters
----------
variant : Variant
exon : pyensembl.Exon
Exon which this variant overlaps
exon_number : int
Index (starting from 1) of the given exon in the transcript's
sequence of exons.
transcript : pyensembl.Transcript | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/effect_prediction.py#L274-L397 | train | This function returns the effect of this variant on a Transcript assuming we already know that this variant overlaps some exon of the transcript. | 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) + '\157' + chr(0b110010) + chr(1505 - 1454) + '\x32', 0o10), nzTpIcepk0o8('\x30' + chr(7489 - 7378) + chr(0b11010 + 0o34), ord("\x08")), nzTpIcepk0o8(chr(1346 - 1298) + chr(0b110001 + 0o76) + chr(0b110100) + chr(48), 0o10), nzTpIcepk0o8(chr(1927 - 1879) + chr(0b1101111) + chr(49) + chr(0b110110) + chr(1436 - 1388), 7635 - 7627), nzTpIcepk0o8(chr(931 - 883) + '\157' + '\x32' + '\x30' + chr(1992 - 1941), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b100010 + 0o115) + '\062' + chr(51), 0o10), nzTpIcepk0o8(chr(1515 - 1467) + chr(111) + chr(0b110011) + '\x34' + chr(0b110001 + 0o1), 0b1000), nzTpIcepk0o8('\060' + chr(7182 - 7071) + chr(1775 - 1726) + chr(0b110011 + 0o2), 30206 - 30198), nzTpIcepk0o8(chr(0b1010 + 0o46) + chr(0b1101111) + chr(0b110011) + chr(54) + '\066', 11762 - 11754), nzTpIcepk0o8(chr(0b110000) + chr(0b111 + 0o150) + chr(2480 - 2429) + chr(49) + chr(0b110010), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x31' + '\x31' + chr(49), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(50) + chr(0b100000 + 0o20), 0b1000), nzTpIcepk0o8(chr(0b101111 + 0o1) + chr(0b11101 + 0o122) + chr(0b110001) + chr(0b1000 + 0o56) + '\x31', 0b1000), nzTpIcepk0o8('\060' + chr(2756 - 2645) + chr(1243 - 1193) + chr(0b110110) + '\x34', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(49) + chr(0b101101 + 0o4) + chr(54), 1909 - 1901), nzTpIcepk0o8(chr(48) + chr(0b100000 + 0o117) + '\061' + '\066', 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(0b110010) + '\067' + '\063', 63312 - 63304), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110101) + chr(0b110110), 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + '\063' + chr(0b100 + 0o61) + chr(0b1100 + 0o44), 0b1000), nzTpIcepk0o8(chr(0b10011 + 0o35) + '\x6f' + chr(2399 - 2349) + chr(0b101 + 0o61) + chr(0b101 + 0o62), 56104 - 56096), nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(0b1101111) + chr(0b110011) + chr(0b10100 + 0o35), 6988 - 6980), nzTpIcepk0o8(chr(1723 - 1675) + chr(0b1101111) + chr(1678 - 1627) + chr(0b10100 + 0o34) + chr(0b110000), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(0b10 + 0o60) + '\x31' + '\067', 0b1000), nzTpIcepk0o8(chr(0b110 + 0o52) + chr(0b1101111) + chr(0b110001) + '\062' + chr(0b10010 + 0o41), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x32' + chr(0b110101) + chr(52), 0o10), nzTpIcepk0o8(chr(1996 - 1948) + chr(0b1101111) + chr(0b110011) + '\063' + '\x37', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x37' + chr(50), 0o10), nzTpIcepk0o8(chr(0b100001 + 0o17) + '\157' + chr(49) + chr(52) + chr(1552 - 1502), 63221 - 63213), nzTpIcepk0o8('\x30' + chr(111) + chr(50) + chr(0b101011 + 0o13) + chr(0b110010), 0b1000), nzTpIcepk0o8('\060' + chr(0b100 + 0o153) + chr(0b100010 + 0o21) + chr(0b110101) + chr(50), 0b1000), nzTpIcepk0o8(chr(992 - 944) + chr(0b1101111) + chr(49) + '\x30' + chr(0b101001 + 0o13), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + '\061' + chr(0b110110) + '\x32', ord("\x08")), nzTpIcepk0o8('\060' + chr(12226 - 12115) + '\062' + chr(0b110010) + chr(55), 0o10), nzTpIcepk0o8(chr(48) + chr(0b111011 + 0o64) + chr(0b10101 + 0o35) + chr(53) + '\x36', 0o10), nzTpIcepk0o8('\060' + chr(0b11100 + 0o123) + chr(2231 - 2182) + chr(54) + '\x31', 8), nzTpIcepk0o8(chr(0b100001 + 0o17) + chr(0b1101111) + chr(51) + chr(0b110111) + chr(0b110001), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(51) + chr(0b10011 + 0o37) + chr(53), 0o10), nzTpIcepk0o8('\060' + chr(111) + '\061' + '\x37' + '\x32', 30863 - 30855), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(641 - 591) + chr(0b110011) + chr(0b10110 + 0o35), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(821 - 770) + chr(0b100111 + 0o17) + chr(55), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + chr(0b101010 + 0o105) + '\065' + '\x30', ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xb4'), chr(0b1100100) + '\x65' + '\143' + chr(111) + chr(0b1100100) + chr(101))(chr(117) + chr(0b1110100) + '\146' + chr(45) + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def c28iNVDft2OW(ZXJSPKxkIyZK, Rxu3AkImGCU1, VaBlaQ94SGbZ, lnOu7fTAiCZI):
EL9M2pbhqIZt = ZXJSPKxkIyZK.trimmed_ref
VVUcV7Q2ITTL = ZXJSPKxkIyZK.trimmed_alt
fvOw4SZvhoGW = ZXJSPKxkIyZK.trimmed_base1_start
QjYr_nlhPhpd = ZXJSPKxkIyZK.trimmed_base1_end
if fvOw4SZvhoGW < roI3spqORKae(Rxu3AkImGCU1, roI3spqORKae(ES5oEprVxulp(b'\xd1WB8\xc5G\x81a\xa9\x86\x02i'), chr(0b1100100) + chr(0b101 + 0o140) + chr(99) + '\x6f' + '\x64' + chr(0b1100101))(chr(117) + '\x74' + '\146' + '\x2d' + chr(56))):
roI3spqORKae(iKLp4UdyhCfx, roI3spqORKae(ES5oEprVxulp(b'\xf3~n\x08\xba_\x95R\xc7\xad;_'), '\144' + chr(0b10000 + 0o125) + chr(4761 - 4662) + chr(0b1101111) + chr(0b1100001 + 0o3) + '\x65')('\x75' + chr(116) + '\146' + '\x2d' + '\x38'))(roI3spqORKae(ES5oEprVxulp(b"\xd7sT\x11\xf7z\x8dc\xd6\xa3'0\x07\xd5<g\xda@\x9c\x97<\xb3\xaf \xd8\xbeH\x16\xc1\xca&\x17\xf1\xc1\x03\x9c\xf5\x1f\xe3\x98\xf4&\x05\x03"), '\x64' + chr(101) + chr(447 - 348) + chr(111) + chr(100) + chr(101))(chr(117) + chr(0b1110100) + chr(0b100010 + 0o104) + chr(0b101101) + '\x38'), ZXJSPKxkIyZK, Rxu3AkImGCU1)
assert ftfygxgFas5X(EL9M2pbhqIZt) > nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(48), 0o10), roI3spqORKae(ES5oEprVxulp(b"\xcfhE\x08\xf3v\x81y\x93\xaeiy\x1f\xc7+|\xcfG\x87\xd99\xa9\xe1'\xc3\xffS\x0c\xc6\x98+\x1c"), chr(0b10111 + 0o115) + chr(0b1100100 + 0o1) + chr(0b1001001 + 0o32) + '\x6f' + chr(4647 - 4547) + '\145')(chr(0b10011 + 0o142) + chr(0b11011 + 0o131) + '\x66' + chr(0b101101) + '\x38')
LJDy7illZV9R = Rxu3AkImGCU1.KQbHFTcl_LKy - fvOw4SZvhoGW
EL9M2pbhqIZt = EL9M2pbhqIZt[LJDy7illZV9R:]
VVUcV7Q2ITTL = VVUcV7Q2ITTL[LJDy7illZV9R:]
DronXG2252Og = Rxu3AkImGCU1.KQbHFTcl_LKy
else:
DronXG2252Og = fvOw4SZvhoGW
if QjYr_nlhPhpd > roI3spqORKae(Rxu3AkImGCU1, roI3spqORKae(ES5oEprVxulp(b'\xd4ow&\xe9R\xb5c\xc6\xa6\x7fD'), '\x64' + '\x65' + '\143' + chr(0b1000011 + 0o54) + chr(0b1100100) + chr(8515 - 8414))(chr(6594 - 6477) + '\x74' + '\146' + chr(838 - 793) + chr(56))):
roI3spqORKae(iKLp4UdyhCfx, roI3spqORKae(ES5oEprVxulp(b'\xf3~n\x08\xba_\x95R\xc7\xad;_'), '\x64' + '\145' + chr(3137 - 3038) + chr(0b1101111) + chr(0b1100100) + '\x65')('\165' + '\164' + chr(4998 - 4896) + chr(0b101101) + '\070'))(roI3spqORKae(ES5oEprVxulp(b"\xd7sT\x11\xf7z\x8dc\xd6\xa3'0\x07\xd5<g\xda@\x9c\x97<\xb3\xaf6\xc2\xbbIB\xd3\x8c0\x17\xe5\x8e\x14\x81\xba\x14\xbb\xd2\xe9"), chr(0b1000101 + 0o37) + chr(101) + '\x63' + '\157' + chr(0b1000010 + 0o42) + chr(0b101100 + 0o71))(chr(10830 - 10713) + chr(4370 - 4254) + chr(0b1100110) + chr(0b1001 + 0o44) + chr(56)), ZXJSPKxkIyZK, Rxu3AkImGCU1)
VxvnwAO58T7L = QjYr_nlhPhpd - Rxu3AkImGCU1.NiWVjAWn0l6T
EL9M2pbhqIZt = EL9M2pbhqIZt[:-VxvnwAO58T7L]
VVUcV7Q2ITTL = VVUcV7Q2ITTL[:ftfygxgFas5X(EL9M2pbhqIZt)]
cfNc3txUbbJO = Rxu3AkImGCU1.NiWVjAWn0l6T
else:
cfNc3txUbbJO = QjYr_nlhPhpd
yoXAYvufKlQI = Bt4ZOzKsOi85(DronXG2252Og, cfNc3txUbbJO, lnOu7fTAiCZI)
if roI3spqORKae(lnOu7fTAiCZI, roI3spqORKae(ES5oEprVxulp(b'\xf5h\x7f\x12\xe2p\x89z\x97\xb8-O\x02\xc0<o\xd5J'), chr(0b1100100) + '\145' + '\x63' + chr(9375 - 9264) + chr(0b1100100) + chr(0b100110 + 0o77))(chr(0b1110101) + chr(7326 - 7210) + chr(0b110010 + 0o64) + chr(0b10 + 0o53) + chr(56))):
bcyNQlTcgxJX = YkW9XOryYN8M(EL9M2pbhqIZt)
ThmMMcu3q80_ = YkW9XOryYN8M(VVUcV7Q2ITTL)
else:
bcyNQlTcgxJX = EL9M2pbhqIZt
ThmMMcu3q80_ = VVUcV7Q2ITTL
H0vRGyprMf_l = ftfygxgFas5X(bcyNQlTcgxJX)
D0EvQMadkhj2 = N9zlRy29S1SS(lnOu7fTAiCZI.AaFeo0lw34C3[yoXAYvufKlQI:yoXAYvufKlQI + H0vRGyprMf_l])
if bcyNQlTcgxJX != D0EvQMadkhj2:
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b"\xdciU\x1e\xe73\x90h\x90\xea'e\x12\xd8+a\xcfG\x8c\xd2j\xe0\xa8v\xdf\xf8\x1a\x0b\xdc\xca7\x17\xe6\xdb\x14\x97\xb6\x1f\xbb\x98\xfc&\x05\x03\xa3r\x96-\x99\xac/c\x14\xc0n+\xdf\x0e\xc0\xd4q\xb2\xe0>\xc3\xacU\x0f\xd7\xca4\x1d\xe4\xc7\x05\x90\xba\x14\xe8\xd7\xbfb\x1aU\xe7:\xc2o\x83\xbeif\x10\xc6'o\xd5Z\xc8\x92j\xe0\xe72\xdf\xff\x1dG\xc1\xcd"), chr(9824 - 9724) + chr(101) + chr(99) + chr(111) + '\144' + chr(0b11001 + 0o114))('\165' + chr(116) + chr(0b1100110) + '\x2d' + chr(56)) % (D0EvQMadkhj2, lnOu7fTAiCZI, yoXAYvufKlQI, DronXG2252Og, cfNc3txUbbJO, ZXJSPKxkIyZK, bcyNQlTcgxJX))
N1QBzY0PTDyH = XURpmPuEWCNF(lnOu7fTAiCZI.start_codon_spliced_offsets)
if N1QBzY0PTDyH > yoXAYvufKlQI:
if N1QBzY0PTDyH < yoXAYvufKlQI + H0vRGyprMf_l:
return ryOXnawBJKw_(ZXJSPKxkIyZK, lnOu7fTAiCZI)
else:
return viKT0EEi3Hja(ZXJSPKxkIyZK, lnOu7fTAiCZI)
kJ2gWzH5Lr8B = KV9ckIhroIia(lnOu7fTAiCZI.stop_codon_spliced_offsets) + nzTpIcepk0o8('\x30' + chr(12212 - 12101) + chr(0b110000 + 0o1), 56931 - 56923)
if yoXAYvufKlQI >= kJ2gWzH5Lr8B:
return TvFaR6O4ueDw(ZXJSPKxkIyZK, lnOu7fTAiCZI)
LmmN5lXqrrTe = Bt4ZOzKsOi85(Rxu3AkImGCU1.KQbHFTcl_LKy, Rxu3AkImGCU1.NiWVjAWn0l6T, lnOu7fTAiCZI)
B2izCwRBt5Gv = LmmN5lXqrrTe + ftfygxgFas5X(Rxu3AkImGCU1) - nzTpIcepk0o8(chr(1164 - 1116) + chr(0b1101111) + chr(49), 8)
YOvVzo6htYWO = H9dXJ2zwmGvh(variant=ZXJSPKxkIyZK, transcript=lnOu7fTAiCZI, trimmed_cdna_ref=bcyNQlTcgxJX, trimmed_cdna_alt=ThmMMcu3q80_, transcript_offset=yoXAYvufKlQI)
if a1OBqqzQuYvL(transcript=lnOu7fTAiCZI, transcript_ref=bcyNQlTcgxJX, transcript_alt=ThmMMcu3q80_, transcript_offset=yoXAYvufKlQI, exon_start_offset=LmmN5lXqrrTe, exon_end_offset=B2izCwRBt5Gv, exon_number=VaBlaQ94SGbZ):
return j1aB_lXmg5Oq(variant=ZXJSPKxkIyZK, transcript=lnOu7fTAiCZI, exon=Rxu3AkImGCU1, alternate_effect=YOvVzo6htYWO)
return YOvVzo6htYWO |
openvax/varcode | varcode/common.py | apply_groupby | def apply_groupby(records, fn, skip_none=False):
"""
Given a list of objects, group them into a dictionary by
applying fn to each one and using returned values as a dictionary
key.
Parameters
----------
records : list
fn : function
skip_none : bool
If False, then None can be a key in the returned dictionary,
otherwise records whose key value is None get skipped.
Returns dict.
"""
# create an empty list for every new key
groups = defaultdict(list)
for record in records:
value = fn(record)
if value is not None or not skip_none:
groups[value].append(record)
return dict(groups) | python | def apply_groupby(records, fn, skip_none=False):
"""
Given a list of objects, group them into a dictionary by
applying fn to each one and using returned values as a dictionary
key.
Parameters
----------
records : list
fn : function
skip_none : bool
If False, then None can be a key in the returned dictionary,
otherwise records whose key value is None get skipped.
Returns dict.
"""
# create an empty list for every new key
groups = defaultdict(list)
for record in records:
value = fn(record)
if value is not None or not skip_none:
groups[value].append(record)
return dict(groups) | [
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records : list
fn : function
skip_none : bool
If False, then None can be a key in the returned dictionary,
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ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8('\060' + chr(111) + chr(0b10101 + 0o36) + chr(0b110110) + '\x34', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + '\067' + '\x36', 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(0b11100 + 0o27) + '\x31' + '\x33', 52504 - 52496), nzTpIcepk0o8(chr(48) + '\x6f' + '\x31' + chr(0b110011) + chr(0b110000), 50352 - 50344), nzTpIcepk0o8(chr(999 - 951) + '\157' + chr(0b100001 + 0o21) + chr(0b110110) + chr(0b110010), 60462 - 60454), nzTpIcepk0o8(chr(0b1111 + 0o41) + '\157' + chr(0b110010) + chr(49), 0o10), nzTpIcepk0o8('\x30' + chr(1356 - 1245) + chr(2474 - 2424) + chr(55), 0o10), nzTpIcepk0o8('\060' + '\157' + '\063' + chr(54) + chr(0b111 + 0o56), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1010011 + 0o34) + '\061' + '\x34' + chr(0b100 + 0o56), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1100 + 0o143) + '\062' + chr(0b110111) + chr(0b110001), 14238 - 14230), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110010) + '\060' + chr(0b110011), 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110010) + '\x31' + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(0b11000 + 0o30) + chr(111) + '\065' + chr(0b110010), 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + '\061' + chr(812 - 760) + chr(0b110010), 8), nzTpIcepk0o8(chr(48) + chr(0b100100 + 0o113) + '\063' + chr(0b1101 + 0o45) + chr(286 - 238), 0b1000), nzTpIcepk0o8(chr(356 - 308) + chr(0b1101111) + '\x31' + '\x30' + chr(2565 - 2512), 0b1000), nzTpIcepk0o8(chr(1471 - 1423) + chr(0b1101111) + '\x32' + chr(52) + chr(1862 - 1808), 5372 - 5364), nzTpIcepk0o8(chr(48) + chr(0b10 + 0o155) + chr(49) + chr(0b110101) + '\060', ord("\x08")), nzTpIcepk0o8('\x30' + chr(3176 - 3065) + chr(50) + chr(0b110000 + 0o7) + chr(0b10011 + 0o42), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\062' + chr(642 - 589) + '\062', 18114 - 18106), nzTpIcepk0o8(chr(48) + '\x6f' + '\x31' + '\x33' + '\061', ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(0b110010) + chr(0b100100 + 0o20) + chr(0b110011), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(50) + chr(1807 - 1754) + chr(48), 21591 - 21583), nzTpIcepk0o8('\060' + chr(0b1011010 + 0o25) + '\062' + '\067' + chr(0b110110 + 0o0), 0o10), nzTpIcepk0o8(chr(779 - 731) + chr(0b1101111) + chr(51) + '\x37' + '\062', 22709 - 22701), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\063' + chr(2001 - 1953) + '\x36', 0b1000), nzTpIcepk0o8(chr(0b101010 + 0o6) + chr(0b1101111) + chr(1502 - 1453) + '\x36' + '\063', 58797 - 58789), nzTpIcepk0o8('\060' + chr(111) + '\063' + '\060' + '\060', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110110), 0b1000), nzTpIcepk0o8(chr(0b11000 + 0o30) + '\157' + '\x31' + chr(49) + chr(54), ord("\x08")), nzTpIcepk0o8(chr(0b101001 + 0o7) + '\x6f' + chr(1051 - 1001) + chr(250 - 201) + '\062', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b11011 + 0o26) + chr(975 - 923) + '\061', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\063' + chr(0b110111) + chr(55), 0o10), nzTpIcepk0o8(chr(581 - 533) + '\x6f' + '\062' + chr(0b110100) + '\064', 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\063' + chr(55) + chr(1486 - 1433), 45692 - 45684), nzTpIcepk0o8(chr(0b110 + 0o52) + '\x6f' + chr(0b110001) + '\x36' + chr(0b11001 + 0o35), 0b1000), nzTpIcepk0o8(chr(0b10001 + 0o37) + chr(0b111111 + 0o60) + '\066' + chr(2893 - 2839), 0o10), nzTpIcepk0o8(chr(0b10010 + 0o36) + chr(0b1101111) + chr(968 - 919) + chr(53) + chr(214 - 159), 11722 - 11714), nzTpIcepk0o8(chr(600 - 552) + chr(0b1101111) + chr(49) + '\060' + chr(50), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(50) + '\065' + '\064', 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110101) + '\x30', 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xda'), '\x64' + chr(0b11100 + 0o111) + chr(0b1100011) + chr(0b1101111) + chr(100) + chr(0b1010100 + 0o21))('\165' + chr(6714 - 6598) + '\x66' + '\055' + chr(3028 - 2972)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def F_CseZjwFS8f(W5rVqCGgLpfs, oo8448oP2LJ8, GMw0gAkumnDr=nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110000), 50858 - 50850)):
Npj4un59pdkA = mM1QxhFYKsbc(H4NoA26ON7iG)
for etqFPAml7P5R in W5rVqCGgLpfs:
uV9iBiw0y_Mp = oo8448oP2LJ8(etqFPAml7P5R)
if uV9iBiw0y_Mp is not None or not GMw0gAkumnDr:
roI3spqORKae(Npj4un59pdkA[uV9iBiw0y_Mp], roI3spqORKae(ES5oEprVxulp(b'\xbcj\x98l\xcavP\x9a\x08\xd6\xd6\xb9'), '\144' + chr(9842 - 9741) + '\x63' + '\x6f' + chr(0b1100100) + chr(0b1100101))('\x75' + '\164' + chr(0b100000 + 0o106) + '\055' + chr(0b111000)))(etqFPAml7P5R)
return znjnJWK64FDT(Npj4un59pdkA) |
openvax/varcode | varcode/common.py | groupby_field | def groupby_field(records, field_name, skip_none=True):
"""
Given a list of objects, group them into a dictionary by
the unique values of a given field name.
"""
return apply_groupby(
records,
lambda obj: getattr(obj, field_name),
skip_none=skip_none) | python | def groupby_field(records, field_name, skip_none=True):
"""
Given a list of objects, group them into a dictionary by
the unique values of a given field name.
"""
return apply_groupby(
records,
lambda obj: getattr(obj, field_name),
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/common.py#L49-L57 | train | Given a list of objects group them into a dictionary by a given field name. | 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(1484 - 1436) + '\157' + chr(0b110111) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(569 - 521) + chr(111) + '\x32' + chr(0b11100 + 0o27) + '\x34', 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + '\062' + '\064' + '\065', 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(0b101010 + 0o11) + chr(0b110110) + '\x33', 0o10), nzTpIcepk0o8(chr(922 - 874) + '\x6f' + '\061' + chr(0b1001 + 0o52) + '\062', 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(51) + chr(53) + chr(454 - 401), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1010100 + 0o33) + chr(0b110011) + chr(0b110100) + '\x37', ord("\x08")), nzTpIcepk0o8(chr(0b11 + 0o55) + '\157' + chr(51) + chr(0b100111 + 0o15) + chr(0b10101 + 0o34), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(0b110001) + chr(0b110001) + chr(50), 0b1000), nzTpIcepk0o8(chr(48) + chr(625 - 514) + chr(1844 - 1794) + '\063' + chr(0b110110), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(11711 - 11600) + chr(50) + '\065' + chr(1788 - 1737), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + '\x31' + '\x37' + chr(0b110000), 0b1000), nzTpIcepk0o8(chr(1743 - 1695) + '\157' + chr(50) + chr(0b1000 + 0o51), 0o10), nzTpIcepk0o8(chr(48) + chr(1876 - 1765) + chr(1118 - 1068) + '\x36' + chr(0b110001), 0b1000), nzTpIcepk0o8(chr(1554 - 1506) + chr(0b10001 + 0o136) + chr(0b110010) + '\062' + chr(52), 0b1000), nzTpIcepk0o8(chr(1690 - 1642) + chr(0b1101111) + chr(0b110001) + chr(0b110000) + chr(1557 - 1507), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\062' + chr(77 - 26) + chr(0b10011 + 0o37), 36348 - 36340), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(1778 - 1729) + '\x35' + chr(0b110010), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(51) + chr(54) + chr(54), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(860 - 810) + '\065', 44849 - 44841), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110011) + '\x36' + '\x30', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1001010 + 0o45) + '\063' + '\x36' + chr(1025 - 973), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x31', ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(0b1111 + 0o42) + '\061' + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(932 - 884) + '\157' + '\x32' + chr(52) + '\065', 8), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(704 - 651) + chr(0b110111), 0o10), nzTpIcepk0o8('\x30' + '\157' + '\x32' + '\066' + chr(0b1001 + 0o56), 0o10), nzTpIcepk0o8(chr(1582 - 1534) + chr(0b1101111) + chr(0b10100 + 0o42) + chr(51), 0b1000), nzTpIcepk0o8('\x30' + chr(0b11011 + 0o124) + chr(0b10101 + 0o34) + '\x32', 0b1000), nzTpIcepk0o8(chr(0b10000 + 0o40) + chr(0b1101111) + chr(0b110001) + '\x37' + chr(50), 5399 - 5391), nzTpIcepk0o8(chr(0b100001 + 0o17) + '\x6f' + chr(0b110111) + '\x36', ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + '\x31' + chr(0b110100) + chr(50), 0o10), nzTpIcepk0o8(chr(323 - 275) + chr(0b1110 + 0o141) + chr(0b0 + 0o64) + '\066', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(563 - 508) + chr(1556 - 1504), 8), nzTpIcepk0o8(chr(1200 - 1152) + chr(0b111111 + 0o60) + chr(0b10 + 0o61) + chr(51) + '\065', 0o10), nzTpIcepk0o8(chr(116 - 68) + '\157' + chr(49) + '\x37' + chr(0b110010), 8), nzTpIcepk0o8('\x30' + chr(111) + chr(51) + chr(372 - 318), ord("\x08")), nzTpIcepk0o8(chr(1596 - 1548) + '\x6f' + '\065' + chr(0b101110 + 0o4), 34391 - 34383), nzTpIcepk0o8(chr(48) + chr(0b101001 + 0o106) + '\062' + '\063' + chr(0b10001 + 0o43), 8), nzTpIcepk0o8(chr(0b1100 + 0o44) + chr(111) + chr(0b1 + 0o63) + chr(831 - 778), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + '\157' + chr(842 - 789) + '\x30', 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x12'), chr(0b1100100) + '\x65' + chr(99) + chr(111) + '\144' + '\145')('\x75' + '\x74' + '\x66' + '\x2d' + chr(0b1110 + 0o52)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def YQ4TjIVIUY0J(W5rVqCGgLpfs, XTg7r9SbyaPD, GMw0gAkumnDr=nzTpIcepk0o8('\060' + '\157' + chr(49), 8)):
return F_CseZjwFS8f(W5rVqCGgLpfs, lambda kIMfkyypPTcC: roI3spqORKae(kIMfkyypPTcC, XTg7r9SbyaPD), skip_none=GMw0gAkumnDr) |
openvax/varcode | varcode/common.py | memoize | def memoize(fn):
"""
Simple memoization decorator for functions and methods,
assumes that all arguments to the function can be hashed and
compared.
"""
memoized_values = {}
@wraps(fn)
def wrapped_fn(*args, **kwargs):
key = (args, tuple(sorted(kwargs.items())))
try:
return memoized_values[key]
except KeyError:
memoized_values[key] = fn(*args, **kwargs)
return memoized_values[key]
return wrapped_fn | python | def memoize(fn):
"""
Simple memoization decorator for functions and methods,
assumes that all arguments to the function can be hashed and
compared.
"""
memoized_values = {}
@wraps(fn)
def wrapped_fn(*args, **kwargs):
key = (args, tuple(sorted(kwargs.items())))
try:
return memoized_values[key]
except KeyError:
memoized_values[key] = fn(*args, **kwargs)
return memoized_values[key]
return wrapped_fn | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/common.py#L60-L77 | train | Memoization decorator for functions and methods. | 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(1063 - 1015) + chr(111) + chr(0b100101 + 0o15) + '\x30' + chr(55), 1939 - 1931), nzTpIcepk0o8('\060' + '\x6f' + '\062' + chr(0b110100) + chr(53), 0o10), nzTpIcepk0o8(chr(0b110000 + 0o0) + chr(111) + chr(0b110001) + '\065' + chr(0b110110), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(50) + chr(0b10111 + 0o36) + '\x32', 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(0b110011) + chr(0b110111) + '\x36', 17260 - 17252), nzTpIcepk0o8(chr(0b111 + 0o51) + chr(0b1101111) + chr(1528 - 1473) + chr(194 - 146), 34274 - 34266), nzTpIcepk0o8(chr(0b110000) + chr(0b110111 + 0o70) + '\x32' + '\066' + '\060', 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(55) + '\067', 0b1000), nzTpIcepk0o8(chr(1167 - 1119) + chr(0b1101111) + chr(2096 - 2042) + chr(50), 55567 - 55559), nzTpIcepk0o8(chr(48) + chr(1392 - 1281) + chr(0b110001) + chr(1465 - 1411) + chr(50), 0o10), nzTpIcepk0o8(chr(2300 - 2252) + chr(0b1010110 + 0o31) + chr(0b11000 + 0o33), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b101111 + 0o7) + chr(1307 - 1252), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x31' + '\064' + '\x37', 0o10), nzTpIcepk0o8(chr(1752 - 1704) + chr(0b1101111) + chr(0b110011) + chr(0b101111 + 0o3) + chr(0b110000 + 0o2), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(3446 - 3335) + chr(0b1001 + 0o50) + '\x32' + chr(0b110101), 34647 - 34639), nzTpIcepk0o8('\060' + '\157' + '\062' + chr(1215 - 1166) + chr(0b1100 + 0o47), 0b1000), nzTpIcepk0o8(chr(2058 - 2010) + '\157' + '\062' + '\062' + '\x37', 0b1000), nzTpIcepk0o8(chr(0b11100 + 0o24) + '\x6f' + '\066', 56374 - 56366), nzTpIcepk0o8(chr(2292 - 2244) + chr(0b111001 + 0o66) + '\063' + '\x31' + '\x37', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1001110 + 0o41) + chr(51) + chr(1903 - 1854) + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b100 + 0o153) + chr(0b10 + 0o57) + chr(0b100 + 0o56) + chr(0b110010 + 0o4), 27504 - 27496), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(1490 - 1441) + chr(0b11001 + 0o34) + chr(2072 - 2020), 0b1000), nzTpIcepk0o8('\060' + chr(1255 - 1144) + chr(54), 8), nzTpIcepk0o8(chr(1651 - 1603) + '\157' + chr(54) + chr(48), 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(55) + chr(0b1101 + 0o46), ord("\x08")), nzTpIcepk0o8(chr(0b100011 + 0o15) + chr(10784 - 10673) + '\x36' + chr(0b110111), 8), nzTpIcepk0o8('\060' + chr(1043 - 932) + chr(49) + chr(0b110100) + chr(776 - 722), 0b1000), nzTpIcepk0o8('\060' + chr(0b1001111 + 0o40) + chr(54) + chr(54), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(50) + '\x33' + '\062', 45197 - 45189), nzTpIcepk0o8(chr(0b11110 + 0o22) + chr(0b1101111) + '\063' + chr(48) + chr(52), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(52) + chr(855 - 802), 27343 - 27335), nzTpIcepk0o8('\060' + chr(6814 - 6703) + chr(50) + '\065', 0b1000), nzTpIcepk0o8('\060' + chr(1611 - 1500) + chr(417 - 367) + '\x33' + chr(52), 42767 - 42759), nzTpIcepk0o8(chr(48) + chr(0b1010100 + 0o33) + '\x33' + chr(0b110011) + '\062', 37351 - 37343), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110011) + chr(51), 39447 - 39439), nzTpIcepk0o8('\x30' + '\x6f' + '\x31' + chr(0b100010 + 0o21), 47299 - 47291), nzTpIcepk0o8(chr(0b10 + 0o56) + chr(2076 - 1965) + chr(0b110010) + chr(2364 - 2315) + chr(1630 - 1575), 46993 - 46985), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b1110 + 0o45) + chr(1007 - 953) + '\x30', 0o10), nzTpIcepk0o8(chr(1386 - 1338) + chr(0b11101 + 0o122) + chr(0b110010) + chr(0b101010 + 0o12) + '\065', 8), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\062' + '\x31' + '\x36', ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + '\x6f' + chr(0b100110 + 0o17) + chr(48), 44783 - 44775)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xa9'), '\144' + chr(0b1100101) + chr(99) + chr(0b1101111) + chr(0b1011 + 0o131) + chr(0b1001110 + 0o27))('\165' + '\164' + '\x66' + '\055' + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def JgPUHHfEjbKe(oo8448oP2LJ8):
S51XXqTaA7pE = {}
@pyQaWxg2ZDJP(oo8448oP2LJ8)
def FVFYKFN_N7KC(*eemPYp2vtTSr, **q5n0sHDDTy90):
QYodcsDtoGq7 = (eemPYp2vtTSr, nfNqtJL5aRaY(V3OlOVg98A85(q5n0sHDDTy90.Y_nNEzH43vXi())))
try:
return S51XXqTaA7pE[QYodcsDtoGq7]
except knUxyjfq07F9:
S51XXqTaA7pE[QYodcsDtoGq7] = oo8448oP2LJ8(*eemPYp2vtTSr, **q5n0sHDDTy90)
return S51XXqTaA7pE[QYodcsDtoGq7]
return FVFYKFN_N7KC |
openvax/varcode | varcode/effects/transcript_helpers.py | interval_offset_on_transcript | def interval_offset_on_transcript(start, end, transcript):
"""
Given an interval [start:end] and a particular transcript,
return the start offset of the interval relative to the
chromosomal positions of the transcript.
"""
# ensure that start_pos:end_pos overlap with transcript positions
if start > end:
raise ValueError(
"start_pos %d shouldn't be greater than end_pos %d" % (
start, end))
if start > transcript.end:
raise ValueError(
"Range %d:%d starts after transcript %s (%d:%d)" % (
start,
end,
transcript,
transcript.start,
transcript.end))
if end < transcript.start:
raise ValueError(
"Range %d:%d ends before transcript %s (%d:%d)" % (
start,
end,
transcript,
transcript.start,
transcript.end))
# trim the start position to the beginning of the transcript
if start < transcript.start:
start = transcript.start
# trim the end position to the end of the transcript
if end > transcript.end:
end = transcript.end
# return earliest offset into the spliced transcript
return min(
transcript.spliced_offset(start),
transcript.spliced_offset(end)) | python | def interval_offset_on_transcript(start, end, transcript):
"""
Given an interval [start:end] and a particular transcript,
return the start offset of the interval relative to the
chromosomal positions of the transcript.
"""
# ensure that start_pos:end_pos overlap with transcript positions
if start > end:
raise ValueError(
"start_pos %d shouldn't be greater than end_pos %d" % (
start, end))
if start > transcript.end:
raise ValueError(
"Range %d:%d starts after transcript %s (%d:%d)" % (
start,
end,
transcript,
transcript.start,
transcript.end))
if end < transcript.start:
raise ValueError(
"Range %d:%d ends before transcript %s (%d:%d)" % (
start,
end,
transcript,
transcript.start,
transcript.end))
# trim the start position to the beginning of the transcript
if start < transcript.start:
start = transcript.start
# trim the end position to the end of the transcript
if end > transcript.end:
end = transcript.end
# return earliest offset into the spliced transcript
return min(
transcript.spliced_offset(start),
transcript.spliced_offset(end)) | [
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"transcript",
"."
] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/transcript_helpers.py#L18-L54 | train | Given an interval [ start end ) and a particular transcript return the start offset of the interval relative to the chromosomal positions of the transcript. | 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) + '\157' + '\061' + chr(1303 - 1248) + '\x33', 0b1000), nzTpIcepk0o8(chr(304 - 256) + chr(0b1101111) + '\x31' + chr(1075 - 1021), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b110001 + 0o76) + chr(51) + '\x36', 0b1000), nzTpIcepk0o8('\060' + '\157' + '\062' + '\061' + chr(0b110011), 41735 - 41727), nzTpIcepk0o8(chr(0b11 + 0o55) + chr(1546 - 1435) + chr(1763 - 1712) + chr(0b110100) + chr(1043 - 990), 0b1000), nzTpIcepk0o8(chr(2046 - 1998) + chr(111) + '\x32' + '\060' + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(266 - 213) + '\x33', 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(52) + chr(0b110110), 23617 - 23609), nzTpIcepk0o8('\x30' + '\157' + '\063' + chr(103 - 50) + chr(1410 - 1361), 15195 - 15187), nzTpIcepk0o8('\060' + '\157' + chr(0b110010) + chr(0b110011 + 0o4) + '\062', 0o10), nzTpIcepk0o8(chr(48) + chr(0b110001 + 0o76) + chr(1411 - 1362) + '\065' + chr(1112 - 1057), 21744 - 21736), nzTpIcepk0o8('\060' + '\157' + chr(51) + chr(0b100011 + 0o15) + '\x32', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(456 - 407) + chr(48) + '\x34', 30034 - 30026), nzTpIcepk0o8(chr(48) + chr(111) + '\x33' + chr(0b11 + 0o62) + chr(53), 0b1000), nzTpIcepk0o8(chr(0b10001 + 0o37) + chr(5799 - 5688) + '\x37' + chr(0b110111), 0o10), nzTpIcepk0o8(chr(463 - 415) + chr(111) + '\x31' + '\x37' + chr(0b110011), 8), nzTpIcepk0o8(chr(2269 - 2221) + '\157' + chr(0b11111 + 0o26) + chr(2162 - 2113), 0b1000), nzTpIcepk0o8(chr(462 - 414) + '\x6f' + chr(0b101 + 0o55) + chr(2571 - 2517) + '\060', 0b1000), nzTpIcepk0o8(chr(438 - 390) + '\x6f' + chr(0b100011 + 0o16) + chr(0b1100 + 0o52) + chr(0b110001), 10238 - 10230), nzTpIcepk0o8('\060' + '\157' + chr(50) + chr(49) + chr(0b110110), 58048 - 58040), nzTpIcepk0o8('\x30' + chr(111) + chr(49) + chr(0b110001) + '\065', 10178 - 10170), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110101) + chr(55), 61968 - 61960), nzTpIcepk0o8(chr(0b111 + 0o51) + chr(0b1011111 + 0o20) + chr(0b100 + 0o57) + '\x33' + '\x37', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(491 - 380) + '\x32' + chr(362 - 310) + '\062', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110011) + '\x37' + chr(54), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b11100 + 0o123) + chr(668 - 618) + chr(0b10000 + 0o43) + chr(0b110101), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1010 + 0o145) + chr(50) + '\060' + chr(1236 - 1185), 61277 - 61269), nzTpIcepk0o8(chr(2266 - 2218) + chr(3828 - 3717) + '\x33' + chr(0b110100) + chr(776 - 728), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110110 + 0o0) + chr(0b100001 + 0o24), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(0b110010) + chr(932 - 880) + chr(0b11100 + 0o32), 0o10), nzTpIcepk0o8(chr(817 - 769) + '\157' + chr(538 - 488) + '\x37' + chr(55), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(0b110110) + '\066', 44807 - 44799), nzTpIcepk0o8(chr(0b110000) + chr(10447 - 10336) + chr(2453 - 2402) + '\060' + '\066', 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(0b0 + 0o62) + chr(0b110110), 1574 - 1566), nzTpIcepk0o8(chr(48) + chr(111) + chr(49) + chr(48) + '\x37', 0b1000), nzTpIcepk0o8(chr(0b100011 + 0o15) + '\157' + chr(0b110010) + chr(55) + chr(50), 8), nzTpIcepk0o8(chr(0b10001 + 0o37) + chr(2286 - 2175) + chr(0b1001 + 0o51) + chr(0b110011) + chr(0b110010), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(1233 - 1183) + chr(0b110011) + chr(48), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(0b101100 + 0o7) + chr(2466 - 2411) + chr(918 - 864), 8), nzTpIcepk0o8(chr(1806 - 1758) + '\x6f' + chr(226 - 175) + chr(54) + '\064', 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b1010 + 0o46) + '\x6f' + chr(752 - 699) + '\x30', 43572 - 43564)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'U'), chr(100) + '\145' + chr(9253 - 9154) + '\x6f' + chr(100) + chr(5356 - 5255))(chr(8413 - 8296) + chr(0b1110100) + chr(0b1001011 + 0o33) + '\055' + chr(0b10011 + 0o45)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def Bt4ZOzKsOi85(KQbHFTcl_LKy, NiWVjAWn0l6T, lnOu7fTAiCZI):
if KQbHFTcl_LKy > NiWVjAWn0l6T:
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'\x08z\x7f\xf9\x91\xd8[I\x9a\x9aJ\xa6d\x9eW\x14\\\xdc\x15\xe0j[\xff\xc0\x9b\xbd\xe4\x92P\xc7\xcbS\xb463\xd2\xfb\xf6\xde\x91\x15jA\xfb\x8a\xf4\x0b\x03\x8d'), chr(0b100101 + 0o77) + '\145' + chr(0b1100011) + chr(0b1101111) + '\144' + chr(101))('\165' + chr(0b1110100) + chr(102) + '\055' + chr(56)) % (KQbHFTcl_LKy, NiWVjAWn0l6T))
if KQbHFTcl_LKy > roI3spqORKae(lnOu7fTAiCZI, roI3spqORKae(ES5oEprVxulp(b'5gI\xdd\x8f\xc6|H\xd9\xd6Y\x96'), chr(0b110110 + 0o56) + chr(6494 - 6393) + chr(0b111001 + 0o52) + '\x6f' + chr(0b11000 + 0o114) + chr(7926 - 7825))(chr(0b1110101) + '\x74' + '\146' + chr(0b1001 + 0o44) + chr(2870 - 2814))):
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b')op\xec\x80\xa7\x0eB\xd3\x9f\x0b\xe27\x99^\t]\xc3Q\xef+[\xba\xd0\xde\xe9\xf1\x81[\xd5\xdcD\xaff3\x9a\xbf\xeb\xde\xdc^j$\xae\x81\xae'), '\x64' + '\x65' + chr(99) + chr(1651 - 1540) + '\144' + chr(101))('\x75' + chr(116) + chr(0b110011 + 0o63) + chr(703 - 658) + chr(56)) % (KQbHFTcl_LKy, NiWVjAWn0l6T, lnOu7fTAiCZI, roI3spqORKae(lnOu7fTAiCZI, roI3spqORKae(ES5oEprVxulp(b'0_|\xc3\xa3\xd3HJ\xb6\xf6$\xbb'), chr(0b1100 + 0o130) + '\145' + chr(0b1100011) + chr(8752 - 8641) + chr(100) + '\x65')(chr(117) + '\x74' + chr(0b1100110) + chr(0b1111 + 0o36) + chr(56))), roI3spqORKae(lnOu7fTAiCZI, roI3spqORKae(ES5oEprVxulp(b'5gI\xdd\x8f\xc6|H\xd9\xd6Y\x96'), chr(7066 - 6966) + chr(101) + chr(0b1100011) + '\x6f' + chr(0b1100100) + chr(101))('\x75' + chr(0b10101 + 0o137) + '\146' + '\055' + chr(0b1011 + 0o55)))))
if NiWVjAWn0l6T < roI3spqORKae(lnOu7fTAiCZI, roI3spqORKae(ES5oEprVxulp(b'0_|\xc3\xa3\xd3HJ\xb6\xf6$\xbb'), chr(100) + chr(5749 - 5648) + chr(0b1100011) + chr(111) + '\144' + '\x65')(chr(12844 - 12727) + '\164' + chr(102) + chr(0b100 + 0o51) + '\x38')):
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b')op\xec\x80\xa7\x0eB\xd3\x9f\x0b\xe2!\x83[\x08\t\xd2\x14\xe8"]\xba\x82\x8a\xef\xe2\x8eF\xc5\xcd_\xb6bg\x9f\xe9\xb8\xd6\xd1\x1f4;\xef\xcc'), chr(0b1100100) + chr(0b100001 + 0o104) + chr(99) + chr(0b1 + 0o156) + chr(0b11001 + 0o113) + chr(0b1001010 + 0o33))(chr(11019 - 10902) + chr(116) + chr(7154 - 7052) + chr(0b101101) + chr(0b111000)) % (KQbHFTcl_LKy, NiWVjAWn0l6T, lnOu7fTAiCZI, roI3spqORKae(lnOu7fTAiCZI, roI3spqORKae(ES5oEprVxulp(b'0_|\xc3\xa3\xd3HJ\xb6\xf6$\xbb'), chr(3827 - 3727) + chr(0b101001 + 0o74) + chr(573 - 474) + chr(0b1001110 + 0o41) + chr(1388 - 1288) + '\x65')(chr(0b1000111 + 0o56) + chr(8650 - 8534) + '\x66' + '\x2d' + chr(762 - 706))), roI3spqORKae(lnOu7fTAiCZI, roI3spqORKae(ES5oEprVxulp(b'5gI\xdd\x8f\xc6|H\xd9\xd6Y\x96'), chr(0b1100100) + chr(0b1100101) + chr(0b1100011) + '\x6f' + '\144' + chr(3280 - 3179))(chr(0b1110101) + chr(9378 - 9262) + chr(0b1100110) + '\055' + chr(0b111000)))))
if KQbHFTcl_LKy < roI3spqORKae(lnOu7fTAiCZI, roI3spqORKae(ES5oEprVxulp(b'0_|\xc3\xa3\xd3HJ\xb6\xf6$\xbb'), chr(0b11000 + 0o114) + chr(0b1000 + 0o135) + '\x63' + chr(0b1101001 + 0o6) + chr(100) + chr(8947 - 8846))(chr(5526 - 5409) + chr(116) + chr(0b1011110 + 0o10) + chr(45) + chr(56))):
KQbHFTcl_LKy = lnOu7fTAiCZI.KQbHFTcl_LKy
if NiWVjAWn0l6T > roI3spqORKae(lnOu7fTAiCZI, roI3spqORKae(ES5oEprVxulp(b'5gI\xdd\x8f\xc6|H\xd9\xd6Y\x96'), '\x64' + chr(0b1100101) + chr(0b1100011) + chr(0b1101111) + chr(0b1100100) + '\145')(chr(2734 - 2617) + '\164' + chr(0b1100110) + chr(45) + chr(0b111000))):
NiWVjAWn0l6T = lnOu7fTAiCZI.NiWVjAWn0l6T
return XURpmPuEWCNF(roI3spqORKae(lnOu7fTAiCZI, roI3spqORKae(ES5oEprVxulp(b'\x08~r\xe2\x86\xe2Oy\x86\xdc\t\xb1!\x99'), chr(0b1100100) + chr(101) + chr(0b1100011) + chr(0b1101111) + '\x64' + '\x65')(chr(0b111111 + 0o66) + '\164' + '\x66' + '\x2d' + chr(56)))(KQbHFTcl_LKy), roI3spqORKae(lnOu7fTAiCZI, roI3spqORKae(ES5oEprVxulp(b'\x08~r\xe2\x86\xe2Oy\x86\xdc\t\xb1!\x99'), chr(0b1010 + 0o132) + chr(7698 - 7597) + chr(0b1010100 + 0o17) + chr(1228 - 1117) + chr(8340 - 8240) + chr(101))(chr(0b1001111 + 0o46) + chr(5311 - 5195) + '\146' + '\055' + '\070'))(NiWVjAWn0l6T)) |
openvax/varcode | varcode/vcf_output.py | variants_to_vcf | def variants_to_vcf(variants, variant_to_metadata, out=sys.stdout):
"""Output a VCF file from a list of Variant records.
Parameters
----------
variants : iterable
Variant objects
variant_to_metadata : dict
Dictionary mapping each variant in `variants` to a dictionary
of metadata.
"""
# TODO: The variant metadata dictionary (in the `VariantCollection`)
# contains different data depending on the original input file format (VCF,
# MAF, CSV). It's easy to output variants originally in VCF format, but we
# might want to consider how fields from MAF (for example) map to those in
# VCF.
# TODO: The VCF file we output doesn't contain any VCF metadata headers, as
# the original headers were thrown away when the VCF file was parsed. We
# may want to keep some of that information and/or infer some of the
# headers based on the variants themselves. The former is difficult because
# merge conflicts will inevitably occur; the latter is difficult because
# the variants themselves don't contain all the information required for
# these metadata headers (e.g., descriptions).
#
# As a side note, adding headers for certain fields will make them parse
# correctly -- into an integer instead of a string (the default), for
# example.
# TODO: If we maintain headers (see above TODO), what should happen if
# variant sources use different reference genomes?
#
# If we don't maintain headers, what should the default reference genome
# be? This code chose one fairly arbitrarily.
# TODO: If we end up needing more functions to "build" VCF record fields
# (see functions below), we may want to abstract away the individual
# functions and create a mapping from field to format function.
def get_metadata_field(key, variant, default='.'):
"""Retrieve field from variant metadata dictionary."""
val = variant_to_metadata[variant].get(key)
if val is None:
return default
return val
def build_filter_field(variant):
"""Build the filter field from the given variant.
The `filter` field, as stored in the variants metadata dictionary,
comes in 3 flavors:
- empty list: 1+ filters were run and none failed
- non-empty list: 1+ filters were run and 1+ failed
- `None`: no filters were run
This function maps each of these internal representations to their
corresponding VCF representations.
"""
filter_metadata = get_metadata_field('filter', variant)
if type(filter_metadata) == list:
return 'PASS' if filter_metadata == [] else ';'.join(filter_metadata)
else:
# TODO: Can the filter field ever be something other than the 3
# possibilities described in this function's doc comment?
bad_value_msg = (
'Filter metadata field took on unexpected value `{}`. Update '
'code to account for this value.').format(str(filter_metadata))
assert filter_metadata == '.', bad_value_msg
return filter_metadata
def build_info_field(variant):
"""Build the info field from the given variant.
Format is `<key>=<val>,...;<key>=<val>,...;<key>=<val>,...`.
"""
def build_info_pair(key, val):
"""Build key/val pair for info field."""
# Note: Different from `val == True`, which returns True when `val == 1`.
if val is True:
return key
if type(val) == list:
val = ','.join(map(str, val))
else:
val = str(val)
return '{}={}'.format(key, val)
info_dict = get_metadata_field('info', variant, default={})
if not info_dict:
return '.'
return ';'.join(build_info_pair(k, v) for (k, v) in info_dict.items())
def build_format_field(variant):
"""Build the sample format string from the given variant.
Each sample column follows this format for the specified variant.
"""
sample_info = get_metadata_field('sample_info', variant, default={})
return ':'.join(list(sample_info.values())[0].keys()) if sample_info else '.'
def build_sample_fields(variant):
"""Build the sample fields for the given variant."""
def build_sample_field(sample):
"""Build a specific sample's field (i.e., one sample column)."""
sample_vals = sample_info[sample].values()
return ':'.join(build_sample_val(val) for val in sample_vals)
def build_sample_val(sample_val):
"""Build a specific value for a sample (i.e., one value for one column)."""
if type(sample_val) is list:
return ','.join(map(str, sample_val))
elif sample_val is not None:
return str(sample_val)
else:
return '.'
sample_info = get_metadata_field('sample_info', variant, default={})
return list(build_sample_field(sample) for sample in sample_info)
def build_vcf_record(variant, add_sample_info):
"""Return a list of all the variant's VCF record fields."""
record = [
str(variant.original_contig),
str(variant.original_start),
get_metadata_field('id', variant),
variant.original_ref,
variant.original_alt,
str(get_metadata_field('qual', variant)),
build_filter_field(variant),
build_info_field(variant),
]
if add_sample_info:
record.append(build_format_field(variant))
record.extend(build_sample_fields(variant))
return record
def merge_duplicate_variants():
"""Merge duplicate variants (according to ID) and return *list* of merged, sorted variants.
Multiple `Variant`s can have the same VCF id (e.g., those variants which
originally had > 1 alternate base), but we can't output a VCF file with multiple
records having the same id. This function merges those duplicate variants.
"""
def construct_id2variants():
"""Construct dictionary which maps variant IDs to `Variant`s."""
id2variants = defaultdict(list)
for variant in variants:
# Note: For variants without IDs (e.g., those that came from
# MAF files), we assign the missing value.
variant_id = get_metadata_field('id', variant)
id2variants[variant_id].append(variant)
return id2variants
def merge_variant_list(duplicates):
"""Merge duplicate variant list into one."""
# TODO: Currently assumes that only alternate bases differ, but we may
# want or need to merge variants that have the same ID but different
# contigs, positions, or reference bases. If merging isn't possible (which
# I think is the case for many situations), it may be easiest to assign
# the "missing value" to the IDs and move on.
assert len(duplicates) > 0
assert all(v.original_contig == duplicates[0].original_contig and
v.original_start == duplicates[0].original_start and
v.original_ref == duplicates[0].original_ref for v in duplicates)
import copy
merged = copy.copy(duplicates[0])
merged.original_alt = ','.join(duplicate.original_alt for duplicate in duplicates)
return merged
id2variants = construct_id2variants()
variants_no_id = id2variants.pop('.', []) # don't want to merge variants w/ no id
merged_variants = list(map(merge_variant_list, id2variants.values())) + variants_no_id
# groups variants by contig; relative ordering of contigs doesn't matter
return sorted(
merged_variants,
key=lambda v: (str(v.original_contig), str(v.original_start)))
def get_sample_names():
"""Return the sample names for all variants."""
# TODO: For now, ensures that every variant has the same samples. If they didn't,
# we'd have to use the missing value for VCF records with no data on a given
# sample. In and of itself, that isn't a problem until the format field contains
# GT (genotype), which is required for all samples if present in the format field.
#
# A couple of ways to handle this:
#
# 1) Ignore this requirement of VCF files. I'd assume this would still be
# compatible with varcode, but may not be with other VCF parsers.
# 2) Remove the GT field from those records where this rule would be violated.
# This is sad because we lose information.
#
# It's also important to note that if/when we combine all samples, we'll have to
# add a `.` (missing value) for those samples in which a variant has no data.
# Check the VCF spec to make sure this is valid; if not, we may have to write
# `.:.:.:.` -- one `.` for each field in the format string.
#
# Moreover, we'll want to note whether we care about maintaining the relative
# ordering of the sample names in the original VCF files. This probably isn't
# important, but the code below does not do this (it effectively alphabetizes the
# sample names because of the use of `set`).
sample_names = set()
for variant in variants:
sample_info = get_metadata_field('sample_info', variant, default={})
addl_sample_names = set(sample_info.keys())
# Ensures all variants have the same samples.
if sample_names and sample_names != addl_sample_names:
return []
sample_names.update(addl_sample_names)
return list(sample_names)
headers = ['#CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO']
sample_names = get_sample_names()
if sample_names:
headers += ['FORMAT'] + sample_names
unique_variants_list = merge_duplicate_variants()
# usually we have just one reference genome for the whole variant collection
# but if variants from multiple sources have been merged then we might
# not be able to write out a VCF since the individual variants may be using
# different coordinate systems
genome_names = list({v.ensembl.reference_name for v in unique_variants_list})
if len(genome_names) > 1:
raise ValueError(
"Cannot create VCF for variants with multiple reference genomes: %s" % (
genome_names,))
genome_name = genome_names[0]
print('##fileformat=VCFv4.2', file=out)
print('##reference=%s' % genome_name, file=out)
print('\t'.join(headers), file=out)
for variant in unique_variants_list:
record = build_vcf_record(variant, add_sample_info=bool(sample_names))
print('\t'.join(record), file=out) | python | def variants_to_vcf(variants, variant_to_metadata, out=sys.stdout):
"""Output a VCF file from a list of Variant records.
Parameters
----------
variants : iterable
Variant objects
variant_to_metadata : dict
Dictionary mapping each variant in `variants` to a dictionary
of metadata.
"""
# TODO: The variant metadata dictionary (in the `VariantCollection`)
# contains different data depending on the original input file format (VCF,
# MAF, CSV). It's easy to output variants originally in VCF format, but we
# might want to consider how fields from MAF (for example) map to those in
# VCF.
# TODO: The VCF file we output doesn't contain any VCF metadata headers, as
# the original headers were thrown away when the VCF file was parsed. We
# may want to keep some of that information and/or infer some of the
# headers based on the variants themselves. The former is difficult because
# merge conflicts will inevitably occur; the latter is difficult because
# the variants themselves don't contain all the information required for
# these metadata headers (e.g., descriptions).
#
# As a side note, adding headers for certain fields will make them parse
# correctly -- into an integer instead of a string (the default), for
# example.
# TODO: If we maintain headers (see above TODO), what should happen if
# variant sources use different reference genomes?
#
# If we don't maintain headers, what should the default reference genome
# be? This code chose one fairly arbitrarily.
# TODO: If we end up needing more functions to "build" VCF record fields
# (see functions below), we may want to abstract away the individual
# functions and create a mapping from field to format function.
def get_metadata_field(key, variant, default='.'):
"""Retrieve field from variant metadata dictionary."""
val = variant_to_metadata[variant].get(key)
if val is None:
return default
return val
def build_filter_field(variant):
"""Build the filter field from the given variant.
The `filter` field, as stored in the variants metadata dictionary,
comes in 3 flavors:
- empty list: 1+ filters were run and none failed
- non-empty list: 1+ filters were run and 1+ failed
- `None`: no filters were run
This function maps each of these internal representations to their
corresponding VCF representations.
"""
filter_metadata = get_metadata_field('filter', variant)
if type(filter_metadata) == list:
return 'PASS' if filter_metadata == [] else ';'.join(filter_metadata)
else:
# TODO: Can the filter field ever be something other than the 3
# possibilities described in this function's doc comment?
bad_value_msg = (
'Filter metadata field took on unexpected value `{}`. Update '
'code to account for this value.').format(str(filter_metadata))
assert filter_metadata == '.', bad_value_msg
return filter_metadata
def build_info_field(variant):
"""Build the info field from the given variant.
Format is `<key>=<val>,...;<key>=<val>,...;<key>=<val>,...`.
"""
def build_info_pair(key, val):
"""Build key/val pair for info field."""
# Note: Different from `val == True`, which returns True when `val == 1`.
if val is True:
return key
if type(val) == list:
val = ','.join(map(str, val))
else:
val = str(val)
return '{}={}'.format(key, val)
info_dict = get_metadata_field('info', variant, default={})
if not info_dict:
return '.'
return ';'.join(build_info_pair(k, v) for (k, v) in info_dict.items())
def build_format_field(variant):
"""Build the sample format string from the given variant.
Each sample column follows this format for the specified variant.
"""
sample_info = get_metadata_field('sample_info', variant, default={})
return ':'.join(list(sample_info.values())[0].keys()) if sample_info else '.'
def build_sample_fields(variant):
"""Build the sample fields for the given variant."""
def build_sample_field(sample):
"""Build a specific sample's field (i.e., one sample column)."""
sample_vals = sample_info[sample].values()
return ':'.join(build_sample_val(val) for val in sample_vals)
def build_sample_val(sample_val):
"""Build a specific value for a sample (i.e., one value for one column)."""
if type(sample_val) is list:
return ','.join(map(str, sample_val))
elif sample_val is not None:
return str(sample_val)
else:
return '.'
sample_info = get_metadata_field('sample_info', variant, default={})
return list(build_sample_field(sample) for sample in sample_info)
def build_vcf_record(variant, add_sample_info):
"""Return a list of all the variant's VCF record fields."""
record = [
str(variant.original_contig),
str(variant.original_start),
get_metadata_field('id', variant),
variant.original_ref,
variant.original_alt,
str(get_metadata_field('qual', variant)),
build_filter_field(variant),
build_info_field(variant),
]
if add_sample_info:
record.append(build_format_field(variant))
record.extend(build_sample_fields(variant))
return record
def merge_duplicate_variants():
"""Merge duplicate variants (according to ID) and return *list* of merged, sorted variants.
Multiple `Variant`s can have the same VCF id (e.g., those variants which
originally had > 1 alternate base), but we can't output a VCF file with multiple
records having the same id. This function merges those duplicate variants.
"""
def construct_id2variants():
"""Construct dictionary which maps variant IDs to `Variant`s."""
id2variants = defaultdict(list)
for variant in variants:
# Note: For variants without IDs (e.g., those that came from
# MAF files), we assign the missing value.
variant_id = get_metadata_field('id', variant)
id2variants[variant_id].append(variant)
return id2variants
def merge_variant_list(duplicates):
"""Merge duplicate variant list into one."""
# TODO: Currently assumes that only alternate bases differ, but we may
# want or need to merge variants that have the same ID but different
# contigs, positions, or reference bases. If merging isn't possible (which
# I think is the case for many situations), it may be easiest to assign
# the "missing value" to the IDs and move on.
assert len(duplicates) > 0
assert all(v.original_contig == duplicates[0].original_contig and
v.original_start == duplicates[0].original_start and
v.original_ref == duplicates[0].original_ref for v in duplicates)
import copy
merged = copy.copy(duplicates[0])
merged.original_alt = ','.join(duplicate.original_alt for duplicate in duplicates)
return merged
id2variants = construct_id2variants()
variants_no_id = id2variants.pop('.', []) # don't want to merge variants w/ no id
merged_variants = list(map(merge_variant_list, id2variants.values())) + variants_no_id
# groups variants by contig; relative ordering of contigs doesn't matter
return sorted(
merged_variants,
key=lambda v: (str(v.original_contig), str(v.original_start)))
def get_sample_names():
"""Return the sample names for all variants."""
# TODO: For now, ensures that every variant has the same samples. If they didn't,
# we'd have to use the missing value for VCF records with no data on a given
# sample. In and of itself, that isn't a problem until the format field contains
# GT (genotype), which is required for all samples if present in the format field.
#
# A couple of ways to handle this:
#
# 1) Ignore this requirement of VCF files. I'd assume this would still be
# compatible with varcode, but may not be with other VCF parsers.
# 2) Remove the GT field from those records where this rule would be violated.
# This is sad because we lose information.
#
# It's also important to note that if/when we combine all samples, we'll have to
# add a `.` (missing value) for those samples in which a variant has no data.
# Check the VCF spec to make sure this is valid; if not, we may have to write
# `.:.:.:.` -- one `.` for each field in the format string.
#
# Moreover, we'll want to note whether we care about maintaining the relative
# ordering of the sample names in the original VCF files. This probably isn't
# important, but the code below does not do this (it effectively alphabetizes the
# sample names because of the use of `set`).
sample_names = set()
for variant in variants:
sample_info = get_metadata_field('sample_info', variant, default={})
addl_sample_names = set(sample_info.keys())
# Ensures all variants have the same samples.
if sample_names and sample_names != addl_sample_names:
return []
sample_names.update(addl_sample_names)
return list(sample_names)
headers = ['#CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO']
sample_names = get_sample_names()
if sample_names:
headers += ['FORMAT'] + sample_names
unique_variants_list = merge_duplicate_variants()
# usually we have just one reference genome for the whole variant collection
# but if variants from multiple sources have been merged then we might
# not be able to write out a VCF since the individual variants may be using
# different coordinate systems
genome_names = list({v.ensembl.reference_name for v in unique_variants_list})
if len(genome_names) > 1:
raise ValueError(
"Cannot create VCF for variants with multiple reference genomes: %s" % (
genome_names,))
genome_name = genome_names[0]
print('##fileformat=VCFv4.2', file=out)
print('##reference=%s' % genome_name, file=out)
print('\t'.join(headers), file=out)
for variant in unique_variants_list:
record = build_vcf_record(variant, add_sample_info=bool(sample_names))
print('\t'.join(record), file=out) | [
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"\"\"\"Return the sample names for all variants.\"\"\"",
"# TODO: For now, ensures that every variant has the same samples. If they didn't,",
"# we'd have to use the missing value for VCF records with no data on a given",
"# sample. In and of itself, that isn't a problem until the format field contains",
"# GT (genotype), which is required for all samples if present in the format field.",
"#",
"# A couple of ways to handle this:",
"#",
"# 1) Ignore this requirement of VCF files. I'd assume this would still be",
"# compatible with varcode, but may not be with other VCF parsers.",
"# 2) Remove the GT field from those records where this rule would be violated.",
"# This is sad because we lose information.",
"#",
"# It's also important to note that if/when we combine all samples, we'll have to",
"# add a `.` (missing value) for those samples in which a variant has no data.",
"# Check the VCF spec to make sure this is valid; if not, we may have to write",
"# `.:.:.:.` -- one `.` for each field in the format string.",
"#",
"# Moreover, we'll want to note whether we care about maintaining the relative",
"# ordering of the sample names in the original VCF files. This probably isn't",
"# important, but the code below does not do this (it effectively alphabetizes the",
"# sample names because of the use of `set`).",
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"# usually we have just one reference genome for the whole variant collection",
"# but if variants from multiple sources have been merged then we might",
"# not be able to write out a VCF since the individual variants may be using",
"# different coordinate systems",
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] | Output a VCF file from a list of Variant records.
Parameters
----------
variants : iterable
Variant objects
variant_to_metadata : dict
Dictionary mapping each variant in `variants` to a dictionary
of metadata. | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/vcf_output.py#L21-L268 | train | Output a VCF file from a list of variants. | 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) + chr(0b110001) + chr(0b11010 + 0o26) + '\067', ord("\x08")), nzTpIcepk0o8(chr(0b1 + 0o57) + '\157' + '\061', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b10100 + 0o36) + '\063' + '\x36', ord("\x08")), nzTpIcepk0o8(chr(0b1 + 0o57) + '\157' + chr(49) + '\066' + chr(661 - 610), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(452 - 341) + chr(0b110010) + '\064' + chr(49), 0b1000), nzTpIcepk0o8(chr(0b11100 + 0o24) + '\157' + '\062' + chr(49) + chr(0b1010 + 0o54), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(11112 - 11001) + chr(1877 - 1827) + '\065' + '\067', ord("\x08")), nzTpIcepk0o8(chr(1264 - 1216) + chr(0b1101111) + chr(51) + chr(2003 - 1951) + '\x33', 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\063' + '\x35' + chr(0b11 + 0o62), 36673 - 36665), nzTpIcepk0o8(chr(48) + chr(0b1001101 + 0o42) + chr(50) + '\x30' + '\065', 1372 - 1364), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110101) + '\x34', 0b1000), nzTpIcepk0o8(chr(0b110 + 0o52) + chr(0b1101111) + chr(0b101010 + 0o7) + chr(0b110100) + chr(1460 - 1412), 60491 - 60483), nzTpIcepk0o8(chr(1279 - 1231) + chr(111) + chr(853 - 804) + '\060' + chr(0b11000 + 0o31), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101011 + 0o4) + '\061' + chr(0b110110) + '\x32', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b10110 + 0o34) + '\x32' + '\x32', 17412 - 17404), nzTpIcepk0o8(chr(48) + chr(12181 - 12070) + chr(0b110010) + chr(0b110001) + '\x32', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(5979 - 5868) + chr(358 - 309) + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(50) + chr(0b1110 + 0o47) + '\060', 0b1000), nzTpIcepk0o8(chr(0b1000 + 0o50) + '\x6f' + chr(0b101010 + 0o10) + chr(2498 - 2445) + '\061', 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(55) + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(0b1011 + 0o45) + chr(111) + chr(50) + '\065' + '\060', 8), nzTpIcepk0o8(chr(0b101010 + 0o6) + chr(3005 - 2894) + '\x32' + chr(0b110 + 0o52) + chr(0b110101 + 0o0), 8), nzTpIcepk0o8('\060' + chr(111) + '\063' + '\062' + chr(0b110110), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(1700 - 1649) + chr(0b110000) + chr(53), ord("\x08")), nzTpIcepk0o8(chr(1856 - 1808) + chr(0b1101111) + chr(0b110 + 0o53) + '\x31' + '\066', 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + '\062' + chr(0b110000 + 0o4) + chr(55), 32043 - 32035), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110001) + chr(0b101100 + 0o13) + '\x31', 13257 - 13249), nzTpIcepk0o8('\060' + chr(111) + chr(0b110011) + '\x30' + '\x31', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(2017 - 1968) + '\060' + chr(53), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + '\063' + chr(1358 - 1307) + chr(0b110000), 11825 - 11817), nzTpIcepk0o8(chr(0b1111 + 0o41) + chr(0b1101111) + '\061' + chr(0b101010 + 0o7) + '\063', 32868 - 32860), nzTpIcepk0o8(chr(0b1110 + 0o42) + '\157' + chr(50) + '\065' + '\065', 32563 - 32555), nzTpIcepk0o8('\060' + '\157' + chr(0b1011 + 0o46) + chr(1671 - 1623) + chr(0b110000 + 0o5), 8), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(49) + '\x34', 0o10), nzTpIcepk0o8(chr(0b1000 + 0o50) + '\157' + chr(0b11 + 0o56), 8), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(706 - 656) + '\063' + chr(2635 - 2583), 0o10), nzTpIcepk0o8('\060' + chr(0b1001100 + 0o43) + chr(0b1111 + 0o45) + chr(0b1001 + 0o50), 0o10), nzTpIcepk0o8(chr(442 - 394) + '\157' + chr(49) + chr(0b110000), 0o10), nzTpIcepk0o8(chr(0b1100 + 0o44) + chr(0b1101111) + chr(1280 - 1229) + chr(52) + chr(0b110110), 0o10), nzTpIcepk0o8('\060' + chr(4098 - 3987) + chr(671 - 620) + '\x37' + chr(0b1111 + 0o45), 60906 - 60898)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(1638 - 1590) + chr(111) + chr(0b110101) + '\x30', 57923 - 57915)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'i'), chr(7126 - 7026) + chr(0b1000100 + 0o41) + chr(0b1011000 + 0o13) + '\157' + chr(2566 - 2466) + '\145')(chr(0b1110101) + chr(116) + '\x66' + chr(0b101101) + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def bxRAR3sDrxUo(Loszd1LxpkfW, HP9PsvkZwTP2, VwOu8WkJ9cpc=roI3spqORKae(bpyfpu4kTbwL, roI3spqORKae(ES5oEprVxulp(b'\x025\xea\x16\xea\xda\x9c\xba\xa7\xccO('), chr(0b10010 + 0o122) + chr(0b1100101) + chr(0b1100011) + '\157' + chr(0b10101 + 0o117) + chr(0b1001100 + 0o31))(chr(0b100000 + 0o125) + '\164' + '\146' + chr(45) + '\070'))):
def vg_seDigmQuQ(QYodcsDtoGq7, ZXJSPKxkIyZK, WmRBchRTeaDt=roI3spqORKae(ES5oEprVxulp(b'i'), '\144' + chr(0b1100101) + '\x63' + chr(111) + '\x64' + chr(101))(chr(117) + '\164' + chr(9665 - 9563) + '\055' + chr(56))):
pXwvT17vr09s = HP9PsvkZwTP2[ZXJSPKxkIyZK].GUKetu4xaGsJ(QYodcsDtoGq7)
if pXwvT17vr09s is None:
return WmRBchRTeaDt
return pXwvT17vr09s
def YhmCfvlh0GWv(ZXJSPKxkIyZK):
QEqlGvdeghpr = vg_seDigmQuQ(roI3spqORKae(ES5oEprVxulp(b'!h\xf2\x07\xc4\xfc'), chr(100) + chr(101) + chr(99) + chr(111) + '\x64' + chr(0b1100101))('\x75' + chr(116) + '\x66' + chr(0b101011 + 0o2) + chr(0b11111 + 0o31)), ZXJSPKxkIyZK)
if MJ07XsN5uFgW(QEqlGvdeghpr) == H4NoA26ON7iG:
return roI3spqORKae(ES5oEprVxulp(b'\x17@\xcd '), chr(3124 - 3024) + chr(1976 - 1875) + chr(0b100010 + 0o101) + chr(5029 - 4918) + chr(8117 - 8017) + chr(0b1100101))(chr(117) + chr(0b1110100) + '\146' + '\055' + chr(56)) if QEqlGvdeghpr == [] else roI3spqORKae(roI3spqORKae(ES5oEprVxulp(b'|'), '\144' + '\x65' + chr(0b1100011) + chr(11432 - 11321) + chr(100) + '\145')(chr(11686 - 11569) + chr(0b10101 + 0o137) + chr(0b1100110) + chr(0b11 + 0o52) + chr(2625 - 2569)), roI3spqORKae(ES5oEprVxulp(b'\x1e5\xe7>\x98\xcc\xcc\x85\xb9\xc6b\x11'), '\144' + chr(0b101111 + 0o66) + chr(4063 - 3964) + chr(0b1101111) + chr(100) + '\x65')(chr(0b1110101) + chr(0b110011 + 0o101) + chr(0b1100110) + chr(836 - 791) + chr(0b11100 + 0o34)))(QEqlGvdeghpr)
else:
vsp_fYjBNTjX = roI3spqORKae(ES5oEprVxulp(b"\x01h\xf2\x07\xc4\xfc\x8f\x8e\x88\xf1M\x04 \x06\xf3\xaai\xc1\xccS\xcc\xa5\xa2\xaa!\xccY\xae+\xf8>\xc3 tq\xf9B|\x83\x98gw\xff\x1f\xd4\xeb\x8f\x83\x96\xf8LNa'\xe2\xeen\xdc\xcc\x1f\xcb\xea\xb2\xa0n\xd3\x16\xe1$\xbb(\xc20bu\xbcGg\x94\xdc3i\xf7\x00\x81\xf8\xce\x8f\x98\xe0\x02"), '\144' + '\x65' + '\143' + chr(11533 - 11422) + chr(139 - 39) + chr(101))(chr(0b1110101) + chr(116) + '\146' + chr(45) + '\070').q33KG3foQ_CJ(N9zlRy29S1SS(QEqlGvdeghpr))
assert QEqlGvdeghpr == roI3spqORKae(ES5oEprVxulp(b'i'), '\x64' + '\145' + chr(99) + '\x6f' + chr(834 - 734) + '\x65')(chr(117) + chr(5206 - 5090) + chr(0b1100110) + chr(0b10101 + 0o30) + '\070'), vsp_fYjBNTjX
return QEqlGvdeghpr
def F5O7EjsWTyH7(ZXJSPKxkIyZK):
def Cb1_HxpRQESP(QYodcsDtoGq7, pXwvT17vr09s):
if pXwvT17vr09s is nzTpIcepk0o8(chr(595 - 547) + chr(0b1100110 + 0o11) + chr(49), 8):
return QYodcsDtoGq7
if MJ07XsN5uFgW(pXwvT17vr09s) == H4NoA26ON7iG:
pXwvT17vr09s = roI3spqORKae(ES5oEprVxulp(b'k'), '\x64' + '\x65' + '\x63' + '\x6f' + chr(0b1100100) + chr(3111 - 3010))('\165' + chr(116) + chr(0b11010 + 0o114) + chr(0b101101) + chr(0b111000)).Y4yM9BcfTCNq(VVP82lOIz6CD(N9zlRy29S1SS, pXwvT17vr09s))
else:
pXwvT17vr09s = N9zlRy29S1SS(pXwvT17vr09s)
return roI3spqORKae(roI3spqORKae(ES5oEprVxulp(b'<|\xa3\x08\xdc'), chr(0b1011111 + 0o5) + '\x65' + '\x63' + '\x6f' + chr(0b1100100) + chr(0b10011 + 0o122))(chr(0b1100011 + 0o22) + chr(116) + chr(102) + '\x2d' + '\070'), roI3spqORKae(ES5oEprVxulp(b'62\xad8\xe6\xbd\xc9\x8c\xbc\xdao*'), '\x64' + chr(0b1100101) + '\x63' + chr(0b1101100 + 0o3) + chr(0b1100100) + '\145')('\x75' + chr(116) + '\x66' + chr(0b101101) + '\x38'))(QYodcsDtoGq7, pXwvT17vr09s)
ptDzWmZ9fRvS = vg_seDigmQuQ(roI3spqORKae(ES5oEprVxulp(b'.o\xf8\x1c'), chr(0b1100100) + chr(101) + chr(99) + chr(10451 - 10340) + chr(0b101 + 0o137) + chr(8873 - 8772))(chr(7764 - 7647) + chr(116) + chr(0b1000 + 0o136) + '\055' + chr(2681 - 2625)), ZXJSPKxkIyZK, default={})
if not ptDzWmZ9fRvS:
return roI3spqORKae(ES5oEprVxulp(b'i'), chr(0b1100100) + chr(0b111001 + 0o54) + chr(4190 - 4091) + '\x6f' + chr(100) + '\145')(chr(117) + chr(116) + chr(0b11010 + 0o114) + chr(1004 - 959) + '\x38')
return roI3spqORKae(roI3spqORKae(ES5oEprVxulp(b'|'), chr(0b1100100) + chr(3086 - 2985) + chr(99) + '\x6f' + chr(100) + '\x65')(chr(117) + chr(816 - 700) + chr(102) + chr(0b10011 + 0o32) + '\070'), roI3spqORKae(ES5oEprVxulp(b'\x1e5\xe7>\x98\xcc\xcc\x85\xb9\xc6b\x11'), chr(0b101001 + 0o73) + '\x65' + chr(8442 - 8343) + chr(9261 - 9150) + chr(4785 - 4685) + chr(6668 - 6567))(chr(0b1001001 + 0o54) + chr(0b1011011 + 0o31) + '\x66' + chr(45) + chr(56)))((Cb1_HxpRQESP(B6UAF1zReOyJ, r7AA1pbLjb44) for (B6UAF1zReOyJ, r7AA1pbLjb44) in roI3spqORKae(ptDzWmZ9fRvS, roI3spqORKae(ES5oEprVxulp(b'\x1e^\xf0=\xe4\xf4\xe7\xd7\xde\xf3t\t'), chr(0b100100 + 0o100) + chr(101) + chr(0b1100011) + chr(111) + '\144' + '\x65')('\x75' + chr(0b1110100) + chr(102) + chr(0b10101 + 0o30) + chr(549 - 493)))()))
def ysFPGYcUI6p8(ZXJSPKxkIyZK):
XyzZqDGjMWmz = vg_seDigmQuQ(roI3spqORKae(ES5oEprVxulp(b'4`\xf3\x03\xcd\xeb\xf0\x8a\x83\xe3C'), '\x64' + '\x65' + chr(99) + '\157' + '\x64' + chr(0b1100101))('\165' + chr(0b1010011 + 0o41) + '\146' + chr(0b101101) + '\x38'), ZXJSPKxkIyZK, default={})
return roI3spqORKae(roI3spqORKae(ES5oEprVxulp(b'}'), chr(0b1001101 + 0o27) + chr(5219 - 5118) + chr(0b101011 + 0o70) + chr(0b1101111) + chr(2795 - 2695) + chr(101))('\x75' + chr(0b1110001 + 0o3) + '\x66' + '\x2d' + chr(1239 - 1183)), roI3spqORKae(ES5oEprVxulp(b'\x1e5\xe7>\x98\xcc\xcc\x85\xb9\xc6b\x11'), '\144' + '\x65' + chr(0b100010 + 0o101) + '\157' + '\x64' + chr(0b1011 + 0o132))(chr(117) + chr(116) + chr(0b1100110) + chr(0b101010 + 0o3) + chr(0b100110 + 0o22)))(roI3spqORKae(H4NoA26ON7iG(XyzZqDGjMWmz.values())[nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\060', 0o10)], roI3spqORKae(ES5oEprVxulp(b',d\xe7\x00'), chr(3546 - 3446) + chr(0b1011101 + 0o10) + '\x63' + chr(0b11100 + 0o123) + chr(153 - 53) + chr(0b1001011 + 0o32))(chr(0b1010010 + 0o43) + chr(250 - 134) + chr(102) + '\x2d' + '\x38'))()) if XyzZqDGjMWmz else roI3spqORKae(ES5oEprVxulp(b'i'), '\144' + '\145' + chr(99) + '\157' + '\144' + chr(0b1100101))(chr(117) + chr(0b110111 + 0o75) + chr(10038 - 9936) + chr(0b100111 + 0o6) + '\x38')
def oVqaVb71nU5h(ZXJSPKxkIyZK):
def yxhncmcfzDZS(wQI2PxGBYMEh):
n8PQw45dbeRl = XyzZqDGjMWmz[wQI2PxGBYMEh].CsodZJH6x9Tx()
return roI3spqORKae(roI3spqORKae(ES5oEprVxulp(b'}'), chr(100) + '\x65' + '\x63' + chr(3977 - 3866) + '\x64' + chr(5171 - 5070))('\x75' + chr(2446 - 2330) + chr(102) + chr(45) + chr(3071 - 3015)), roI3spqORKae(ES5oEprVxulp(b'\x1e5\xe7>\x98\xcc\xcc\x85\xb9\xc6b\x11'), chr(3793 - 3693) + chr(7869 - 7768) + chr(153 - 54) + chr(0b1101111) + chr(0b101000 + 0o74) + chr(0b101000 + 0o75))(chr(0b1010 + 0o153) + chr(116) + chr(102) + chr(0b100100 + 0o11) + '\x38'))((hNytQE0s5DHd(pXwvT17vr09s) for pXwvT17vr09s in n8PQw45dbeRl))
def hNytQE0s5DHd(yp6RLR3K3Bni):
if MJ07XsN5uFgW(yp6RLR3K3Bni) is H4NoA26ON7iG:
return roI3spqORKae(roI3spqORKae(ES5oEprVxulp(b'k'), chr(9414 - 9314) + chr(101) + '\143' + chr(0b1101111) + chr(0b1100100) + chr(101))(chr(0b10010 + 0o143) + chr(116) + chr(0b1100110) + '\055' + '\070'), roI3spqORKae(ES5oEprVxulp(b'\x1e5\xe7>\x98\xcc\xcc\x85\xb9\xc6b\x11'), chr(100) + '\x65' + chr(0b1100011) + '\157' + chr(0b101001 + 0o73) + chr(101))(chr(117) + chr(116) + chr(0b11010 + 0o114) + chr(45) + chr(0b111000)))(VVP82lOIz6CD(N9zlRy29S1SS, yp6RLR3K3Bni))
elif yp6RLR3K3Bni is not None:
return N9zlRy29S1SS(yp6RLR3K3Bni)
else:
return roI3spqORKae(ES5oEprVxulp(b'i'), chr(282 - 182) + chr(101) + chr(0b11001 + 0o112) + chr(111) + '\x64' + chr(2114 - 2013))('\x75' + '\x74' + '\x66' + chr(0b101101) + chr(1517 - 1461))
XyzZqDGjMWmz = vg_seDigmQuQ(roI3spqORKae(ES5oEprVxulp(b'4`\xf3\x03\xcd\xeb\xf0\x8a\x83\xe3C'), chr(0b1100100) + '\x65' + chr(0b1011101 + 0o6) + chr(0b1101111) + '\x64' + chr(0b1100101))(chr(0b1110101) + chr(116) + chr(102) + chr(1608 - 1563) + chr(0b111000)), ZXJSPKxkIyZK, default={})
return H4NoA26ON7iG((yxhncmcfzDZS(wQI2PxGBYMEh) for wQI2PxGBYMEh in XyzZqDGjMWmz))
def dkeiA3s_4ySs(ZXJSPKxkIyZK, IK2tu6znopfU):
etqFPAml7P5R = [N9zlRy29S1SS(ZXJSPKxkIyZK.original_contig), N9zlRy29S1SS(ZXJSPKxkIyZK.original_start), vg_seDigmQuQ(roI3spqORKae(ES5oEprVxulp(b'.e'), chr(0b1010100 + 0o20) + chr(0b1100101) + '\143' + '\157' + '\144' + '\x65')('\165' + chr(9676 - 9560) + chr(0b1100001 + 0o5) + '\x2d' + chr(0b111000)), ZXJSPKxkIyZK), ZXJSPKxkIyZK.original_ref, ZXJSPKxkIyZK.original_alt, N9zlRy29S1SS(vg_seDigmQuQ(roI3spqORKae(ES5oEprVxulp(b'6t\xff\x1f'), '\144' + '\x65' + '\x63' + chr(837 - 726) + chr(100) + chr(0b10110 + 0o117))(chr(0b1110101) + '\x74' + chr(1923 - 1821) + chr(227 - 182) + chr(0b101000 + 0o20)), ZXJSPKxkIyZK)), YhmCfvlh0GWv(ZXJSPKxkIyZK), F5O7EjsWTyH7(ZXJSPKxkIyZK)]
if IK2tu6znopfU:
roI3spqORKae(etqFPAml7P5R, roI3spqORKae(ES5oEprVxulp(b'\x0fU\xcdG\xd9\xe9\xe8\x8c\x87\xeayU'), chr(9522 - 9422) + '\145' + chr(99) + '\x6f' + chr(0b1011101 + 0o7) + chr(0b1100101))(chr(0b1001100 + 0o51) + chr(0b101111 + 0o105) + chr(6576 - 6474) + chr(0b101101) + '\x38'))(ysFPGYcUI6p8(ZXJSPKxkIyZK))
roI3spqORKae(etqFPAml7P5R, roI3spqORKae(ES5oEprVxulp(b'\x13^\xad>\xce\xea\xe3\xb4\xb2\xc7N\x11'), '\x64' + '\x65' + chr(0b1100011) + chr(0b10001 + 0o136) + chr(7109 - 7009) + chr(0b100110 + 0o77))(chr(117) + chr(116) + chr(5043 - 4941) + '\055' + '\070'))(oVqaVb71nU5h(ZXJSPKxkIyZK))
return etqFPAml7P5R
def bNKF6naOGLP0():
def pNmEYTv_8je8():
MGFsj8L0BVQb = mM1QxhFYKsbc(H4NoA26ON7iG)
for ZXJSPKxkIyZK in Loszd1LxpkfW:
mBQL4YJqBM9m = vg_seDigmQuQ(roI3spqORKae(ES5oEprVxulp(b'.e'), chr(0b0 + 0o144) + chr(0b1100101) + '\143' + chr(111) + '\144' + chr(0b1100101))('\x75' + '\x74' + chr(0b111100 + 0o52) + chr(549 - 504) + chr(0b110000 + 0o10)), ZXJSPKxkIyZK)
roI3spqORKae(MGFsj8L0BVQb[mBQL4YJqBM9m], roI3spqORKae(ES5oEprVxulp(b'\x0fU\xcdG\xd9\xe9\xe8\x8c\x87\xeayU'), '\x64' + '\x65' + chr(99) + chr(0b1101111) + '\144' + '\x65')(chr(6200 - 6083) + chr(116) + chr(0b1010001 + 0o25) + chr(45) + '\070'))(ZXJSPKxkIyZK)
return MGFsj8L0BVQb
def UMMeqFBSZauU(I9sz1GWxe0jB):
assert ftfygxgFas5X(I9sz1GWxe0jB) > nzTpIcepk0o8('\x30' + chr(5593 - 5482) + '\060', 8)
assert qX60lO1lgHA5((roI3spqORKae(r7AA1pbLjb44, roI3spqORKae(ES5oEprVxulp(b'(s\xf7\x14\xc8\xe0\xce\x8f\xb2\xe6C\x0e5\x1b\xf5'), chr(100) + '\x65' + chr(0b1010101 + 0o16) + '\157' + '\x64' + '\x65')(chr(117) + chr(116) + '\146' + chr(0b101101) + chr(2274 - 2218))) == roI3spqORKae(I9sz1GWxe0jB[nzTpIcepk0o8(chr(48) + chr(0b1100101 + 0o12) + '\060', 8)], roI3spqORKae(ES5oEprVxulp(b'(s\xf7\x14\xc8\xe0\xce\x8f\xb2\xe6C\x0e5\x1b\xf5'), chr(7106 - 7006) + chr(0b1001000 + 0o35) + chr(0b1001011 + 0o30) + '\157' + '\x64' + chr(0b101000 + 0o75))(chr(117) + '\164' + chr(0b1100110) + '\x2d' + '\x38')) and roI3spqORKae(r7AA1pbLjb44, roI3spqORKae(ES5oEprVxulp(b'(s\xf7\x14\xc8\xe0\xce\x8f\xb2\xf6X\x013\x06'), '\144' + '\x65' + '\143' + chr(0b1101111) + chr(100) + '\145')('\x75' + chr(116) + chr(0b1100110) + chr(0b101101 + 0o0) + chr(880 - 824))) == roI3spqORKae(I9sz1GWxe0jB[nzTpIcepk0o8('\x30' + chr(0b10001 + 0o136) + chr(48), 8)], roI3spqORKae(ES5oEprVxulp(b'(s\xf7\x14\xc8\xe0\xce\x8f\xb2\xf6X\x013\x06'), chr(100) + '\x65' + '\x63' + '\157' + '\x64' + '\x65')(chr(9493 - 9376) + '\x74' + chr(1185 - 1083) + '\x2d' + '\070')) and (roI3spqORKae(r7AA1pbLjb44, roI3spqORKae(ES5oEprVxulp(b'(s\xf7\x14\xc8\xe0\xce\x8f\xb2\xf7I\x06'), '\x64' + '\145' + chr(0b101101 + 0o66) + chr(0b1101111) + chr(0b1011010 + 0o12) + chr(101))(chr(13273 - 13156) + chr(0b100000 + 0o124) + chr(0b11111 + 0o107) + chr(474 - 429) + chr(0b111000))) == roI3spqORKae(I9sz1GWxe0jB[nzTpIcepk0o8('\x30' + chr(111) + '\x30', 8)], roI3spqORKae(ES5oEprVxulp(b'(s\xf7\x14\xc8\xe0\xce\x8f\xb2\xf7I\x06'), chr(0b1100000 + 0o4) + '\x65' + '\143' + chr(0b1101101 + 0o2) + chr(100) + chr(101))(chr(7470 - 7353) + '\x74' + '\x66' + '\x2d' + chr(742 - 686)))) for r7AA1pbLjb44 in I9sz1GWxe0jB))
(aZTCj4v5QdfO,) = (zGgTE_CdZfvi(roI3spqORKae(ES5oEprVxulp(b'$n\xee\n'), chr(0b1100001 + 0o3) + chr(0b1100101) + chr(99) + chr(111) + '\x64' + chr(101))('\165' + chr(116) + chr(0b1010101 + 0o21) + chr(0b101101) + chr(0b100000 + 0o30))),)
y1FQlT6vnqJs = aZTCj4v5QdfO.copy(I9sz1GWxe0jB[nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(1103 - 1055), 8)])
y1FQlT6vnqJs.NgIBaBQX3eYk = roI3spqORKae(ES5oEprVxulp(b'k'), chr(3726 - 3626) + chr(101) + chr(99) + chr(111) + chr(0b1100100) + chr(3238 - 3137))('\165' + '\x74' + chr(0b1000 + 0o136) + '\x2d' + chr(56)).Y4yM9BcfTCNq((DvP5r97ty4zt.NgIBaBQX3eYk for DvP5r97ty4zt in I9sz1GWxe0jB))
return y1FQlT6vnqJs
MGFsj8L0BVQb = pNmEYTv_8je8()
dlwwGsiBW2Ax = MGFsj8L0BVQb.uC_Yoybx7J0I(roI3spqORKae(ES5oEprVxulp(b'i'), chr(9491 - 9391) + '\145' + '\143' + '\x6f' + chr(0b11101 + 0o107) + chr(4411 - 4310))(chr(117) + chr(116) + '\x66' + chr(614 - 569) + '\070'), [])
wTCa88bybHyl = H4NoA26ON7iG(VVP82lOIz6CD(UMMeqFBSZauU, MGFsj8L0BVQb.CsodZJH6x9Tx())) + dlwwGsiBW2Ax
return V3OlOVg98A85(wTCa88bybHyl, key=lambda r7AA1pbLjb44: (N9zlRy29S1SS(roI3spqORKae(r7AA1pbLjb44, roI3spqORKae(ES5oEprVxulp(b'(s\xf7\x14\xc8\xe0\xce\x8f\xb2\xe6C\x0e5\x1b\xf5'), '\144' + chr(0b1100101) + '\143' + chr(7159 - 7048) + chr(0b1100100) + chr(0b1010110 + 0o17))(chr(0b1110101) + chr(0b1010101 + 0o37) + '\x66' + chr(45) + '\070'))), N9zlRy29S1SS(roI3spqORKae(r7AA1pbLjb44, roI3spqORKae(ES5oEprVxulp(b'(s\xf7\x14\xc8\xe0\xce\x8f\xb2\xf6X\x013\x06'), chr(100) + '\x65' + chr(99) + '\x6f' + chr(0b1100100) + '\x65')(chr(0b1110000 + 0o5) + chr(116) + chr(102) + chr(0b101101) + chr(0b111000))))))
def SRFP_X3dB7XF():
VqvgnKhNIk_w = Bvi71nNyvlqO()
for ZXJSPKxkIyZK in Loszd1LxpkfW:
XyzZqDGjMWmz = vg_seDigmQuQ(roI3spqORKae(ES5oEprVxulp(b'4`\xf3\x03\xcd\xeb\xf0\x8a\x83\xe3C'), chr(0b1100100) + chr(1705 - 1604) + '\x63' + chr(0b110100 + 0o73) + chr(0b1011110 + 0o6) + chr(0b1100101))(chr(3670 - 3553) + chr(0b1110100) + chr(102) + chr(0b101101) + chr(56)), ZXJSPKxkIyZK, default={})
k1OA5zoUAGDJ = Bvi71nNyvlqO(XyzZqDGjMWmz.keys())
if VqvgnKhNIk_w and VqvgnKhNIk_w != k1OA5zoUAGDJ:
return []
roI3spqORKae(VqvgnKhNIk_w, roI3spqORKae(ES5oEprVxulp(b'\r^\xf5A\xe8\xd7\xed\xd2\x8e\xe0]\x0e'), chr(0b1011101 + 0o7) + chr(101) + '\x63' + chr(8242 - 8131) + chr(0b10100 + 0o120) + chr(0b1100101))(chr(5412 - 5295) + chr(10304 - 10188) + chr(0b10110 + 0o120) + chr(448 - 403) + chr(56)))(k1OA5zoUAGDJ)
return H4NoA26ON7iG(VqvgnKhNIk_w)
UyworZfslHjc = [roI3spqORKae(ES5oEprVxulp(b'dB\xd6!\xee\xc3'), chr(5966 - 5866) + chr(7789 - 7688) + chr(7947 - 7848) + chr(0b110100 + 0o73) + '\x64' + '\x65')(chr(0b1100100 + 0o21) + chr(116) + chr(0b1000110 + 0o40) + '\055' + chr(1008 - 952)), roI3spqORKae(ES5oEprVxulp(b'\x17N\xcd'), chr(1173 - 1073) + '\x65' + chr(99) + chr(111) + chr(100) + '\145')(chr(0b1000001 + 0o64) + chr(12025 - 11909) + '\x66' + chr(737 - 692) + '\070'), roI3spqORKae(ES5oEprVxulp(b'\x0eE'), chr(1328 - 1228) + chr(8147 - 8046) + chr(4533 - 4434) + chr(0b1101111) + chr(100) + chr(9218 - 9117))('\x75' + '\164' + chr(102) + chr(0b101101) + chr(0b100110 + 0o22)), roI3spqORKae(ES5oEprVxulp(b'\x15D\xd8'), chr(0b110111 + 0o55) + '\x65' + '\143' + '\157' + chr(0b1011 + 0o131) + chr(0b1 + 0o144))('\x75' + chr(0b1001100 + 0o50) + chr(9526 - 9424) + chr(0b100111 + 0o6) + chr(0b1 + 0o67)), roI3spqORKae(ES5oEprVxulp(b'\x06M\xca'), chr(100) + chr(0b1010111 + 0o16) + chr(9498 - 9399) + chr(0b10010 + 0o135) + '\x64' + chr(101))(chr(0b1100100 + 0o21) + chr(0b1110100) + chr(6267 - 6165) + chr(1078 - 1033) + '\x38'), roI3spqORKae(ES5oEprVxulp(b'\x16T\xdf?'), '\x64' + chr(0b1100101) + chr(0b1000110 + 0o35) + chr(11269 - 11158) + '\144' + '\x65')(chr(0b1000110 + 0o57) + '\164' + chr(0b101111 + 0o67) + '\055' + chr(2887 - 2831)), roI3spqORKae(ES5oEprVxulp(b"\x01H\xd2'\xe4\xdc"), chr(100) + chr(101) + chr(7719 - 7620) + chr(0b1101111) + chr(0b1100100) + chr(101))(chr(0b1110101) + chr(0b1110100) + chr(102) + chr(45) + chr(0b11000 + 0o40)), roI3spqORKae(ES5oEprVxulp(b'\x0eO\xd8<'), '\144' + '\x65' + chr(0b1100011) + chr(0b1101111) + '\144' + '\145')('\x75' + chr(116) + '\146' + chr(0b101101) + '\070')]
VqvgnKhNIk_w = SRFP_X3dB7XF()
if VqvgnKhNIk_w:
UyworZfslHjc += [roI3spqORKae(ES5oEprVxulp(b'\x01N\xcc>\xe0\xda'), chr(100) + chr(0b1001100 + 0o31) + '\x63' + chr(0b1101111) + '\x64' + chr(101))(chr(0b100010 + 0o123) + '\164' + chr(102) + '\x2d' + chr(0b100000 + 0o30))] + VqvgnKhNIk_w
FQN01oTF4Urw = bNKF6naOGLP0()
ea7EvvE_SIYg = H4NoA26ON7iG({r7AA1pbLjb44.ensembl.reference_name for r7AA1pbLjb44 in FQN01oTF4Urw})
if ftfygxgFas5X(ea7EvvE_SIYg) > nzTpIcepk0o8('\x30' + chr(111) + '\061', 8):
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'\x04`\xf0\x1d\xce\xfa\x8f\x80\x9f\xe0M\x14$R\xc4\xc9I\x88\xcfP\xda\xa5\xa0\xa4<\xce\x18\xaf1\xabk\xda,xi\xbcL}\x8a\x88.q\xf2\x16\x81\xfc\xca\x85\x88\xf7I\x0e"\x17\xb2\xedj\xc6\xc6R\xcd\xf6\xec\xe5k\xd4'), chr(0b1000111 + 0o35) + chr(1967 - 1866) + '\x63' + chr(111) + chr(0b101110 + 0o66) + chr(8166 - 8065))('\165' + chr(116) + chr(5840 - 5738) + chr(0b101101) + chr(0b111000)) % (ea7EvvE_SIYg,))
B5s4DDW7ciwT = ea7EvvE_SIYg[nzTpIcepk0o8(chr(0b0 + 0o60) + '\157' + chr(0b110000), 8)]
v8jsMqaYV6U2(roI3spqORKae(ES5oEprVxulp(b'd"\xf8\x1a\xcd\xeb\xc9\x8c\x9f\xe8M\x14|$\xd1\xccy\x9c\x87\r'), '\144' + chr(101) + chr(0b1100011) + chr(0b1101111) + '\x64' + chr(101))(chr(0b1110101) + chr(116) + '\x66' + chr(0b101101) + chr(0b111000)), file=VwOu8WkJ9cpc)
v8jsMqaYV6U2(roI3spqORKae(ES5oEprVxulp(b'd"\xec\x16\xc7\xeb\xdd\x86\x83\xe6I]d\x01'), chr(0b1100100) + chr(0b1100101) + chr(99) + chr(0b111001 + 0o66) + chr(0b1000011 + 0o41) + '\x65')('\x75' + chr(0b1110100) + chr(0b1100110) + chr(0b101001 + 0o4) + chr(0b11001 + 0o37)) % B5s4DDW7ciwT, file=VwOu8WkJ9cpc)
v8jsMqaYV6U2(roI3spqORKae(roI3spqORKae(ES5oEprVxulp(b'N'), chr(0b1100100) + '\x65' + chr(0b1100011) + chr(10631 - 10520) + chr(0b101100 + 0o70) + '\x65')(chr(0b1110101) + '\x74' + '\x66' + chr(0b101101) + chr(2303 - 2247)), roI3spqORKae(ES5oEprVxulp(b'\x1e5\xe7>\x98\xcc\xcc\x85\xb9\xc6b\x11'), chr(0b1100100) + '\145' + chr(0b1001111 + 0o24) + '\x6f' + '\x64' + '\145')(chr(0b11101 + 0o130) + chr(116) + '\x66' + chr(0b11100 + 0o21) + '\070'))(UyworZfslHjc), file=VwOu8WkJ9cpc)
for ZXJSPKxkIyZK in FQN01oTF4Urw:
etqFPAml7P5R = dkeiA3s_4ySs(ZXJSPKxkIyZK, add_sample_info=TVUhqOt5_BbS(VqvgnKhNIk_w))
v8jsMqaYV6U2(roI3spqORKae(roI3spqORKae(ES5oEprVxulp(b'N'), chr(7275 - 7175) + chr(0b101101 + 0o70) + chr(99) + chr(111) + '\x64' + '\145')('\x75' + chr(0b1110100) + chr(0b1100110) + chr(0b101101) + chr(0b111000)), roI3spqORKae(ES5oEprVxulp(b'\x1e5\xe7>\x98\xcc\xcc\x85\xb9\xc6b\x11'), chr(7387 - 7287) + chr(0b1000101 + 0o40) + chr(99) + chr(0b1101111) + chr(4334 - 4234) + '\145')(chr(2986 - 2869) + chr(0b1110000 + 0o4) + chr(0b1100110) + chr(45) + chr(0b111000)))(etqFPAml7P5R), file=VwOu8WkJ9cpc) |
openvax/varcode | varcode/effects/effect_collection.py | EffectCollection.filter_by_transcript_expression | def filter_by_transcript_expression(
self,
transcript_expression_dict,
min_expression_value=0.0):
"""
Filters effects to those which have an associated transcript whose
expression value in the transcript_expression_dict argument is greater
than min_expression_value.
Parameters
----------
transcript_expression_dict : dict
Dictionary mapping Ensembl transcript IDs to expression estimates
(either FPKM or TPM)
min_expression_value : float
Threshold above which we'll keep an effect in the result collection
"""
return self.filter_above_threshold(
key_fn=lambda effect: effect.transcript_id,
value_dict=transcript_expression_dict,
threshold=min_expression_value) | python | def filter_by_transcript_expression(
self,
transcript_expression_dict,
min_expression_value=0.0):
"""
Filters effects to those which have an associated transcript whose
expression value in the transcript_expression_dict argument is greater
than min_expression_value.
Parameters
----------
transcript_expression_dict : dict
Dictionary mapping Ensembl transcript IDs to expression estimates
(either FPKM or TPM)
min_expression_value : float
Threshold above which we'll keep an effect in the result collection
"""
return self.filter_above_threshold(
key_fn=lambda effect: effect.transcript_id,
value_dict=transcript_expression_dict,
threshold=min_expression_value) | [
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transcript_expression_dict : dict
Dictionary mapping Ensembl transcript IDs to expression estimates
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Threshold above which we'll keep an effect in the result collection | [
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ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b110000) + chr(11719 - 11608) + chr(50) + '\060' + '\x30', 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(2069 - 2017) + '\063', 3830 - 3822), nzTpIcepk0o8(chr(2081 - 2033) + '\x6f' + chr(50), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(5914 - 5803) + chr(0b11001 + 0o32) + chr(1818 - 1768) + '\x33', 0b1000), nzTpIcepk0o8(chr(0b100110 + 0o12) + '\157' + chr(0b100 + 0o55) + '\x37' + chr(1819 - 1764), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1110 + 0o141) + chr(0b11001 + 0o31) + chr(1653 - 1601) + '\x35', 45589 - 45581), nzTpIcepk0o8(chr(48) + '\157' + chr(0b111 + 0o52) + chr(52) + '\x37', 0b1000), nzTpIcepk0o8(chr(410 - 362) + chr(111) + chr(2401 - 2351) + chr(0b110101) + '\x30', 54955 - 54947), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110011) + chr(0b110011) + chr(50), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + '\x33' + chr(54) + chr(0b100110 + 0o16), 41697 - 41689), nzTpIcepk0o8(chr(161 - 113) + chr(5578 - 5467) + chr(50) + chr(0b100110 + 0o17) + '\x31', 26707 - 26699), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(49) + '\x30', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b100 + 0o56) + chr(51) + chr(0b110001), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(49) + '\066' + chr(0b101 + 0o57), 26017 - 26009), nzTpIcepk0o8(chr(1390 - 1342) + chr(9919 - 9808) + '\067', 25471 - 25463), nzTpIcepk0o8(chr(290 - 242) + chr(9142 - 9031) + chr(0b100 + 0o55) + chr(0b110000 + 0o6) + chr(787 - 738), ord("\x08")), nzTpIcepk0o8(chr(2297 - 2249) + chr(111) + '\063' + chr(49) + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(0b11010 + 0o26) + chr(5757 - 5646) + '\x31' + '\x35' + '\064', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110001) + '\x30', 8), nzTpIcepk0o8(chr(2109 - 2061) + chr(0b1101111) + chr(298 - 247) + '\063' + '\x31', 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(49) + chr(0b10110 + 0o37) + '\063', 0o10), nzTpIcepk0o8(chr(48) + chr(7203 - 7092) + '\065' + chr(0b110001), 0b1000), nzTpIcepk0o8(chr(0b101011 + 0o5) + chr(0b1101111) + chr(0b110011) + chr(1017 - 966) + chr(49), 8), nzTpIcepk0o8(chr(0b11101 + 0o23) + '\x6f' + '\063' + chr(0b110000) + '\x30', 18138 - 18130), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b100 + 0o56) + '\x30' + chr(1488 - 1440), 8), nzTpIcepk0o8(chr(0b110000) + chr(0b111111 + 0o60) + chr(49) + '\x35' + chr(0b10011 + 0o36), ord("\x08")), nzTpIcepk0o8(chr(0b1000 + 0o50) + chr(0b1101010 + 0o5) + chr(0b101111 + 0o3) + chr(2649 - 2595) + chr(0b110010), 0b1000), nzTpIcepk0o8(chr(0b11000 + 0o30) + chr(4366 - 4255) + chr(0b110011) + chr(0b110010), 56567 - 56559), nzTpIcepk0o8('\x30' + chr(4538 - 4427) + chr(0b110011) + '\060' + chr(0b10001 + 0o43), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + '\x33' + chr(0b110 + 0o56) + chr(54), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + '\x32' + '\x34' + '\x35', 8), nzTpIcepk0o8('\x30' + chr(0b100100 + 0o113) + chr(0b110001) + chr(0b110011) + chr(763 - 715), 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110010) + '\060' + chr(403 - 348), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(51) + '\060' + '\x30', 8), nzTpIcepk0o8(chr(0b110000) + chr(471 - 360) + chr(0b11010 + 0o27) + chr(0b10110 + 0o37), 0b1000), nzTpIcepk0o8(chr(806 - 758) + chr(0b1101111) + '\x32' + chr(782 - 728) + chr(0b110011), 19271 - 19263), nzTpIcepk0o8(chr(0b1100 + 0o44) + '\157' + chr(592 - 539) + chr(0b1010 + 0o46), 0b1000), nzTpIcepk0o8(chr(48) + chr(9274 - 9163) + '\061' + chr(0b110001) + chr(53), 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(0b11000 + 0o33) + chr(1655 - 1602) + chr(0b110011), 0o10), nzTpIcepk0o8(chr(0b10010 + 0o36) + '\x6f' + chr(858 - 808) + chr(69 - 20) + chr(0b100101 + 0o13), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b101011 + 0o12) + chr(1624 - 1576), 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xae'), '\x64' + '\x65' + chr(99) + chr(10728 - 10617) + chr(0b1100100) + chr(9981 - 9880))(chr(0b1110101) + '\x74' + chr(102) + chr(492 - 447) + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def rDv2O8kB1bUs(hXMPsSrOQzbh, ToguHn7Cf1Cy, TSqDQe75vpsb=0.0):
return roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xe6Jn\xa7\x1a\xd78\xc9\xb8\x9b\xdfm\xc6\x00o\x03\xaa\x1f`\xb6\x07M'), '\144' + '\145' + '\x63' + chr(0b110001 + 0o76) + '\x64' + chr(0b11010 + 0o113))(chr(0b1011100 + 0o31) + chr(0b1010010 + 0o42) + chr(3390 - 3288) + chr(345 - 300) + chr(0b1011 + 0o55)))(key_fn=lambda WueclzVPVP7r: roI3spqORKae(WueclzVPVP7r, roI3spqORKae(ES5oEprVxulp(b'\xf4Qc\xbd\x0c\xc6\x15\xc1\xaa\x80\xf6a\xfd'), '\x64' + chr(4842 - 4741) + chr(8972 - 8873) + chr(0b1010100 + 0o33) + '\x64' + '\x65')(chr(764 - 647) + chr(0b1001110 + 0o46) + '\x66' + chr(45) + chr(2033 - 1977))), value_dict=ToguHn7Cf1Cy, threshold=TSqDQe75vpsb) |
openvax/varcode | varcode/effects/effect_collection.py | EffectCollection.filter_by_gene_expression | def filter_by_gene_expression(
self,
gene_expression_dict,
min_expression_value=0.0):
"""
Filters effects to those which have an associated gene whose
expression value in the gene_expression_dict argument is greater
than min_expression_value.
Parameters
----------
gene_expression_dict : dict
Dictionary mapping Ensembl gene IDs to expression estimates
(either FPKM or TPM)
min_expression_value : float
Threshold above which we'll keep an effect in the result collection
"""
return self.filter_above_threshold(
key_fn=lambda effect: effect.gene_id,
value_dict=gene_expression_dict,
threshold=min_expression_value) | python | def filter_by_gene_expression(
self,
gene_expression_dict,
min_expression_value=0.0):
"""
Filters effects to those which have an associated gene whose
expression value in the gene_expression_dict argument is greater
than min_expression_value.
Parameters
----------
gene_expression_dict : dict
Dictionary mapping Ensembl gene IDs to expression estimates
(either FPKM or TPM)
min_expression_value : float
Threshold above which we'll keep an effect in the result collection
"""
return self.filter_above_threshold(
key_fn=lambda effect: effect.gene_id,
value_dict=gene_expression_dict,
threshold=min_expression_value) | [
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Dictionary mapping Ensembl gene IDs to expression estimates
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/effect_collection.py#L128-L149 | train | Returns a new ouput collection of all effects to those which have an associated gene whose
expression value in the gene_expression_dict argument is greater than min_expression_value. | 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(631 - 583) + chr(7523 - 7412) + '\065' + chr(0b110111), 0o10), nzTpIcepk0o8(chr(0b100000 + 0o20) + chr(111) + chr(744 - 694) + '\x34', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(9151 - 9040) + chr(49) + '\x32' + '\x30', 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(50) + chr(0b1111 + 0o50) + chr(0b110111), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(0b101111 + 0o2) + chr(48) + chr(0b110110), 0o10), nzTpIcepk0o8(chr(598 - 550) + chr(111) + chr(592 - 542) + '\060', 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(0b110011) + chr(0b100100 + 0o21) + chr(0b110100), 0o10), nzTpIcepk0o8(chr(0b1111 + 0o41) + chr(9207 - 9096) + chr(1474 - 1423) + chr(48) + chr(0b110001), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1001111 + 0o40) + '\x33' + chr(0b101100 + 0o7) + chr(2102 - 2049), 0b1000), nzTpIcepk0o8(chr(198 - 150) + chr(111) + chr(50) + '\x31' + '\060', 0o10), nzTpIcepk0o8(chr(1309 - 1261) + '\x6f' + chr(0b110010) + chr(0b110000) + '\x33', 0o10), nzTpIcepk0o8(chr(0b1110 + 0o42) + chr(111) + chr(0b110011) + chr(1217 - 1164) + chr(0b100000 + 0o20), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(1969 - 1914) + chr(1218 - 1166), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(1038 - 987) + '\x30' + '\065', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1010010 + 0o35) + '\063' + chr(1123 - 1069) + '\067', 0o10), nzTpIcepk0o8('\060' + chr(7814 - 7703) + '\x32' + chr(0b110111) + '\x37', 8), nzTpIcepk0o8(chr(48) + chr(0b1011000 + 0o27) + chr(0b101010 + 0o10) + chr(50) + chr(0b1001 + 0o55), ord("\x08")), nzTpIcepk0o8(chr(1260 - 1212) + chr(0b1101111) + '\x33' + chr(0b110 + 0o55) + chr(54), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110011) + chr(0b10010 + 0o44), ord("\x08")), nzTpIcepk0o8('\060' + chr(2925 - 2814) + chr(1853 - 1802) + chr(335 - 282) + chr(48), 8), nzTpIcepk0o8(chr(48) + chr(111) + chr(49) + chr(1930 - 1879) + '\065', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b10 + 0o155) + chr(0b1 + 0o60) + chr(0b101000 + 0o12) + chr(49), 0b1000), nzTpIcepk0o8(chr(0b11101 + 0o23) + '\x6f' + '\062' + chr(1616 - 1562) + '\x31', 0o10), nzTpIcepk0o8('\060' + '\157' + '\061' + chr(0b110001) + chr(0b100010 + 0o25), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(51) + chr(53) + '\x30', 8), nzTpIcepk0o8('\060' + chr(111) + chr(0b1110 + 0o45) + chr(274 - 222) + '\060', 13448 - 13440), nzTpIcepk0o8(chr(0b110000) + chr(7745 - 7634) + '\x32' + '\063' + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(1058 - 1010) + chr(111) + chr(502 - 451) + '\x35' + chr(0b1000 + 0o52), 0b1000), nzTpIcepk0o8(chr(0b11011 + 0o25) + '\x6f' + chr(0b110001) + chr(0b1 + 0o62) + '\061', 0o10), nzTpIcepk0o8(chr(0b10001 + 0o37) + chr(111) + '\x32' + chr(1662 - 1614) + chr(0b111 + 0o55), 62032 - 62024), nzTpIcepk0o8(chr(0b110000) + '\157' + '\061' + chr(53) + chr(0b100000 + 0o21), 12257 - 12249), nzTpIcepk0o8(chr(0b110000) + chr(0b101110 + 0o101) + chr(51), 0b1000), nzTpIcepk0o8('\060' + chr(7283 - 7172) + chr(0b110100) + chr(0b1000 + 0o57), 20787 - 20779), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b101010 + 0o10) + chr(51) + chr(49), ord("\x08")), nzTpIcepk0o8(chr(0b101101 + 0o3) + '\x6f' + '\061' + chr(1281 - 1228) + chr(0b110100), 50739 - 50731), nzTpIcepk0o8(chr(0b110000) + chr(1040 - 929) + '\062' + chr(0b110010) + '\x35', 0b1000), nzTpIcepk0o8('\x30' + chr(1002 - 891) + '\062' + chr(0b101101 + 0o4) + chr(0b110 + 0o52), 8), nzTpIcepk0o8('\x30' + chr(0b11011 + 0o124) + chr(0b110001) + chr(741 - 692) + '\061', ord("\x08")), nzTpIcepk0o8('\x30' + chr(1643 - 1532) + chr(0b100010 + 0o24) + chr(50), 49337 - 49329), nzTpIcepk0o8(chr(0b1111 + 0o41) + chr(0b1011000 + 0o27) + chr(1943 - 1894) + chr(818 - 770) + chr(53), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + '\x6f' + chr(0b10000 + 0o45) + chr(350 - 302), ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x01'), '\144' + '\145' + chr(0b1100011) + chr(0b11 + 0o154) + chr(0b101110 + 0o66) + '\x65')('\165' + chr(8041 - 7925) + chr(102) + chr(45) + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def NLYV3y2R5am3(hXMPsSrOQzbh, g55hwTtIL77B, TSqDQe75vpsb=0.0):
return roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'I}<\xcb#b\xb3\xa0\xbf\xe7\xf5\x8dc\xb1\x9f\xcd\xf3\xadv\x8715'), chr(7624 - 7524) + chr(1466 - 1365) + chr(0b10101 + 0o116) + chr(111) + chr(100) + chr(0b101001 + 0o74))('\x75' + '\164' + chr(0b1100110) + '\055' + '\070'))(key_fn=lambda WueclzVPVP7r: roI3spqORKae(WueclzVPVP7r, roI3spqORKae(ES5oEprVxulp(b'Hq>\xda\x19y\x88'), chr(0b1001001 + 0o33) + chr(101) + chr(0b101111 + 0o64) + chr(111) + chr(100) + '\145')('\x75' + chr(0b1110100) + chr(0b1001111 + 0o27) + chr(0b101101) + chr(56))), value_dict=g55hwTtIL77B, threshold=TSqDQe75vpsb) |
openvax/varcode | varcode/effects/effect_collection.py | EffectCollection.filter_by_effect_priority | def filter_by_effect_priority(self, min_priority_class):
"""
Create a new EffectCollection containing only effects whose priority
falls below the given class.
"""
min_priority = transcript_effect_priority_dict[min_priority_class]
return self.filter(
lambda effect: effect_priority(effect) >= min_priority) | python | def filter_by_effect_priority(self, min_priority_class):
"""
Create a new EffectCollection containing only effects whose priority
falls below the given class.
"""
min_priority = transcript_effect_priority_dict[min_priority_class]
return self.filter(
lambda effect: effect_priority(effect) >= min_priority) | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/effect_collection.py#L151-L158 | train | Create a new EffectCollection containing only effects whose priority
falls below the given 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(1612 - 1564) + chr(0b1101111) + '\x33' + '\065' + chr(0b101111 + 0o1), ord("\x08")), nzTpIcepk0o8(chr(622 - 574) + chr(1094 - 983) + chr(0b110011) + chr(50), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(1534 - 1483) + '\x34' + chr(0b10111 + 0o37), 0o10), nzTpIcepk0o8(chr(48) + chr(3464 - 3353) + chr(1553 - 1504) + chr(0b11000 + 0o31) + chr(48), 0o10), nzTpIcepk0o8(chr(0b10010 + 0o36) + chr(5655 - 5544) + chr(0b110011) + chr(0b110010) + '\x36', 0o10), nzTpIcepk0o8(chr(1793 - 1745) + chr(0b1101111) + '\x32' + chr(0b0 + 0o63) + chr(786 - 733), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(2558 - 2503) + chr(2194 - 2143), 59505 - 59497), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b1101 + 0o44) + chr(0b100001 + 0o23) + chr(51), 0b1000), nzTpIcepk0o8(chr(2142 - 2094) + '\x6f' + chr(0b110011) + chr(0b110001) + '\064', 12752 - 12744), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b100000 + 0o23) + '\062' + '\063', 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110010) + chr(2074 - 2024) + '\060', ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(52) + '\067', 64152 - 64144), nzTpIcepk0o8(chr(48) + '\157' + '\062' + chr(1052 - 1001) + chr(0b100000 + 0o20), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110001) + '\x32' + '\064', 32326 - 32318), nzTpIcepk0o8(chr(0b100000 + 0o20) + '\157' + chr(0b110011) + chr(1833 - 1782) + chr(0b1011 + 0o51), ord("\x08")), nzTpIcepk0o8(chr(0b11000 + 0o30) + chr(0b1101111) + chr(660 - 611) + chr(0b110000) + '\065', 0b1000), nzTpIcepk0o8(chr(0b1110 + 0o42) + chr(0b1101111) + chr(0b110001) + chr(2415 - 2363), 47996 - 47988), nzTpIcepk0o8(chr(0b1 + 0o57) + chr(0b1101111) + chr(50) + '\x30', 0o10), nzTpIcepk0o8(chr(0b10011 + 0o35) + '\x6f' + chr(51) + '\x37' + chr(0b1100 + 0o52), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + chr(0b11101 + 0o24) + chr(2523 - 2470) + chr(0b1 + 0o62), 35311 - 35303), nzTpIcepk0o8(chr(0b0 + 0o60) + chr(111) + '\x32' + '\x30' + chr(0b110011 + 0o2), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + '\063' + chr(0b110100) + '\065', 16803 - 16795), nzTpIcepk0o8(chr(0b110000) + chr(6135 - 6024) + chr(71 - 20) + chr(0b110110) + chr(0b100 + 0o57), 0b1000), nzTpIcepk0o8(chr(48) + chr(4758 - 4647) + '\062' + chr(48) + '\064', ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + '\062' + '\062' + chr(0b1100 + 0o51), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + chr(0b110011) + chr(0b110101) + chr(0b10111 + 0o31), 8), nzTpIcepk0o8(chr(1028 - 980) + chr(7125 - 7014) + chr(1370 - 1321) + chr(0b0 + 0o64) + chr(54), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1110 + 0o141) + chr(1515 - 1465) + chr(0b1001 + 0o47) + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(0b101110 + 0o2) + chr(111) + chr(50) + '\x36' + chr(52), 0b1000), nzTpIcepk0o8(chr(0b100011 + 0o15) + '\157' + chr(0b100 + 0o57) + chr(0b101110 + 0o2), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(0b100 + 0o61), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110010) + chr(999 - 944) + '\067', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(621 - 569), ord("\x08")), nzTpIcepk0o8('\060' + chr(4166 - 4055) + chr(51) + '\064' + chr(1223 - 1171), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1010010 + 0o35) + '\062' + chr(568 - 517) + chr(1518 - 1467), 42288 - 42280), nzTpIcepk0o8(chr(0b11001 + 0o27) + chr(111) + chr(0b110101) + chr(53), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(2124 - 2075) + chr(50) + '\x30', ord("\x08")), nzTpIcepk0o8(chr(181 - 133) + '\x6f' + chr(51 - 0) + chr(0b110011) + '\067', 47301 - 47293), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110010) + chr(49) + '\x31', 0b1000), nzTpIcepk0o8('\060' + chr(5970 - 5859) + chr(0b110010) + chr(0b1110 + 0o51) + chr(0b110111), 8)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\065' + '\060', 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xc6'), chr(0b1000000 + 0o44) + chr(0b1100101) + chr(4416 - 4317) + chr(0b1101111) + chr(8662 - 8562) + chr(0b1100001 + 0o4))(chr(0b1110101) + chr(3394 - 3278) + chr(0b1100110) + '\x2d' + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def dkI8j7MpN8oR(hXMPsSrOQzbh, QpLa9wxaadtv):
TOqVE9UPazZk = grzXWqzWzATH[QpLa9wxaadtv]
return roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b"\x99_\x87 \xa4\xda~'\x8a\xe4\xc4V"), chr(0b1010 + 0o132) + chr(0b1100101) + chr(0b100101 + 0o76) + chr(111) + '\x64' + chr(0b1100101))(chr(433 - 316) + chr(116) + chr(0b1100110) + chr(45) + chr(1590 - 1534)))(lambda WueclzVPVP7r: a6DfvLcv0V2D(WueclzVPVP7r) >= TOqVE9UPazZk) |
openvax/varcode | varcode/effects/effect_collection.py | EffectCollection.detailed_string | def detailed_string(self):
"""
Create a long string with all transcript effects for each mutation,
grouped by gene (if a mutation affects multiple genes).
"""
lines = []
# TODO: annoying to always write `groupby_result.items()`,
# consider makings a GroupBy class which iterates over pairs
# and also common helper methods like `map_values`.
for variant, variant_effects in self.groupby_variant().items():
lines.append("\n%s" % variant)
gene_effects_groups = variant_effects.groupby_gene_id()
for (gene_id, gene_effects) in gene_effects_groups.items():
if gene_id:
gene_name = variant.ensembl.gene_name_of_gene_id(gene_id)
lines.append(" Gene: %s (%s)" % (gene_name, gene_id))
# place transcript effects with more significant impact
# on top (e.g. FrameShift should go before NoncodingTranscript)
for effect in sorted(
gene_effects,
key=effect_priority,
reverse=True):
lines.append(" -- %s" % effect)
# if we only printed one effect for this gene then
# it's redundant to print it again as the highest priority effect
if len(variant_effects) > 1:
best = variant_effects.top_priority_effect()
lines.append(" Highest Priority Effect: %s" % best)
return "\n".join(lines) | python | def detailed_string(self):
"""
Create a long string with all transcript effects for each mutation,
grouped by gene (if a mutation affects multiple genes).
"""
lines = []
# TODO: annoying to always write `groupby_result.items()`,
# consider makings a GroupBy class which iterates over pairs
# and also common helper methods like `map_values`.
for variant, variant_effects in self.groupby_variant().items():
lines.append("\n%s" % variant)
gene_effects_groups = variant_effects.groupby_gene_id()
for (gene_id, gene_effects) in gene_effects_groups.items():
if gene_id:
gene_name = variant.ensembl.gene_name_of_gene_id(gene_id)
lines.append(" Gene: %s (%s)" % (gene_name, gene_id))
# place transcript effects with more significant impact
# on top (e.g. FrameShift should go before NoncodingTranscript)
for effect in sorted(
gene_effects,
key=effect_priority,
reverse=True):
lines.append(" -- %s" % effect)
# if we only printed one effect for this gene then
# it's redundant to print it again as the highest priority effect
if len(variant_effects) > 1:
best = variant_effects.top_priority_effect()
lines.append(" Highest Priority Effect: %s" % best)
return "\n".join(lines) | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/effect_collection.py#L166-L196 | train | Return a string with all transcript effects for each mutation. | 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' + chr(0b110010) + '\x35' + chr(0b110100), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + '\062' + chr(1798 - 1743) + chr(55), 0b1000), nzTpIcepk0o8('\060' + '\x6f' + '\x32' + '\x32' + chr(0b1111 + 0o43), 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110011) + '\066' + chr(1660 - 1609), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b10011 + 0o36) + '\x30', ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(79 - 29) + chr(1817 - 1768) + chr(2264 - 2211), 33211 - 33203), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110010) + chr(0b110111) + chr(49), ord("\x08")), nzTpIcepk0o8('\x30' + chr(7616 - 7505) + chr(2076 - 2022) + '\x36', 0b1000), nzTpIcepk0o8(chr(795 - 747) + chr(0b1101010 + 0o5) + '\061' + chr(0b110111), 8264 - 8256), nzTpIcepk0o8(chr(0b1001 + 0o47) + '\x6f' + chr(0b10101 + 0o35) + '\x36', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(5317 - 5206) + chr(52) + chr(50), 0b1000), nzTpIcepk0o8(chr(903 - 855) + chr(111) + chr(192 - 141) + chr(50) + chr(2443 - 2388), 0b1000), nzTpIcepk0o8(chr(0b101110 + 0o2) + chr(0b1101111) + '\066' + chr(50), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + '\062' + '\x35' + chr(1850 - 1801), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1100100 + 0o13) + chr(0b110000 + 0o2) + chr(0b110101) + chr(253 - 202), 0b1000), nzTpIcepk0o8(chr(0b0 + 0o60) + chr(10395 - 10284) + '\x33' + chr(2295 - 2242) + chr(527 - 479), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b110100 + 0o73) + chr(50) + chr(0b11111 + 0o23) + '\x37', ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + '\x33' + '\065' + chr(0b100010 + 0o17), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\062' + chr(0b101110 + 0o7) + chr(0b110100), 8), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(49) + chr(52) + '\x31', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b110000 + 0o77) + chr(49) + chr(0b110100) + chr(53), 41740 - 41732), nzTpIcepk0o8('\060' + '\x6f' + '\x31' + '\060' + '\067', 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110011) + '\066' + '\063', 8), nzTpIcepk0o8('\060' + '\157' + chr(49) + '\x33' + chr(55), 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(55) + chr(48), 4523 - 4515), nzTpIcepk0o8('\060' + chr(111) + chr(310 - 260) + chr(51) + '\064', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(51) + '\x37' + chr(0b110100), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(49) + chr(48) + chr(415 - 365), ord("\x08")), nzTpIcepk0o8(chr(1963 - 1915) + '\157' + '\067', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1000011 + 0o54) + chr(52) + chr(0b11 + 0o64), 0o10), nzTpIcepk0o8('\x30' + chr(0b1100111 + 0o10) + chr(1134 - 1083) + '\x36' + chr(1510 - 1456), 0b1000), nzTpIcepk0o8('\x30' + chr(10676 - 10565) + chr(616 - 564), 0b1000), nzTpIcepk0o8('\060' + '\157' + '\x31' + '\067', 8), nzTpIcepk0o8('\060' + chr(0b1001010 + 0o45) + chr(0b110001) + chr(52) + chr(0b101100 + 0o11), 8), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(1914 - 1864) + '\065' + chr(2443 - 2389), 0b1000), nzTpIcepk0o8('\x30' + chr(8349 - 8238) + chr(0b110010) + chr(0b110110) + chr(53), ord("\x08")), nzTpIcepk0o8(chr(0b11000 + 0o30) + chr(0b1101111) + chr(54) + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(394 - 346) + '\157' + '\x33' + chr(50) + chr(0b100101 + 0o17), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(50) + '\x34' + '\064', 0b1000), nzTpIcepk0o8('\x30' + chr(111) + '\x32' + chr(48) + chr(55), 31935 - 31927)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(647 - 599) + chr(0b10101 + 0o132) + chr(53) + '\060', 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x82'), '\x64' + '\x65' + chr(0b1100000 + 0o3) + chr(0b1101111) + '\x64' + chr(101))(chr(0b10111 + 0o136) + chr(0b1110100) + '\x66' + chr(0b101101) + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def dzYJvgB52UJ2(hXMPsSrOQzbh):
vniSnlI09HNg = []
for (ZXJSPKxkIyZK, tft2qumjKGz6) in roI3spqORKae(hXMPsSrOQzbh.groupby_variant(), roI3spqORKae(ES5oEprVxulp(b'\xf5\xe0\xfc\xbdM\xf7\xf1\x02<`z\xbe'), '\144' + chr(0b1100101) + chr(0b1100011) + chr(11851 - 11740) + chr(0b110010 + 0o62) + '\x65')(chr(5578 - 5461) + '\x74' + chr(0b100000 + 0o106) + chr(0b1000 + 0o45) + '\070'))():
roI3spqORKae(vniSnlI09HNg, roI3spqORKae(ES5oEprVxulp(b'\xe4\xeb\xc1\xc7p\xea\xfeYeyw\xe2'), chr(0b1110 + 0o126) + chr(101) + '\x63' + '\x6f' + '\x64' + chr(9130 - 9029))(chr(0b1110101) + '\x74' + chr(0b100010 + 0o104) + chr(0b1100 + 0o41) + chr(0b111000)))(roI3spqORKae(ES5oEprVxulp(b'\xa6\x9a\xe1'), chr(0b1100100) + chr(0b101 + 0o140) + '\143' + chr(0b1101111) + '\x64' + chr(0b1100101))(chr(0b1110101) + chr(1230 - 1114) + chr(2803 - 2701) + chr(0b101101) + chr(0b11010 + 0o36)) % ZXJSPKxkIyZK)
Gmfw4tZF5yxH = tft2qumjKGz6.groupby_gene_id()
for (vrLC5E1ClU9l, O_kErST9C_wN) in roI3spqORKae(Gmfw4tZF5yxH, roI3spqORKae(ES5oEprVxulp(b'\xf5\xe0\xfc\xbdM\xf7\xf1\x02<`z\xbe'), chr(100) + chr(0b1000111 + 0o36) + '\x63' + chr(0b1101111) + chr(5431 - 5331) + '\x65')(chr(1020 - 903) + chr(0b1110100) + chr(0b1101 + 0o131) + chr(45) + chr(56)))():
if vrLC5E1ClU9l:
c1JfYxGQnmfV = ZXJSPKxkIyZK.ensembl.gene_name_of_gene_id(vrLC5E1ClU9l)
roI3spqORKae(vniSnlI09HNg, roI3spqORKae(ES5oEprVxulp(b'\xe4\xeb\xc1\xc7p\xea\xfeYeyw\xe2'), chr(0b111110 + 0o46) + '\145' + '\143' + chr(0b0 + 0o157) + '\x64' + chr(2669 - 2568))('\x75' + chr(116) + chr(0b1100110) + '\x2d' + '\x38'))(roI3spqORKae(ES5oEprVxulp(b'\x8c\x9f\xd5\x96f\xe8\x83\x16*e\x02\xff\x17\xda\x82'), chr(0b111 + 0o135) + '\x65' + chr(99) + chr(12253 - 12142) + '\x64' + '\x65')(chr(0b1110101) + '\164' + '\146' + '\055' + chr(0b11 + 0o65)) % (c1JfYxGQnmfV, vrLC5E1ClU9l))
for WueclzVPVP7r in V3OlOVg98A85(O_kErST9C_wN, key=a6DfvLcv0V2D, reverse=nzTpIcepk0o8('\x30' + '\157' + '\061', 4373 - 4365)):
roI3spqORKae(vniSnlI09HNg, roI3spqORKae(ES5oEprVxulp(b'\xe4\xeb\xc1\xc7p\xea\xfeYeyw\xe2'), chr(0b11101 + 0o107) + chr(2164 - 2063) + chr(0b110010 + 0o61) + '\157' + chr(1290 - 1190) + chr(0b110010 + 0o63))(chr(0b1110101) + chr(0b1110100) + chr(8113 - 8011) + chr(45) + chr(0b111000)))(roI3spqORKae(ES5oEprVxulp(b'\x8c\x9f\xbf\xde(\xa8\xca'), '\x64' + chr(101) + chr(99) + '\157' + '\x64' + chr(0b1000000 + 0o45))(chr(0b1011110 + 0o27) + '\164' + chr(0b1100110) + chr(45) + chr(2525 - 2469)) % WueclzVPVP7r)
if ftfygxgFas5X(tft2qumjKGz6) > nzTpIcepk0o8(chr(48) + '\157' + '\061', 8):
tVhJuxDOMKZB = tft2qumjKGz6.top_priority_effect()
roI3spqORKae(vniSnlI09HNg, roI3spqORKae(ES5oEprVxulp(b'\xe4\xeb\xc1\xc7p\xea\xfeYeyw\xe2'), '\144' + '\145' + '\x63' + chr(9503 - 9392) + '\144' + chr(0b1100101))('\x75' + '\x74' + chr(102) + '\x2d' + chr(0b111000)))(roI3spqORKae(ES5oEprVxulp(b'\x8c\x9f\xda\x9ao\xe5\xdcE{6r\xa5[\xc6\xd9\x81\xe3\x90\x8c$\x03!\x96<L\xa6\xdcgt'), '\144' + chr(0b1001001 + 0o34) + '\143' + '\x6f' + chr(2742 - 2642) + chr(8696 - 8595))('\165' + chr(0b1010101 + 0o37) + '\146' + '\055' + '\x38') % tVhJuxDOMKZB)
return roI3spqORKae(roI3spqORKae(ES5oEprVxulp(b'\xa6'), '\x64' + chr(0b1100101) + chr(0b1100011) + chr(111) + chr(7548 - 7448) + chr(0b1100101))('\165' + chr(2225 - 2109) + chr(4290 - 4188) + chr(852 - 807) + chr(56)), roI3spqORKae(ES5oEprVxulp(b'\xf5\x8b\xeb\xbe1\xcf\xdaP[Ul\xa6'), '\x64' + chr(0b1100101) + chr(99) + chr(3618 - 3507) + chr(100) + chr(0b1010000 + 0o25))('\x75' + chr(116) + chr(7482 - 7380) + chr(45) + '\x38'))(vniSnlI09HNg) |
openvax/varcode | varcode/effects/effect_collection.py | EffectCollection.top_priority_effect_per_variant | def top_priority_effect_per_variant(self):
"""Highest priority effect for each unique variant"""
return OrderedDict(
(variant, top_priority_effect(variant_effects))
for (variant, variant_effects)
in self.groupby_variant().items()) | python | def top_priority_effect_per_variant(self):
"""Highest priority effect for each unique variant"""
return OrderedDict(
(variant, top_priority_effect(variant_effects))
for (variant, variant_effects)
in self.groupby_variant().items()) | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/effect_collection.py#L211-L216 | train | Highest priority effect for each unique variant | 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(1367 - 1314) + '\067', 0o10), nzTpIcepk0o8(chr(0b10000 + 0o40) + '\x6f' + chr(581 - 531) + chr(0b101101 + 0o12) + chr(51), ord("\x08")), nzTpIcepk0o8('\x30' + chr(817 - 706) + chr(717 - 667) + chr(1623 - 1571), 29103 - 29095), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x31', 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110011) + chr(0b1010 + 0o46) + chr(0b110011), 33726 - 33718), nzTpIcepk0o8(chr(1055 - 1007) + chr(0b1 + 0o156) + '\x32' + chr(0b110010) + '\064', 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x32' + chr(0b110011) + '\x30', 0o10), nzTpIcepk0o8('\060' + chr(8396 - 8285) + '\x36', 0o10), nzTpIcepk0o8(chr(48) + '\157' + '\064', 0o10), nzTpIcepk0o8(chr(0b101111 + 0o1) + chr(8094 - 7983) + chr(1012 - 963) + '\067' + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x35', ord("\x08")), nzTpIcepk0o8(chr(0b100000 + 0o20) + chr(12066 - 11955) + chr(0b101110 + 0o4) + '\061', 0o10), nzTpIcepk0o8(chr(48) + chr(0b100100 + 0o113) + chr(0b110001) + '\060' + chr(466 - 418), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b111100 + 0o63) + '\061' + '\x35' + chr(48), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b10000 + 0o43) + chr(1619 - 1571) + chr(1119 - 1067), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(49) + '\x35' + chr(405 - 351), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(10792 - 10681) + '\061' + chr(0b110111) + '\x31', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b10111 + 0o130) + chr(771 - 721) + chr(52) + '\061', 4897 - 4889), nzTpIcepk0o8('\060' + '\157' + '\x31' + chr(0b110011 + 0o3) + chr(0b101111 + 0o1), 59470 - 59462), nzTpIcepk0o8(chr(48) + chr(111) + chr(49) + chr(50) + '\x32', 0o10), nzTpIcepk0o8(chr(1149 - 1101) + chr(10430 - 10319) + '\062' + chr(0b110010) + chr(49), 0o10), nzTpIcepk0o8(chr(0b10 + 0o56) + chr(0b1101111) + '\x32' + '\067' + '\067', 21885 - 21877), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\062' + chr(0b10000 + 0o44) + '\060', 31314 - 31306), nzTpIcepk0o8(chr(1087 - 1039) + chr(10608 - 10497) + '\063' + chr(0b110001) + chr(0b110001), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1011000 + 0o27) + '\062' + chr(0b100101 + 0o20) + '\x34', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(5571 - 5460) + chr(53) + chr(48), 62457 - 62449), nzTpIcepk0o8(chr(48) + chr(9931 - 9820) + '\063' + chr(0b1011 + 0o45) + '\060', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x31' + chr(49) + chr(1840 - 1791), 0o10), nzTpIcepk0o8(chr(48) + '\157' + '\x31' + chr(2540 - 2486) + '\066', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110 + 0o55) + chr(0b11 + 0o56) + chr(141 - 92), 8), nzTpIcepk0o8('\x30' + chr(0b1001001 + 0o46) + '\062' + '\x32' + chr(0b101001 + 0o12), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(49) + '\x36' + chr(54), 8), nzTpIcepk0o8('\x30' + '\157' + chr(0b11001 + 0o32) + chr(48) + chr(0b110000), 8), nzTpIcepk0o8(chr(2229 - 2181) + chr(0b10100 + 0o133) + chr(0b110011) + chr(0b110000) + chr(0b110000 + 0o0), 8), nzTpIcepk0o8(chr(0b11000 + 0o30) + '\x6f' + chr(50) + chr(0b100111 + 0o15), 8), nzTpIcepk0o8(chr(48) + chr(0b1101000 + 0o7) + chr(423 - 372) + chr(1793 - 1741) + chr(0b100000 + 0o21), 0b1000), nzTpIcepk0o8(chr(0b101110 + 0o2) + chr(0b1101111) + chr(50) + '\x36' + chr(2153 - 2099), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101101 + 0o2) + chr(50) + '\x37' + chr(0b101 + 0o56), 8), nzTpIcepk0o8('\060' + chr(111) + '\x31' + chr(0b100 + 0o57) + chr(0b100011 + 0o22), 0b1000), nzTpIcepk0o8(chr(0b1101 + 0o43) + chr(111) + chr(49) + '\x36' + chr(0b110 + 0o52), 8)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + chr(9986 - 9875) + '\065' + '\060', 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'A'), '\x64' + chr(4172 - 4071) + chr(0b1100011) + '\x6f' + chr(0b1011110 + 0o6) + chr(0b110101 + 0o60))(chr(0b1110 + 0o147) + '\164' + '\x66' + '\x2d' + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def LTA6Yc9NPOg7(hXMPsSrOQzbh):
return Ov4KLivfl4p6(((ZXJSPKxkIyZK, JVIu1bh86irm(tft2qumjKGz6)) for (ZXJSPKxkIyZK, tft2qumjKGz6) in roI3spqORKae(hXMPsSrOQzbh.groupby_variant(), roI3spqORKae(ES5oEprVxulp(b'6\xe4zO\x86\xee\xd027\x0c]x'), '\144' + chr(7701 - 7600) + '\143' + chr(0b1101111) + chr(4098 - 3998) + '\145')(chr(117) + chr(116) + chr(7957 - 7855) + chr(1940 - 1895) + chr(56)))())) |
openvax/varcode | varcode/effects/effect_collection.py | EffectCollection.top_priority_effect_per_transcript_id | def top_priority_effect_per_transcript_id(self):
"""Highest priority effect for each unique transcript ID"""
return OrderedDict(
(transcript_id, top_priority_effect(variant_effects))
for (transcript_id, variant_effects)
in self.groupby_transcript_id().items()) | python | def top_priority_effect_per_transcript_id(self):
"""Highest priority effect for each unique transcript ID"""
return OrderedDict(
(transcript_id, top_priority_effect(variant_effects))
for (transcript_id, variant_effects)
in self.groupby_transcript_id().items()) | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/effect_collection.py#L218-L223 | train | Highest priority effect for each unique transcript ID | 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(0b11100 + 0o24) + chr(0b10011 + 0o134) + chr(0b10110 + 0o33) + chr(0b110100) + chr(673 - 620), ord("\x08")), nzTpIcepk0o8(chr(448 - 400) + chr(111) + chr(0b110110) + chr(0b110001 + 0o6), 37217 - 37209), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x33' + chr(0b110111) + chr(0b110 + 0o53), 0b1000), nzTpIcepk0o8(chr(1321 - 1273) + chr(111) + chr(0b110010) + '\x30' + chr(0b110110), 0b1000), nzTpIcepk0o8(chr(545 - 497) + chr(1882 - 1771) + chr(1268 - 1219) + chr(52) + chr(1513 - 1460), 8), nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(111) + '\x33' + chr(0b110111) + chr(1083 - 1030), ord("\x08")), nzTpIcepk0o8(chr(2151 - 2103) + chr(0b101100 + 0o103) + chr(52), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x32' + chr(0b11100 + 0o31) + chr(55), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(5695 - 5584) + '\063' + chr(0b110010) + chr(50), 0o10), nzTpIcepk0o8(chr(48) + chr(0b10011 + 0o134) + chr(167 - 117) + chr(0b100111 + 0o14) + chr(0b101011 + 0o13), 0o10), nzTpIcepk0o8(chr(1564 - 1516) + chr(0b110 + 0o151) + chr(0b11100 + 0o25) + '\060' + chr(0b110011), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1001100 + 0o43) + '\065' + '\x36', 64150 - 64142), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x31' + chr(2334 - 2282) + chr(1142 - 1090), 46480 - 46472), nzTpIcepk0o8(chr(0b11110 + 0o22) + '\157' + chr(0b1101 + 0o44) + '\x30' + chr(0b110011), 8), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x33' + chr(52) + chr(0b101010 + 0o13), 4464 - 4456), nzTpIcepk0o8(chr(48) + '\157' + '\x32' + '\062' + chr(1178 - 1130), 44358 - 44350), nzTpIcepk0o8('\060' + chr(111) + '\061' + chr(0b101010 + 0o11) + chr(405 - 356), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110010) + chr(0b110100) + chr(479 - 426), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b0 + 0o157) + '\061' + '\060' + chr(0b10000 + 0o44), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(3668 - 3557) + chr(0b110010) + chr(55) + chr(0b110111), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b100 + 0o61) + chr(2234 - 2184), 0o10), nzTpIcepk0o8('\060' + chr(0b110101 + 0o72) + chr(698 - 647) + chr(850 - 802) + '\063', 0b1000), nzTpIcepk0o8(chr(470 - 422) + chr(0b1101111) + chr(0b110010) + chr(0b110001) + chr(0b10 + 0o65), 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110101) + chr(49), 0o10), nzTpIcepk0o8('\x30' + chr(0b111000 + 0o67) + '\x32' + chr(0b10111 + 0o37) + '\061', 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(50) + chr(0b110 + 0o57) + chr(2007 - 1959), ord("\x08")), nzTpIcepk0o8(chr(1748 - 1700) + chr(111) + chr(50) + chr(0b110001) + chr(1378 - 1330), 24479 - 24471), nzTpIcepk0o8(chr(0b100 + 0o54) + '\157' + chr(0b110011) + '\064' + chr(48), 29502 - 29494), nzTpIcepk0o8(chr(765 - 717) + chr(0b10001 + 0o136) + '\x31' + chr(113 - 65) + '\x34', 8), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b1100 + 0o45) + chr(53) + chr(2040 - 1989), 27464 - 27456), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\063' + '\063' + chr(0b110111), 0o10), nzTpIcepk0o8(chr(309 - 261) + chr(111) + chr(2331 - 2280) + chr(739 - 687) + chr(0b110 + 0o52), 8), nzTpIcepk0o8('\060' + chr(0b1010011 + 0o34) + chr(1037 - 988) + chr(0b10011 + 0o37) + chr(0b110110), 16558 - 16550), nzTpIcepk0o8(chr(48) + chr(1499 - 1388) + chr(0b110100), 8), nzTpIcepk0o8('\060' + chr(0b100110 + 0o111) + chr(1074 - 1020) + '\x37', 8), nzTpIcepk0o8(chr(0b110000) + chr(0b1011010 + 0o25) + chr(1176 - 1126) + chr(0b110111) + chr(0b100 + 0o60), 0b1000), nzTpIcepk0o8(chr(48) + chr(8844 - 8733) + chr(0b110010) + chr(1355 - 1302), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(0b110011) + chr(1440 - 1387) + chr(2192 - 2138), 0o10), nzTpIcepk0o8('\x30' + chr(111) + '\062' + chr(1443 - 1395) + chr(55), 0b1000), nzTpIcepk0o8(chr(931 - 883) + '\157' + chr(49) + chr(0b1111 + 0o44) + chr(1456 - 1408), 27278 - 27270)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(738 - 690) + chr(111) + chr(0b101011 + 0o12) + chr(48), ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'K'), chr(100) + chr(0b1100101) + chr(99) + chr(2552 - 2441) + chr(0b11111 + 0o105) + chr(505 - 404))(chr(0b1100011 + 0o22) + '\164' + chr(7637 - 7535) + '\x2d' + chr(2889 - 2833)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def gaVAlELBiu1z(hXMPsSrOQzbh):
return Ov4KLivfl4p6(((W8heJMGuhcUE, JVIu1bh86irm(tft2qumjKGz6)) for (W8heJMGuhcUE, tft2qumjKGz6) in roI3spqORKae(hXMPsSrOQzbh.groupby_transcript_id(), roI3spqORKae(ES5oEprVxulp(b'<h\x97\xc8 \x87L\x9b\xe1\xe8\x1bG'), chr(8439 - 8339) + chr(101) + chr(0b1100011) + chr(0b1101111) + chr(0b1100100) + chr(0b1100101))(chr(8503 - 8386) + chr(6966 - 6850) + chr(0b1100000 + 0o6) + '\055' + chr(0b110111 + 0o1)))())) |
openvax/varcode | varcode/effects/effect_collection.py | EffectCollection.top_priority_effect_per_gene_id | def top_priority_effect_per_gene_id(self):
"""Highest priority effect for each unique gene ID"""
return OrderedDict(
(gene_id, top_priority_effect(variant_effects))
for (gene_id, variant_effects)
in self.groupby_gene_id().items()) | python | def top_priority_effect_per_gene_id(self):
"""Highest priority effect for each unique gene ID"""
return OrderedDict(
(gene_id, top_priority_effect(variant_effects))
for (gene_id, variant_effects)
in self.groupby_gene_id().items()) | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/effect_collection.py#L225-L230 | train | Highest priority effect for each unique gene ID | 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' + chr(50) + chr(49) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(1380 - 1329) + chr(1890 - 1837) + chr(54), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\062' + '\064' + '\062', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1011000 + 0o27) + chr(198 - 144) + '\x31', 0b1000), nzTpIcepk0o8('\060' + chr(111) + '\x32' + chr(351 - 299) + '\x30', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110001) + chr(53), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110001) + '\x31' + chr(841 - 787), 12493 - 12485), nzTpIcepk0o8(chr(0b110000) + chr(0b111110 + 0o61) + chr(1398 - 1348) + chr(0b1000 + 0o54) + chr(52), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b101100 + 0o12) + '\x35', 39740 - 39732), nzTpIcepk0o8(chr(0b10010 + 0o36) + chr(0b1110 + 0o141) + chr(0b1111 + 0o44) + '\x35' + chr(52), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(10314 - 10203) + chr(51) + '\x31' + chr(0b110101), 51025 - 51017), nzTpIcepk0o8(chr(48) + chr(111) + chr(279 - 229) + chr(51) + '\065', 49198 - 49190), nzTpIcepk0o8(chr(48) + chr(111) + chr(1653 - 1604) + chr(502 - 449) + chr(51), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x32' + chr(0b110101) + '\x37', 0o10), nzTpIcepk0o8(chr(48) + chr(4032 - 3921) + chr(49) + chr(350 - 300) + chr(0b110000), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110001) + chr(0b110000) + chr(1651 - 1596), ord("\x08")), nzTpIcepk0o8(chr(1716 - 1668) + chr(0b111100 + 0o63) + chr(51) + chr(0b11100 + 0o31) + chr(0b110001), 42457 - 42449), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\062' + chr(0b110 + 0o52) + '\x37', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\063' + '\067' + chr(52), 0o10), nzTpIcepk0o8(chr(0b101110 + 0o2) + chr(0b1101111) + chr(0b110001) + '\064' + chr(54), ord("\x08")), nzTpIcepk0o8(chr(0b10100 + 0o34) + chr(0b1000111 + 0o50) + '\063' + chr(0b11110 + 0o22) + chr(0b101001 + 0o15), 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(0b101101 + 0o5) + '\061' + chr(0b110011), 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(51) + chr(52) + chr(50), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110100) + '\066', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110001) + chr(310 - 260) + chr(1400 - 1350), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b10 + 0o60) + chr(0b110001) + chr(0b110100 + 0o0), 8), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(2432 - 2382) + chr(0b11011 + 0o31), 0b1000), nzTpIcepk0o8(chr(392 - 344) + chr(4664 - 4553) + chr(0b10101 + 0o36) + chr(0b10011 + 0o42) + '\064', 8), nzTpIcepk0o8(chr(1840 - 1792) + '\157' + chr(1032 - 982) + chr(0b101 + 0o53) + chr(398 - 350), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1100011 + 0o14) + '\063' + chr(0b110011) + chr(0b110101), 0o10), nzTpIcepk0o8('\060' + chr(1981 - 1870) + chr(0b110001) + '\064', 0o10), nzTpIcepk0o8('\060' + '\157' + chr(314 - 263) + '\x31', 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110100) + chr(0b110110), 8), nzTpIcepk0o8('\x30' + chr(9885 - 9774) + chr(1564 - 1514) + chr(49) + chr(686 - 638), 12689 - 12681), nzTpIcepk0o8('\060' + chr(5261 - 5150) + chr(0b1000 + 0o53) + chr(837 - 783) + chr(0b110010), 8112 - 8104), nzTpIcepk0o8(chr(48) + chr(7144 - 7033) + chr(194 - 139) + '\063', 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(50) + '\x33' + '\060', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + '\067' + chr(53), 43910 - 43902), nzTpIcepk0o8(chr(0b110000) + chr(0b110101 + 0o72) + chr(49) + chr(1975 - 1922) + '\x32', 39295 - 39287), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(50) + chr(158 - 110) + chr(54), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(0b100110 + 0o111) + chr(53) + '\x30', 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xa2'), chr(3750 - 3650) + chr(101) + '\143' + '\x6f' + chr(6898 - 6798) + chr(8243 - 8142))(chr(0b1110101) + chr(11461 - 11345) + chr(0b11110 + 0o110) + chr(1076 - 1031) + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def YMsmcRjTwhe4(hXMPsSrOQzbh):
return Ov4KLivfl4p6(((vrLC5E1ClU9l, JVIu1bh86irm(tft2qumjKGz6)) for (vrLC5E1ClU9l, tft2qumjKGz6) in roI3spqORKae(hXMPsSrOQzbh.groupby_gene_id(), roI3spqORKae(ES5oEprVxulp(b'\xd5\xb1\xcc\x7f\xe5w\x06\x90\x06\x9a\x95\xf4'), chr(0b101100 + 0o70) + chr(0b1100001 + 0o4) + '\143' + chr(0b1101111) + chr(100) + chr(0b1100101))(chr(0b11010 + 0o133) + '\164' + '\146' + '\x2d' + '\x38'))())) |
openvax/varcode | varcode/effects/effect_collection.py | EffectCollection.effect_expression | def effect_expression(self, expression_levels):
"""
Parameters
----------
expression_levels : dict
Dictionary mapping transcript IDs to length-normalized expression
levels (either FPKM or TPM)
Returns dictionary mapping each transcript effect to an expression
quantity. Effects that don't have an associated transcript
(e.g. Intergenic) will not be included.
"""
return OrderedDict(
(effect, expression_levels.get(effect.transcript.id, 0.0))
for effect in self
if effect.transcript is not None) | python | def effect_expression(self, expression_levels):
"""
Parameters
----------
expression_levels : dict
Dictionary mapping transcript IDs to length-normalized expression
levels (either FPKM or TPM)
Returns dictionary mapping each transcript effect to an expression
quantity. Effects that don't have an associated transcript
(e.g. Intergenic) will not be included.
"""
return OrderedDict(
(effect, expression_levels.get(effect.transcript.id, 0.0))
for effect in self
if effect.transcript is not None) | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/effect_collection.py#L232-L247 | train | Returns a dictionary mapping each transcript effect to an expression level. | 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(187 - 139) + chr(111) + chr(0b110100) + '\063', 26842 - 26834), nzTpIcepk0o8(chr(0b100010 + 0o16) + '\157' + chr(0b110001) + chr(0b11 + 0o63) + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(1935 - 1886) + '\062' + '\067', 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(1519 - 1470) + chr(0b1100 + 0o50), 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(0b110001) + chr(0b110001) + chr(2403 - 2350), 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(0b101010 + 0o10) + chr(866 - 811) + chr(2040 - 1985), ord("\x08")), nzTpIcepk0o8(chr(0b1001 + 0o47) + '\157' + '\061' + chr(0b110001) + chr(0b100001 + 0o20), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + '\065' + chr(0b111 + 0o54), 50147 - 50139), nzTpIcepk0o8(chr(0b11111 + 0o21) + chr(2646 - 2535) + chr(0b110010) + '\x33' + chr(0b1010 + 0o54), 55889 - 55881), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b1111 + 0o42) + chr(0b110101) + '\060', 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110011) + '\064' + '\067', 0b1000), nzTpIcepk0o8(chr(317 - 269) + chr(111) + chr(49) + chr(0b100011 + 0o15) + chr(655 - 603), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b1001 + 0o52) + chr(1888 - 1838) + '\061', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110001) + '\x31' + chr(51), 0o10), nzTpIcepk0o8(chr(0b11100 + 0o24) + '\x6f' + '\062' + '\064' + chr(1103 - 1054), 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(50) + chr(1656 - 1602) + chr(0b110000), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(51) + chr(50) + chr(50), 0o10), nzTpIcepk0o8('\060' + chr(0b1110 + 0o141) + chr(630 - 578) + chr(2153 - 2104), 33126 - 33118), nzTpIcepk0o8('\060' + chr(0b10110 + 0o131) + '\063' + '\x35' + '\x35', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110010) + '\x37' + chr(53), 47832 - 47824), nzTpIcepk0o8(chr(48) + chr(0b100011 + 0o114) + chr(0b1000 + 0o52) + chr(0b100010 + 0o23) + chr(1880 - 1825), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1000 + 0o147) + chr(0b10001 + 0o41) + '\x35' + chr(0b101 + 0o62), 8), nzTpIcepk0o8(chr(0b10 + 0o56) + '\157' + chr(0b1100 + 0o45) + '\061' + chr(270 - 215), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + '\063' + chr(0b110110), 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110011) + '\066' + '\x33', 18681 - 18673), nzTpIcepk0o8(chr(48) + '\157' + '\x31' + chr(51), 0o10), nzTpIcepk0o8(chr(2269 - 2221) + chr(0b1101111) + chr(0b10 + 0o61) + chr(0b11110 + 0o24) + chr(0b101111 + 0o6), 45068 - 45060), nzTpIcepk0o8(chr(562 - 514) + '\x6f' + '\062' + chr(0b110011) + chr(0b10110 + 0o34), 61481 - 61473), nzTpIcepk0o8(chr(0b101100 + 0o4) + '\157' + '\063' + chr(54) + chr(0b101111 + 0o7), ord("\x08")), nzTpIcepk0o8(chr(194 - 146) + chr(0b1101111) + chr(51) + chr(489 - 436) + '\066', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b111111 + 0o60) + '\x33' + chr(0b110000) + chr(0b110010), 21373 - 21365), nzTpIcepk0o8(chr(1463 - 1415) + '\x6f' + chr(379 - 330) + chr(48) + chr(912 - 864), 0o10), nzTpIcepk0o8('\x30' + chr(111) + '\x31' + chr(50) + chr(1893 - 1845), 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(0b101111 + 0o4) + chr(2161 - 2113) + chr(1781 - 1733), ord("\x08")), nzTpIcepk0o8(chr(2057 - 2009) + chr(0b1101111) + '\x37' + '\060', 64205 - 64197), nzTpIcepk0o8('\060' + chr(111) + '\x33' + chr(55) + '\x31', 24560 - 24552), nzTpIcepk0o8(chr(0b1101 + 0o43) + chr(5244 - 5133) + chr(0b110111) + chr(0b110101), 21129 - 21121), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\062' + chr(0b11010 + 0o33) + '\064', 0o10), nzTpIcepk0o8(chr(48) + chr(0b10011 + 0o134) + chr(0b110100) + chr(0b110001), 8), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(1457 - 1406) + chr(48) + chr(0b110111), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + chr(111) + chr(1630 - 1577) + '\060', 29356 - 29348)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\r'), chr(0b1011100 + 0o10) + chr(5599 - 5498) + chr(0b1100011) + chr(111) + chr(100) + '\145')(chr(0b1110101) + chr(7806 - 7690) + chr(102) + chr(0b100110 + 0o7) + chr(2765 - 2709)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def tuEAgog2vNiM(hXMPsSrOQzbh, OSW3kTdKrKc2):
return Ov4KLivfl4p6(((WueclzVPVP7r, roI3spqORKae(OSW3kTdKrKc2, roI3spqORKae(ES5oEprVxulp(b'd \x1ci9\xca}S\xff/\x94\x0e'), chr(0b0 + 0o144) + chr(0b11101 + 0o110) + chr(0b1100011) + chr(111) + chr(0b1011111 + 0o5) + '\145')(chr(0b1110101) + chr(5805 - 5689) + chr(0b1100110) + '\055' + '\070'))(roI3spqORKae(WueclzVPVP7r.transcript, roI3spqORKae(ES5oEprVxulp(b'N\x14\x1bb\x01\xd8qd\xab\x12\xb7\x10'), chr(0b10001 + 0o123) + chr(3042 - 2941) + '\x63' + chr(0b1101000 + 0o7) + chr(3132 - 3032) + chr(101))(chr(0b1110101) + chr(0b1110100) + chr(0b1100110) + '\x2d' + '\x38')), 0.0)) for WueclzVPVP7r in hXMPsSrOQzbh if roI3spqORKae(WueclzVPVP7r, roI3spqORKae(ES5oEprVxulp(b'W\x076b>\xdc;B\xee\x1c'), '\x64' + '\145' + chr(99) + chr(111) + chr(0b1100100) + chr(0b10110 + 0o117))('\x75' + chr(116) + '\x66' + chr(45) + '\070')) is not None)) |
openvax/varcode | varcode/effects/effect_collection.py | EffectCollection.top_expression_effect | def top_expression_effect(self, expression_levels):
"""
Return effect whose transcript has the highest expression level.
If none of the effects are expressed or have associated transcripts,
then return None. In case of ties, add lexicographical sorting by
effect priority and transcript length.
"""
effect_expression_dict = self.effect_expression(expression_levels)
if len(effect_expression_dict) == 0:
return None
def key_fn(effect_fpkm_pair):
"""
Sort effects primarily by their expression level
and secondarily by the priority logic used in
`top_priority_effect`.
"""
(effect, fpkm) = effect_fpkm_pair
return (fpkm, multi_gene_effect_sort_key(effect))
return max(effect_expression_dict.items(), key=key_fn)[0] | python | def top_expression_effect(self, expression_levels):
"""
Return effect whose transcript has the highest expression level.
If none of the effects are expressed or have associated transcripts,
then return None. In case of ties, add lexicographical sorting by
effect priority and transcript length.
"""
effect_expression_dict = self.effect_expression(expression_levels)
if len(effect_expression_dict) == 0:
return None
def key_fn(effect_fpkm_pair):
"""
Sort effects primarily by their expression level
and secondarily by the priority logic used in
`top_priority_effect`.
"""
(effect, fpkm) = effect_fpkm_pair
return (fpkm, multi_gene_effect_sort_key(effect))
return max(effect_expression_dict.items(), key=key_fn)[0] | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/effect_collection.py#L249-L270 | train | Return the highest expression effect that has the highest expression level. | 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(79 - 28) + chr(0b110010) + '\064', 54614 - 54606), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110010) + chr(0b11101 + 0o27) + chr(2026 - 1978), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b101000 + 0o13) + chr(405 - 353) + '\x36', 0o10), nzTpIcepk0o8(chr(0b100010 + 0o16) + chr(0b10101 + 0o132) + '\x31' + '\x31' + '\060', 0b1000), nzTpIcepk0o8(chr(1060 - 1012) + chr(0b1101111) + chr(386 - 335) + chr(0b101101 + 0o11) + chr(267 - 217), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(50) + chr(2722 - 2668) + chr(49), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x31' + '\x31', 0b1000), nzTpIcepk0o8(chr(0b11000 + 0o30) + chr(0b110001 + 0o76) + chr(0b110001) + chr(53) + chr(211 - 159), 0b1000), nzTpIcepk0o8(chr(0b100001 + 0o17) + '\x6f' + chr(1180 - 1131) + chr(1597 - 1548) + chr(48), 8), nzTpIcepk0o8(chr(2286 - 2238) + '\157' + chr(51) + '\x36', 0b1000), nzTpIcepk0o8('\060' + chr(3848 - 3737) + chr(0b110001) + chr(0b1001 + 0o54) + chr(0b100011 + 0o23), 22834 - 22826), nzTpIcepk0o8(chr(0b110000) + chr(6007 - 5896) + chr(50) + '\x34' + chr(48), 8), nzTpIcepk0o8(chr(0b11000 + 0o30) + '\157' + chr(0b101001 + 0o12) + chr(55) + chr(0b101110 + 0o4), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(490 - 441) + chr(0b110001) + '\x32', ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + '\063' + '\x34' + chr(0b0 + 0o60), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(0b100101 + 0o16) + '\062' + '\060', ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(49) + '\x31' + chr(0b10000 + 0o41), 0b1000), nzTpIcepk0o8(chr(0b100001 + 0o17) + chr(0b1101111) + chr(49) + chr(0b110000), 0o10), nzTpIcepk0o8(chr(1779 - 1731) + '\x6f' + chr(51) + chr(1036 - 982) + '\x30', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(8564 - 8453) + '\066' + '\064', 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(805 - 756) + chr(0b10110 + 0o40) + chr(48), 0o10), nzTpIcepk0o8(chr(144 - 96) + chr(0b1011000 + 0o27) + '\x33' + chr(1607 - 1558) + chr(0b110001 + 0o6), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(249 - 200) + '\060' + '\x37', ord("\x08")), nzTpIcepk0o8(chr(1460 - 1412) + chr(0b11001 + 0o126) + chr(0b1001 + 0o50) + '\065', ord("\x08")), nzTpIcepk0o8(chr(2091 - 2043) + chr(0b100111 + 0o110) + '\063' + chr(1213 - 1162) + '\061', 0o10), nzTpIcepk0o8(chr(0b100 + 0o54) + chr(5324 - 5213) + '\x32' + chr(49) + chr(49), 3797 - 3789), nzTpIcepk0o8('\060' + '\157' + '\x31' + chr(52) + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(1777 - 1729) + chr(111) + '\x33' + chr(0b110011) + chr(0b101 + 0o56), 63730 - 63722), nzTpIcepk0o8('\x30' + chr(111) + chr(0b11110 + 0o24) + '\061' + chr(0b11101 + 0o31), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b10111 + 0o32) + chr(0b110011) + '\062', 41555 - 41547), nzTpIcepk0o8('\060' + chr(5585 - 5474) + '\x33' + chr(0b1001 + 0o54) + chr(53), 0b1000), nzTpIcepk0o8(chr(0b0 + 0o60) + chr(111) + chr(49) + chr(640 - 589) + chr(0b10010 + 0o43), 41466 - 41458), nzTpIcepk0o8(chr(1602 - 1554) + '\x6f' + '\063' + '\066' + chr(0b10110 + 0o40), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b0 + 0o157) + chr(0b0 + 0o61) + chr(0b1111 + 0o50) + chr(49), 62013 - 62005), nzTpIcepk0o8('\x30' + '\x6f' + chr(49) + chr(0b11001 + 0o30) + '\067', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b1011 + 0o47) + '\x37' + chr(55), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(3534 - 3423) + chr(0b1010 + 0o50) + chr(0b101011 + 0o14) + chr(0b110111), 8), nzTpIcepk0o8(chr(0b110000) + chr(3524 - 3413) + chr(51) + chr(983 - 930) + '\x30', 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(51) + '\060' + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(725 - 677) + '\157' + chr(2067 - 2016) + '\x31' + chr(0b10110 + 0o41), 8)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b101111 + 0o1) + chr(0b1101111) + '\x35' + chr(48), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xfa'), '\144' + chr(0b1011010 + 0o13) + chr(0b110001 + 0o62) + chr(4227 - 4116) + chr(7565 - 7465) + chr(0b111100 + 0o51))(chr(10985 - 10868) + chr(13133 - 13017) + chr(6237 - 6135) + chr(69 - 24) + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def SSoT_dg6rXVq(hXMPsSrOQzbh, OSW3kTdKrKc2):
K58z6udqfNtY = hXMPsSrOQzbh.effect_expression(OSW3kTdKrKc2)
if ftfygxgFas5X(K58z6udqfNtY) == nzTpIcepk0o8(chr(48) + '\x6f' + chr(328 - 280), 22367 - 22359):
return None
def PBvuaW9OOPCV(gO2OGsqKQJGG):
(WueclzVPVP7r, symZFUmSLaph) = gO2OGsqKQJGG
return (symZFUmSLaph, IEpds8shfG9T(WueclzVPVP7r))
return KV9ckIhroIia(roI3spqORKae(K58z6udqfNtY, roI3spqORKae(ES5oEprVxulp(b'\x8d\xff\x88\x06\xb7\xcbAX{h6\xc9'), chr(7274 - 7174) + chr(101) + chr(9173 - 9074) + chr(0b1010 + 0o145) + '\144' + '\145')(chr(7913 - 7796) + chr(116) + chr(0b10110 + 0o120) + '\x2d' + chr(1920 - 1864)))(), key=PBvuaW9OOPCV)[nzTpIcepk0o8(chr(562 - 514) + chr(6501 - 6390) + '\060', 8)] |
openvax/varcode | varcode/effects/effect_collection.py | EffectCollection.to_dataframe | def to_dataframe(self):
"""Build a dataframe from the effect collection"""
# list of properties to extract from Variant objects if they're
# not None
variant_properties = [
"contig",
"start",
"ref",
"alt",
"is_snv",
"is_transversion",
"is_transition"
]
def row_from_effect(effect):
row = OrderedDict()
row['variant'] = str(effect.variant.short_description)
for field_name in variant_properties:
# if effect.variant is None then this column value will be None
row[field_name] = getattr(effect.variant, field_name, None)
row['gene_id'] = effect.gene_id
row['gene_name'] = effect.gene_name
row['transcript_id'] = effect.transcript_id
row['transcript_name'] = effect.transcript_name
row['effect_type'] = effect.__class__.__name__
row['effect'] = effect.short_description
return row
return pd.DataFrame.from_records([row_from_effect(effect) for effect in self]) | python | def to_dataframe(self):
"""Build a dataframe from the effect collection"""
# list of properties to extract from Variant objects if they're
# not None
variant_properties = [
"contig",
"start",
"ref",
"alt",
"is_snv",
"is_transversion",
"is_transition"
]
def row_from_effect(effect):
row = OrderedDict()
row['variant'] = str(effect.variant.short_description)
for field_name in variant_properties:
# if effect.variant is None then this column value will be None
row[field_name] = getattr(effect.variant, field_name, None)
row['gene_id'] = effect.gene_id
row['gene_name'] = effect.gene_name
row['transcript_id'] = effect.transcript_id
row['transcript_name'] = effect.transcript_name
row['effect_type'] = effect.__class__.__name__
row['effect'] = effect.short_description
return row
return pd.DataFrame.from_records([row_from_effect(effect) for effect in self]) | [
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"effect",
"collection"
] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/effects/effect_collection.py#L272-L301 | train | Build a dataframe from the effect collection | 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(50) + chr(1599 - 1546) + chr(0b1100 + 0o45), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\063' + '\062' + chr(1254 - 1199), 0o10), nzTpIcepk0o8(chr(48) + chr(0b111110 + 0o61) + chr(49) + chr(2379 - 2326), 21318 - 21310), nzTpIcepk0o8(chr(0b110000) + chr(7233 - 7122) + '\063' + '\061' + '\060', ord("\x08")), nzTpIcepk0o8(chr(0b10111 + 0o31) + chr(0b1101111) + chr(0b1100 + 0o46) + chr(322 - 273) + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110001) + '\065', 8), nzTpIcepk0o8(chr(1011 - 963) + chr(0b1000100 + 0o53) + chr(0b110001) + chr(0b110110) + chr(0b1101 + 0o45), 0o10), nzTpIcepk0o8(chr(73 - 25) + chr(0b1101111) + chr(0b110010) + chr(1309 - 1261) + '\064', 31290 - 31282), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(50) + chr(0b110101) + '\x35', 51273 - 51265), nzTpIcepk0o8(chr(0b100101 + 0o13) + '\x6f' + '\066' + chr(0b110000), 0b1000), nzTpIcepk0o8(chr(2294 - 2246) + '\x6f' + '\063' + chr(0b110101), 13729 - 13721), nzTpIcepk0o8(chr(48) + chr(3030 - 2919) + chr(51) + chr(0b110110 + 0o1) + chr(55), 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(51) + chr(0b1101 + 0o52) + chr(0b1010 + 0o52), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x36' + '\065', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x31' + '\x32' + '\062', 0b1000), nzTpIcepk0o8('\060' + chr(0b1001010 + 0o45) + chr(0b1001 + 0o50) + '\x35', 8), nzTpIcepk0o8(chr(48) + chr(7852 - 7741) + chr(50) + chr(707 - 657) + chr(1277 - 1226), ord("\x08")), nzTpIcepk0o8(chr(1904 - 1856) + chr(0b1100110 + 0o11) + '\061' + '\x37' + '\061', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(4653 - 4542) + '\x31' + chr(0b110000) + chr(48), 0o10), nzTpIcepk0o8(chr(128 - 80) + chr(111) + '\x31' + chr(49) + '\061', 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110000 + 0o3) + chr(0b110000) + chr(0b110001), 0o10), nzTpIcepk0o8('\060' + chr(0b1011001 + 0o26) + chr(2101 - 2050) + chr(54), ord("\x08")), nzTpIcepk0o8(chr(619 - 571) + chr(111) + '\062' + chr(687 - 638) + '\067', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b110111 + 0o70) + chr(1214 - 1164) + chr(0b11011 + 0o26) + chr(0b1111 + 0o43), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1011110 + 0o21) + chr(0b110011) + chr(50) + '\060', ord("\x08")), nzTpIcepk0o8(chr(0b1011 + 0o45) + chr(11422 - 11311) + '\x33' + chr(0b11000 + 0o30) + chr(53), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(49) + chr(0b110000) + chr(676 - 621), 54836 - 54828), nzTpIcepk0o8(chr(0b10010 + 0o36) + '\x6f' + chr(50) + '\067', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x32' + chr(0b110010) + '\060', 11737 - 11729), nzTpIcepk0o8(chr(48) + chr(8636 - 8525) + chr(49) + chr(623 - 570) + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(49) + '\x36' + chr(0b10011 + 0o41), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(50) + chr(2442 - 2391) + chr(0b110011), 0o10), nzTpIcepk0o8(chr(1360 - 1312) + '\157' + '\x37' + '\062', 63147 - 63139), nzTpIcepk0o8('\060' + '\x6f' + chr(50) + chr(0b100100 + 0o20) + '\x31', 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(1499 - 1450) + '\x35' + '\062', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(138 - 87) + chr(53) + '\062', 52946 - 52938), nzTpIcepk0o8(chr(1894 - 1846) + chr(111) + chr(982 - 929) + chr(0b101110 + 0o6), 0o10), nzTpIcepk0o8('\060' + chr(8051 - 7940) + chr(49) + chr(0b11011 + 0o27) + chr(2520 - 2466), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b11000 + 0o127) + '\x33' + chr(0b1100 + 0o52) + '\064', 6122 - 6114), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x33' + chr(55) + chr(0b110110), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(685 - 637) + chr(0b1101111) + chr(0b101111 + 0o6) + '\060', 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x87'), chr(100) + '\x65' + chr(826 - 727) + chr(10080 - 9969) + chr(3699 - 3599) + '\145')('\165' + chr(116) + '\146' + chr(332 - 287) + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def ZQVHZJY0d7Ug(hXMPsSrOQzbh):
ghtcPb7lJdQ_ = [roI3spqORKae(ES5oEprVxulp(b'\xca\xb8c\xbc\xe1j'), chr(0b1100100) + '\x65' + chr(0b1100011) + chr(111) + chr(0b1100100) + '\x65')(chr(0b101010 + 0o113) + chr(0b1100011 + 0o21) + chr(0b101101 + 0o71) + '\055' + chr(0b11010 + 0o36)), roI3spqORKae(ES5oEprVxulp(b'\xda\xa3l\xba\xfc'), chr(0b1001101 + 0o27) + chr(5246 - 5145) + chr(0b110011 + 0o60) + chr(111) + '\144' + chr(0b1100101))(chr(117) + chr(0b101011 + 0o111) + chr(0b1100110) + chr(0b101101) + chr(287 - 231)), roI3spqORKae(ES5oEprVxulp(b'\xdb\xb2k'), chr(0b1001000 + 0o34) + chr(101) + chr(0b1100 + 0o127) + chr(0b1101111) + '\x64' + chr(0b11 + 0o142))(chr(11711 - 11594) + '\x74' + chr(0b1100110) + '\x2d' + chr(3045 - 2989)), roI3spqORKae(ES5oEprVxulp(b'\xc8\xbby'), '\x64' + chr(0b11110 + 0o107) + '\x63' + chr(7333 - 7222) + chr(100) + '\x65')(chr(3640 - 3523) + '\164' + '\146' + chr(45) + chr(56)), roI3spqORKae(ES5oEprVxulp(b'\xc0\xa4R\xbb\xe6{'), chr(1608 - 1508) + chr(101) + chr(0b1011111 + 0o4) + chr(1506 - 1395) + chr(100) + chr(2576 - 2475))('\165' + chr(0b10 + 0o162) + chr(0b1100110) + chr(45) + chr(0b1 + 0o67)), roI3spqORKae(ES5oEprVxulp(b'\xc0\xa4R\xbc\xfal\x1c\xf7\xdbUo\x8c\x95Z<'), chr(0b1100100) + chr(101) + '\x63' + chr(3101 - 2990) + chr(0b1100100) + '\x65')(chr(0b11110 + 0o127) + chr(0b1100111 + 0o15) + chr(0b11110 + 0o110) + chr(584 - 539) + chr(0b10010 + 0o46)), roI3spqORKae(ES5oEprVxulp(b'\xc0\xa4R\xbc\xfal\x1c\xf7\xc4Dt\x90\x92'), chr(1659 - 1559) + chr(6919 - 6818) + '\143' + '\157' + chr(0b1010101 + 0o17) + '\x65')('\165' + '\x74' + chr(0b1100110) + chr(0b10111 + 0o26) + chr(56))]
def HNLusP6IdoEv(WueclzVPVP7r):
o6UWUO21mH25 = Ov4KLivfl4p6()
o6UWUO21mH25[roI3spqORKae(ES5oEprVxulp(b'\xdf\xb6\x7f\xa1\xe9c\x06'), chr(346 - 246) + '\x65' + chr(0b1100011) + chr(0b1011101 + 0o22) + chr(100) + '\x65')(chr(9510 - 9393) + chr(0b1100100 + 0o20) + chr(4580 - 4478) + '\x2d' + chr(0b110011 + 0o5))] = N9zlRy29S1SS(WueclzVPVP7r.variant.wscK6j25Wew0)
for XTg7r9SbyaPD in ghtcPb7lJdQ_:
o6UWUO21mH25[XTg7r9SbyaPD] = roI3spqORKae(WueclzVPVP7r.variant, XTg7r9SbyaPD, None)
o6UWUO21mH25[roI3spqORKae(ES5oEprVxulp(b'\xce\xb2c\xad\xd7d\x16'), chr(3396 - 3296) + chr(101) + '\143' + chr(111) + '\144' + '\145')(chr(117) + chr(1730 - 1614) + chr(0b1100110) + '\055' + chr(0b111000))] = WueclzVPVP7r.gene_id
o6UWUO21mH25[roI3spqORKae(ES5oEprVxulp(b'\xce\xb2c\xad\xd7c\x13\xe9\xc8'), '\144' + chr(0b1011 + 0o132) + chr(5454 - 5355) + '\x6f' + '\144' + chr(0b1100101))('\165' + chr(116) + chr(8553 - 8451) + '\055' + chr(56))] = WueclzVPVP7r.gene_name
o6UWUO21mH25[roI3spqORKae(ES5oEprVxulp(b'\xdd\xa5l\xa6\xfbn\x00\xed\xddDB\x96\x98'), chr(1604 - 1504) + '\145' + chr(99) + chr(12260 - 12149) + '\144' + chr(1095 - 994))('\165' + chr(8831 - 8715) + chr(0b1100110) + chr(0b100010 + 0o13) + chr(1234 - 1178))] = WueclzVPVP7r.transcript_id
o6UWUO21mH25[roI3spqORKae(ES5oEprVxulp(b'\xdd\xa5l\xa6\xfbn\x00\xed\xddDB\x91\x9dX7'), chr(100) + '\x65' + '\143' + chr(0b1001000 + 0o47) + '\x64' + chr(4037 - 3936))(chr(0b1100101 + 0o20) + '\164' + '\x66' + chr(45) + chr(0b111000))] = WueclzVPVP7r.transcript_name
o6UWUO21mH25[roI3spqORKae(ES5oEprVxulp(b'\xcc\xb1k\xad\xeby-\xf0\xd4@x'), chr(9108 - 9008) + chr(0b101111 + 0o66) + chr(99) + chr(2535 - 2424) + chr(0b110011 + 0o61) + '\x65')(chr(0b111011 + 0o72) + '\164' + chr(0b1100110) + '\055' + '\x38')] = WueclzVPVP7r.__class__.AYtDRlqeP0tq
o6UWUO21mH25[roI3spqORKae(ES5oEprVxulp(b'\xcc\xb1k\xad\xeby'), '\144' + '\145' + chr(99) + chr(0b111000 + 0o67) + '\x64' + chr(0b110 + 0o137))(chr(117) + chr(0b1110100) + '\x66' + '\055' + chr(0b111000))] = WueclzVPVP7r.wscK6j25Wew0
return o6UWUO21mH25
return roI3spqORKae(HLKt4sa1j9hm.DataFrame, roI3spqORKae(ES5oEprVxulp(b'\xcf\xa5b\xa5\xd7\x7f\x17\xe7\xc2By\x8c'), '\x64' + chr(4493 - 4392) + chr(99) + chr(0b1101111) + chr(100) + chr(0b1100101))(chr(117) + '\164' + chr(0b1100110) + chr(892 - 847) + '\x38'))([HNLusP6IdoEv(WueclzVPVP7r) for WueclzVPVP7r in hXMPsSrOQzbh]) |
openvax/varcode | varcode/util.py | random_variants | def random_variants(
count,
genome_name="GRCh38",
deletions=True,
insertions=True,
random_seed=None):
"""
Generate a VariantCollection with random variants that overlap
at least one complete coding transcript.
"""
rng = random.Random(random_seed)
ensembl = genome_for_reference_name(genome_name)
if ensembl in _transcript_ids_cache:
transcript_ids = _transcript_ids_cache[ensembl]
else:
transcript_ids = ensembl.transcript_ids()
_transcript_ids_cache[ensembl] = transcript_ids
variants = []
# we should finish way before this loop is over but just in case
# something is wrong with PyEnsembl we want to avoid an infinite loop
for _ in range(count * 100):
if len(variants) < count:
transcript_id = rng.choice(transcript_ids)
transcript = ensembl.transcript_by_id(transcript_id)
if not transcript.complete:
continue
exon = rng.choice(transcript.exons)
base1_genomic_position = rng.randint(exon.start, exon.end)
transcript_offset = transcript.spliced_offset(base1_genomic_position)
seq = transcript.sequence
ref = str(seq[transcript_offset])
if transcript.on_backward_strand:
ref = reverse_complement(ref)
alt_nucleotides = [x for x in STANDARD_NUCLEOTIDES if x != ref]
if insertions:
nucleotide_pairs = [
x + y
for x in STANDARD_NUCLEOTIDES
for y in STANDARD_NUCLEOTIDES
]
alt_nucleotides.extend(nucleotide_pairs)
if deletions:
alt_nucleotides.append("")
alt = rng.choice(alt_nucleotides)
variant = Variant(
transcript.contig,
base1_genomic_position,
ref=ref,
alt=alt,
ensembl=ensembl)
variants.append(variant)
else:
return VariantCollection(variants)
raise ValueError(
("Unable to generate %d random variants, "
"there may be a problem with PyEnsembl") % count) | python | def random_variants(
count,
genome_name="GRCh38",
deletions=True,
insertions=True,
random_seed=None):
"""
Generate a VariantCollection with random variants that overlap
at least one complete coding transcript.
"""
rng = random.Random(random_seed)
ensembl = genome_for_reference_name(genome_name)
if ensembl in _transcript_ids_cache:
transcript_ids = _transcript_ids_cache[ensembl]
else:
transcript_ids = ensembl.transcript_ids()
_transcript_ids_cache[ensembl] = transcript_ids
variants = []
# we should finish way before this loop is over but just in case
# something is wrong with PyEnsembl we want to avoid an infinite loop
for _ in range(count * 100):
if len(variants) < count:
transcript_id = rng.choice(transcript_ids)
transcript = ensembl.transcript_by_id(transcript_id)
if not transcript.complete:
continue
exon = rng.choice(transcript.exons)
base1_genomic_position = rng.randint(exon.start, exon.end)
transcript_offset = transcript.spliced_offset(base1_genomic_position)
seq = transcript.sequence
ref = str(seq[transcript_offset])
if transcript.on_backward_strand:
ref = reverse_complement(ref)
alt_nucleotides = [x for x in STANDARD_NUCLEOTIDES if x != ref]
if insertions:
nucleotide_pairs = [
x + y
for x in STANDARD_NUCLEOTIDES
for y in STANDARD_NUCLEOTIDES
]
alt_nucleotides.extend(nucleotide_pairs)
if deletions:
alt_nucleotides.append("")
alt = rng.choice(alt_nucleotides)
variant = Variant(
transcript.contig,
base1_genomic_position,
ref=ref,
alt=alt,
ensembl=ensembl)
variants.append(variant)
else:
return VariantCollection(variants)
raise ValueError(
("Unable to generate %d random variants, "
"there may be a problem with PyEnsembl") % count) | [
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] | 981633db45ca2b31f76c06894a7360ea5d70a9b8 | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/util.py#L29-L92 | train | Generate a VariantCollection with random variants that overlap at least one complete coding transcript. | 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(0b10010 + 0o135) + chr(477 - 428), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + '\061' + '\066' + '\x30', 0o10), nzTpIcepk0o8('\x30' + '\x6f' + '\x34' + '\066', 33085 - 33077), nzTpIcepk0o8(chr(1741 - 1693) + '\157' + '\063' + chr(2380 - 2328) + chr(54), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110010) + '\061' + chr(0b110101 + 0o0), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110001) + '\x34', 60835 - 60827), nzTpIcepk0o8('\x30' + '\157' + '\x31' + chr(0b110001 + 0o0) + '\x36', 0o10), nzTpIcepk0o8('\x30' + chr(0b10000 + 0o137) + chr(0b110010) + chr(0b110101) + '\x37', 6015 - 6007), nzTpIcepk0o8(chr(48) + chr(10233 - 10122) + '\x34' + chr(0b110101), 58225 - 58217), nzTpIcepk0o8(chr(1621 - 1573) + chr(245 - 134) + chr(51) + chr(0b110010 + 0o1) + chr(0b110001), 0o10), nzTpIcepk0o8(chr(48) + chr(0b101101 + 0o102) + chr(819 - 769) + '\x33' + chr(0b110010), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b11110 + 0o26), 0o10), nzTpIcepk0o8(chr(48) + chr(7840 - 7729) + chr(404 - 354) + chr(0b110010) + chr(0b10 + 0o60), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(10438 - 10327) + '\067', ord("\x08")), nzTpIcepk0o8(chr(0b11001 + 0o27) + chr(6943 - 6832) + '\063' + '\x30' + '\064', ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b1000 + 0o51) + chr(50) + '\062', 63901 - 63893), nzTpIcepk0o8('\060' + chr(10723 - 10612) + '\063' + chr(55) + '\x30', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b100111 + 0o12) + '\062' + '\x34', 757 - 749), nzTpIcepk0o8(chr(1648 - 1600) + chr(0b1101111) + chr(0b110010) + chr(0b110000 + 0o7) + chr(1312 - 1258), 0o10), nzTpIcepk0o8(chr(0b11000 + 0o30) + '\x6f' + '\x31' + chr(52) + chr(443 - 393), 0o10), nzTpIcepk0o8(chr(1002 - 954) + '\157' + chr(0b110001) + '\067' + chr(54), ord("\x08")), nzTpIcepk0o8(chr(215 - 167) + chr(111) + '\062' + chr(0b100101 + 0o14) + chr(0b1110 + 0o47), 8), nzTpIcepk0o8('\060' + chr(5500 - 5389) + chr(0b110001) + chr(0b110110) + '\x32', 3327 - 3319), nzTpIcepk0o8(chr(0b101110 + 0o2) + chr(0b1101111) + chr(50) + chr(55) + chr(0b101111 + 0o6), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(0b110001) + '\061' + chr(52), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(483 - 434) + chr(441 - 391) + chr(55), 0b1000), nzTpIcepk0o8(chr(1508 - 1460) + '\157' + '\x33' + chr(0b110011) + '\x33', ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(51) + chr(1960 - 1906) + '\x34', 0b1000), nzTpIcepk0o8(chr(0b10001 + 0o37) + chr(6678 - 6567) + chr(0b110010) + '\066', 0b1000), nzTpIcepk0o8(chr(1858 - 1810) + '\x6f' + '\063' + '\x33' + chr(0b100010 + 0o23), 25939 - 25931), nzTpIcepk0o8('\060' + chr(8454 - 8343) + chr(0b100110 + 0o14) + chr(0b1111 + 0o45) + chr(52), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\061' + chr(54) + chr(0b110011), 0o10), nzTpIcepk0o8('\x30' + '\157' + '\066' + chr(0b101100 + 0o5), 34429 - 34421), nzTpIcepk0o8('\x30' + chr(3221 - 3110) + chr(0b100100 + 0o17) + chr(0b110101) + chr(0b110111), 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(0b10101 + 0o34) + '\x35', 33100 - 33092), nzTpIcepk0o8(chr(0b10000 + 0o40) + chr(12301 - 12190) + '\x33' + '\062' + chr(48), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b101000 + 0o107) + chr(0b110011) + '\063' + chr(1321 - 1272), 8), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b101111 + 0o3) + chr(51) + '\x33', 0o10), nzTpIcepk0o8(chr(1793 - 1745) + chr(0b1101111) + chr(0b100111 + 0o12) + chr(48) + chr(0b110111), ord("\x08")), nzTpIcepk0o8('\060' + chr(9852 - 9741) + chr(1603 - 1553) + chr(2220 - 2168), 50789 - 50781)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(2275 - 2227) + '\x6f' + chr(53) + '\x30', 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'/'), '\x64' + '\145' + chr(0b1100011) + '\157' + chr(2474 - 2374) + '\x65')(chr(0b1000100 + 0o61) + chr(116) + chr(0b1011001 + 0o15) + '\x2d' + chr(0b1101 + 0o53)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def AfmaklqH2IJn(sQSWKlURp7QK, B5s4DDW7ciwT=roI3spqORKae(ES5oEprVxulp(b'F"e\x8e\xbe4'), chr(0b1100100) + '\145' + chr(0b1100011) + '\157' + chr(100) + '\145')(chr(2573 - 2456) + chr(10557 - 10441) + '\146' + '\x2d' + chr(56)), NWOVMdyfqeot=nzTpIcepk0o8(chr(148 - 100) + chr(197 - 86) + chr(0b100110 + 0o13), 8), pwpNKlKwab9j=nzTpIcepk0o8(chr(0b101110 + 0o2) + chr(0b1101111) + '\061', 8), b_yicrCODGH3=None):
x_UFAccWeIYv = PNI8nORkWcyJ.Random(b_yicrCODGH3)
NorgxGKZkMaz = coA7E3pLHPgE(B5s4DDW7ciwT)
if NorgxGKZkMaz in KERQGHuDZJja:
TBWgDyhycJQZ = KERQGHuDZJja[NorgxGKZkMaz]
else:
TBWgDyhycJQZ = NorgxGKZkMaz.transcript_ids()
KERQGHuDZJja[NorgxGKZkMaz] = TBWgDyhycJQZ
Loszd1LxpkfW = []
for zIqcgNgQ9U6F in bbT2xIe5pzk7(sQSWKlURp7QK * nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(49) + chr(52) + chr(0b110100), 0b1000)):
if ftfygxgFas5X(Loszd1LxpkfW) < sQSWKlURp7QK:
W8heJMGuhcUE = x_UFAccWeIYv.choice(TBWgDyhycJQZ)
lnOu7fTAiCZI = NorgxGKZkMaz.transcript_by_id(W8heJMGuhcUE)
if not roI3spqORKae(lnOu7fTAiCZI, roI3spqORKae(ES5oEprVxulp(b'U\x14S\xb3\xd8`\x1b\xc4r\x89\xe92'), chr(6368 - 6268) + chr(101) + '\x63' + chr(0b111011 + 0o64) + chr(5949 - 5849) + '\145')(chr(0b1101101 + 0o10) + chr(0b101011 + 0o111) + chr(0b101011 + 0o73) + '\055' + chr(0b111000))):
continue
Rxu3AkImGCU1 = x_UFAccWeIYv.choice(lnOu7fTAiCZI.exons)
kKLisrkL4vpU = x_UFAccWeIYv.randint(Rxu3AkImGCU1.KQbHFTcl_LKy, Rxu3AkImGCU1.NiWVjAWn0l6T)
yoXAYvufKlQI = lnOu7fTAiCZI.spliced_offset(kKLisrkL4vpU)
ftk9lc7G5FOo = lnOu7fTAiCZI.AaFeo0lw34C3
CmNScfxJ1Uih = N9zlRy29S1SS(ftk9lc7G5FOo[yoXAYvufKlQI])
if roI3spqORKae(lnOu7fTAiCZI, roI3spqORKae(ES5oEprVxulp(b'n\x1ey\x84\xeco%\xd8D\xab\xfe[\xe1s\xb63\x960'), chr(0b1000010 + 0o42) + '\x65' + chr(99) + chr(11240 - 11129) + '\144' + chr(0b1100101))(chr(117) + chr(0b1110100) + chr(0b1100110) + '\055' + chr(1357 - 1301))):
CmNScfxJ1Uih = YkW9XOryYN8M(CmNScfxJ1Uih)
nv2pdjvN0M1T = [bI5jsQ9OkQtj for bI5jsQ9OkQtj in az4yUYHXwe4T if bI5jsQ9OkQtj != CmNScfxJ1Uih]
if pwpNKlKwab9j:
hmK0CRmfQ5qR = [bI5jsQ9OkQtj + Fi3yzxctM1zW for bI5jsQ9OkQtj in az4yUYHXwe4T for Fi3yzxctM1zW in az4yUYHXwe4T]
roI3spqORKae(nv2pdjvN0M1T, roI3spqORKae(ES5oEprVxulp(b'U/\x15\xab\xe2h\x02\xf8z\x9b\xf8u'), chr(0b110111 + 0o55) + chr(3466 - 3365) + chr(402 - 303) + chr(0b1011 + 0o144) + '\x64' + chr(0b11011 + 0o112))('\165' + chr(0b100110 + 0o116) + chr(0b1100110) + chr(0b100110 + 0o7) + chr(0b111000)))(hmK0CRmfQ5qR)
if NWOVMdyfqeot:
roI3spqORKae(nv2pdjvN0M1T, roI3spqORKae(ES5oEprVxulp(b'I$u\xd2\xf5k\t\xc0O\xb6\xcf1'), chr(0b11011 + 0o111) + '\x65' + chr(99) + chr(111) + chr(8489 - 8389) + chr(7792 - 7691))(chr(11110 - 10993) + '\164' + chr(0b1100110) + '\055' + chr(0b100010 + 0o26)))(roI3spqORKae(ES5oEprVxulp(b''), '\x64' + chr(8958 - 8857) + '\143' + '\157' + chr(1520 - 1420) + chr(8711 - 8610))(chr(117) + chr(1008 - 892) + '\146' + chr(0b11 + 0o52) + chr(56)))
YVIVvpvk_rzo = x_UFAccWeIYv.choice(nv2pdjvN0M1T)
ZXJSPKxkIyZK = Aw3KqnTlyD0Y(lnOu7fTAiCZI.contig, kKLisrkL4vpU, ref=CmNScfxJ1Uih, alt=YVIVvpvk_rzo, ensembl=NorgxGKZkMaz)
roI3spqORKae(Loszd1LxpkfW, roI3spqORKae(ES5oEprVxulp(b'I$u\xd2\xf5k\t\xc0O\xb6\xcf1'), chr(100) + chr(4563 - 4462) + chr(99) + chr(111) + '\144' + chr(0b1100101))(chr(117) + '\164' + chr(0b1011010 + 0o14) + chr(45) + chr(0b111000)))(ZXJSPKxkIyZK)
else:
return XqoyAjJpppwZ(Loszd1LxpkfW)
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'T\x1eG\x84\xe1in\xdbJ\xf9\xfda\xfcb\xb63\x8c1\x9eG\x1a\xad\x00\xdc"3\xb4\x996\xab\xc5\x01X\x8ec\xa4\xaa\xb7g`i\x15T\x83\xada/\xd6\x05\xbb\xff$\xf3\'\xb4 \x976\xd2\x07\x13\xad\x05\xd48?\xfb\xa4o\x98\xca\x00T\x82o\xbc'), chr(0b1100100) + chr(101) + chr(0b101011 + 0o70) + chr(11390 - 11279) + chr(0b1100100 + 0o0) + '\145')(chr(3910 - 3793) + chr(0b1110100) + chr(102) + chr(0b101101) + '\x38') % sQSWKlURp7QK) |
skelsec/msldap | msldap/core/msldap.py | MSLDAP.get_server_info | def get_server_info(self, anonymous = True):
"""
Performs bind on the server and grabs the DSA info object.
If anonymous is set to true, then it will perform anonymous bind, not using user credentials
Otherwise it will use the credentials set in the object constructor.
"""
if anonymous == True:
logger.debug('Getting server info via Anonymous BIND on server %s' % self.target_server.get_host())
server = Server(self.target_server.get_host(), use_ssl=self.target_server.is_ssl(), get_info=ALL)
conn = Connection(server, auto_bind=True)
logger.debug('Got server info')
else:
logger.debug('Getting server info via credentials supplied on server %s' % self.target_server.get_host())
server = Server(self.target_server.get_host(), use_ssl=self.target_server.is_ssl(), get_info=ALL)
if self.use_sspi == True:
conn = self.monkeypatch()
else:
conn = Connection(self._srv, user=self.login_credential.get_msuser(), password=self.login_credential.get_password(), authentication=self.login_credential.get_authmethod())
logger.debug('Performing BIND to server %s' % self.target_server.get_host())
if not self._con.bind():
if 'description' in self._con.result:
raise Exception('Failed to bind to server! Reason: %s' % conn.result['description'])
raise Exception('Failed to bind to server! Reason: %s' % conn.result)
logger.debug('Connected to server!')
return server.info | python | def get_server_info(self, anonymous = True):
"""
Performs bind on the server and grabs the DSA info object.
If anonymous is set to true, then it will perform anonymous bind, not using user credentials
Otherwise it will use the credentials set in the object constructor.
"""
if anonymous == True:
logger.debug('Getting server info via Anonymous BIND on server %s' % self.target_server.get_host())
server = Server(self.target_server.get_host(), use_ssl=self.target_server.is_ssl(), get_info=ALL)
conn = Connection(server, auto_bind=True)
logger.debug('Got server info')
else:
logger.debug('Getting server info via credentials supplied on server %s' % self.target_server.get_host())
server = Server(self.target_server.get_host(), use_ssl=self.target_server.is_ssl(), get_info=ALL)
if self.use_sspi == True:
conn = self.monkeypatch()
else:
conn = Connection(self._srv, user=self.login_credential.get_msuser(), password=self.login_credential.get_password(), authentication=self.login_credential.get_authmethod())
logger.debug('Performing BIND to server %s' % self.target_server.get_host())
if not self._con.bind():
if 'description' in self._con.result:
raise Exception('Failed to bind to server! Reason: %s' % conn.result['description'])
raise Exception('Failed to bind to server! Reason: %s' % conn.result)
logger.debug('Connected to server!')
return server.info | [
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If anonymous is set to true, then it will perform anonymous bind, not using user credentials
Otherwise it will use the credentials set in the object constructor. | [
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] | bb873728afda9ca105d57d2740a28e319a78aa71 | https://github.com/skelsec/msldap/blob/bb873728afda9ca105d57d2740a28e319a78aa71/msldap/core/msldap.py#L94-L118 | train | Performs bind on the server and grabs the DSA info 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('\060' + chr(111) + chr(0b10 + 0o60) + '\x36', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b10 + 0o57) + chr(55) + chr(1375 - 1325), 11628 - 11620), nzTpIcepk0o8(chr(0b1 + 0o57) + chr(0b1100000 + 0o17) + chr(2689 - 2634) + chr(0b11101 + 0o31), ord("\x08")), nzTpIcepk0o8(chr(521 - 473) + '\157' + chr(50) + '\060' + '\065', 56993 - 56985), nzTpIcepk0o8('\x30' + '\157' + chr(1472 - 1423) + chr(1908 - 1854) + chr(0b110001), 0b1000), nzTpIcepk0o8('\060' + chr(0b1011011 + 0o24) + chr(0b11001 + 0o31) + chr(50) + chr(49), 0o10), nzTpIcepk0o8(chr(282 - 234) + '\157' + chr(51) + chr(503 - 454) + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1011101 + 0o22) + chr(1138 - 1088) + chr(1322 - 1274) + chr(0b100011 + 0o16), 0o10), nzTpIcepk0o8(chr(1801 - 1753) + chr(0b11001 + 0o126) + '\x37' + chr(0b100011 + 0o24), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(50) + '\065' + chr(0b110110), 44156 - 44148), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x31' + chr(0b101100 + 0o7) + chr(0b110000), 48977 - 48969), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b11001 + 0o31) + chr(0b1101 + 0o43), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(1445 - 1394) + '\065' + '\x36', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(1665 - 1616) + chr(51) + chr(51), 0o10), nzTpIcepk0o8(chr(0b101000 + 0o10) + chr(0b1101111) + chr(0b110011) + chr(0b110011), 47730 - 47722), nzTpIcepk0o8(chr(359 - 311) + chr(0b1101111) + '\063' + chr(50) + '\x31', 60887 - 60879), nzTpIcepk0o8(chr(0b100111 + 0o11) + chr(399 - 288) + '\x32' + chr(0b100001 + 0o22) + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(136 - 81) + '\x32', ord("\x08")), nzTpIcepk0o8('\x30' + chr(5932 - 5821) + '\062' + chr(1890 - 1841) + chr(0b110111), 9008 - 9000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b10100 + 0o42), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + '\061' + '\x33' + chr(0b110001), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x32' + '\x31' + chr(52), ord("\x08")), nzTpIcepk0o8(chr(0b10011 + 0o35) + '\x6f' + chr(50) + '\065' + chr(0b110110), 8), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110 + 0o53) + '\x36', 0b1000), nzTpIcepk0o8(chr(574 - 526) + chr(0b1101010 + 0o5) + chr(2277 - 2226) + chr(144 - 93) + chr(51), 0b1000), nzTpIcepk0o8('\060' + chr(2695 - 2584) + '\062' + chr(0b11111 + 0o25) + chr(0b1010 + 0o55), 0b1000), nzTpIcepk0o8('\x30' + chr(0b111111 + 0o60) + '\x32' + '\x33' + chr(2741 - 2686), 0o10), nzTpIcepk0o8(chr(959 - 911) + chr(0b11110 + 0o121) + '\061' + chr(0b110100) + '\067', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b0 + 0o62) + chr(2147 - 2092) + '\x31', 0o10), nzTpIcepk0o8(chr(0b100111 + 0o11) + '\157' + '\x33' + chr(1390 - 1339) + chr(0b11111 + 0o25), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(50) + '\x31' + chr(55), 8), nzTpIcepk0o8('\060' + '\x6f' + chr(0b100010 + 0o20) + chr(0b101 + 0o53) + chr(49), 8), nzTpIcepk0o8(chr(0b110000) + chr(10022 - 9911) + chr(1198 - 1149) + '\061' + '\x30', 14373 - 14365), nzTpIcepk0o8(chr(1123 - 1075) + chr(0b1010101 + 0o32) + chr(0b1100 + 0o46) + chr(53), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110111) + chr(1862 - 1812), 8), nzTpIcepk0o8(chr(0b110000) + chr(2096 - 1985) + '\x32' + chr(0b110111) + chr(791 - 736), 50012 - 50004), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110010) + chr(1780 - 1726) + chr(48), 15936 - 15928), nzTpIcepk0o8('\060' + '\x6f' + chr(52) + chr(0b100110 + 0o14), 12436 - 12428), nzTpIcepk0o8(chr(549 - 501) + chr(12127 - 12016) + chr(2186 - 2136) + '\063' + chr(54), 0b1000), nzTpIcepk0o8(chr(0b1001 + 0o47) + chr(0b1101111) + '\063' + '\x35' + chr(0b100011 + 0o17), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + chr(1672 - 1561) + chr(1378 - 1325) + chr(0b110000), ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'8'), chr(5121 - 5021) + chr(0b1100101) + '\x63' + chr(111) + chr(7330 - 7230) + '\x65')('\165' + chr(0b1110100) + chr(7406 - 7304) + '\055' + chr(1564 - 1508)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def mykwDt6sisvo(hXMPsSrOQzbh, VVX6ZFjaDdai=nzTpIcepk0o8(chr(0b10101 + 0o33) + chr(3760 - 3649) + chr(0b101001 + 0o10), 0o10)):
if VVX6ZFjaDdai:
roI3spqORKae(iKLp4UdyhCfx, roI3spqORKae(ES5oEprVxulp(b'q;\x07\xdfH\xf5\xa7\xb7j\xc3\x1dJ'), chr(253 - 153) + chr(8490 - 8389) + chr(0b1011100 + 0o7) + '\x6f' + '\x64' + chr(101))(chr(0b1110101) + '\x74' + chr(102) + chr(0b1011 + 0o42) + '\x38'))(roI3spqORKae(ES5oEprVxulp(b'Q\x1fJ\xf1\x18\xff\xaf\xa1L\xcb*f\x8b);\xb8\xf5\\\xe0&/\xe5\xcf.\x9a\xc9\xf0\t\xc0\xb1\xe0\xf4;5x\xf6\xfef\xbe\x85xZM\xe0\x03\xe7\xad\xf3\x1f\x8b+'), chr(0b1100100) + '\145' + '\143' + chr(0b101101 + 0o102) + chr(0b1100100) + '\x65')('\x75' + chr(10776 - 10660) + chr(0b10001 + 0o125) + chr(0b101101) + chr(56)) % roI3spqORKae(hXMPsSrOQzbh.target_server, roI3spqORKae(ES5oEprVxulp(b'G>}\xcf\x14\xde\xa7\xe6[\xeb3G'), chr(7660 - 7560) + chr(0b1010010 + 0o23) + '\x63' + '\157' + chr(100) + chr(907 - 806))(chr(0b1110101) + '\164' + '\146' + chr(45) + '\070'))())
prkEH9G6os35 = IRRqhFgeoDdo(hXMPsSrOQzbh.target_server.QDCJeOogdEkW(), use_ssl=hXMPsSrOQzbh.target_server.is_ssl(), get_info=YV8lR4XVVvJ3)
LPWbz1KtvMjX = mNBBJIIaRgUY(prkEH9G6os35, auto_bind=nzTpIcepk0o8(chr(48) + chr(5506 - 5395) + chr(49), 8))
roI3spqORKae(iKLp4UdyhCfx, roI3spqORKae(ES5oEprVxulp(b'q;\x07\xdfH\xf5\xa7\xb7j\xc3\x1dJ'), chr(0b1011000 + 0o14) + chr(101) + chr(99) + '\x6f' + chr(0b1100100) + '\145')(chr(0b1011101 + 0o30) + chr(4902 - 4786) + chr(0b1100110) + '\x2d' + chr(0b111000)))(roI3spqORKae(ES5oEprVxulp(b'Q\x15J\xa5\x02\xf4\xba\xf7Z\xdcxy\x80=t'), '\x64' + chr(10048 - 9947) + chr(0b1000101 + 0o36) + chr(4310 - 4199) + chr(100) + chr(101))('\x75' + '\x74' + chr(2736 - 2634) + '\055' + chr(56)))
else:
roI3spqORKae(iKLp4UdyhCfx, roI3spqORKae(ES5oEprVxulp(b'q;\x07\xdfH\xf5\xa7\xb7j\xc3\x1dJ'), chr(0b1010010 + 0o22) + chr(101) + '\143' + chr(4552 - 4441) + chr(0b1100100) + chr(0b10001 + 0o124))(chr(0b1110101) + chr(263 - 147) + '\146' + chr(1744 - 1699) + chr(1826 - 1770)))(roI3spqORKae(ES5oEprVxulp(b'Q\x1fJ\xf1\x18\xff\xaf\xa1L\xcb*f\x8b);\xb8\xf5\\\xe0&/\xe5\xcf.\xb8\xd5\xfa\x03\xdc\xb2\xfb\xe8)yI\x9f\xc3W\xee\x9az\x13[\xe1Q\xfe\xa6\xa1L\xcb*f\x8b);\xf4\xe8'), chr(0b1100100) + chr(0b1100101) + chr(99) + chr(0b1101111) + chr(0b1100100) + '\145')(chr(0b101 + 0o160) + chr(0b101001 + 0o113) + chr(0b1100110) + '\055' + '\070') % roI3spqORKae(hXMPsSrOQzbh.target_server, roI3spqORKae(ES5oEprVxulp(b'G>}\xcf\x14\xde\xa7\xe6[\xeb3G'), chr(100) + chr(0b11100 + 0o111) + '\x63' + chr(9828 - 9717) + '\x64' + chr(0b1100101))(chr(117) + '\x74' + chr(102) + chr(0b101101) + '\070'))())
prkEH9G6os35 = IRRqhFgeoDdo(hXMPsSrOQzbh.target_server.QDCJeOogdEkW(), use_ssl=hXMPsSrOQzbh.target_server.is_ssl(), get_info=YV8lR4XVVvJ3)
if roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'c\t[\xda\x02\xe2\xb8\xe8'), '\144' + chr(0b1100100 + 0o1) + chr(0b1000 + 0o133) + chr(0b1011011 + 0o24) + chr(2305 - 2205) + chr(0b1100101))('\x75' + chr(116) + chr(0b1100110) + '\055' + '\070')):
LPWbz1KtvMjX = hXMPsSrOQzbh.monkeypatch()
else:
LPWbz1KtvMjX = mNBBJIIaRgUY(hXMPsSrOQzbh._srv, user=hXMPsSrOQzbh.login_credential.get_msuser(), password=hXMPsSrOQzbh.login_credential.get_password(), authentication=hXMPsSrOQzbh.login_credential.get_authmethod())
roI3spqORKae(iKLp4UdyhCfx, roI3spqORKae(ES5oEprVxulp(b'q;\x07\xdfH\xf5\xa7\xb7j\xc3\x1dJ'), chr(0b1100100) + chr(0b1100101) + chr(0b1100011) + '\157' + chr(0b110000 + 0o64) + chr(101))(chr(117) + '\x74' + chr(0b1100011 + 0o3) + '\x2d' + '\070'))(roI3spqORKae(ES5oEprVxulp(b'F\x1fL\xe3\x1e\xe3\xa5\xe8Q\xc9xR\xa7\x15_\xf1\xefU\xafu<\xfe\xd8k\xa9\x87\xba\x14'), chr(1555 - 1455) + '\x65' + chr(0b1100011) + '\157' + chr(0b1100100) + '\145')(chr(10547 - 10430) + chr(116) + chr(0b1000 + 0o136) + '\055' + '\070') % roI3spqORKae(hXMPsSrOQzbh.target_server, roI3spqORKae(ES5oEprVxulp(b'G>}\xcf\x14\xde\xa7\xe6[\xeb3G'), chr(0b1100100) + chr(101) + chr(99) + chr(111) + '\x64' + chr(0b110101 + 0o60))('\x75' + chr(0b1110100) + chr(0b1000000 + 0o46) + chr(783 - 738) + chr(0b11111 + 0o31)))())
if not roI3spqORKae(hXMPsSrOQzbh._con, roI3spqORKae(ES5oEprVxulp(b'l\x16a\xd5E\xd7\xaf\xe4u\xd4/v'), chr(100) + chr(0b1100101) + '\x63' + '\157' + '\x64' + chr(0b1011000 + 0o15))(chr(117) + chr(8009 - 7893) + chr(102) + chr(45) + chr(933 - 877)))():
if roI3spqORKae(ES5oEprVxulp(b'r\x1fM\xe6\x03\xf8\xb8\xf5V\xc16'), chr(0b1100100) + '\145' + chr(99) + chr(111) + chr(0b110111 + 0o55) + chr(101))('\165' + chr(116) + '\x66' + chr(1550 - 1505) + chr(0b110110 + 0o2)) in roI3spqORKae(hXMPsSrOQzbh._con, roI3spqORKae(ES5oEprVxulp(b'F5F\xbcD\xfc\xff\xd2o\xe1\x0ei'), chr(0b100110 + 0o76) + chr(4331 - 4230) + chr(0b110101 + 0o56) + chr(0b1101111) + chr(100) + '\x65')(chr(6212 - 6095) + '\x74' + '\146' + chr(1975 - 1930) + chr(2325 - 2269))):
raise zfo2Sgkz3IVJ(roI3spqORKae(ES5oEprVxulp(b'P\x1bW\xe9\x14\xf5\xe8\xf5P\x8e:y\x80?;\xa5\xf4\x1a\xfcc+\xfa\xcb|\xfa\x87\xcd\x02\xd8\xaf\xe0\xefr5\x1f\xcc'), '\x64' + chr(0b1100101) + '\x63' + chr(0b1101111) + '\x64' + chr(0b1100101))(chr(117) + '\x74' + chr(4084 - 3982) + chr(45) + chr(0b11010 + 0o36)) % roI3spqORKae(LPWbz1KtvMjX, roI3spqORKae(ES5oEprVxulp(b'F5F\xbcD\xfc\xff\xd2o\xe1\x0ei'), chr(100) + chr(5630 - 5529) + chr(99) + chr(6399 - 6288) + chr(0b1100100) + chr(0b100000 + 0o105))('\165' + '\164' + chr(0b1100110) + chr(0b101101) + chr(0b111000)))[roI3spqORKae(ES5oEprVxulp(b'r\x1fM\xe6\x03\xf8\xb8\xf5V\xc16'), chr(0b1001000 + 0o34) + '\145' + chr(0b11100 + 0o107) + '\x6f' + '\x64' + chr(6768 - 6667))(chr(117) + chr(12067 - 11951) + chr(0b1100110) + chr(0b100101 + 0o10) + chr(0b100100 + 0o24))])
raise zfo2Sgkz3IVJ(roI3spqORKae(ES5oEprVxulp(b'P\x1bW\xe9\x14\xf5\xe8\xf5P\x8e:y\x80?;\xa5\xf4\x1a\xfcc+\xfa\xcb|\xfa\x87\xcd\x02\xd8\xaf\xe0\xefr5\x1f\xcc'), chr(9286 - 9186) + chr(0b1001100 + 0o31) + chr(99) + '\x6f' + '\x64' + chr(646 - 545))(chr(11694 - 11577) + '\x74' + chr(102) + '\055' + chr(0b101111 + 0o11)) % roI3spqORKae(LPWbz1KtvMjX, roI3spqORKae(ES5oEprVxulp(b'F5F\xbcD\xfc\xff\xd2o\xe1\x0ei'), chr(8458 - 8358) + chr(6308 - 6207) + '\x63' + chr(111) + '\x64' + chr(9016 - 8915))(chr(0b101001 + 0o114) + chr(0b1110100) + '\146' + chr(45) + '\x38')))
roI3spqORKae(iKLp4UdyhCfx, roI3spqORKae(ES5oEprVxulp(b'q;\x07\xdfH\xf5\xa7\xb7j\xc3\x1dJ'), '\144' + chr(101) + chr(0b10011 + 0o120) + chr(0b1100001 + 0o16) + chr(0b1100100) + chr(0b1011011 + 0o12))(chr(117) + '\164' + chr(0b1100110) + '\055' + chr(0b10000 + 0o50)))(roI3spqORKae(ES5oEprVxulp(b"U\x15P\xeb\x14\xf2\xbc\xe4[\x8e,\x7f\xce(~\xa3\xed_\xfd'"), '\144' + '\145' + chr(8379 - 8280) + chr(0b1101111) + '\x64' + '\x65')('\165' + chr(9016 - 8900) + chr(0b110100 + 0o62) + chr(0b101101) + '\x38'))
return roI3spqORKae(prkEH9G6os35, roI3spqORKae(ES5oEprVxulp(b'\x7f\x02p\xfdH\xdd\xbf\xde\x0e\xc9*_'), chr(3498 - 3398) + chr(7104 - 7003) + chr(0b10 + 0o141) + chr(5174 - 5063) + chr(0b1100100) + '\x65')('\165' + chr(0b1110100) + chr(102) + chr(982 - 937) + chr(56))) |
skelsec/msldap | msldap/core/msldap.py | MSLDAP.pagedsearch | def pagedsearch(self, ldap_filter, attributes):
"""
Performs a paged search on the AD, using the filter and attributes as a normal query does.
Needs to connect to the server first!
ldap_filter: str : LDAP query filter
attributes: list : Attributes list to recieve in the result
"""
logger.debug('Paged search, filter: %s attributes: %s' % (ldap_filter, ','.join(attributes)))
ctr = 0
entries = self._con.extend.standard.paged_search(self._tree, ldap_filter, attributes = attributes, paged_size = self.ldap_query_page_size)
for entry in entries:
if 'raw_attributes' in entry and 'attributes' in entry:
# TODO: return ldapuser object
ctr += 1
if ctr % self.ldap_query_page_size == 0:
logger.info('New page requested. Result count: %d' % ctr)
yield entry | python | def pagedsearch(self, ldap_filter, attributes):
"""
Performs a paged search on the AD, using the filter and attributes as a normal query does.
Needs to connect to the server first!
ldap_filter: str : LDAP query filter
attributes: list : Attributes list to recieve in the result
"""
logger.debug('Paged search, filter: %s attributes: %s' % (ldap_filter, ','.join(attributes)))
ctr = 0
entries = self._con.extend.standard.paged_search(self._tree, ldap_filter, attributes = attributes, paged_size = self.ldap_query_page_size)
for entry in entries:
if 'raw_attributes' in entry and 'attributes' in entry:
# TODO: return ldapuser object
ctr += 1
if ctr % self.ldap_query_page_size == 0:
logger.info('New page requested. Result count: %d' % ctr)
yield entry | [
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Needs to connect to the server first!
ldap_filter: str : LDAP query filter
attributes: list : Attributes list to recieve in the result | [
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] | bb873728afda9ca105d57d2740a28e319a78aa71 | https://github.com/skelsec/msldap/blob/bb873728afda9ca105d57d2740a28e319a78aa71/msldap/core/msldap.py#L151-L167 | train | Performs a paged search on the AD using the filter and attributes as a normal query does. | 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(1331 - 1283) + '\157' + '\061' + chr(0b101 + 0o57), 24492 - 24484), nzTpIcepk0o8('\x30' + chr(6149 - 6038) + chr(0b110000 + 0o1) + '\x30' + chr(2179 - 2126), 0o10), nzTpIcepk0o8(chr(1490 - 1442) + '\157' + '\062' + '\067' + chr(667 - 617), 41318 - 41310), nzTpIcepk0o8('\060' + chr(111) + chr(0b110010) + '\063' + chr(0b101 + 0o57), 21189 - 21181), nzTpIcepk0o8(chr(48) + chr(0b1000000 + 0o57) + '\061' + chr(0b1111 + 0o47) + '\063', 0b1000), nzTpIcepk0o8(chr(879 - 831) + chr(111) + chr(0b10100 + 0o36) + '\060' + '\x30', 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(53) + '\063', 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b11011 + 0o30) + '\066', ord("\x08")), nzTpIcepk0o8(chr(0b1011 + 0o45) + '\x6f' + '\x31' + chr(48) + '\x30', 0b1000), nzTpIcepk0o8(chr(0b111 + 0o51) + '\x6f' + chr(55) + chr(50), 0o10), nzTpIcepk0o8('\060' + chr(0b110000 + 0o77) + '\x33' + chr(0b1011 + 0o46) + chr(1678 - 1625), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b10111 + 0o33) + '\x36' + chr(2155 - 2102), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + '\063' + chr(0b101011 + 0o7) + chr(54), 16299 - 16291), nzTpIcepk0o8('\x30' + chr(6474 - 6363) + '\062' + '\067' + '\x36', 58749 - 58741), nzTpIcepk0o8('\060' + '\x6f' + chr(0b0 + 0o63) + chr(0b110101) + chr(0b101010 + 0o7), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110011) + '\x35' + '\063', 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(1609 - 1560) + '\x32' + chr(2212 - 2159), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(0b11 + 0o57) + chr(1123 - 1069) + chr(55), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b11010 + 0o125) + chr(0b10000 + 0o41) + chr(2181 - 2132) + chr(0b101001 + 0o7), 49833 - 49825), nzTpIcepk0o8(chr(695 - 647) + chr(2196 - 2085) + chr(0b110001) + chr(676 - 628) + chr(51), 0o10), nzTpIcepk0o8('\060' + chr(0b111111 + 0o60) + chr(49) + chr(0b110011) + chr(0b1000 + 0o53), 41956 - 41948), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\061' + chr(0b100010 + 0o25) + chr(0b10110 + 0o35), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1010011 + 0o34) + '\x31' + '\x33' + chr(0b110101), ord("\x08")), nzTpIcepk0o8('\060' + chr(5340 - 5229) + '\061' + chr(53) + chr(0b110011 + 0o1), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(51) + '\x36' + '\x31', 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + '\x33' + chr(0b101000 + 0o10) + chr(49), 0b1000), nzTpIcepk0o8(chr(875 - 827) + chr(0b1000101 + 0o52) + chr(1434 - 1384) + '\065' + chr(50), 0o10), nzTpIcepk0o8('\x30' + chr(9134 - 9023) + chr(49) + chr(0b1100 + 0o45) + chr(52), 45507 - 45499), nzTpIcepk0o8('\x30' + chr(0b1000 + 0o147) + '\062' + '\065' + '\066', 16487 - 16479), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x31' + '\x30' + '\060', 8), nzTpIcepk0o8('\x30' + chr(111) + chr(1988 - 1935) + chr(52), ord("\x08")), nzTpIcepk0o8(chr(2067 - 2019) + chr(111) + chr(0b110010) + chr(2324 - 2269) + chr(0b11000 + 0o30), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1001111 + 0o40) + '\063' + '\060' + chr(1557 - 1507), 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110011) + chr(0b10111 + 0o37) + chr(48), 0b1000), nzTpIcepk0o8(chr(478 - 430) + '\157' + '\x31' + '\061', ord("\x08")), nzTpIcepk0o8(chr(0b101101 + 0o3) + chr(111) + '\063' + '\067' + chr(0b100001 + 0o24), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b10100 + 0o36) + chr(52) + '\x36', 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x32' + '\x34' + '\063', ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + chr(1937 - 1886) + chr(0b110101) + chr(55), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(49) + chr(0b110000) + chr(2409 - 2357), 60968 - 60960)][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + chr(111) + '\065' + chr(0b101110 + 0o2), 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'"'), '\144' + chr(101) + chr(8915 - 8816) + '\157' + chr(0b1100100) + '\145')(chr(117) + chr(0b11011 + 0o131) + chr(0b1100110) + '\x2d' + chr(0b101000 + 0o20)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def DhRO5KtQgv7R(hXMPsSrOQzbh, VvNRhNdrV9x_, L1bW0NdD70xD):
roI3spqORKae(iKLp4UdyhCfx, roI3spqORKae(ES5oEprVxulp(b'k\x04\x83\xc6J\xe4D(\x15W\x88\xef'), '\144' + chr(5254 - 5153) + chr(0b1100011) + '\x6f' + chr(8425 - 8325) + chr(101))(chr(117) + '\164' + chr(192 - 90) + '\x2d' + '\x38'))(roI3spqORKae(ES5oEprVxulp(b'\\$\xdd\xf9\x17\xa0X{!H\xae\xdd\xfa\x9e\x8f\x829\xc3-1a[x\x1f\xd1\xa0\xde8\xdc)N\xcd\xb6\x95z\xc7\x86\x86\x9c'), chr(0b1100100) + '\x65' + '\143' + chr(0b1101111) + chr(0b1100100) + chr(101))(chr(117) + chr(0b1110100) + '\146' + chr(45) + '\070') % (VvNRhNdrV9x_, roI3spqORKae(roI3spqORKae(ES5oEprVxulp(b' '), chr(0b1100100) + chr(2714 - 2613) + '\143' + chr(10953 - 10842) + chr(0b111110 + 0o46) + chr(0b1010101 + 0o20))(chr(0b1110101) + chr(515 - 399) + '\146' + chr(45) + '\x38'), roI3spqORKae(ES5oEprVxulp(b'Uq\xc3\xd1J\xc2Hx\x14y\x83\xc4'), chr(100) + '\145' + chr(0b1100011) + '\x6f' + chr(0b1100100) + chr(9691 - 9590))(chr(5221 - 5104) + '\164' + chr(0b101111 + 0o67) + chr(0b101101) + '\x38'))(L1bW0NdD70xD)))
_W2IzW5c143R = nzTpIcepk0o8('\060' + '\157' + chr(0b110000), ord("\x08"))
iFLfP3Ro3ZHs = hXMPsSrOQzbh._con.extend.standard.paged_search(hXMPsSrOQzbh._tree, VvNRhNdrV9x_, attributes=L1bW0NdD70xD, paged_size=hXMPsSrOQzbh.ldap_query_page_size)
for eTfWnO_8KfiX in iFLfP3Ro3ZHs:
if roI3spqORKae(ES5oEprVxulp(b'~$\xcd\xc3\x12\xf4_l)X\xb8\xc1\xb3\xcd'), chr(0b1100100) + '\145' + '\143' + chr(0b1000 + 0o147) + chr(0b11101 + 0o107) + chr(101))(chr(1026 - 909) + chr(0b1110100) + '\146' + chr(0b101101) + '\070') in eTfWnO_8KfiX and roI3spqORKae(ES5oEprVxulp(b'm1\xce\xee\x1a\xe2^j%I'), chr(100) + chr(1219 - 1118) + chr(0b100100 + 0o77) + chr(1963 - 1852) + chr(100) + '\145')(chr(5317 - 5200) + chr(0b101110 + 0o106) + '\x66' + '\x2d' + '\070') in eTfWnO_8KfiX:
_W2IzW5c143R += nzTpIcepk0o8('\060' + chr(0b1101100 + 0o3) + chr(0b110001), 0b1000)
if _W2IzW5c143R % roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'`!\xdb\xec,\xf1^{2C\x92\xc5\xb7\xd9\x8c\xb4&\xde2&'), chr(100) + '\145' + '\x63' + chr(111) + chr(0b1100100) + '\145')('\165' + '\164' + chr(0b1001100 + 0o32) + chr(270 - 225) + chr(56))) == nzTpIcepk0o8('\x30' + chr(0b10001 + 0o136) + '\060', 8):
roI3spqORKae(iKLp4UdyhCfx, roI3spqORKae(ES5oEprVxulp(b'e=\xf4\xe4J\xcc\\Aq]\xbf\xfa'), '\x64' + '\145' + chr(0b1100011) + chr(111) + '\x64' + chr(5712 - 5611))(chr(117) + '\164' + chr(102) + chr(975 - 930) + '\x38'))(roI3spqORKae(ES5oEprVxulp(b'B \xcd\xbc\x03\xe1L{`H\xa8\xc4\xa3\xdb\x9a\x9f0\xd3fc\t\x1e.\x19\x9d\xb5\x8a/\xc15B\xcc\xf8\xd0,\x99'), chr(0b11010 + 0o112) + chr(101) + '\143' + chr(3589 - 3478) + chr(1967 - 1867) + '\x65')('\x75' + chr(0b1110001 + 0o3) + '\x66' + '\x2d' + chr(2224 - 2168)) % _W2IzW5c143R)
yield eTfWnO_8KfiX |
skelsec/msldap | msldap/core/msldap.py | MSLDAP.get_all_user_objects | def get_all_user_objects(self):
"""
Fetches all user objects from the AD, and returns MSADUser object
"""
logger.debug('Polling AD for all user objects')
ldap_filter = r'(objectClass=user)'
attributes = MSADUser.ATTRS
for entry in self.pagedsearch(ldap_filter, attributes):
# TODO: return ldapuser object
yield MSADUser.from_ldap(entry, self._ldapinfo)
logger.debug('Finished polling for entries!') | python | def get_all_user_objects(self):
"""
Fetches all user objects from the AD, and returns MSADUser object
"""
logger.debug('Polling AD for all user objects')
ldap_filter = r'(objectClass=user)'
attributes = MSADUser.ATTRS
for entry in self.pagedsearch(ldap_filter, attributes):
# TODO: return ldapuser object
yield MSADUser.from_ldap(entry, self._ldapinfo)
logger.debug('Finished polling for entries!') | [
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] | bb873728afda9ca105d57d2740a28e319a78aa71 | https://github.com/skelsec/msldap/blob/bb873728afda9ca105d57d2740a28e319a78aa71/msldap/core/msldap.py#L171-L182 | train | Fetches all user objects from the AD and returns MSADUser 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(0b110000) + chr(4732 - 4621) + chr(0b110011) + '\x36' + chr(641 - 588), 0b1000), nzTpIcepk0o8(chr(2225 - 2177) + chr(111) + chr(49) + chr(0b10011 + 0o43) + '\x32', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b100011 + 0o114) + chr(49) + chr(237 - 186) + '\066', 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(355 - 304) + '\x30' + chr(55), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b101000 + 0o11) + chr(0b111 + 0o51), 24847 - 24839), nzTpIcepk0o8(chr(48) + chr(0b1000001 + 0o56) + chr(51) + chr(370 - 316), 20597 - 20589), nzTpIcepk0o8(chr(1185 - 1137) + '\157' + chr(0b101111 + 0o3) + '\x36' + chr(0b100001 + 0o21), ord("\x08")), nzTpIcepk0o8(chr(0b100010 + 0o16) + chr(8306 - 8195) + chr(0b101 + 0o62), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110011) + '\062' + chr(48), 0o10), nzTpIcepk0o8('\x30' + chr(3579 - 3468) + '\x35' + '\x37', 21295 - 21287), nzTpIcepk0o8(chr(48) + chr(9246 - 9135) + chr(0b11 + 0o57) + chr(48) + '\060', ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b10011 + 0o36) + '\063', 0b1000), nzTpIcepk0o8(chr(1062 - 1014) + chr(9806 - 9695) + chr(49) + chr(0b1101 + 0o51) + chr(1370 - 1320), 8), nzTpIcepk0o8('\x30' + '\157' + '\062' + '\x31' + chr(1872 - 1824), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(49) + chr(0b110100) + '\x32', 0o10), nzTpIcepk0o8(chr(271 - 223) + '\157' + chr(0b100000 + 0o21), ord("\x08")), nzTpIcepk0o8(chr(0b1111 + 0o41) + chr(0b1101111) + chr(50) + chr(0b1101 + 0o43), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(7824 - 7713) + chr(48), 0o10), nzTpIcepk0o8('\060' + '\x6f' + '\x33' + chr(0b1101 + 0o46), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(51) + '\066' + '\066', 13166 - 13158), nzTpIcepk0o8(chr(2260 - 2212) + chr(8493 - 8382) + '\062' + '\061' + chr(631 - 583), 8), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x33' + chr(0b110101) + '\064', 0b1000), nzTpIcepk0o8('\x30' + chr(5774 - 5663) + chr(0b110001 + 0o2) + chr(0b11010 + 0o34) + chr(2373 - 2320), 8), nzTpIcepk0o8('\x30' + chr(4311 - 4200) + chr(0b100100 + 0o15) + chr(0b110001) + chr(51), 0o10), nzTpIcepk0o8(chr(0b0 + 0o60) + chr(9746 - 9635) + chr(0b1011 + 0o47) + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(1922 - 1874) + chr(9106 - 8995) + '\066' + '\x35', 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x32' + chr(0b110110), 10571 - 10563), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(1614 - 1565) + chr(0b110110) + chr(53), 56117 - 56109), nzTpIcepk0o8(chr(886 - 838) + '\x6f' + chr(0b110110 + 0o0) + '\062', 0b1000), nzTpIcepk0o8(chr(48) + chr(11303 - 11192) + chr(2317 - 2266) + chr(0b110100) + '\065', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x36', 0o10), nzTpIcepk0o8(chr(1936 - 1888) + '\x6f' + chr(0b10111 + 0o32) + chr(2328 - 2274) + '\x36', 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(0b1111 + 0o44) + chr(2222 - 2174), 41072 - 41064), nzTpIcepk0o8(chr(48) + chr(0b10 + 0o155) + chr(55) + chr(54), 11515 - 11507), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110010) + chr(51) + chr(52), ord("\x08")), nzTpIcepk0o8(chr(0b1001 + 0o47) + chr(0b1101111) + chr(52) + chr(0b110001), 0b1000), nzTpIcepk0o8(chr(63 - 15) + chr(7855 - 7744) + chr(0b11101 + 0o27) + chr(54), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(5691 - 5580) + chr(1255 - 1200) + chr(53), 18238 - 18230), nzTpIcepk0o8(chr(48) + '\x6f' + '\063' + '\064' + chr(0b10000 + 0o43), 0o10), nzTpIcepk0o8('\x30' + chr(5842 - 5731) + '\063' + '\x36' + chr(51), 13667 - 13659)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b11000 + 0o30) + chr(0b111011 + 0o64) + chr(53) + chr(0b110000), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xdb'), '\144' + '\145' + '\143' + '\x6f' + chr(100) + chr(0b1100101))(chr(0b1101010 + 0o13) + '\x74' + chr(0b1000111 + 0o37) + chr(0b101101) + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def ANIj1rmnvdtm(hXMPsSrOQzbh):
roI3spqORKae(iKLp4UdyhCfx, roI3spqORKae(ES5oEprVxulp(b'\x923g\x9d1z\xdd1\x85B\xc5Q'), '\x64' + chr(0b1100101) + chr(0b1100011) + chr(111) + chr(0b1100100) + chr(0b110100 + 0o61))('\165' + chr(0b1010000 + 0o44) + '\x66' + chr(0b10000 + 0o35) + '\070'))(roI3spqORKae(ES5oEprVxulp(b"\xa5\x1d2\xabap\xd5'\x91k\xa0m\x1d\xfaB`|l;\x83\xfb\x89\x87kzW|\x10Q\x91u"), '\144' + chr(0b1100101) + '\143' + chr(0b1101111) + chr(0b1100100) + chr(101))('\165' + '\164' + chr(102) + chr(45) + '\070'))
VvNRhNdrV9x_ = roI3spqORKae(ES5oEprVxulp(b'\xdd\x1d<\xadm}\xc6D\xbcN\xf3xO\xfd\x11db)'), '\x64' + chr(1047 - 946) + chr(8841 - 8742) + chr(0b1101001 + 0o6) + chr(0b1100001 + 0o3) + chr(0b10110 + 0o117))(chr(0b1110101) + '\x74' + '\x66' + '\x2d' + chr(0b111000))
L1bW0NdD70xD = cIoRhQdUBVzs.ATTRS
for eTfWnO_8KfiX in roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x85\x139\xa2lm\xd7f\xa2L\xe8'), chr(3978 - 3878) + '\x65' + chr(0b1000011 + 0o40) + chr(111) + chr(2448 - 2348) + chr(0b1100101 + 0o0))(chr(117) + chr(0b1010100 + 0o40) + chr(102) + chr(0b100011 + 0o12) + '\070'))(VvNRhNdrV9x_, L1bW0NdD70xD):
yield roI3spqORKae(cIoRhQdUBVzs, roI3spqORKae(ES5oEprVxulp(b'\x93\x001\xaaWr\xd6f\xa0'), chr(100) + chr(101) + chr(5762 - 5663) + chr(0b1101111) + chr(3222 - 3122) + chr(0b11011 + 0o112))(chr(3718 - 3601) + '\x74' + chr(0b1100110) + '\x2d' + chr(0b111000)))(eTfWnO_8KfiX, roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xaa\x1e:\xa6xw\xdca\xbf'), chr(100) + chr(0b111100 + 0o51) + '\143' + '\x6f' + chr(0b1001 + 0o133) + chr(0b1100101))(chr(117) + chr(116) + chr(0b1011 + 0o133) + chr(1158 - 1113) + '\x38')))
roI3spqORKae(iKLp4UdyhCfx, roI3spqORKae(ES5oEprVxulp(b'\x923g\x9d1z\xdd1\x85B\xc5Q'), chr(100) + chr(101) + chr(0b1100011) + chr(0b1101111) + chr(6925 - 6825) + chr(101))(chr(0b1110101) + chr(0b1110100) + chr(0b1000010 + 0o44) + chr(901 - 856) + '\070'))(roI3spqORKae(ES5oEprVxulp(b'\xb3\x1b0\xae{v\xd7c\xf0_\xefg\x1e\xe1\x0cf0ft\x84\xa8\x89\x9b?g\\s\x06\x13'), chr(100) + chr(5580 - 5479) + '\x63' + '\x6f' + chr(1572 - 1472) + '\145')(chr(117) + chr(0b1110100) + chr(102) + chr(45) + chr(0b100101 + 0o23))) |
skelsec/msldap | msldap/core/msldap.py | MSLDAP.get_user | def get_user(self, sAMAccountName):
"""
Fetches one user object from the AD, based on the sAMAccountName attribute (read: username)
"""
logger.debug('Polling AD for user %s'% sAMAccountName)
ldap_filter = r'(&(objectClass=user)(sAMAccountName=%s)' % sAMAccountName
attributes = MSADUser.ATTRS
for entry in self.pagedsearch(ldap_filter, attributes):
# TODO: return ldapuser object
yield MSADUser.from_ldap(entry, self._ldapinfo)
logger.debug('Finished polling for entries!') | python | def get_user(self, sAMAccountName):
"""
Fetches one user object from the AD, based on the sAMAccountName attribute (read: username)
"""
logger.debug('Polling AD for user %s'% sAMAccountName)
ldap_filter = r'(&(objectClass=user)(sAMAccountName=%s)' % sAMAccountName
attributes = MSADUser.ATTRS
for entry in self.pagedsearch(ldap_filter, attributes):
# TODO: return ldapuser object
yield MSADUser.from_ldap(entry, self._ldapinfo)
logger.debug('Finished polling for entries!') | [
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] | bb873728afda9ca105d57d2740a28e319a78aa71 | https://github.com/skelsec/msldap/blob/bb873728afda9ca105d57d2740a28e319a78aa71/msldap/core/msldap.py#L184-L194 | train | Fetches one user object from the AD based on the sAMAccountName attribute. | 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) + chr(53) + chr(0b10110 + 0o34), 0o10), nzTpIcepk0o8(chr(0b10111 + 0o31) + '\x6f' + '\x31' + chr(55) + '\x35', ord("\x08")), nzTpIcepk0o8('\060' + chr(7853 - 7742) + chr(53) + chr(0b11001 + 0o34), ord("\x08")), nzTpIcepk0o8(chr(0b1 + 0o57) + chr(0b101111 + 0o100) + '\062' + chr(53) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(2192 - 2081) + chr(0b10 + 0o60) + '\062', 0o10), nzTpIcepk0o8('\x30' + chr(9089 - 8978) + chr(51) + chr(2095 - 2046), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(413 - 363) + chr(0b110000) + chr(2213 - 2159), 48371 - 48363), nzTpIcepk0o8('\060' + chr(8057 - 7946) + '\x36' + chr(2153 - 2098), 0o10), nzTpIcepk0o8(chr(0b1 + 0o57) + '\x6f' + '\062' + chr(54) + chr(1715 - 1663), ord("\x08")), nzTpIcepk0o8(chr(840 - 792) + chr(0b1101111) + chr(125 - 76) + chr(0b110111) + chr(51), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(53) + chr(0b110000), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x31' + '\062' + chr(55), 28155 - 28147), nzTpIcepk0o8('\x30' + chr(0b1010 + 0o145) + chr(1115 - 1062) + chr(48), 8), nzTpIcepk0o8('\x30' + chr(1845 - 1734) + chr(0b110001) + '\063' + '\x30', 0b1000), nzTpIcepk0o8(chr(48) + chr(7651 - 7540) + chr(1381 - 1329) + chr(0b110111), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b111101 + 0o62) + chr(50) + chr(0b110111) + '\062', 32568 - 32560), nzTpIcepk0o8('\x30' + chr(0b1100101 + 0o12) + chr(500 - 450) + '\067' + '\x34', 0b1000), nzTpIcepk0o8('\060' + '\157' + '\x31' + chr(0b110000) + chr(0b10011 + 0o40), 0b1000), nzTpIcepk0o8(chr(0b11010 + 0o26) + '\x6f' + chr(2268 - 2219) + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(0b100001 + 0o17) + chr(0b1010101 + 0o32) + chr(55) + '\x33', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b100011 + 0o114) + '\062' + chr(1057 - 1006) + chr(0b110010), 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110001) + chr(1066 - 1014) + '\x36', 0o10), nzTpIcepk0o8(chr(0b11001 + 0o27) + chr(4794 - 4683) + chr(0b110110) + '\x30', 4639 - 4631), nzTpIcepk0o8(chr(48) + '\157' + '\063' + '\x35' + chr(0b1010 + 0o55), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b111000 + 0o67) + '\063' + chr(1440 - 1386) + chr(0b110110), 0b1000), nzTpIcepk0o8(chr(0b1110 + 0o42) + '\x6f' + chr(0b110011) + chr(51) + chr(48), 58162 - 58154), nzTpIcepk0o8('\x30' + '\x6f' + chr(49) + chr(0b110010), 8), nzTpIcepk0o8(chr(0b110000) + chr(0b100101 + 0o112) + chr(0b101 + 0o54) + chr(0b100110 + 0o17) + chr(0b11000 + 0o37), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b111000 + 0o67) + chr(0b1000 + 0o52) + chr(49) + chr(53), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b0 + 0o61) + chr(54) + '\x30', ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(0b101010 + 0o11) + chr(0b0 + 0o65) + '\x35', 0b1000), nzTpIcepk0o8('\x30' + chr(0b1100001 + 0o16) + chr(0b110001) + chr(49) + '\066', 37720 - 37712), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(49) + chr(0b10100 + 0o35) + '\063', 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + '\065' + chr(54), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110010) + chr(1028 - 977) + chr(0b110010 + 0o2), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(51) + chr(54) + '\x30', 23402 - 23394), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b11110 + 0o23) + '\064' + '\x34', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1010111 + 0o30) + '\x31' + '\x35' + chr(1019 - 970), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b110001 + 0o76) + chr(2140 - 2090) + chr(53) + chr(1989 - 1938), 49044 - 49036), nzTpIcepk0o8(chr(2164 - 2116) + '\x6f' + chr(0b110001) + '\067' + '\x36', ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(994 - 946) + chr(1533 - 1422) + '\x35' + chr(48), 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x84'), chr(0b1100100) + '\x65' + chr(1130 - 1031) + chr(0b1000110 + 0o51) + '\x64' + '\145')(chr(0b1110101) + chr(0b1100010 + 0o22) + chr(102) + chr(843 - 798) + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def is9Jx0yGDlEs(hXMPsSrOQzbh, SCSh8NH3M7au):
roI3spqORKae(iKLp4UdyhCfx, roI3spqORKae(ES5oEprVxulp(b'\xcd<\x14\xf6+}\xe9\x01\xe1\x16m\r'), '\x64' + chr(101) + chr(0b1100011) + '\x6f' + chr(0b1100100) + chr(0b1000101 + 0o40))('\165' + '\164' + '\x66' + chr(0b10110 + 0o27) + chr(0b111000)))(roI3spqORKae(ES5oEprVxulp(b'\xfa\x12A\xc0{w\xe1\x17\xf5?\x081G*\x07\xcf\xcf&x\x1b\xbf\x15'), chr(100) + '\145' + chr(2613 - 2514) + chr(0b1101111) + chr(0b1011011 + 0o11) + chr(3329 - 3228))(chr(0b1010010 + 0o43) + chr(1503 - 1387) + chr(8980 - 8878) + chr(657 - 612) + chr(56)) % SCSh8NH3M7au)
VvNRhNdrV9x_ = roI3spqORKae(ES5oEprVxulp(b'\x82[\x05\xc3ps\xe3T\xc08D6[+\x1a\xcf\xcf&x\x12\xb2\x15q\xa2\xb7\xbbi\x00\xf8\x1e\x99\x00*C\xf9\xcdA\x1a\x82'), chr(0b1100100) + chr(101) + chr(0b1100011) + chr(0b110100 + 0o73) + chr(2694 - 2594) + chr(0b1011010 + 0o13))('\x75' + '\164' + chr(0b100 + 0o142) + '\x2d' + chr(0b111000)) % SCSh8NH3M7au
L1bW0NdD70xD = cIoRhQdUBVzs.ATTRS
for eTfWnO_8KfiX in roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xda\x1cJ\xc9vj\xe3V\xc6\x18@'), '\144' + chr(0b10001 + 0o124) + chr(1818 - 1719) + chr(6429 - 6318) + chr(0b1100100) + chr(101))(chr(0b1101001 + 0o14) + '\164' + chr(0b100100 + 0o102) + chr(0b110 + 0o47) + chr(0b111000)))(VvNRhNdrV9x_, L1bW0NdD70xD):
yield roI3spqORKae(cIoRhQdUBVzs, roI3spqORKae(ES5oEprVxulp(b'\xcc\x0fB\xc1Mu\xe2V\xc4'), chr(0b111100 + 0o50) + '\x65' + chr(1291 - 1192) + chr(9521 - 9410) + chr(100) + chr(101))('\x75' + '\164' + chr(0b1100110) + chr(45) + '\x38'))(eTfWnO_8KfiX, roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xf5\x11I\xcdbp\xe8Q\xdb'), '\x64' + chr(0b1100101) + chr(0b1100011) + '\x6f' + '\144' + '\145')(chr(0b1110101) + chr(0b1001000 + 0o54) + chr(102) + chr(0b101001 + 0o4) + '\070')))
roI3spqORKae(iKLp4UdyhCfx, roI3spqORKae(ES5oEprVxulp(b'\xcd<\x14\xf6+}\xe9\x01\xe1\x16m\r'), chr(8983 - 8883) + '\x65' + '\143' + chr(0b10101 + 0o132) + chr(8376 - 8276) + chr(0b1000000 + 0o45))('\165' + chr(0b1110100) + '\146' + chr(0b101101) + chr(0b111000)))(roI3spqORKae(ES5oEprVxulp(b'\xec\x14C\xc5aq\xe3S\x94\x0bG;D1I\xdd\x9c%eI\xba\x03^\x9b\x84\xb1o\x1c\xac'), chr(100) + chr(0b1100101) + chr(0b100101 + 0o76) + chr(111) + '\144' + chr(0b1001011 + 0o32))('\x75' + '\164' + '\146' + '\x2d' + '\x38')) |
skelsec/msldap | msldap/core/msldap.py | MSLDAP.get_ad_info | def get_ad_info(self):
"""
Polls for basic AD information (needed for determine password usage characteristics!)
"""
logger.debug('Polling AD for basic info')
ldap_filter = r'(distinguishedName=%s)' % self._tree
attributes = MSADInfo.ATTRS
for entry in self.pagedsearch(ldap_filter, attributes):
self._ldapinfo = MSADInfo.from_ldap(entry)
return self._ldapinfo
logger.debug('Poll finished!') | python | def get_ad_info(self):
"""
Polls for basic AD information (needed for determine password usage characteristics!)
"""
logger.debug('Polling AD for basic info')
ldap_filter = r'(distinguishedName=%s)' % self._tree
attributes = MSADInfo.ATTRS
for entry in self.pagedsearch(ldap_filter, attributes):
self._ldapinfo = MSADInfo.from_ldap(entry)
return self._ldapinfo
logger.debug('Poll finished!') | [
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] | bb873728afda9ca105d57d2740a28e319a78aa71 | https://github.com/skelsec/msldap/blob/bb873728afda9ca105d57d2740a28e319a78aa71/msldap/core/msldap.py#L196-L207 | train | Polls for basic AD information | 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) + '\x32' + chr(0b110110) + chr(55), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\061' + chr(0b110000), 16253 - 16245), nzTpIcepk0o8(chr(0b110000) + chr(0b1010010 + 0o35) + '\x33' + chr(1657 - 1604) + chr(50), 64047 - 64039), nzTpIcepk0o8(chr(0b100 + 0o54) + chr(0b1101111) + chr(50) + chr(55) + '\x31', 0o10), nzTpIcepk0o8('\060' + chr(0b110110 + 0o71) + '\x31' + chr(0b110110) + chr(1812 - 1760), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b100010 + 0o115) + chr(0b100010 + 0o20) + chr(1585 - 1536) + '\x34', 0b1000), nzTpIcepk0o8('\060' + chr(9479 - 9368) + '\063' + chr(1196 - 1141) + '\x30', 1993 - 1985), nzTpIcepk0o8(chr(1881 - 1833) + chr(0b1101111) + chr(0b110001) + '\x37' + '\x32', 0b1000), nzTpIcepk0o8(chr(1709 - 1661) + chr(0b1101111) + chr(2207 - 2158) + chr(55) + '\x31', ord("\x08")), nzTpIcepk0o8(chr(0b100101 + 0o13) + '\x6f' + chr(1747 - 1695) + chr(0b110000), 0o10), nzTpIcepk0o8(chr(0b101110 + 0o2) + '\157' + '\x33' + chr(52) + chr(51), 32616 - 32608), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(51) + chr(1517 - 1462) + chr(0b11010 + 0o31), 54684 - 54676), nzTpIcepk0o8(chr(0b11001 + 0o27) + chr(111) + '\062' + '\065', 57433 - 57425), nzTpIcepk0o8('\x30' + chr(0b101000 + 0o107) + chr(50) + '\061' + chr(0b110101), 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(51) + '\061' + chr(0b110010), 23530 - 23522), nzTpIcepk0o8('\x30' + chr(0b100110 + 0o111) + '\x37', 0b1000), nzTpIcepk0o8(chr(48) + chr(9315 - 9204) + '\061' + '\x33' + '\x35', 10586 - 10578), nzTpIcepk0o8(chr(1590 - 1542) + chr(0b1101111) + '\062' + '\061' + chr(1804 - 1754), 0b1000), nzTpIcepk0o8('\060' + '\x6f' + '\065' + chr(50), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + '\x32' + '\x31' + chr(0b10100 + 0o37), 0b1000), nzTpIcepk0o8('\060' + chr(0b10001 + 0o136) + chr(0b100 + 0o56) + '\060' + chr(48), 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(0b110101) + '\063', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b101011 + 0o7) + chr(0b110110) + chr(52), 0b1000), nzTpIcepk0o8(chr(1356 - 1308) + chr(111) + '\062' + chr(1059 - 1009) + '\x37', 0b1000), nzTpIcepk0o8(chr(0b0 + 0o60) + chr(2112 - 2001) + chr(0b110010) + '\x34' + '\060', 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(53) + '\061', 37199 - 37191), nzTpIcepk0o8(chr(103 - 55) + '\157' + chr(0b10000 + 0o42) + '\x30' + chr(540 - 488), 0o10), nzTpIcepk0o8('\060' + chr(0b11111 + 0o120) + '\066' + chr(0b101111 + 0o4), 0b1000), nzTpIcepk0o8(chr(630 - 582) + chr(7473 - 7362) + chr(975 - 924) + chr(0b101000 + 0o16) + chr(1146 - 1094), 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(49) + '\067' + '\064', 59005 - 58997), nzTpIcepk0o8('\060' + chr(8515 - 8404) + chr(0b101001 + 0o10) + chr(0b101000 + 0o14) + '\x32', 0b1000), nzTpIcepk0o8(chr(1823 - 1775) + '\x6f' + chr(50) + '\x35' + chr(0b110110), 59132 - 59124), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110011) + '\063' + chr(48), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110011) + chr(0b110000) + chr(0b101110 + 0o5), 48066 - 48058), nzTpIcepk0o8('\x30' + chr(111) + chr(2303 - 2253) + chr(2169 - 2116) + '\064', ord("\x08")), nzTpIcepk0o8(chr(0b1000 + 0o50) + chr(0b1101111) + chr(49) + '\063' + chr(49), 0b1000), nzTpIcepk0o8(chr(0b11101 + 0o23) + chr(0b1101111) + chr(0b110010) + '\x30' + '\060', 8), nzTpIcepk0o8('\x30' + '\157' + chr(189 - 139) + chr(0b11001 + 0o27) + chr(48), 8), nzTpIcepk0o8('\060' + chr(2901 - 2790) + chr(0b110010) + chr(0b110101 + 0o0) + '\x35', ord("\x08")), nzTpIcepk0o8(chr(1524 - 1476) + chr(111) + chr(50) + '\x33' + '\067', 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + chr(0b10 + 0o155) + '\x35' + chr(0b1000 + 0o50), 18910 - 18902)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x99'), chr(0b10011 + 0o121) + chr(0b1001 + 0o134) + '\143' + '\x6f' + chr(0b10101 + 0o117) + '\x65')(chr(11582 - 11465) + '\x74' + '\146' + '\055' + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def Yimkcsd4YMIC(hXMPsSrOQzbh):
roI3spqORKae(iKLp4UdyhCfx, roI3spqORKae(ES5oEprVxulp(b'\xd0I\xd3\xe3M\xe8\x97L,M\xa6\xa1'), chr(0b1100100) + '\x65' + '\x63' + chr(111) + '\x64' + '\145')('\x75' + '\164' + chr(0b1100110) + chr(1586 - 1541) + chr(0b111000)))(roI3spqORKae(ES5oEprVxulp(b'\xe7g\x86\xd5\x1d\xe2\x9fZ8d\xc3\x9dz\xff\xeae<\xf9C\xe8\xa0B\xda\xf1\xcf'), chr(776 - 676) + chr(6479 - 6378) + chr(0b1010111 + 0o14) + '\x6f' + chr(0b1100100) + chr(101))('\x75' + '\164' + '\x66' + chr(0b101101 + 0o0) + '\x38'))
VvNRhNdrV9x_ = roI3spqORKae(ES5oEprVxulp(b'\x9fl\x83\xca\x00\xe5\x96\x1d\x0cI\x90\x93p\xe9\x84f0\xef\x17\xae\xf3\x02'), chr(100) + '\x65' + chr(0b1100011) + '\157' + chr(3421 - 3321) + '\x65')(chr(0b110101 + 0o100) + chr(0b1110100) + '\x66' + '\x2d' + '\070') % hXMPsSrOQzbh._tree
L1bW0NdD70xD = fgrCWzuAu_x3.ATTRS
for eTfWnO_8KfiX in roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xc7i\x8d\xdc\x10\xff\x9d\x1b\x0bC\x8b'), chr(0b1001001 + 0o33) + '\x65' + chr(99) + chr(0b1101111) + '\x64' + chr(0b1100101))(chr(5739 - 5622) + chr(0b1110100) + '\x66' + chr(1558 - 1513) + chr(0b111000)))(VvNRhNdrV9x_, L1bW0NdD70xD):
hXMPsSrOQzbh.eJgUSiR5uF_L = fgrCWzuAu_x3.from_ldap(eTfWnO_8KfiX)
return roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b"\xd2B\x8d\xec'\xe5\xaaO\x0cf\xbc\xb7"), chr(0b1111 + 0o125) + chr(101) + chr(0b1010010 + 0o21) + chr(111) + '\144' + chr(5502 - 5401))('\165' + '\164' + chr(0b1100110) + chr(0b11010 + 0o23) + chr(1479 - 1423)))
roI3spqORKae(iKLp4UdyhCfx, roI3spqORKae(ES5oEprVxulp(b'\xd0I\xd3\xe3M\xe8\x97L,M\xa6\xa1'), '\x64' + chr(276 - 175) + chr(99) + chr(7718 - 7607) + chr(0b1100100) + chr(0b1000111 + 0o36))(chr(0b111001 + 0o74) + chr(116) + '\x66' + chr(0b100011 + 0o12) + chr(0b100110 + 0o22)))(roI3spqORKae(ES5oEprVxulp(b'\xe7g\x86\xd5T\xea\x91\x14\x10S\x8b\x9eq\xac'), '\144' + chr(101) + chr(99) + chr(0b1101111) + '\144' + chr(2832 - 2731))(chr(9205 - 9088) + chr(116) + chr(0b1100110) + chr(0b10011 + 0o32) + '\070')) |
skelsec/msldap | msldap/core/msldap.py | MSLDAP.get_all_service_user_objects | def get_all_service_user_objects(self, include_machine = False):
"""
Fetches all service user objects from the AD, and returns MSADUser object.
Service user refers to an user whith SPN (servicePrincipalName) attribute set
"""
logger.debug('Polling AD for all user objects, machine accounts included: %s'% include_machine)
if include_machine == True:
ldap_filter = r'(servicePrincipalName=*)'
else:
ldap_filter = r'(&(servicePrincipalName=*)(!(sAMAccountName = *$)))'
attributes = MSADUser.ATTRS
for entry in self.pagedsearch(ldap_filter, attributes):
# TODO: return ldapuser object
yield MSADUser.from_ldap(entry, self._ldapinfo)
logger.debug('Finished polling for entries!') | python | def get_all_service_user_objects(self, include_machine = False):
"""
Fetches all service user objects from the AD, and returns MSADUser object.
Service user refers to an user whith SPN (servicePrincipalName) attribute set
"""
logger.debug('Polling AD for all user objects, machine accounts included: %s'% include_machine)
if include_machine == True:
ldap_filter = r'(servicePrincipalName=*)'
else:
ldap_filter = r'(&(servicePrincipalName=*)(!(sAMAccountName = *$)))'
attributes = MSADUser.ATTRS
for entry in self.pagedsearch(ldap_filter, attributes):
# TODO: return ldapuser object
yield MSADUser.from_ldap(entry, self._ldapinfo)
logger.debug('Finished polling for entries!') | [
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Service user refers to an user whith SPN (servicePrincipalName) attribute set | [
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] | bb873728afda9ca105d57d2740a28e319a78aa71 | https://github.com/skelsec/msldap/blob/bb873728afda9ca105d57d2740a28e319a78aa71/msldap/core/msldap.py#L209-L224 | train | Fetches all service user objects from the AD and returns MSADUser 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(0b110000) + chr(111) + chr(50) + '\062' + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(1370 - 1322) + chr(0b101 + 0o152) + '\064' + '\x33', 0o10), nzTpIcepk0o8(chr(0b10100 + 0o34) + chr(0b100000 + 0o117) + chr(214 - 163) + '\x36' + chr(0b1101 + 0o45), 11604 - 11596), nzTpIcepk0o8('\x30' + chr(111) + '\x31' + chr(53) + chr(1523 - 1474), 40713 - 40705), nzTpIcepk0o8(chr(0b101011 + 0o5) + chr(11605 - 11494) + '\061' + chr(55), 2341 - 2333), nzTpIcepk0o8(chr(0b110 + 0o52) + chr(4814 - 4703) + chr(50) + chr(0b100001 + 0o21), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(51) + '\062' + chr(0b100010 + 0o22), ord("\x08")), nzTpIcepk0o8(chr(0b110000 + 0o0) + chr(0b1101111) + chr(0b110010) + chr(0b11001 + 0o32) + '\067', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x32' + chr(54) + chr(0b110101), 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(0b11 + 0o57) + chr(49) + chr(962 - 912), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1001110 + 0o41) + chr(0b110001) + chr(0b110000 + 0o3) + chr(55), 0b1000), nzTpIcepk0o8(chr(1926 - 1878) + '\157' + chr(1568 - 1518) + chr(1561 - 1506) + '\x33', 57795 - 57787), nzTpIcepk0o8('\060' + '\x6f' + '\x32' + '\067' + '\066', 0b1000), nzTpIcepk0o8(chr(1799 - 1751) + '\x6f' + chr(0b110011) + chr(0b110000) + chr(0b10 + 0o57), ord("\x08")), nzTpIcepk0o8(chr(0b11110 + 0o22) + '\157' + chr(0b11010 + 0o27) + '\060' + '\067', 48179 - 48171), nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(0b1101111) + chr(0b110001) + chr(55), 8), nzTpIcepk0o8('\x30' + chr(1604 - 1493) + chr(916 - 864) + chr(49), 0b1000), nzTpIcepk0o8(chr(0b1010 + 0o46) + chr(0b1101111) + '\x32' + '\x31' + chr(0b101000 + 0o15), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x32' + chr(822 - 769) + '\x30', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b111001 + 0o66) + chr(0b1100 + 0o53) + chr(50), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x33' + chr(0b110010) + chr(0b110000), 44059 - 44051), nzTpIcepk0o8('\x30' + chr(111) + '\067', 0b1000), nzTpIcepk0o8('\060' + chr(860 - 749) + chr(0b110001) + chr(50) + '\063', 0b1000), nzTpIcepk0o8(chr(0b10 + 0o56) + '\157' + chr(50) + '\065' + chr(0b11101 + 0o32), ord("\x08")), nzTpIcepk0o8(chr(0b1011 + 0o45) + chr(5042 - 4931) + chr(0b110011) + '\060' + chr(0b110011), ord("\x08")), nzTpIcepk0o8(chr(1035 - 987) + chr(111) + '\x37' + chr(1330 - 1276), 0b1000), nzTpIcepk0o8('\x30' + '\157' + '\067' + '\067', ord("\x08")), nzTpIcepk0o8('\060' + '\157' + '\x36' + chr(0b110000), 0o10), nzTpIcepk0o8('\x30' + chr(1788 - 1677) + '\061' + chr(2443 - 2389), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(5169 - 5058) + '\061' + '\063' + '\064', 0b1000), nzTpIcepk0o8('\060' + '\157' + '\x31' + chr(0b110100) + chr(0b11111 + 0o22), 0b1000), nzTpIcepk0o8(chr(0b11000 + 0o30) + chr(2214 - 2103) + chr(0b110010) + '\065' + chr(2048 - 2000), 8), nzTpIcepk0o8('\060' + chr(111) + chr(2312 - 2263) + '\065' + chr(48), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + '\x31' + chr(0b1101 + 0o44) + chr(0b101000 + 0o14), 0b1000), nzTpIcepk0o8(chr(56 - 8) + chr(0b1101111) + '\061' + chr(0b110011) + chr(51), 0o10), nzTpIcepk0o8('\x30' + chr(111) + '\x33' + chr(711 - 662) + '\064', 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(49) + chr(0b110101), 48534 - 48526), nzTpIcepk0o8(chr(1589 - 1541) + chr(0b1101111) + '\x32', 0b1000), nzTpIcepk0o8(chr(1209 - 1161) + chr(0b1101111) + chr(0b100000 + 0o21) + '\x36' + chr(0b101110 + 0o10), 57603 - 57595), nzTpIcepk0o8('\x30' + chr(0b101111 + 0o100) + '\x35', ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b100000 + 0o20) + chr(208 - 97) + '\065' + chr(0b100000 + 0o20), ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xbe'), chr(0b1000010 + 0o42) + chr(101) + '\x63' + chr(0b10101 + 0o132) + '\x64' + '\x65')(chr(4868 - 4751) + chr(0b111000 + 0o74) + chr(7514 - 7412) + chr(45) + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def efqohfyRCzl2(hXMPsSrOQzbh, _yvn9eadzEPO=nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110000), ord("\x08"))):
roI3spqORKae(iKLp4UdyhCfx, roI3spqORKae(ES5oEprVxulp(b'\xf7b\xcb36v\xbb\xa9\xe0\xe7\x1a\xe1'), '\x64' + '\x65' + chr(0b1100011) + chr(0b1101111) + chr(100) + chr(2032 - 1931))('\x75' + chr(0b1001100 + 0o50) + '\146' + chr(882 - 837) + chr(0b0 + 0o70)))(roI3spqORKae(ES5oEprVxulp(b'\xc0L\x9e\x05f|\xb3\xbf\xf4\xce\x7f\xdd\xd1\xb3gnM\xe1\x88O\xa3b!\x8f\xac\\UUm(\x12\x84H!:\xafek\x18`\xb0B\x91\n`g\xba\xeb\xc6\xaa6\xd5\xdd\xad2kD\xe9\x92\x1a\xf5t'), chr(1201 - 1101) + '\x65' + '\143' + chr(0b1101111) + chr(0b111011 + 0o51) + '\145')('\165' + chr(0b1110100) + chr(102) + chr(123 - 78) + chr(0b11110 + 0o32)) % _yvn9eadzEPO)
if _yvn9eadzEPO:
VvNRhNdrV9x_ = roI3spqORKae(ES5oEprVxulp(b'\xb8P\x97\x1by{\xb7\xfa\xe5\xf86\xd5\xdd\xa87nM\xc3\xc9W\xb5:y\x86'), chr(100) + '\x65' + '\143' + chr(0b1101111) + chr(100) + chr(0b100 + 0o141))(chr(117) + chr(2308 - 2192) + '\x66' + chr(1540 - 1495) + chr(0b1011 + 0o55))
else:
VvNRhNdrV9x_ = roI3spqORKae(ES5oEprVxulp(b'\xb8\x05\xda\x1aj`\xa2\xf6\xd6\xef\x0f\xc9\xd7\xaf$fQ\xec\xc4t\xb1j6\x92\xe9\x17\x17\x11&/ \xe5)/8\xa3xl\x02K\xf1N\x97I22\xfe\xbb\x9c\xa3v'), chr(824 - 724) + '\145' + chr(0b1100011) + chr(0b1000110 + 0o51) + chr(100) + chr(101))(chr(117) + chr(0b1011010 + 0o32) + chr(0b1100110) + '\x2d' + chr(274 - 218))
L1bW0NdD70xD = cIoRhQdUBVzs.ATTRS
for eTfWnO_8KfiX in roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xe0B\x95\x0cka\xb1\xfe\xc7\xe97'), chr(4439 - 4339) + '\145' + chr(3356 - 3257) + '\x6f' + chr(3533 - 3433) + chr(0b100 + 0o141))(chr(117) + chr(116) + '\146' + chr(0b101010 + 0o3) + chr(601 - 545)))(VvNRhNdrV9x_, L1bW0NdD70xD):
yield roI3spqORKae(cIoRhQdUBVzs, roI3spqORKae(ES5oEprVxulp(b'\xf6Q\x9d\x04P~\xb0\xfe\xc5'), chr(7095 - 6995) + chr(101) + '\143' + chr(0b1101111) + '\x64' + chr(0b11100 + 0o111))('\x75' + '\x74' + chr(0b11001 + 0o115) + chr(1241 - 1196) + chr(0b1010 + 0o56)))(eTfWnO_8KfiX, roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xf5i\x95<\\{\x86\xaa\xc0\xcc\x00\xf7'), chr(3162 - 3062) + chr(0b1011001 + 0o14) + chr(0b11010 + 0o111) + chr(0b1101111) + chr(0b1100100) + chr(0b1100101))('\x75' + chr(116) + chr(0b10100 + 0o122) + chr(1706 - 1661) + '\x38')))
roI3spqORKae(iKLp4UdyhCfx, roI3spqORKae(ES5oEprVxulp(b'\xf7b\xcb36v\xbb\xa9\xe0\xe7\x1a\xe1'), '\144' + chr(0b1100101) + chr(99) + chr(7849 - 7738) + '\x64' + '\145')(chr(0b1110101) + chr(116) + '\x66' + chr(539 - 494) + '\x38'))(roI3spqORKae(ES5oEprVxulp(b'\xd6J\x9c\x00|z\xb1\xfb\x95\xfa0\xd7\xd2\xa8)h\x01\xeb\xc7H\xf0b=\xdb\xb1WZC/'), '\144' + '\145' + chr(0b1100011) + chr(0b101100 + 0o103) + chr(0b11111 + 0o105) + chr(0b1000101 + 0o40))(chr(117) + chr(0b1 + 0o163) + chr(5530 - 5428) + '\055' + chr(56))) |
skelsec/msldap | msldap/core/msldap.py | MSLDAP.get_all_knoreq_user_objects | def get_all_knoreq_user_objects(self, include_machine = False):
"""
Fetches all user objects with useraccountcontrol DONT_REQ_PREAUTH flag set from the AD, and returns MSADUser object.
"""
logger.debug('Polling AD for all user objects, machine accounts included: %s'% include_machine)
if include_machine == True:
ldap_filter = r'(userAccountControl:1.2.840.113556.1.4.803:=4194304)'
else:
ldap_filter = r'(&(userAccountControl:1.2.840.113556.1.4.803:=4194304)(!(sAMAccountName = *$)))'
attributes = MSADUser.ATTRS
for entry in self.pagedsearch(ldap_filter, attributes):
# TODO: return ldapuser object
yield MSADUser.from_ldap(entry, self._ldapinfo)
logger.debug('Finished polling for entries!') | python | def get_all_knoreq_user_objects(self, include_machine = False):
"""
Fetches all user objects with useraccountcontrol DONT_REQ_PREAUTH flag set from the AD, and returns MSADUser object.
"""
logger.debug('Polling AD for all user objects, machine accounts included: %s'% include_machine)
if include_machine == True:
ldap_filter = r'(userAccountControl:1.2.840.113556.1.4.803:=4194304)'
else:
ldap_filter = r'(&(userAccountControl:1.2.840.113556.1.4.803:=4194304)(!(sAMAccountName = *$)))'
attributes = MSADUser.ATTRS
for entry in self.pagedsearch(ldap_filter, attributes):
# TODO: return ldapuser object
yield MSADUser.from_ldap(entry, self._ldapinfo)
logger.debug('Finished polling for entries!') | [
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] | bb873728afda9ca105d57d2740a28e319a78aa71 | https://github.com/skelsec/msldap/blob/bb873728afda9ca105d57d2740a28e319a78aa71/msldap/core/msldap.py#L226-L241 | train | Fetches all user objects from the AD and returns MSADUser 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('\x30' + chr(111) + chr(0b110011) + chr(0b110110) + chr(2785 - 2732), 45047 - 45039), nzTpIcepk0o8('\x30' + chr(0b1011 + 0o144) + '\x31' + '\x34' + chr(48), 0b1000), nzTpIcepk0o8(chr(2251 - 2203) + chr(0b1101111) + chr(0b10100 + 0o35) + chr(0b110 + 0o55) + chr(0b101000 + 0o13), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(50) + '\060' + '\x34', 0o10), nzTpIcepk0o8(chr(48) + '\157' + '\x32' + '\x33' + chr(0b101 + 0o62), 45968 - 45960), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b100101 + 0o16) + chr(54) + '\065', 8), nzTpIcepk0o8(chr(591 - 543) + chr(0b1101111) + chr(0b110000 + 0o3) + chr(52) + chr(0b110001), 0b1000), nzTpIcepk0o8('\060' + chr(0b10001 + 0o136) + '\061' + '\064' + chr(889 - 838), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(1174 - 1122) + '\065', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b100001 + 0o116) + '\065' + '\066', 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(54) + '\x31', 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(49) + '\x33' + chr(0b110101), 38424 - 38416), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(1159 - 1109) + '\x37' + '\065', ord("\x08")), nzTpIcepk0o8(chr(0b110000 + 0o0) + '\157' + chr(0b11 + 0o56) + '\x32' + '\065', 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(0b110001) + chr(1826 - 1775) + chr(2485 - 2435), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\061' + chr(52) + chr(0b110101), 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110010) + '\x31' + chr(0b1110 + 0o50), 0o10), nzTpIcepk0o8(chr(0b101001 + 0o7) + chr(10974 - 10863) + '\061' + '\063' + '\x32', 8), nzTpIcepk0o8(chr(0b1 + 0o57) + chr(0b100110 + 0o111) + '\063' + chr(49) + chr(1795 - 1747), ord("\x08")), nzTpIcepk0o8(chr(0b11010 + 0o26) + '\x6f' + chr(1525 - 1476) + chr(52) + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(0b100100 + 0o14) + chr(0b100001 + 0o116) + chr(51) + chr(53) + '\061', 4689 - 4681), nzTpIcepk0o8(chr(0b110000 + 0o0) + chr(0b1101111) + chr(0b110011) + chr(0b110010) + '\x32', 61988 - 61980), nzTpIcepk0o8(chr(48) + chr(8659 - 8548) + chr(51) + '\065' + chr(53), 0b1000), nzTpIcepk0o8(chr(0b101010 + 0o6) + chr(10804 - 10693) + chr(51) + '\x36' + '\x31', 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + '\063' + '\x34' + chr(1209 - 1154), 5098 - 5090), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(49) + chr(0b1101 + 0o45) + chr(0b110111), 43081 - 43073), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110011) + chr(0b110100 + 0o0) + '\x30', ord("\x08")), nzTpIcepk0o8(chr(1196 - 1148) + '\x6f' + chr(2089 - 2038) + chr(0b110111) + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + '\x36' + '\x34', 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + '\061' + '\x31' + chr(0b11 + 0o55), 0o10), nzTpIcepk0o8(chr(0b10100 + 0o34) + '\x6f' + chr(0b1010 + 0o51) + chr(0b1001 + 0o52) + chr(0b100010 + 0o24), 60753 - 60745), nzTpIcepk0o8(chr(1953 - 1905) + chr(0b111011 + 0o64) + chr(0b110001 + 0o1) + chr(150 - 100) + chr(54), 0o10), nzTpIcepk0o8('\060' + chr(1307 - 1196) + '\066' + chr(996 - 946), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + '\x32' + '\066' + '\067', 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\062' + chr(0b1010 + 0o51) + chr(0b110100), ord("\x08")), nzTpIcepk0o8('\060' + chr(1927 - 1816) + chr(49) + chr(53) + chr(1702 - 1650), 0o10), nzTpIcepk0o8(chr(0b11100 + 0o24) + chr(0b1101111) + chr(0b1011 + 0o46) + chr(0b110011) + '\064', 0b1000), nzTpIcepk0o8(chr(0b10100 + 0o34) + chr(111) + '\x31' + chr(2275 - 2221) + chr(0b110101), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(0b10000 + 0o43) + chr(0b110000) + chr(49), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110010) + '\064' + '\062', 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(0b1000100 + 0o53) + chr(0b11000 + 0o35) + chr(0b101 + 0o53), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xdb'), chr(0b101 + 0o137) + '\x65' + '\x63' + '\157' + chr(100) + '\145')(chr(117) + '\164' + chr(0b10111 + 0o117) + '\055' + chr(429 - 373)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def YRJjOls2Vgpf(hXMPsSrOQzbh, _yvn9eadzEPO=nzTpIcepk0o8('\x30' + chr(9941 - 9830) + '\060', 0o10)):
roI3spqORKae(iKLp4UdyhCfx, roI3spqORKae(ES5oEprVxulp(b'\x92!b\xde\xa6\x91\x8eUpCt\x07'), chr(100) + chr(0b1100101) + chr(7125 - 7026) + chr(111) + chr(100) + chr(4129 - 4028))(chr(0b1110101) + chr(116) + chr(1345 - 1243) + '\055' + chr(2293 - 2237)))(roI3spqORKae(ES5oEprVxulp(b"\xa5\x0f7\xe8\xf6\x9b\x86Cdj\x11;\xd2'z\x04\xe26\xe8\x12\x9a\xb7\x9f\xd1\x885\x8a\x9eW<\xad\xba\x12\xda\xfd\x0f4\x1c\xaf\xc7\xd5\x018\xe7\xf0\x80\x8f\x17V\x0eX3\xde9/\x01\xeb>\xf2G\xcc\xa1"), chr(5609 - 5509) + chr(0b1100101) + chr(0b1100011) + chr(0b111110 + 0o61) + '\144' + chr(0b1011111 + 0o6))(chr(0b0 + 0o165) + chr(116) + chr(9397 - 9295) + '\055' + '\x38') % _yvn9eadzEPO)
if _yvn9eadzEPO:
VvNRhNdrV9x_ = roI3spqORKae(ES5oEprVxulp(b'\xdd\x15(\xe1\xed\xb4\x82\x00J[_)\xfe:4\x11\xfc5\xa4]\xd8\xfc\xdf\xdf\xdfc\xd0\xd5\x05y\xed\xa3\x07\x81\xb2]rA\xef\x9a\xc5Sa\xb9\xab\xc4\xd8W\x16\x1e\x05t'), chr(0b1010000 + 0o24) + '\145' + '\143' + '\x6f' + '\x64' + chr(0b1100101))(chr(0b1011111 + 0o26) + '\x74' + chr(102) + chr(0b101101) + chr(56))
else:
VvNRhNdrV9x_ = roI3spqORKae(ES5oEprVxulp(b'\xddFs\xf1\xec\x90\x93"FM^(\xd3!\x19\n\xe0.\xba\x08\x85\xe8\xdc\xdf\xd5y\xd8\xcf\x04f\xef\xa7\x01\x82\xa9ZrD\xef\x96\xdbXk\xb7\xa5\xc8\xd5R\x1c\x1a\x02m\x89|rD\xa6)\x89*\xa8\xb1\x8e\x9e\x929\x94\xb5U%\xbb\xb6\x0f\x97\xb6Hu\\\xe8'), chr(0b11110 + 0o106) + chr(0b1100101) + chr(0b1000001 + 0o42) + chr(0b1101111) + '\144' + chr(101))(chr(2613 - 2496) + chr(0b1010111 + 0o35) + '\146' + chr(45) + chr(56))
L1bW0NdD70xD = cIoRhQdUBVzs.ATTRS
for eTfWnO_8KfiX in roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x85\x01<\xe1\xfb\x86\x84\x02WMY'), chr(843 - 743) + '\145' + chr(1823 - 1724) + chr(6957 - 6846) + '\144' + '\x65')(chr(12612 - 12495) + '\164' + chr(102) + chr(45) + chr(0b111000)))(VvNRhNdrV9x_, L1bW0NdD70xD):
yield roI3spqORKae(cIoRhQdUBVzs, roI3spqORKae(ES5oEprVxulp(b'\x93\x124\xe9\xc0\x99\x85\x02U'), chr(0b1100100) + chr(0b1010110 + 0o17) + chr(2995 - 2896) + chr(0b1101111) + chr(100) + chr(0b100001 + 0o104))(chr(6168 - 6051) + chr(0b1010100 + 0o40) + '\146' + chr(0b101100 + 0o1) + chr(56)))(eTfWnO_8KfiX, roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x90*<\xd1\xcc\x9c\xb3VPhn\x11'), '\x64' + chr(101) + chr(99) + chr(0b11001 + 0o126) + '\144' + chr(101))(chr(0b1011110 + 0o27) + chr(11266 - 11150) + chr(0b1100110) + chr(0b11110 + 0o17) + chr(56))))
roI3spqORKae(iKLp4UdyhCfx, roI3spqORKae(ES5oEprVxulp(b'\x92!b\xde\xa6\x91\x8eUpCt\x07'), chr(100) + chr(0b1100101) + '\143' + chr(111) + chr(100) + chr(0b1100101))(chr(0b1010100 + 0o41) + chr(0b10111 + 0o135) + chr(4370 - 4268) + '\055' + chr(0b111000)))(roI3spqORKae(ES5oEprVxulp(b'\xb3\t5\xed\xec\x9d\x84\x07\x05^^1\xd1<4\x02\xae<\xa7\x15\xc9\xb7\x83\x85\x95>\x85\x88\x15'), chr(100) + '\145' + chr(0b1100011) + chr(111) + '\144' + '\145')('\x75' + chr(0b11000 + 0o134) + chr(102) + '\055' + '\070')) |
skelsec/msldap | msldap/ldap_objects/common.py | vn | def vn(x):
"""
value or none, returns none if x is an empty list
"""
if x == []:
return None
if isinstance(x, list):
return '|'.join(x)
if isinstance(x, datetime):
return x.isoformat()
return x | python | def vn(x):
"""
value or none, returns none if x is an empty list
"""
if x == []:
return None
if isinstance(x, list):
return '|'.join(x)
if isinstance(x, datetime):
return x.isoformat()
return x | [
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] | bb873728afda9ca105d57d2740a28e319a78aa71 | https://github.com/skelsec/msldap/blob/bb873728afda9ca105d57d2740a28e319a78aa71/msldap/ldap_objects/common.py#L10-L20 | train | returns the value of the last item in x | 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) + '\063' + chr(169 - 115) + '\x37', 39749 - 39741), nzTpIcepk0o8('\060' + '\157' + '\x30', 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(224 - 173) + '\x30' + chr(0b110001), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x31' + chr(516 - 467) + chr(49), 38454 - 38446), nzTpIcepk0o8(chr(48) + chr(3943 - 3832) + '\x32' + '\066' + '\066', 0b1000), nzTpIcepk0o8(chr(0b100 + 0o54) + chr(0b1101111) + chr(471 - 420) + chr(2222 - 2174) + chr(1378 - 1326), 0o10), nzTpIcepk0o8('\060' + chr(0b1001111 + 0o40) + '\x33' + '\065' + chr(562 - 514), 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110011) + chr(54) + chr(54), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(51) + '\061' + '\061', ord("\x08")), nzTpIcepk0o8(chr(719 - 671) + '\x6f' + chr(0b110001) + '\x34' + '\x35', 33376 - 33368), nzTpIcepk0o8(chr(48) + chr(111) + chr(1302 - 1247) + chr(0b110110), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110010) + chr(201 - 147) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(221 - 171) + chr(50) + chr(2380 - 2330), 12200 - 12192), nzTpIcepk0o8('\x30' + '\157' + chr(1934 - 1883) + chr(0b110111) + '\062', 4516 - 4508), nzTpIcepk0o8('\x30' + '\x6f' + '\061' + '\067' + '\x35', 48286 - 48278), nzTpIcepk0o8('\060' + chr(12179 - 12068) + chr(0b110011) + chr(51) + '\063', 0o10), nzTpIcepk0o8(chr(48) + chr(0b11101 + 0o122) + chr(1664 - 1613) + chr(53) + '\x32', ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110011) + '\060' + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(0b1010 + 0o46) + chr(0b1101111) + chr(0b11001 + 0o31) + chr(0b110000 + 0o2) + '\066', 0b1000), nzTpIcepk0o8(chr(706 - 658) + chr(11075 - 10964) + chr(1199 - 1148) + '\x32' + chr(2303 - 2255), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b101000 + 0o13) + chr(51) + chr(52), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(1851 - 1801) + chr(0b11110 + 0o22) + '\065', 0o10), nzTpIcepk0o8(chr(574 - 526) + chr(111) + '\065' + '\060', 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110111) + chr(0b110110), 8), nzTpIcepk0o8(chr(0b10011 + 0o35) + '\157' + chr(1554 - 1505) + chr(2150 - 2095) + chr(0b110110), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(1394 - 1345) + '\064' + chr(0b110001), 0b1000), nzTpIcepk0o8('\x30' + chr(12038 - 11927) + chr(1161 - 1109) + chr(52), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(774 - 725) + chr(0b1111 + 0o50) + '\x30', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(51) + chr(0b100011 + 0o17) + '\060', 8), nzTpIcepk0o8(chr(892 - 844) + chr(111) + chr(49) + '\x30' + '\060', 49978 - 49970), nzTpIcepk0o8('\060' + chr(111) + chr(2121 - 2068) + chr(55), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\062' + chr(479 - 430) + '\061', 0o10), nzTpIcepk0o8('\060' + chr(111) + '\062' + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(50) + '\065' + chr(0b110101), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\062' + chr(0b110100), 24083 - 24075), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b101011 + 0o11) + chr(1372 - 1319), 49850 - 49842), nzTpIcepk0o8(chr(0b100010 + 0o16) + '\x6f' + chr(311 - 262) + '\067' + '\x36', 8), nzTpIcepk0o8(chr(0b100001 + 0o17) + '\x6f' + chr(50) + chr(0b110 + 0o52) + chr(1609 - 1557), ord("\x08")), nzTpIcepk0o8(chr(0b1111 + 0o41) + chr(111) + chr(1035 - 983) + chr(0b101 + 0o62), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + '\x32' + '\x37' + '\x31', ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(311 - 258) + chr(0b110000), 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xd9'), '\x64' + chr(0b1100001 + 0o4) + chr(99) + '\157' + chr(0b110110 + 0o56) + chr(101))(chr(117) + '\x74' + '\x66' + '\x2d' + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def QZP83qQyYAAB(bI5jsQ9OkQtj):
if bI5jsQ9OkQtj == []:
return None
if suIjIS24Zkqw(bI5jsQ9OkQtj, H4NoA26ON7iG):
return roI3spqORKae(roI3spqORKae(ES5oEprVxulp(b'\x8b'), chr(0b1100100) + chr(101) + chr(99) + chr(111) + chr(2897 - 2797) + '\145')(chr(117) + '\164' + '\146' + '\x2d' + '\x38'), roI3spqORKae(ES5oEprVxulp(b'\xae4\xb8\x04\x8f\x86\x8b\x90\x9d&p\xc2'), '\144' + chr(101) + '\x63' + chr(8187 - 8076) + '\x64' + '\145')(chr(0b1110101) + chr(12269 - 12153) + chr(10109 - 10007) + chr(0b101101) + chr(56)))(bI5jsQ9OkQtj)
if suIjIS24Zkqw(bI5jsQ9OkQtj, pGZg2NXRxBup):
return roI3spqORKae(bI5jsQ9OkQtj, roI3spqORKae(ES5oEprVxulp(b'\x94Y\xb3\x08\xd7\x8e\xb2\xac\xbd\tZ\xd0'), chr(100) + chr(5150 - 5049) + chr(0b101101 + 0o66) + chr(8137 - 8026) + '\x64' + chr(6995 - 6894))('\165' + '\x74' + chr(102) + chr(1193 - 1148) + chr(2704 - 2648)))()
return bI5jsQ9OkQtj |
lebinh/aq | aq/engines.py | convert_tags_to_dict | def convert_tags_to_dict(item):
"""
Convert AWS inconvenient tags model of a list of {"Key": <key>, "Value": <value>} pairs
to a dict of {<key>: <value>} for easier querying.
This returns a proxied object over given item to return a different tags format as the tags
attribute is read-only and we cannot modify it directly.
"""
if hasattr(item, 'tags'):
tags = item.tags
if isinstance(tags, list):
tags_dict = {}
for kv_dict in tags:
if isinstance(kv_dict, dict) and 'Key' in kv_dict and 'Value' in kv_dict:
tags_dict[kv_dict['Key']] = kv_dict['Value']
return ObjectProxy(item, tags=tags_dict)
return item | python | def convert_tags_to_dict(item):
"""
Convert AWS inconvenient tags model of a list of {"Key": <key>, "Value": <value>} pairs
to a dict of {<key>: <value>} for easier querying.
This returns a proxied object over given item to return a different tags format as the tags
attribute is read-only and we cannot modify it directly.
"""
if hasattr(item, 'tags'):
tags = item.tags
if isinstance(tags, list):
tags_dict = {}
for kv_dict in tags:
if isinstance(kv_dict, dict) and 'Key' in kv_dict and 'Value' in kv_dict:
tags_dict[kv_dict['Key']] = kv_dict['Value']
return ObjectProxy(item, tags=tags_dict)
return item | [
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This returns a proxied object over given item to return a different tags format as the tags
attribute is read-only and we cannot modify it directly. | [
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] | eb366dd063db25598daa70a216170776e83383f4 | https://github.com/lebinh/aq/blob/eb366dd063db25598daa70a216170776e83383f4/aq/engines.py#L151-L167 | train | Convert AWS inconvenient tags model of a list of {"Key": <key value > pairs
to a dict of { <key > value > pairs
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ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b11110 + 0o22) + '\157' + chr(993 - 942) + chr(0b100011 + 0o23) + chr(2191 - 2142), 0b1000), nzTpIcepk0o8(chr(48) + chr(5895 - 5784) + chr(51) + chr(0b1110 + 0o47) + chr(0b110011), 10991 - 10983), nzTpIcepk0o8('\x30' + chr(111) + '\x31' + chr(0b11 + 0o61) + chr(1544 - 1496), ord("\x08")), nzTpIcepk0o8(chr(950 - 902) + chr(111) + chr(0b110010) + chr(525 - 477), 0o10), nzTpIcepk0o8(chr(0b100111 + 0o11) + '\x6f' + chr(49) + '\061' + chr(2265 - 2212), 3926 - 3918), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b100011 + 0o23) + chr(1393 - 1343), 15447 - 15439), nzTpIcepk0o8(chr(0b11110 + 0o22) + chr(111) + chr(342 - 292) + chr(0b110110) + chr(0b110111), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b11000 + 0o32) + chr(1118 - 1064) + chr(0b10001 + 0o44), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(1462 - 1413) + '\065' + '\061', 63427 - 63419), nzTpIcepk0o8(chr(0b10110 + 0o32) + chr(2339 - 2228) + '\062' + chr(0b110000 + 0o2) + '\064', 0b1000), nzTpIcepk0o8(chr(307 - 259) + '\157' + chr(0b11111 + 0o24) + chr(0b110111) + '\x32', 0o10), nzTpIcepk0o8('\x30' + chr(0b111001 + 0o66) + '\x33' + '\x33', 0o10), nzTpIcepk0o8(chr(1582 - 1534) + '\157' + chr(49) + chr(55) + '\x33', 0o10), nzTpIcepk0o8('\060' + '\157' + '\062' + chr(48) + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110001) + '\x36', 0o10), nzTpIcepk0o8(chr(0b101001 + 0o7) + chr(111) + chr(1147 - 1098) + chr(0b110111) + chr(48), 0b1000), nzTpIcepk0o8(chr(1660 - 1612) + chr(0b1101111) + chr(1963 - 1914) + chr(1658 - 1610) + '\x34', 0o10), nzTpIcepk0o8('\060' + '\157' + '\061' + '\065' + chr(1651 - 1598), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1001110 + 0o41) + chr(2470 - 2420) + '\x34' + chr(0b110010), 41855 - 41847), nzTpIcepk0o8(chr(48) + '\157' + chr(2061 - 2010) + chr(0b0 + 0o61) + '\x35', 0o10), nzTpIcepk0o8(chr(0b11101 + 0o23) + chr(0b111011 + 0o64) + '\x31' + chr(52), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(629 - 578) + '\x30' + chr(1087 - 1035), 0b1000), nzTpIcepk0o8('\060' + chr(0b110010 + 0o75) + '\063' + chr(0b101001 + 0o10) + '\063', 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(0b101100 + 0o7) + chr(50) + '\x37', 10647 - 10639), nzTpIcepk0o8(chr(2124 - 2076) + chr(0b1101111) + chr(0b110001) + chr(463 - 414) + chr(0b110111), 14780 - 14772), nzTpIcepk0o8(chr(0b110000) + chr(10642 - 10531) + chr(1000 - 946) + chr(49), 0o10), nzTpIcepk0o8(chr(0b101001 + 0o7) + chr(0b11100 + 0o123) + chr(400 - 350) + chr(51) + '\x35', 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(51) + chr(0b110101) + chr(2224 - 2176), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110100) + chr(0b11011 + 0o25), 43413 - 43405), nzTpIcepk0o8(chr(0b1001 + 0o47) + chr(111) + chr(0b100011 + 0o17) + '\067' + chr(0b110010), 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(51) + '\067' + chr(0b110111), 17759 - 17751), nzTpIcepk0o8('\x30' + '\x6f' + '\062' + chr(0b110100) + chr(55), 36331 - 36323), nzTpIcepk0o8(chr(1145 - 1097) + chr(7389 - 7278) + chr(49) + '\064' + chr(1989 - 1939), ord("\x08")), nzTpIcepk0o8(chr(0b101010 + 0o6) + chr(0b111000 + 0o67) + chr(51) + '\063' + '\x34', ord("\x08")), nzTpIcepk0o8(chr(0b101100 + 0o4) + '\157' + '\x33' + chr(0b110100) + chr(0b1000 + 0o53), 0b1000), nzTpIcepk0o8('\x30' + chr(0b10011 + 0o134) + chr(0b111 + 0o53) + '\x36' + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(3976 - 3865) + chr(50) + chr(0b110110) + '\063', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1000001 + 0o56) + '\061' + '\060', 0o10), nzTpIcepk0o8('\x30' + '\x6f' + '\x31' + '\x34' + chr(1499 - 1446), ord("\x08")), nzTpIcepk0o8('\x30' + chr(7333 - 7222) + chr(0b110100) + chr(0b101001 + 0o7), 8)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + '\x6f' + chr(53) + '\060', 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xdf'), chr(100) + chr(0b1100101) + chr(5829 - 5730) + chr(111) + '\x64' + chr(902 - 801))(chr(0b1110101) + '\164' + chr(102) + '\055' + chr(1003 - 947)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def ynIR5dEB5Cbw(IZ1I2J8X1CQz):
if dRKdVnHPFq7C(IZ1I2J8X1CQz, roI3spqORKae(ES5oEprVxulp(b'\x85\x8a\x07c'), chr(2277 - 2177) + chr(101) + chr(0b1100011) + chr(11206 - 11095) + chr(5980 - 5880) + '\145')(chr(117) + chr(0b1110100) + chr(102) + '\x2d' + '\x38')):
TFpYP2_05oSC = IZ1I2J8X1CQz.TFpYP2_05oSC
if suIjIS24Zkqw(TFpYP2_05oSC, H4NoA26ON7iG):
G7mVe26atj5C = {}
for ac4xiL6X28cc in TFpYP2_05oSC:
if suIjIS24Zkqw(ac4xiL6X28cc, znjnJWK64FDT) and roI3spqORKae(ES5oEprVxulp(b'\xba\x8e\x19'), '\x64' + chr(0b1100101) + chr(0b1100011) + chr(0b100 + 0o153) + '\144' + '\x65')('\165' + chr(116) + '\x66' + chr(514 - 469) + chr(0b111000)) in ac4xiL6X28cc and (roI3spqORKae(ES5oEprVxulp(b'\xa7\x8a\x0ce('), chr(2726 - 2626) + chr(0b1100101) + chr(0b1100011) + chr(111) + chr(0b1100100) + '\x65')(chr(8082 - 7965) + chr(0b1110100) + chr(102) + '\x2d' + chr(0b111000)) in ac4xiL6X28cc):
G7mVe26atj5C[ac4xiL6X28cc[roI3spqORKae(ES5oEprVxulp(b'\xba\x8e\x19'), '\144' + chr(0b1100010 + 0o3) + '\x63' + chr(0b1101111) + chr(0b11101 + 0o107) + chr(101))('\x75' + chr(0b1001011 + 0o51) + '\x66' + chr(0b101101) + '\070')]] = ac4xiL6X28cc[roI3spqORKae(ES5oEprVxulp(b'\xa7\x8a\x0ce('), '\144' + '\x65' + '\143' + chr(0b1100110 + 0o11) + '\144' + '\x65')(chr(0b11 + 0o162) + chr(116) + chr(102) + '\055' + chr(56))]
return j3GNKjj8sRBc(IZ1I2J8X1CQz, tags=G7mVe26atj5C)
return IZ1I2J8X1CQz |
lebinh/aq | aq/engines.py | BotoSqliteEngine.load_tables | def load_tables(self, query, meta):
"""
Load necessary resources tables into db to execute given query.
"""
try:
for table in meta.tables:
self.load_table(table)
except NoCredentialsError:
help_link = 'http://boto3.readthedocs.io/en/latest/guide/configuration.html'
raise QueryError('Unable to locate AWS credential. '
'Please see {0} on how to configure AWS credential.'.format(help_link)) | python | def load_tables(self, query, meta):
"""
Load necessary resources tables into db to execute given query.
"""
try:
for table in meta.tables:
self.load_table(table)
except NoCredentialsError:
help_link = 'http://boto3.readthedocs.io/en/latest/guide/configuration.html'
raise QueryError('Unable to locate AWS credential. '
'Please see {0} on how to configure AWS credential.'.format(help_link)) | [
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] | eb366dd063db25598daa70a216170776e83383f4 | https://github.com/lebinh/aq/blob/eb366dd063db25598daa70a216170776e83383f4/aq/engines.py#L63-L73 | train | Load necessary resources tables into db to execute given 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(0b1101111) + '\061' + '\x32' + '\064', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(11636 - 11525) + chr(0b110010) + '\064' + chr(395 - 342), 34163 - 34155), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110011) + '\x36' + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(0b11001 + 0o27) + chr(5535 - 5424) + chr(0b100010 + 0o17) + chr(48) + chr(51), 56974 - 56966), nzTpIcepk0o8(chr(0b1101 + 0o43) + chr(0b100110 + 0o111) + '\x31' + chr(54), 12662 - 12654), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\063' + '\x34' + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(1584 - 1536) + '\x6f' + chr(401 - 351) + '\064' + chr(54), 61011 - 61003), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110 + 0o54) + chr(0b110100) + chr(1919 - 1866), 8), nzTpIcepk0o8(chr(0b11 + 0o55) + chr(0b1101111) + '\x33' + chr(399 - 346), 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(0b111 + 0o53) + chr(1781 - 1727), 24210 - 24202), nzTpIcepk0o8('\x30' + chr(0b1011110 + 0o21) + chr(0b110011) + chr(0b10010 + 0o41) + chr(2403 - 2352), 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110010) + chr(0b110110) + '\060', 60432 - 60424), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b1010 + 0o47) + '\061', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110010) + chr(0b110010) + chr(55), 9982 - 9974), nzTpIcepk0o8(chr(2159 - 2111) + '\157' + '\x32' + chr(0b110011) + chr(0b1001 + 0o52), 0o10), nzTpIcepk0o8(chr(1881 - 1833) + chr(0b1010111 + 0o30) + chr(49) + '\065' + chr(0b110001), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1011000 + 0o27) + chr(0b11010 + 0o33) + '\x35', ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(2005 - 1954) + chr(53) + chr(0b110101), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + '\063' + chr(2660 - 2607) + chr(0b110101), 8), nzTpIcepk0o8('\060' + '\157' + chr(51) + chr(693 - 643) + chr(2477 - 2423), 0o10), nzTpIcepk0o8('\060' + chr(0b110 + 0o151) + chr(2340 - 2289) + chr(54) + '\x30', 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(51) + '\x30' + chr(51), 0o10), nzTpIcepk0o8('\060' + '\157' + '\x31' + chr(0b110011) + '\067', 26122 - 26114), nzTpIcepk0o8('\x30' + '\157' + chr(0b110011) + chr(1006 - 957) + '\x30', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(2071 - 1960) + chr(0b1001 + 0o52) + chr(0b110110) + chr(1034 - 984), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(10385 - 10274) + chr(1072 - 1023) + '\060' + chr(0b101101 + 0o11), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(52) + chr(383 - 328), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\061' + chr(51) + chr(0b110111), 8), nzTpIcepk0o8('\060' + chr(0b1010101 + 0o32) + chr(774 - 725) + chr(49) + chr(0b10001 + 0o37), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(10774 - 10663) + '\x32' + '\x34', 0b1000), nzTpIcepk0o8('\060' + '\157' + '\x32' + '\x37' + chr(1291 - 1237), 42456 - 42448), nzTpIcepk0o8(chr(48) + chr(11957 - 11846) + chr(0b11001 + 0o27), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1001000 + 0o47) + chr(0b110011) + chr(0b100001 + 0o23) + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b111110 + 0o61) + '\x33' + '\060' + chr(0b110000), 25426 - 25418), nzTpIcepk0o8('\x30' + chr(0b110101 + 0o72) + chr(0b110010) + chr(2452 - 2402) + '\065', ord("\x08")), nzTpIcepk0o8(chr(1646 - 1598) + chr(111) + chr(1894 - 1844) + chr(50) + chr(53), 8), nzTpIcepk0o8(chr(48) + chr(1652 - 1541) + chr(54) + '\064', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(8341 - 8230) + '\061' + chr(0b10000 + 0o41) + chr(55), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101100 + 0o3) + '\x31' + chr(0b110010) + chr(51), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1001011 + 0o44) + '\063' + chr(1999 - 1947), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110 + 0o52) + '\x6f' + chr(1246 - 1193) + chr(48), 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'z'), chr(4760 - 4660) + chr(0b1000110 + 0o37) + chr(99) + chr(0b1101111) + chr(0b1100100) + chr(101))('\x75' + '\x74' + chr(0b11111 + 0o107) + '\055' + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def ZWmNLgqwlpdi(hXMPsSrOQzbh, wKKXKFBlqW0G, DCKHhI6xLX9g):
try:
for JlcDRbBtmPwV in roI3spqORKae(DCKHhI6xLX9g, roI3spqORKae(ES5oEprVxulp(b'\x03\xc2\x80\x10D\xba\x96\xd6TO\xab\xfc'), chr(0b1100100) + chr(2597 - 2496) + '\x63' + chr(0b1101100 + 0o3) + '\x64' + '\x65')(chr(0b1110101) + chr(824 - 708) + chr(0b1100110) + chr(0b1110 + 0o37) + '\x38')):
roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b"8\xca\x95'Q\x96\xc7\xc7qs"), chr(0b1100100) + '\145' + '\143' + chr(11361 - 11250) + chr(7951 - 7851) + '\145')(chr(0b1100111 + 0o16) + chr(116) + '\x66' + chr(1802 - 1757) + chr(0b111000)))(JlcDRbBtmPwV)
except MK4tLc_SQkei:
YEwpwKiWKUwV = roI3spqORKae(ES5oEprVxulp(b"<\xd1\x8034\xcd\x89\xc7rb\xb4\x83'\xe5\xfe\x08I\x99\x85\xb3\x94\xac<\xbb\xdc/Hp-z\x91l\x86\xb4\xf0\xe6@`4i=\xc1\x91lm\x8d\xc8\xc3tq\xae\xc2h\xe3\xf2\x06C\xc3\x85\xa2\x9d\xaf"), chr(0b111000 + 0o54) + chr(0b101100 + 0o71) + chr(0b1100011) + '\157' + chr(8455 - 8355) + chr(6980 - 6879))(chr(0b1110101) + chr(116) + chr(0b110 + 0o140) + chr(0b101100 + 0o1) + '\070')
raise B_3wvd3kWd38(roI3spqORKae(roI3spqORKae(ES5oEprVxulp(b"\x01\xcb\x95!b\x87\x86\xd1r6\xb7\xdfj\xf6\xef\x0c\r\xac\xba\x85\xd0\xa0-\xad\x96#I+!u\xd2.\xc7\x90\xf9\xf0U<6<'\xc0\x91cu\xd2\xdb\x85rx\xfb\xd8f\xe0\xbb\x1dB\xcd\x8e\xb9\x9e\xa56\xaf\x874B\x7f\tC\xed \x84\xb2\xf0\xf1Q!'u5\xc9\xda"), chr(100) + chr(0b1000100 + 0o41) + '\143' + '\157' + chr(0b1010000 + 0o24) + chr(101))(chr(0b1110101) + '\164' + chr(3554 - 3452) + chr(45) + chr(0b111000)), roI3spqORKae(ES5oEprVxulp(b'%\x96\xc7\x08I\xd1\xc0\xcaLI\x98\xfa'), '\144' + '\145' + '\143' + '\157' + chr(100) + chr(0b100000 + 0o105))('\165' + chr(0b1110100 + 0o0) + chr(102) + chr(45) + chr(56)))(YEwpwKiWKUwV)) |
lebinh/aq | aq/engines.py | BotoSqliteEngine.load_table | def load_table(self, table):
"""
Load resources as specified by given table into our db.
"""
region = table.database if table.database else self.default_region
resource_name, collection_name = table.table.split('_', 1)
# we use underscore "_" instead of dash "-" for region name but boto3 need dash
boto_region_name = region.replace('_', '-')
resource = self.boto3_session.resource(resource_name, region_name=boto_region_name)
if not hasattr(resource, collection_name):
raise QueryError(
'Unknown collection <{0}> of resource <{1}>'.format(collection_name, resource_name))
self.attach_region(region)
self.refresh_table(region, table.table, resource, getattr(resource, collection_name)) | python | def load_table(self, table):
"""
Load resources as specified by given table into our db.
"""
region = table.database if table.database else self.default_region
resource_name, collection_name = table.table.split('_', 1)
# we use underscore "_" instead of dash "-" for region name but boto3 need dash
boto_region_name = region.replace('_', '-')
resource = self.boto3_session.resource(resource_name, region_name=boto_region_name)
if not hasattr(resource, collection_name):
raise QueryError(
'Unknown collection <{0}> of resource <{1}>'.format(collection_name, resource_name))
self.attach_region(region)
self.refresh_table(region, table.table, resource, getattr(resource, collection_name)) | [
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] | eb366dd063db25598daa70a216170776e83383f4 | https://github.com/lebinh/aq/blob/eb366dd063db25598daa70a216170776e83383f4/aq/engines.py#L75-L89 | train | Load resources as specified by given table into our db. | 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(2273 - 2225) + '\157' + '\063' + chr(0b10000 + 0o46) + chr(52), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(49) + chr(55) + chr(49), 38806 - 38798), nzTpIcepk0o8('\x30' + chr(111) + chr(1460 - 1410) + chr(0b101110 + 0o2), 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(51) + chr(0b110110) + '\x35', 0o10), nzTpIcepk0o8('\060' + chr(0b10000 + 0o137) + '\x37' + chr(0b100 + 0o54), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + '\063' + '\x33' + chr(0b110100), ord("\x08")), nzTpIcepk0o8('\x30' + chr(8978 - 8867) + chr(0b110011) + chr(1040 - 985) + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\061' + '\066' + chr(2472 - 2418), 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(0b110010) + '\x36' + chr(1946 - 1895), 22872 - 22864), nzTpIcepk0o8(chr(0b110000) + chr(0b110101 + 0o72) + '\062' + '\064' + '\x34', 29532 - 29524), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110001) + chr(55) + chr(50), ord("\x08")), nzTpIcepk0o8(chr(194 - 146) + chr(0b1101111) + '\x33' + chr(52) + chr(52), 0o10), nzTpIcepk0o8(chr(0b10001 + 0o37) + chr(2431 - 2320) + '\061' + chr(53) + chr(49), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b100110 + 0o15) + chr(0b110000) + chr(1486 - 1435), 0b1000), nzTpIcepk0o8(chr(2034 - 1986) + '\x6f' + '\061' + chr(0b111 + 0o54) + chr(50), 0b1000), nzTpIcepk0o8(chr(0b11011 + 0o25) + chr(0b1010111 + 0o30) + chr(0b110010) + chr(0b1111 + 0o50) + '\x36', 0b1000), nzTpIcepk0o8(chr(0b100011 + 0o15) + '\x6f' + chr(1319 - 1270) + chr(2115 - 2061) + '\x36', 8), nzTpIcepk0o8(chr(0b110000) + chr(5470 - 5359) + chr(0b100111 + 0o13) + chr(0b10 + 0o65) + '\063', 46424 - 46416), nzTpIcepk0o8(chr(0b101011 + 0o5) + chr(0b101011 + 0o104) + chr(49) + chr(0b110111), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(51) + chr(54) + chr(0b11111 + 0o21), 26841 - 26833), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110010) + '\065' + '\060', 39408 - 39400), nzTpIcepk0o8('\x30' + chr(0b1011101 + 0o22) + chr(0b110001) + chr(1784 - 1730) + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(0b101110 + 0o2) + '\157' + chr(2428 - 2377) + '\064' + chr(0b110100), 8), nzTpIcepk0o8(chr(2238 - 2190) + chr(0b1010010 + 0o35) + '\x31' + chr(0b11110 + 0o27) + chr(53), ord("\x08")), nzTpIcepk0o8(chr(809 - 761) + chr(0b1101111) + chr(49) + '\060', 36875 - 36867), nzTpIcepk0o8('\060' + chr(8708 - 8597) + chr(1521 - 1470) + chr(0b11110 + 0o26) + chr(0b100101 + 0o15), 46514 - 46506), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110011) + chr(0b110001), 7049 - 7041), nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(0b1101111) + '\x33' + '\063' + chr(1667 - 1616), ord("\x08")), nzTpIcepk0o8(chr(0b11001 + 0o27) + chr(7991 - 7880) + chr(54) + '\x32', 13561 - 13553), nzTpIcepk0o8(chr(48) + chr(111) + '\x31' + '\065' + chr(52), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x35' + chr(0b110101), ord("\x08")), nzTpIcepk0o8('\060' + chr(857 - 746) + '\x31' + chr(0b110010) + chr(2470 - 2420), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b100011 + 0o114) + chr(205 - 154) + chr(0b1000 + 0o53) + '\061', 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110010) + chr(0b110110) + '\x34', 11342 - 11334), nzTpIcepk0o8(chr(0b11 + 0o55) + chr(0b1101111) + chr(2100 - 2049) + '\x34' + chr(0b110010), 8), nzTpIcepk0o8(chr(0b110000) + chr(3681 - 3570) + chr(51) + '\063' + chr(0b110011), 8), nzTpIcepk0o8('\x30' + '\157' + chr(0b100110 + 0o20) + '\061', 0b1000), nzTpIcepk0o8(chr(320 - 272) + chr(8758 - 8647) + chr(0b110111) + chr(2369 - 2319), 41100 - 41092), nzTpIcepk0o8(chr(503 - 455) + chr(111) + chr(0b110001) + chr(48) + chr(55), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(111) + 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'\xda'), chr(0b1100100) + '\x65' + '\x63' + '\x6f' + '\144' + '\x65')(chr(11942 - 11825) + chr(0b110000 + 0o104) + '\146' + chr(0b101101) + chr(2647 - 2591)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def su5EAo21TYT7(hXMPsSrOQzbh, JlcDRbBtmPwV):
SiTpDn8thAb3 = JlcDRbBtmPwV.IGOEKnm_tONS if JlcDRbBtmPwV.IGOEKnm_tONS else hXMPsSrOQzbh.xWakBHgZsMT5
(bgROwQpU4HNC, b5GWyQ19IkYp) = JlcDRbBtmPwV.table.LfRrQOxuDvnC(roI3spqORKae(ES5oEprVxulp(b'\xab'), chr(139 - 39) + chr(9659 - 9558) + chr(0b10000 + 0o123) + '\157' + chr(0b1011011 + 0o11) + '\x65')(chr(0b1110101) + chr(116) + chr(102) + chr(714 - 669) + '\x38'), nzTpIcepk0o8(chr(48) + '\x6f' + chr(1068 - 1019), 0o10))
snj4OxgpPYmn = SiTpDn8thAb3.E91dbqOZXBpJ(roI3spqORKae(ES5oEprVxulp(b'\xab'), chr(0b1100100) + '\x65' + chr(99) + chr(10811 - 10700) + '\144' + chr(101))(chr(2684 - 2567) + chr(7281 - 7165) + '\146' + '\x2d' + chr(56)), roI3spqORKae(ES5oEprVxulp(b'\xd9'), '\x64' + '\145' + '\x63' + chr(111) + chr(2283 - 2183) + chr(0b1100101))(chr(0b1100001 + 0o24) + chr(0b1010101 + 0o37) + '\146' + '\x2d' + '\x38'))
Touxl2u0siZW = hXMPsSrOQzbh.boto3_session.Touxl2u0siZW(bgROwQpU4HNC, region_name=snj4OxgpPYmn)
if not dRKdVnHPFq7C(Touxl2u0siZW, b5GWyQ19IkYp):
raise B_3wvd3kWd38(roI3spqORKae(roI3spqORKae(ES5oEprVxulp(b"\xa1\x17{\x9bW\xab\x93#\x15\xdc\xc8\x16\x81\n\xb73\xd1\x18\x9b3\x8b\x98\r\xdaMg\x849\xa9W\x1fB'\xab\xd7\x87\xfb\rAv\x89G"), chr(0b101010 + 0o72) + '\x65' + chr(0b1011101 + 0o6) + chr(3960 - 3849) + chr(100) + chr(101))(chr(0b1110101) + '\x74' + '\146' + chr(45) + '\070'), roI3spqORKae(ES5oEprVxulp(b"\x85J#\xbe\x7f\xef\x9bl'\xec\xe70"), chr(0b1011000 + 0o14) + '\x65' + '\143' + chr(0b1101111) + chr(0b1100100) + chr(5809 - 5708))(chr(117) + '\164' + chr(0b111110 + 0o50) + chr(315 - 270) + chr(2084 - 2028)))(b5GWyQ19IkYp, bgROwQpU4HNC))
roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x95\rd\x94[\xb4\xa2q\x13\xd4\xcd\x15\x8a'), '\144' + '\x65' + '\x63' + chr(0b11 + 0o154) + '\144' + chr(101))(chr(117) + chr(116) + '\146' + chr(129 - 84) + chr(0b101100 + 0o14)))(SiTpDn8thAb3)
roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x86\x1cv\x87]\xaf\x95\\\x02\xd2\xc6\x16\x81'), '\x64' + '\x65' + chr(5269 - 5170) + chr(0b1101111) + chr(0b1010000 + 0o24) + chr(0b1100101))(chr(0b1110101) + '\x74' + '\x66' + chr(0b101101) + chr(0b11101 + 0o33)))(SiTpDn8thAb3, roI3spqORKae(JlcDRbBtmPwV, roI3spqORKae(ES5oEprVxulp(b'\xbe\x15s\xb1j\xbe\xbfw\x1b\xe3\xd3,'), '\x64' + '\x65' + '\x63' + chr(111) + '\x64' + '\x65')(chr(0b1110101) + '\x74' + chr(0b1100110) + chr(0b101101) + '\070')), Touxl2u0siZW, roI3spqORKae(Touxl2u0siZW, b5GWyQ19IkYp)) |
lebinh/aq | aq/sqlite_util.py | json_serialize | def json_serialize(obj):
"""
Simple generic JSON serializer for common objects.
"""
if isinstance(obj, datetime):
return obj.isoformat()
if hasattr(obj, 'id'):
return jsonify(obj.id)
if hasattr(obj, 'name'):
return jsonify(obj.name)
raise TypeError('{0} is not JSON serializable'.format(obj)) | python | def json_serialize(obj):
"""
Simple generic JSON serializer for common objects.
"""
if isinstance(obj, datetime):
return obj.isoformat()
if hasattr(obj, 'id'):
return jsonify(obj.id)
if hasattr(obj, 'name'):
return jsonify(obj.name)
raise TypeError('{0} is not JSON serializable'.format(obj)) | [
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] | eb366dd063db25598daa70a216170776e83383f4 | https://github.com/lebinh/aq/blob/eb366dd063db25598daa70a216170776e83383f4/aq/sqlite_util.py#L20-L33 | train | Simple generic JSON serializer for common objects. | 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(0b101 + 0o53) + chr(9497 - 9386) + '\x31' + chr(0b1001 + 0o51) + chr(53), ord("\x08")), nzTpIcepk0o8(chr(0b111 + 0o51) + '\x6f' + '\061' + chr(0b110101) + chr(1398 - 1346), 3443 - 3435), nzTpIcepk0o8(chr(1985 - 1937) + chr(7054 - 6943) + '\x33' + chr(54) + '\064', 0b1000), nzTpIcepk0o8(chr(48) + '\157' + '\063' + chr(0b110110) + '\067', ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(1428 - 1377) + chr(0b11111 + 0o23) + chr(0b110000), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b11100 + 0o123) + chr(50) + '\x37' + chr(53), 0o10), nzTpIcepk0o8(chr(219 - 171) + chr(8999 - 8888) + '\x31' + chr(0b110000) + chr(0b110110), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(2613 - 2502) + chr(0b110010) + chr(1943 - 1889) + chr(1233 - 1183), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + '\061' + '\x31' + '\x32', 53662 - 53654), nzTpIcepk0o8('\060' + chr(6706 - 6595) + chr(52) + chr(48), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1001100 + 0o43) + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(1208 - 1160) + '\157' + '\x31' + '\x34' + '\x30', 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(50) + '\060' + chr(0b101101 + 0o10), ord("\x08")), nzTpIcepk0o8(chr(0b10101 + 0o33) + '\x6f' + '\062' + '\x36' + chr(2163 - 2113), 8), nzTpIcepk0o8(chr(0b10000 + 0o40) + '\x6f' + '\x32' + chr(0b101111 + 0o4) + '\065', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x31', 41407 - 41399), nzTpIcepk0o8(chr(0b110000) + '\157' + '\062' + chr(775 - 724) + chr(1741 - 1691), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x34' + chr(0b101001 + 0o10), 0o10), nzTpIcepk0o8(chr(493 - 445) + chr(0b1101111) + chr(1088 - 1033) + chr(2362 - 2309), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\063' + '\x37' + '\x33', ord("\x08")), nzTpIcepk0o8(chr(1356 - 1308) + '\157' + chr(0b110001 + 0o2) + chr(0b110101) + chr(0b11101 + 0o23), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(50) + '\065' + chr(0b110101), 50652 - 50644), nzTpIcepk0o8('\060' + '\157' + chr(0b110001 + 0o0) + chr(726 - 672), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110001) + chr(48) + '\061', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b11 + 0o154) + chr(2323 - 2273) + chr(0b110010) + '\065', ord("\x08")), nzTpIcepk0o8(chr(1127 - 1079) + chr(0b1101111) + chr(0b110001) + chr(48) + chr(2020 - 1966), 8), nzTpIcepk0o8('\060' + '\157' + chr(0b110111), 8), nzTpIcepk0o8(chr(48) + chr(111) + chr(485 - 435) + chr(49) + chr(0b101111 + 0o10), 12221 - 12213), nzTpIcepk0o8(chr(48) + chr(111) + chr(50) + chr(48) + chr(1556 - 1501), 60407 - 60399), nzTpIcepk0o8(chr(0b110000) + '\157' + '\061' + chr(0b110001) + chr(1128 - 1074), ord("\x08")), nzTpIcepk0o8(chr(1608 - 1560) + chr(111) + chr(2458 - 2408) + chr(53) + chr(54), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(0b110001) + chr(0b100100 + 0o17) + '\x36', ord("\x08")), nzTpIcepk0o8('\x30' + chr(5657 - 5546) + chr(0b101111 + 0o4) + chr(0b110011) + chr(596 - 547), ord("\x08")), nzTpIcepk0o8(chr(2173 - 2125) + chr(0b1101111) + '\062' + chr(646 - 594) + chr(762 - 714), 52500 - 52492), nzTpIcepk0o8('\x30' + '\157' + chr(49) + chr(49) + chr(55), 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(2079 - 2028) + '\067' + '\x36', ord("\x08")), nzTpIcepk0o8(chr(1283 - 1235) + chr(6001 - 5890) + chr(0b100111 + 0o13) + chr(0b100011 + 0o20) + '\x30', ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110010) + chr(50) + chr(55), 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(49) + chr(1441 - 1391) + chr(2122 - 2072), 9062 - 9054), nzTpIcepk0o8(chr(0b1 + 0o57) + chr(0b101011 + 0o104) + chr(0b110001) + chr(0b101 + 0o60) + '\x30', ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b10111 + 0o36) + chr(0b11111 + 0o21), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'{'), '\x64' + chr(3265 - 3164) + '\143' + chr(8895 - 8784) + chr(0b110001 + 0o63) + '\145')(chr(117) + '\164' + chr(0b101100 + 0o72) + chr(0b101101) + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def otPJ9DwBlNP2(kIMfkyypPTcC):
if suIjIS24Zkqw(kIMfkyypPTcC, pGZg2NXRxBup):
return roI3spqORKae(kIMfkyypPTcC, roI3spqORKae(ES5oEprVxulp(b'65\x86\xb6\xb1\xf7\x1c\xe8>Lc\x03'), '\144' + chr(0b110110 + 0o57) + chr(0b100101 + 0o76) + '\157' + chr(100) + chr(0b1100101))(chr(117) + chr(1383 - 1267) + chr(102) + chr(0b101101) + chr(0b111000)))()
if dRKdVnHPFq7C(kIMfkyypPTcC, roI3spqORKae(ES5oEprVxulp(b'<\x08'), chr(0b1100100) + chr(1767 - 1666) + '\143' + chr(1137 - 1026) + chr(0b1100100) + '\145')(chr(0b1001 + 0o154) + chr(0b1110100) + '\x66' + chr(70 - 25) + chr(56))):
return KX6AkKujYHMO(roI3spqORKae(kIMfkyypPTcC, roI3spqORKae(ES5oEprVxulp(b'8\r\xb8\x99\x9c\xda~\xfd\x7fZW4'), '\144' + chr(0b1100101) + chr(4110 - 4011) + chr(0b1101111) + chr(4940 - 4840) + '\x65')(chr(0b1001 + 0o154) + chr(116) + chr(0b1100110) + chr(0b101101) + '\070')))
if dRKdVnHPFq7C(kIMfkyypPTcC, roI3spqORKae(ES5oEprVxulp(b';\r\x99\x92'), '\144' + '\145' + chr(0b101010 + 0o71) + chr(0b1101111) + chr(100) + '\145')('\165' + chr(0b1110100) + chr(5139 - 5037) + chr(0b101101) + '\x38')):
return KX6AkKujYHMO(roI3spqORKae(kIMfkyypPTcC, roI3spqORKae(ES5oEprVxulp(b'\x06 \xa2\xb5\xe2\xff\x16\xf3\x15MN\x05'), chr(100) + '\145' + chr(786 - 687) + chr(187 - 76) + chr(0b1101 + 0o127) + chr(0b100110 + 0o77))(chr(117) + chr(0b1110100) + chr(102) + chr(45) + '\070')))
raise jZIjKu8IFANs(roI3spqORKae(roI3spqORKae(ES5oEprVxulp(b".\\\x89\xd7\xb9\xcef\xdc%T'*\xd6\xfd\xd3!\xe9DO\x92\x89\xc1g;\xf4$k\xea"), chr(0b1100100) + chr(0b1100101) + '\143' + chr(111) + '\144' + chr(0b1100101))(chr(0b1110101) + '\164' + chr(0b1100110) + '\055' + chr(56)), roI3spqORKae(ES5oEprVxulp(b'$_\xc7\xbc\x97\x8e \xdd\x1b\x7fD*'), chr(0b1000111 + 0o35) + chr(0b1010111 + 0o16) + chr(0b1100011) + chr(0b1101111) + '\144' + '\145')(chr(0b1110101) + '\x74' + '\x66' + chr(0b101010 + 0o3) + chr(0b110 + 0o62)))(kIMfkyypPTcC)) |
lebinh/aq | aq/sqlite_util.py | json_get | def json_get(serialized_object, field):
"""
This emulates the HSTORE `->` get value operation.
It get value from JSON serialized column by given key and return `null` if not present.
Key can be either an integer for array index access or a string for object field access.
:return: JSON serialized value of key in object
"""
# return null if serialized_object is null or "serialized null"
if serialized_object is None:
return None
obj = json.loads(serialized_object)
if obj is None:
return None
if isinstance(field, int):
# array index access
res = obj[field] if 0 <= field < len(obj) else None
else:
# object field access
res = obj.get(field)
if not isinstance(res, (int, float, string_types)):
res = json.dumps(res)
return res | python | def json_get(serialized_object, field):
"""
This emulates the HSTORE `->` get value operation.
It get value from JSON serialized column by given key and return `null` if not present.
Key can be either an integer for array index access or a string for object field access.
:return: JSON serialized value of key in object
"""
# return null if serialized_object is null or "serialized null"
if serialized_object is None:
return None
obj = json.loads(serialized_object)
if obj is None:
return None
if isinstance(field, int):
# array index access
res = obj[field] if 0 <= field < len(obj) else None
else:
# object field access
res = obj.get(field)
if not isinstance(res, (int, float, string_types)):
res = json.dumps(res)
return res | [
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It get value from JSON serialized column by given key and return `null` if not present.
Key can be either an integer for array index access or a string for object field access.
:return: JSON serialized value of key in object | [
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] | eb366dd063db25598daa70a216170776e83383f4 | https://github.com/lebinh/aq/blob/eb366dd063db25598daa70a216170776e83383f4/aq/sqlite_util.py#L36-L61 | train | This emulates the HSTORE get value operation. It get value from JSON serialized column by given key and return null if not present. | 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(10195 - 10084) + chr(55) + chr(1515 - 1467), 0b1000), nzTpIcepk0o8(chr(60 - 12) + '\157' + chr(2260 - 2211) + chr(0b1111 + 0o50) + '\066', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b110000 + 0o77) + chr(0b110001) + '\061' + chr(0b110001), 54557 - 54549), nzTpIcepk0o8('\060' + '\157' + chr(1119 - 1068) + chr(52), 49647 - 49639), nzTpIcepk0o8(chr(249 - 201) + chr(8744 - 8633) + chr(51) + chr(48) + chr(0b100111 + 0o11), 0b1000), nzTpIcepk0o8(chr(1647 - 1599) + chr(0b1101111) + chr(51) + chr(2204 - 2154), 37813 - 37805), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110010) + chr(0b10000 + 0o40) + chr(55), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(50) + chr(1868 - 1817) + chr(0b10101 + 0o41), 52086 - 52078), nzTpIcepk0o8(chr(0b101 + 0o53) + chr(6215 - 6104) + '\063' + '\x37', 0b1000), nzTpIcepk0o8(chr(1760 - 1712) + chr(111) + chr(1874 - 1824) + chr(0b110000) + chr(0b100 + 0o54), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b101011 + 0o104) + '\x31' + chr(52) + '\064', 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\061' + chr(0b11 + 0o57) + chr(0b0 + 0o61), 40380 - 40372), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\063' + chr(50) + '\064', 0b1000), nzTpIcepk0o8(chr(1558 - 1510) + chr(7291 - 7180) + '\062' + chr(1384 - 1332) + chr(1857 - 1807), 0b1000), nzTpIcepk0o8(chr(1471 - 1423) + '\x6f' + chr(50) + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(1242 - 1194) + chr(12191 - 12080) + chr(0b110011) + '\067' + chr(0b110111), 7718 - 7710), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110011) + chr(1650 - 1600) + chr(384 - 332), 8), nzTpIcepk0o8(chr(1539 - 1491) + chr(0b1011 + 0o144) + chr(53), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + '\064' + '\062', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1100101 + 0o12) + chr(0b101011 + 0o7) + chr(1307 - 1259) + chr(1231 - 1179), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(181 - 130) + chr(2563 - 2512) + chr(48), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x33' + chr(0b11011 + 0o33) + chr(148 - 98), 0o10), nzTpIcepk0o8(chr(1591 - 1543) + chr(111) + chr(0b101100 + 0o6) + chr(0b0 + 0o65) + chr(55), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b11100 + 0o25) + chr(0b110111) + chr(1296 - 1242), 8), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(49) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(651 - 603) + '\157' + '\x31' + '\062' + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(0b1001 + 0o47) + chr(6920 - 6809) + '\062' + chr(0b10001 + 0o44) + '\067', 8), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(2355 - 2304) + '\x33' + '\065', 60744 - 60736), nzTpIcepk0o8('\060' + '\x6f' + chr(51) + chr(0b1 + 0o64), 0b1000), nzTpIcepk0o8('\060' + chr(0b101111 + 0o100) + chr(0b110101) + '\x37', 0b1000), nzTpIcepk0o8(chr(1186 - 1138) + '\x6f' + chr(0b100111 + 0o12) + '\060' + '\061', 1222 - 1214), nzTpIcepk0o8('\x30' + chr(2996 - 2885) + '\x32' + chr(2366 - 2314) + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(0b100101 + 0o13) + '\x6f' + '\062' + '\x31' + chr(0b110111), 0b1000), nzTpIcepk0o8('\x30' + '\157' + '\067' + chr(54), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x32' + chr(1376 - 1323) + chr(0b1101 + 0o44), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b1100 + 0o47) + '\060' + chr(384 - 333), ord("\x08")), nzTpIcepk0o8(chr(0b100101 + 0o13) + chr(0b1101111) + '\063' + chr(0b10100 + 0o35) + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + '\062' + '\x33' + '\x36', 8), nzTpIcepk0o8('\060' + chr(5489 - 5378) + chr(0b110 + 0o57) + chr(54), 45167 - 45159), nzTpIcepk0o8(chr(0b110000) + chr(4704 - 4593) + chr(0b110001) + chr(49) + chr(53), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(813 - 765) + '\157' + chr(0b101001 + 0o14) + chr(48), 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x16'), chr(0b1100100) + '\145' + chr(99) + chr(1768 - 1657) + chr(0b1100100) + '\145')(chr(0b1110101) + '\164' + chr(0b1100110) + '\x2d' + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def stzphUpPMbn9(GZZjbnt11v5X, uF4zwjUGNIxR):
if GZZjbnt11v5X is None:
return None
kIMfkyypPTcC = LNUKEwZDIbyb.OiapAM4bM0Ea(GZZjbnt11v5X)
if kIMfkyypPTcC is None:
return None
if suIjIS24Zkqw(uF4zwjUGNIxR, nzTpIcepk0o8):
_XdQFJpnzJor = kIMfkyypPTcC[uF4zwjUGNIxR] if nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\060', 52533 - 52525) <= uF4zwjUGNIxR < ftfygxgFas5X(kIMfkyypPTcC) else None
else:
_XdQFJpnzJor = kIMfkyypPTcC.GUKetu4xaGsJ(uF4zwjUGNIxR)
if not suIjIS24Zkqw(_XdQFJpnzJor, (nzTpIcepk0o8, jLW6pRf2DSRk, Q9V5WOaImAwl)):
_XdQFJpnzJor = LNUKEwZDIbyb.Zjglmm8uenkC(_XdQFJpnzJor)
return _XdQFJpnzJor |
lebinh/aq | aq/sqlite_util.py | create_table | def create_table(db, schema_name, table_name, columns):
"""
Create a table, schema_name.table_name, in given database with given list of column names.
"""
table = '{0}.{1}'.format(schema_name, table_name) if schema_name else table_name
db.execute('DROP TABLE IF EXISTS {0}'.format(table))
columns_list = ', '.join(columns)
db.execute('CREATE TABLE {0} ({1})'.format(table, columns_list)) | python | def create_table(db, schema_name, table_name, columns):
"""
Create a table, schema_name.table_name, in given database with given list of column names.
"""
table = '{0}.{1}'.format(schema_name, table_name) if schema_name else table_name
db.execute('DROP TABLE IF EXISTS {0}'.format(table))
columns_list = ', '.join(columns)
db.execute('CREATE TABLE {0} ({1})'.format(table, columns_list)) | [
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] | eb366dd063db25598daa70a216170776e83383f4 | https://github.com/lebinh/aq/blob/eb366dd063db25598daa70a216170776e83383f4/aq/sqlite_util.py#L64-L71 | train | Create a table in given database with given list of column 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(0b101101 + 0o3) + '\157' + chr(49) + chr(0b11100 + 0o33) + chr(0b110110), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b10011 + 0o37) + chr(732 - 679) + '\x31', 57548 - 57540), nzTpIcepk0o8(chr(0b110000) + chr(0b11 + 0o154) + chr(0b110011) + '\062' + chr(0b100000 + 0o25), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x35' + chr(2220 - 2171), 62214 - 62206), nzTpIcepk0o8(chr(0b11101 + 0o23) + chr(0b11100 + 0o123) + '\061' + '\x31' + chr(909 - 858), 0o10), nzTpIcepk0o8('\x30' + chr(8556 - 8445) + chr(414 - 363) + chr(0b1101 + 0o47) + '\062', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b110101 + 0o72) + '\063' + chr(1400 - 1348) + chr(52), 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(50) + '\x34' + chr(48), 7628 - 7620), nzTpIcepk0o8('\060' + chr(111) + chr(0b1111 + 0o43) + '\063' + chr(1452 - 1401), 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(49) + chr(0b101011 + 0o12) + '\062', 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(51) + chr(2314 - 2263) + chr(0b1101 + 0o51), 11626 - 11618), nzTpIcepk0o8('\x30' + chr(1126 - 1015) + chr(49) + '\x33' + '\x30', 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110001) + chr(52) + chr(2577 - 2525), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(1647 - 1596) + '\x31' + chr(0b110110), 60770 - 60762), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\063' + '\060' + '\063', 4079 - 4071), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(1906 - 1855) + '\x32' + '\064', 51104 - 51096), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x31' + chr(2237 - 2189) + chr(0b1011 + 0o51), 49874 - 49866), nzTpIcepk0o8(chr(705 - 657) + chr(0b1001011 + 0o44) + chr(49) + '\065' + chr(50), 8), nzTpIcepk0o8('\060' + '\157' + '\063', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\063' + chr(52) + chr(0b1001 + 0o50), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(1728 - 1676) + chr(55), 0o10), nzTpIcepk0o8('\060' + '\x6f' + '\x33' + chr(0b11100 + 0o30) + chr(0b100101 + 0o13), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(49) + chr(0b110010 + 0o0) + chr(512 - 464), 0o10), nzTpIcepk0o8(chr(0b10001 + 0o37) + chr(0b1101111) + chr(53) + '\061', 8), nzTpIcepk0o8('\060' + chr(6115 - 6004) + chr(49) + chr(0b110011) + '\x37', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(9207 - 9096) + chr(1058 - 1005) + '\065', ord("\x08")), nzTpIcepk0o8('\060' + '\157' + '\x33' + chr(48) + chr(0b10 + 0o56), 0b1000), nzTpIcepk0o8('\060' + chr(10283 - 10172) + chr(0b110010 + 0o5) + '\x33', 0b1000), nzTpIcepk0o8(chr(1521 - 1473) + chr(0b1101111) + chr(0b100010 + 0o21) + '\064' + '\x35', ord("\x08")), nzTpIcepk0o8(chr(2292 - 2244) + '\157' + '\061' + '\067' + chr(0b100001 + 0o23), 0b1000), nzTpIcepk0o8('\060' + chr(0b10011 + 0o134) + chr(0b110010) + '\060' + chr(645 - 595), 49431 - 49423), nzTpIcepk0o8(chr(0b110000) + chr(0b1100111 + 0o10) + '\x32' + chr(0b110001) + chr(55), 22796 - 22788), nzTpIcepk0o8('\060' + '\x6f' + '\x32' + chr(2405 - 2350) + chr(0b11100 + 0o33), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(523 - 412) + '\062' + chr(0b110010), 0o10), nzTpIcepk0o8(chr(48) + chr(11725 - 11614) + chr(0b110 + 0o60) + chr(0b110100), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1011001 + 0o26) + chr(0b1011 + 0o47) + chr(51) + chr(0b110100), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(1079 - 1030) + '\066' + chr(2282 - 2232), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b101111 + 0o100) + '\061' + chr(1033 - 982) + chr(52), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x33' + '\067' + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(1512 - 1464) + chr(0b1101111) + '\062' + chr(51) + '\x32', 17309 - 17301)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(0b110000 + 0o77) + chr(2623 - 2570) + chr(399 - 351), 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'P'), '\144' + chr(101) + '\x63' + chr(7108 - 6997) + '\144' + chr(0b101111 + 0o66))(chr(0b1110101) + chr(0b1000110 + 0o56) + chr(102) + '\x2d' + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def CZv75EkBKH7o(HW7Cf8GRrz2A, dLZ3Z3RyCgN2, kR9bIddrApHD, U39jSiI54Mlp):
JlcDRbBtmPwV = roI3spqORKae(ES5oEprVxulp(b'\x05\x99\xa8\x070\xd3\x99'), '\x64' + chr(101) + chr(0b1100011) + '\x6f' + chr(100) + chr(101))('\x75' + '\164' + chr(7538 - 7436) + '\055' + '\070').q33KG3foQ_CJ(dLZ3Z3RyCgN2, kR9bIddrApHD) if dLZ3Z3RyCgN2 else kR9bIddrApHD
roI3spqORKae(HW7Cf8GRrz2A, roI3spqORKae(ES5oEprVxulp(b'=\xfa\xe1z|\xb0\x88\xee\xff>\xad!'), chr(0b1011001 + 0o13) + chr(6254 - 6153) + chr(99) + chr(111) + '\x64' + '\x65')(chr(8928 - 8811) + chr(0b1110100) + chr(0b1100110) + chr(0b101 + 0o50) + chr(364 - 308)))(roI3spqORKae(roI3spqORKae(ES5oEprVxulp(b':\xfb\x9ayk\xb6\xa5\xe2\xd7/\xfe\x11"\xee\x86\x8c\r9W\xb2\x07\x9b`T'), chr(0b1100100) + '\x65' + chr(7188 - 7089) + '\157' + chr(0b1000001 + 0o43) + chr(101))(chr(117) + chr(0b1110100) + chr(0b1000110 + 0o40) + chr(45) + chr(56)), roI3spqORKae(ES5oEprVxulp(b'\x0f\x9a\xe6b\x0c\xd1\x82\xcf\xca5\x9d\x12'), chr(0b1010000 + 0o24) + chr(4479 - 4378) + chr(0b1011001 + 0o12) + '\157' + chr(0b1100100) + chr(0b1100101))('\165' + '\164' + chr(0b1100110) + chr(0b101101) + chr(56)))(JlcDRbBtmPwV))
X7DvycdFVrSb = roI3spqORKae(ES5oEprVxulp(b'R\x89'), chr(100) + chr(101) + '\x63' + chr(111) + chr(9512 - 9412) + chr(0b1100010 + 0o3))(chr(0b1101101 + 0o10) + '\164' + '\x66' + chr(0b101101) + chr(1940 - 1884)).Y4yM9BcfTCNq(U39jSiI54Mlp)
roI3spqORKae(HW7Cf8GRrz2A, roI3spqORKae(ES5oEprVxulp(b'=\xfa\xe1z|\xb0\x88\xee\xff>\xad!'), chr(100) + chr(101) + chr(99) + chr(8964 - 8853) + chr(0b1100100) + chr(893 - 792))('\165' + chr(11679 - 11563) + chr(4032 - 3930) + '\x2d' + chr(2893 - 2837)))(roI3spqORKae(roI3spqORKae(ES5oEprVxulp(b'=\xfb\x90h\x1f\xa7\xc4\xf4\xda(\x92\x1dD\xb5\xf3\xa9dBx\xd0Z\xc9'), chr(0b1000001 + 0o43) + chr(0b1100101) + chr(99) + '\x6f' + '\144' + '\145')('\165' + '\164' + '\146' + chr(0b101101) + '\x38'), roI3spqORKae(ES5oEprVxulp(b'\x0f\x9a\xe6b\x0c\xd1\x82\xcf\xca5\x9d\x12'), chr(100) + '\x65' + chr(0b1010010 + 0o21) + '\157' + chr(6194 - 6094) + '\145')(chr(2805 - 2688) + '\x74' + chr(2167 - 2065) + '\x2d' + chr(0b10111 + 0o41)))(JlcDRbBtmPwV, X7DvycdFVrSb)) |
lebinh/aq | aq/sqlite_util.py | insert_all | def insert_all(db, schema_name, table_name, columns, items):
"""
Insert all item in given items list into the specified table, schema_name.table_name.
"""
table = '{0}.{1}'.format(schema_name, table_name) if schema_name else table_name
columns_list = ', '.join(columns)
values_list = ', '.join(['?'] * len(columns))
query = 'INSERT INTO {table} ({columns}) VALUES ({values})'.format(
table=table, columns=columns_list, values=values_list)
for item in items:
values = [getattr(item, col) for col in columns]
db.execute(query, values) | python | def insert_all(db, schema_name, table_name, columns, items):
"""
Insert all item in given items list into the specified table, schema_name.table_name.
"""
table = '{0}.{1}'.format(schema_name, table_name) if schema_name else table_name
columns_list = ', '.join(columns)
values_list = ', '.join(['?'] * len(columns))
query = 'INSERT INTO {table} ({columns}) VALUES ({values})'.format(
table=table, columns=columns_list, values=values_list)
for item in items:
values = [getattr(item, col) for col in columns]
db.execute(query, values) | [
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"table_name",
"."
] | eb366dd063db25598daa70a216170776e83383f4 | https://github.com/lebinh/aq/blob/eb366dd063db25598daa70a216170776e83383f4/aq/sqlite_util.py#L74-L85 | train | Insert all items in given items list into the specified table. | 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) + '\157' + chr(0b111 + 0o54) + chr(0b110000) + chr(48), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(0b101101 + 0o6) + chr(1087 - 1039) + '\x31', 37721 - 37713), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\063' + chr(0b11010 + 0o30) + '\062', ord("\x08")), nzTpIcepk0o8(chr(0b10 + 0o56) + chr(0b1101111) + '\x36' + '\x36', ord("\x08")), nzTpIcepk0o8(chr(2014 - 1966) + chr(0b1101111) + chr(2507 - 2454) + '\x33', 29120 - 29112), nzTpIcepk0o8('\060' + '\x6f' + chr(2181 - 2131) + chr(49) + chr(0b11111 + 0o25), 0o10), nzTpIcepk0o8(chr(983 - 935) + '\157' + chr(50) + chr(0b110110) + chr(1253 - 1202), 0o10), nzTpIcepk0o8(chr(0b101111 + 0o1) + '\x6f' + chr(2215 - 2161) + '\061', 0b1000), nzTpIcepk0o8('\x30' + chr(5930 - 5819) + chr(0b110001) + chr(0b100111 + 0o20) + '\067', 53993 - 53985), nzTpIcepk0o8('\x30' + chr(11926 - 11815) + chr(50) + chr(48) + chr(0b10001 + 0o44), 54298 - 54290), nzTpIcepk0o8(chr(48) + chr(0b11110 + 0o121) + '\x32' + chr(52) + '\060', ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + '\062' + chr(2341 - 2288) + chr(1015 - 965), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(0b110001) + chr(52) + chr(0b1111 + 0o43), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1000010 + 0o55) + chr(0b110011) + '\x34' + chr(0b110001), 0b1000), nzTpIcepk0o8('\060' + '\157' + '\062' + chr(50) + chr(0b1111 + 0o47), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\063' + '\x37' + chr(0b1111 + 0o43), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b100001 + 0o116) + '\x34' + chr(51), 0b1000), nzTpIcepk0o8(chr(48) + chr(10360 - 10249) + chr(1694 - 1644) + chr(0b100000 + 0o22) + chr(0b10010 + 0o44), 8), nzTpIcepk0o8(chr(0b11111 + 0o21) + chr(0b1101111) + '\x36' + '\x36', 8), nzTpIcepk0o8(chr(0b100101 + 0o13) + chr(2535 - 2424) + chr(0b10111 + 0o34) + chr(1805 - 1751) + chr(776 - 726), ord("\x08")), nzTpIcepk0o8(chr(0b101111 + 0o1) + chr(0b1100101 + 0o12) + chr(0b101100 + 0o7) + chr(53) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(1895 - 1847) + chr(111) + chr(0b101110 + 0o10) + chr(51), 11427 - 11419), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b10101 + 0o35) + '\x35' + chr(346 - 291), 10269 - 10261), nzTpIcepk0o8('\060' + chr(1560 - 1449) + '\x31' + chr(0b11111 + 0o21) + chr(51), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1100110 + 0o11) + chr(0b110011) + '\x31' + '\x33', 0b1000), nzTpIcepk0o8(chr(1404 - 1356) + chr(0b1101111) + chr(50) + chr(54) + chr(53), 48819 - 48811), nzTpIcepk0o8(chr(0b1111 + 0o41) + '\157' + chr(640 - 591) + '\x37' + chr(1169 - 1118), ord("\x08")), nzTpIcepk0o8(chr(0b101000 + 0o10) + '\x6f' + '\x31' + '\x35' + chr(49), 0b1000), nzTpIcepk0o8(chr(531 - 483) + chr(0b1101111) + '\063' + chr(2444 - 2391) + '\x30', 16526 - 16518), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x33' + chr(50) + chr(0b10001 + 0o42), 0b1000), nzTpIcepk0o8('\x30' + chr(2988 - 2877) + chr(51) + '\x35' + chr(51), 8), nzTpIcepk0o8(chr(0b110000) + chr(0b110001 + 0o76) + chr(62 - 11) + chr(0b1000 + 0o52) + chr(0b110100), 30719 - 30711), nzTpIcepk0o8(chr(2256 - 2208) + chr(4949 - 4838) + chr(0b110111) + '\x37', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(370 - 259) + chr(51) + chr(0b101110 + 0o4) + '\060', 0o10), nzTpIcepk0o8(chr(1967 - 1919) + chr(0b1101111) + '\061' + chr(0b110111), 8611 - 8603), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x33' + chr(2222 - 2170) + chr(0b10111 + 0o32), 8), nzTpIcepk0o8(chr(0b11111 + 0o21) + chr(5507 - 5396) + '\063' + chr(1797 - 1749), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(803 - 754) + chr(49) + chr(1580 - 1527), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b101011 + 0o6) + chr(0b110001) + '\064', ord("\x08")), nzTpIcepk0o8(chr(1201 - 1153) + chr(0b1101111) + chr(0b110010) + chr(2682 - 2630) + chr(268 - 215), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + chr(0b1101100 + 0o3) + chr(0b110101) + '\060', 42050 - 42042)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xee'), chr(0b1100100) + '\145' + chr(99) + chr(0b1101111) + '\x64' + chr(0b111100 + 0o51))(chr(0b1110101) + chr(116) + '\146' + chr(0b101101) + chr(0b10 + 0o66)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def IJWZYoY4w8qT(HW7Cf8GRrz2A, dLZ3Z3RyCgN2, kR9bIddrApHD, U39jSiI54Mlp, Y_nNEzH43vXi):
JlcDRbBtmPwV = roI3spqORKae(ES5oEprVxulp(b'\xbb\xf1\xaf\x18P\xbd\xce'), '\144' + chr(101) + chr(0b111100 + 0o47) + '\157' + chr(0b1000100 + 0o40) + '\145')('\165' + chr(0b1110100) + '\146' + chr(0b10011 + 0o32) + chr(471 - 415)).q33KG3foQ_CJ(dLZ3Z3RyCgN2, kR9bIddrApHD) if dLZ3Z3RyCgN2 else kR9bIddrApHD
X7DvycdFVrSb = roI3spqORKae(ES5oEprVxulp(b'\xec\xe1'), chr(100) + chr(9470 - 9369) + chr(598 - 499) + chr(111) + chr(0b111001 + 0o53) + chr(1310 - 1209))('\165' + chr(13222 - 13106) + chr(854 - 752) + '\055' + chr(1290 - 1234)).Y4yM9BcfTCNq(U39jSiI54Mlp)
NergWdyig884 = roI3spqORKae(ES5oEprVxulp(b'\xec\xe1'), chr(9616 - 9516) + chr(101) + '\x63' + chr(7776 - 7665) + chr(100) + '\145')(chr(117) + chr(10769 - 10653) + chr(0b11 + 0o143) + chr(1032 - 987) + chr(0b100110 + 0o22)).Y4yM9BcfTCNq([roI3spqORKae(ES5oEprVxulp(b'\xff'), '\x64' + chr(3662 - 3561) + '\143' + '\x6f' + chr(0b1100100) + '\145')(chr(117) + chr(0b1110100) + chr(0b1 + 0o145) + chr(0b101101) + '\070')] * ftfygxgFas5X(U39jSiI54Mlp))
wKKXKFBlqW0G = roI3spqORKae(ES5oEprVxulp(b'\x89\x8f\x81sy\xd8\x93x1\xd1\xef\x8a\x19\x95\xf7\x98O\xf3K\xd2\xc3H\xcc,\xa7\xc0\x16\x07\x9b\xae\xc2\xf4i\x91C\xb4]\x1el\x8d\xbb\xb7\xb3Z^\xe9\xc0LV'), chr(4902 - 4802) + chr(0b110100 + 0o61) + chr(0b11100 + 0o107) + '\x6f' + '\x64' + '\x65')(chr(9183 - 9066) + '\x74' + chr(0b1100110) + chr(0b101101) + chr(0b111000)).q33KG3foQ_CJ(table=JlcDRbBtmPwV, columns=X7DvycdFVrSb, values=NergWdyig884)
for IZ1I2J8X1CQz in Y_nNEzH43vXi:
CsodZJH6x9Tx = [roI3spqORKae(IZ1I2J8X1CQz, hRTUxJgvuslu) for hRTUxJgvuslu in U39jSiI54Mlp]
roI3spqORKae(HW7Cf8GRrz2A, roI3spqORKae(ES5oEprVxulp(b'\x83\x92\xe6e\x1c\xde\xdf\x7f\x1b\xd1\xd3\xd3'), '\x64' + chr(101) + chr(4339 - 4240) + chr(0b1101111) + '\x64' + '\145')('\x75' + chr(9339 - 9223) + '\x66' + chr(45) + chr(56)))(wKKXKFBlqW0G, CsodZJH6x9Tx) |
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