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cggh/scikit-allel | allel/stats/sf.py | joint_sfs_folded_scaled | def joint_sfs_folded_scaled(ac1, ac2, n1=None, n2=None):
"""Compute the joint folded site frequency spectrum between two
populations, scaled such that a constant value is expected across the
spectrum for neutral variation, constant population size and unrelated
populations.
Parameters
----------
ac1 : array_like, int, shape (n_variants, 2)
Allele counts for the first population.
ac2 : array_like, int, shape (n_variants, 2)
Allele counts for the second population.
n1, n2 : int, optional
The total number of chromosomes called in each population.
Returns
-------
joint_sfs_folded_scaled : ndarray, int, shape (n1//2 + 1, n2//2 + 1)
Array where the (i, j)th element is the scaled frequency of variant
sites with a minor allele count of i in the first population and j
in the second population.
""" # noqa
# check inputs
ac1, n1 = _check_ac_n(ac1, n1)
ac2, n2 = _check_ac_n(ac2, n2)
# compute site frequency spectrum
s = joint_sfs_folded(ac1, ac2, n1=n1, n2=n2)
# apply scaling
s = scale_joint_sfs_folded(s, n1, n2)
return s | python | def joint_sfs_folded_scaled(ac1, ac2, n1=None, n2=None):
"""Compute the joint folded site frequency spectrum between two
populations, scaled such that a constant value is expected across the
spectrum for neutral variation, constant population size and unrelated
populations.
Parameters
----------
ac1 : array_like, int, shape (n_variants, 2)
Allele counts for the first population.
ac2 : array_like, int, shape (n_variants, 2)
Allele counts for the second population.
n1, n2 : int, optional
The total number of chromosomes called in each population.
Returns
-------
joint_sfs_folded_scaled : ndarray, int, shape (n1//2 + 1, n2//2 + 1)
Array where the (i, j)th element is the scaled frequency of variant
sites with a minor allele count of i in the first population and j
in the second population.
""" # noqa
# check inputs
ac1, n1 = _check_ac_n(ac1, n1)
ac2, n2 = _check_ac_n(ac2, n2)
# compute site frequency spectrum
s = joint_sfs_folded(ac1, ac2, n1=n1, n2=n2)
# apply scaling
s = scale_joint_sfs_folded(s, n1, n2)
return s | [
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Allele counts for the first population.
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Allele counts for the second population.
n1, n2 : int, optional
The total number of chromosomes called in each population.
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joint_sfs_folded_scaled : ndarray, int, shape (n1//2 + 1, n2//2 + 1)
Array where the (i, j)th element is the scaled frequency of variant
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ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8('\x30' + '\x6f' + '\062' + chr(0b101100 + 0o13) + chr(243 - 193), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(51) + chr(2398 - 2347) + chr(2413 - 2361), 7603 - 7595), nzTpIcepk0o8(chr(0b110000 + 0o0) + '\157' + '\x34' + chr(54), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110010) + chr(52) + chr(0b110001 + 0o0), 20116 - 20108), nzTpIcepk0o8(chr(178 - 130) + '\157' + chr(1459 - 1408) + chr(0b101110 + 0o11), 8326 - 8318), nzTpIcepk0o8(chr(0b11100 + 0o24) + chr(0b1101111) + chr(1421 - 1370) + chr(0b11100 + 0o32) + chr(301 - 251), 0b1000), nzTpIcepk0o8('\060' + chr(9902 - 9791) + '\x31' + '\062' + chr(54), 0b1000), nzTpIcepk0o8(chr(1867 - 1819) + chr(0b101 + 0o152) + '\x32' + chr(0b100011 + 0o20) + chr(1838 - 1787), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110001) + chr(55) + '\x31', 11481 - 11473), nzTpIcepk0o8('\060' + chr(0b1111 + 0o140) + chr(0b110011) + chr(48), 58840 - 58832), nzTpIcepk0o8(chr(48) + chr(111) + '\064' + chr(1278 - 1230), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1001110 + 0o41) + chr(0b110001) + chr(50) + chr(0b110100), 0o10), nzTpIcepk0o8(chr(0b11010 + 0o26) + chr(0b1101111) + '\x31' + chr(418 - 366) + '\x33', 18549 - 18541), nzTpIcepk0o8('\x30' + '\x6f' + chr(127 - 76) + '\062' + chr(50), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110001) + '\060' + chr(0b10110 + 0o34), 10750 - 10742), nzTpIcepk0o8(chr(48) + chr(7308 - 7197) + chr(48), 0b1000), nzTpIcepk0o8(chr(1395 - 1347) + chr(0b1000011 + 0o54) + '\065' + chr(50), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(468 - 418) + chr(0b110110) + '\x31', ord("\x08")), nzTpIcepk0o8(chr(1098 - 1050) + chr(5689 - 5578) + chr(49) + chr(1393 - 1344) + chr(0b0 + 0o66), 6176 - 6168), nzTpIcepk0o8(chr(0b11000 + 0o30) + chr(111) + '\x32' + chr(50) + chr(221 - 167), 0o10), nzTpIcepk0o8(chr(0b11111 + 0o21) + chr(0b1101111) + '\062' + chr(386 - 332) + chr(54), 0b1000), nzTpIcepk0o8(chr(1337 - 1289) + '\157' + chr(0b110011) + chr(0b1101 + 0o51) + '\x30', ord("\x08")), nzTpIcepk0o8(chr(0b10011 + 0o35) + chr(0b1101111) + chr(50) + chr(0b110000) + chr(2329 - 2277), 14769 - 14761), nzTpIcepk0o8('\060' + '\x6f' + '\064' + chr(1808 - 1757), 37954 - 37946), nzTpIcepk0o8('\060' + '\x6f' + chr(1688 - 1636) + chr(612 - 560), 40074 - 40066), nzTpIcepk0o8(chr(0b11100 + 0o24) + chr(0b1101111) + chr(507 - 458) + chr(0b110101) + chr(51), 0b1000), nzTpIcepk0o8(chr(566 - 518) + chr(7352 - 7241) + chr(49) + chr(52) + '\x32', ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110011) + '\x34' + chr(0b111 + 0o54), 0o10), nzTpIcepk0o8(chr(1485 - 1437) + chr(111) + chr(0b1110 + 0o45) + '\x35', 56238 - 56230), nzTpIcepk0o8('\060' + '\157' + '\061' + chr(48) + '\060', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(1606 - 1557) + '\064' + chr(0b110011), 8), nzTpIcepk0o8(chr(0b11101 + 0o23) + '\157' + chr(50) + '\x33' + chr(0b100011 + 0o15), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + '\062' + chr(178 - 124) + '\x34', 19347 - 19339), nzTpIcepk0o8(chr(794 - 746) + chr(111) + chr(51) + chr(1717 - 1664) + chr(0b110111), 0o10), nzTpIcepk0o8(chr(48) + chr(4570 - 4459) + chr(50) + chr(0b11000 + 0o32) + '\x34', ord("\x08")), nzTpIcepk0o8('\060' + chr(8775 - 8664) + '\062' + '\x31', 0o10), nzTpIcepk0o8(chr(0b101000 + 0o10) + chr(0b10111 + 0o130) + chr(897 - 843) + chr(52), 0o10), nzTpIcepk0o8(chr(0b110 + 0o52) + chr(0b101000 + 0o107) + '\x32' + '\066' + '\x36', 8), nzTpIcepk0o8('\x30' + chr(6721 - 6610) + chr(1857 - 1805) + '\x37', 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110001) + '\x36' + '\x33', 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + chr(0b1101111) + '\065' + '\x30', 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x94'), chr(328 - 228) + chr(7869 - 7768) + chr(0b1 + 0o142) + chr(973 - 862) + chr(0b0 + 0o144) + chr(7654 - 7553))('\x75' + chr(11191 - 11075) + chr(0b1100110) + '\055' + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def GhU5BQrnBR2u(kqnbwhK0EBnP, S9W4ddqb2HVR, YYJGqULB4ite=None, vX1Eq0k9zbZq=None):
(kqnbwhK0EBnP, YYJGqULB4ite) = Bg7TKbEgPrRI(kqnbwhK0EBnP, YYJGqULB4ite)
(S9W4ddqb2HVR, vX1Eq0k9zbZq) = Bg7TKbEgPrRI(S9W4ddqb2HVR, vX1Eq0k9zbZq)
PmE5_h409JAA = DK1OdcdBGZjg(kqnbwhK0EBnP, S9W4ddqb2HVR, n1=YYJGqULB4ite, n2=vX1Eq0k9zbZq)
PmE5_h409JAA = PDIHFOcFsp3w(PmE5_h409JAA, YYJGqULB4ite, vX1Eq0k9zbZq)
return PmE5_h409JAA |
cggh/scikit-allel | allel/stats/sf.py | scale_joint_sfs_folded | def scale_joint_sfs_folded(s, n1, n2):
"""Scale a folded joint site frequency spectrum.
Parameters
----------
s : array_like, int, shape (m_chromosomes//2, n_chromosomes//2)
Folded joint site frequency spectrum.
n1, n2 : int, optional
The total number of chromosomes called in each population.
Returns
-------
joint_sfs_folded_scaled : ndarray, int, shape (m_chromosomes//2, n_chromosomes//2)
Scaled folded joint site frequency spectrum.
""" # noqa
out = np.empty_like(s)
for i in range(s.shape[0]):
for j in range(s.shape[1]):
out[i, j] = s[i, j] * i * j * (n1 - i) * (n2 - j)
return out | python | def scale_joint_sfs_folded(s, n1, n2):
"""Scale a folded joint site frequency spectrum.
Parameters
----------
s : array_like, int, shape (m_chromosomes//2, n_chromosomes//2)
Folded joint site frequency spectrum.
n1, n2 : int, optional
The total number of chromosomes called in each population.
Returns
-------
joint_sfs_folded_scaled : ndarray, int, shape (m_chromosomes//2, n_chromosomes//2)
Scaled folded joint site frequency spectrum.
""" # noqa
out = np.empty_like(s)
for i in range(s.shape[0]):
for j in range(s.shape[1]):
out[i, j] = s[i, j] * i * j * (n1 - i) * (n2 - j)
return out | [
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Folded joint site frequency spectrum.
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The total number of chromosomes called in each population.
Returns
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/stats/sf.py#L370-L390 | train | Scale a folded joint site frequency spectrum. | 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(0b1101010 + 0o5) + chr(0b110110) + chr(51), 26578 - 26570), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110011) + chr(0b110101) + chr(0b110001), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110011) + '\x35' + chr(0b110001), 8), nzTpIcepk0o8(chr(0b100010 + 0o16) + chr(0b1101111) + chr(50) + chr(50) + '\x36', 17833 - 17825), nzTpIcepk0o8('\x30' + chr(8246 - 8135) + '\x35' + chr(967 - 913), ord("\x08")), nzTpIcepk0o8(chr(0b100101 + 0o13) + chr(111) + '\063' + chr(0b100100 + 0o16), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(53) + chr(0b110011), ord("\x08")), nzTpIcepk0o8(chr(0b11101 + 0o23) + chr(7538 - 7427) + chr(0b110110) + '\066', ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(50) + '\060' + chr(48), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110010) + chr(48) + '\x35', 62981 - 62973), nzTpIcepk0o8('\060' + chr(0b1101110 + 0o1) + chr(0b110010) + '\x36' + '\063', ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(0b10011 + 0o40) + chr(55) + chr(2014 - 1959), 0b1000), nzTpIcepk0o8(chr(1858 - 1810) + chr(0b1101111) + chr(0b11011 + 0o26) + '\x36' + chr(0b1110 + 0o51), 0b1000), nzTpIcepk0o8(chr(0b1011 + 0o45) + chr(111) + chr(54) + chr(55), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b101001 + 0o106) + '\063' + '\x30', 10851 - 10843), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(1137 - 1088) + '\067' + chr(1775 - 1723), 20245 - 20237), nzTpIcepk0o8(chr(48) + chr(1569 - 1458) + chr(0b10000 + 0o44), ord("\x08")), nzTpIcepk0o8(chr(0b1010 + 0o46) + chr(0b1101111) + '\063' + chr(2393 - 2340) + '\x33', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b11010 + 0o27) + chr(0b10000 + 0o46) + chr(120 - 70), 0o10), nzTpIcepk0o8(chr(288 - 240) + chr(0b1101111) + chr(0b0 + 0o61) + chr(54), 10088 - 10080), nzTpIcepk0o8('\x30' + chr(111) + '\063' + chr(0b110010) + '\x36', 0b1000), nzTpIcepk0o8(chr(987 - 939) + chr(0b1101111) + chr(0b101111 + 0o4) + '\067' + chr(0b100 + 0o55), 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(0b10111 + 0o33) + '\x35' + '\x33', 36555 - 36547), nzTpIcepk0o8(chr(1243 - 1195) + chr(0b11110 + 0o121) + '\x31' + chr(0b1000 + 0o53) + chr(51), 0o10), nzTpIcepk0o8('\060' + '\x6f' + '\x32' + chr(1631 - 1582) + chr(960 - 911), 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(0b10100 + 0o36) + chr(54) + chr(0b110111), 36430 - 36422), nzTpIcepk0o8(chr(0b110000) + chr(0b1000011 + 0o54) + '\063' + chr(0b10011 + 0o42) + chr(0b11 + 0o56), 8), nzTpIcepk0o8('\060' + chr(0b111110 + 0o61) + '\066' + chr(0b110000), 0b1000), nzTpIcepk0o8(chr(0b10000 + 0o40) + '\157' + chr(0b100110 + 0o14) + chr(2696 - 2643) + chr(2067 - 2019), 45271 - 45263), nzTpIcepk0o8(chr(1618 - 1570) + chr(111) + '\062' + chr(1546 - 1491), 11831 - 11823), nzTpIcepk0o8(chr(0b110000) + chr(0b101100 + 0o103) + chr(0b1101 + 0o46) + chr(2068 - 2013) + chr(0b1100 + 0o44), 0o10), nzTpIcepk0o8(chr(1679 - 1631) + chr(0b1101111) + '\x32' + chr(49) + chr(0b110111 + 0o0), 23570 - 23562), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(50) + '\x34' + chr(0b101101 + 0o11), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + chr(0b110011) + '\065', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x32' + '\x33' + chr(51), 57077 - 57069), nzTpIcepk0o8('\060' + '\157' + chr(55) + chr(53), 0o10), nzTpIcepk0o8('\060' + chr(8008 - 7897) + '\061' + chr(0b110101) + '\x37', ord("\x08")), nzTpIcepk0o8(chr(0b110000 + 0o0) + '\157' + chr(50) + '\x31' + chr(48), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b1010 + 0o50) + chr(0b110011) + chr(1841 - 1789), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(555 - 504) + chr(55) + chr(679 - 626), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + chr(7601 - 7490) + chr(0b100 + 0o61) + chr(0b110000), 64355 - 64347)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x1d'), '\144' + chr(101) + '\x63' + '\157' + chr(8859 - 8759) + chr(0b1100101))('\165' + chr(12920 - 12804) + chr(4362 - 4260) + chr(45) + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def PDIHFOcFsp3w(PmE5_h409JAA, YYJGqULB4ite, vX1Eq0k9zbZq):
VwOu8WkJ9cpc = nDF4gVNx0u9Q.sAjSkFBTxPdS(PmE5_h409JAA)
for ZlbFMSG8gCoF in bbT2xIe5pzk7(roI3spqORKae(PmE5_h409JAA, roI3spqORKae(ES5oEprVxulp(b'_\x81\x8b\xdb\x1e#\x19w\xc6\xd2\x8b\x99'), chr(100) + chr(4142 - 4041) + '\143' + chr(111) + chr(9344 - 9244) + '\x65')(chr(1002 - 885) + chr(0b1010011 + 0o41) + chr(0b1100110) + chr(0b101101) + '\x38'))[nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b1010 + 0o46), 40669 - 40661)]):
for sChW4gUsXrIC in bbT2xIe5pzk7(roI3spqORKae(PmE5_h409JAA, roI3spqORKae(ES5oEprVxulp(b'_\x81\x8b\xdb\x1e#\x19w\xc6\xd2\x8b\x99'), chr(0b1101 + 0o127) + chr(101) + chr(0b10000 + 0o123) + chr(0b1101111) + chr(6169 - 6069) + chr(5771 - 5670))('\x75' + chr(116) + chr(10023 - 9921) + '\x2d' + '\070'))[nzTpIcepk0o8(chr(48) + '\157' + '\x31', 0b1000)]):
VwOu8WkJ9cpc[ZlbFMSG8gCoF, sChW4gUsXrIC] = PmE5_h409JAA[ZlbFMSG8gCoF, sChW4gUsXrIC] * ZlbFMSG8gCoF * sChW4gUsXrIC * (YYJGqULB4ite - ZlbFMSG8gCoF) * (vX1Eq0k9zbZq - sChW4gUsXrIC)
return VwOu8WkJ9cpc |
cggh/scikit-allel | allel/stats/sf.py | fold_sfs | def fold_sfs(s, n):
"""Fold a site frequency spectrum.
Parameters
----------
s : array_like, int, shape (n_chromosomes,)
Site frequency spectrum
n : int
Total number of chromosomes called.
Returns
-------
sfs_folded : ndarray, int
Folded site frequency spectrum
"""
# check inputs
s = asarray_ndim(s, 1)
assert s.shape[0] <= n + 1, 'invalid number of chromosomes'
# need to check s has all entries up to n
if s.shape[0] < n + 1:
sn = np.zeros(n + 1, dtype=s.dtype)
sn[:s.shape[0]] = s
s = sn
# fold
nf = (n + 1) // 2
n = nf * 2
o = s[:nf] + s[nf:n][::-1]
return o | python | def fold_sfs(s, n):
"""Fold a site frequency spectrum.
Parameters
----------
s : array_like, int, shape (n_chromosomes,)
Site frequency spectrum
n : int
Total number of chromosomes called.
Returns
-------
sfs_folded : ndarray, int
Folded site frequency spectrum
"""
# check inputs
s = asarray_ndim(s, 1)
assert s.shape[0] <= n + 1, 'invalid number of chromosomes'
# need to check s has all entries up to n
if s.shape[0] < n + 1:
sn = np.zeros(n + 1, dtype=s.dtype)
sn[:s.shape[0]] = s
s = sn
# fold
nf = (n + 1) // 2
n = nf * 2
o = s[:nf] + s[nf:n][::-1]
return o | [
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Folded site frequency spectrum | [
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"."
] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/stats/sf.py#L393-L425 | train | Fold a site frequency spectrum. | 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(1337 - 1289) + '\157' + chr(0b110010) + chr(0b11 + 0o64) + '\067', 31857 - 31849), nzTpIcepk0o8('\060' + '\x6f' + chr(48), ord("\x08")), nzTpIcepk0o8(chr(1866 - 1818) + chr(0b1000000 + 0o57) + chr(51) + '\062' + chr(0b101001 + 0o10), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + '\x36' + '\067', 16129 - 16121), nzTpIcepk0o8(chr(48) + chr(111) + chr(50) + chr(0b110010 + 0o1) + chr(0b110000), 45001 - 44993), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110010) + '\x32' + '\063', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1110 + 0o141) + '\063' + '\066' + chr(53), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110011) + chr(0b110111) + chr(0b11111 + 0o24), 0o10), nzTpIcepk0o8(chr(1757 - 1709) + chr(0b1101111) + chr(50) + chr(2402 - 2349) + chr(0b10110 + 0o34), 32359 - 32351), nzTpIcepk0o8(chr(48) + chr(1668 - 1557) + chr(50) + '\063' + chr(0b101110 + 0o3), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(938 - 888) + '\x33' + '\067', 5673 - 5665), nzTpIcepk0o8(chr(431 - 383) + chr(0b1000110 + 0o51) + chr(0b110010) + '\x35' + chr(0b110001), 52185 - 52177), nzTpIcepk0o8('\x30' + '\x6f' + '\x31' + chr(0b110101 + 0o0) + chr(0b0 + 0o61), 7084 - 7076), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110001) + '\x33', 0o10), nzTpIcepk0o8(chr(205 - 157) + chr(0b1101111) + chr(0b110001) + chr(55) + '\x37', 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(1781 - 1730) + '\066' + chr(48), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x33' + '\x33', 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(0b110011) + '\066' + chr(0b101111 + 0o6), 8), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x31' + chr(2646 - 2593) + '\067', 25005 - 24997), nzTpIcepk0o8(chr(2216 - 2168) + '\x6f' + '\x32' + chr(0b110000) + chr(860 - 808), ord("\x08")), nzTpIcepk0o8(chr(0b10110 + 0o32) + chr(111) + chr(0b110010) + chr(0b10 + 0o63) + '\067', 10992 - 10984), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\063' + chr(52) + '\061', ord("\x08")), nzTpIcepk0o8(chr(131 - 83) + chr(0b1101111) + '\x32' + chr(2318 - 2269) + chr(0b110010 + 0o0), ord("\x08")), nzTpIcepk0o8(chr(0b110 + 0o52) + chr(2302 - 2191) + '\061' + '\065' + chr(2266 - 2214), ord("\x08")), nzTpIcepk0o8(chr(663 - 615) + '\157' + chr(1699 - 1648) + chr(52) + chr(1860 - 1810), ord("\x08")), nzTpIcepk0o8(chr(0b10000 + 0o40) + chr(0b1001110 + 0o41) + chr(0b110010) + chr(51) + chr(0b1101 + 0o46), 0o10), nzTpIcepk0o8(chr(266 - 218) + chr(3482 - 3371) + '\061' + chr(2002 - 1950) + '\x31', 12371 - 12363), nzTpIcepk0o8('\060' + '\157' + chr(1716 - 1666) + '\x37' + chr(49), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(50) + chr(0b11001 + 0o27) + chr(1431 - 1378), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(1516 - 1466) + chr(0b110110) + chr(0b1101 + 0o43), 0b1000), nzTpIcepk0o8(chr(0b11101 + 0o23) + chr(0b1101111) + chr(1947 - 1898) + chr(2638 - 2584) + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(54) + chr(0b1000 + 0o56), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(8836 - 8725) + '\063' + chr(50), 57955 - 57947), nzTpIcepk0o8(chr(48) + '\x6f' + '\061' + chr(0b110100) + chr(0b110101), 0b1000), nzTpIcepk0o8('\x30' + chr(0b10111 + 0o130) + chr(0b110011) + chr(0b100100 + 0o22) + '\x36', 34199 - 34191), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(2230 - 2179) + '\x31', ord("\x08")), nzTpIcepk0o8(chr(0b101000 + 0o10) + '\x6f' + '\x33' + chr(0b100100 + 0o14) + '\060', ord("\x08")), nzTpIcepk0o8('\x30' + chr(10873 - 10762) + chr(1533 - 1482) + chr(607 - 552) + chr(387 - 337), 5400 - 5392), nzTpIcepk0o8('\060' + chr(0b1000 + 0o147) + '\x33' + '\x30' + chr(51), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110010) + chr(52), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + chr(0b1101111) + '\065' + '\x30', 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x91'), chr(0b1011111 + 0o5) + chr(0b111101 + 0o50) + '\x63' + chr(0b1101111) + chr(0b1100100) + '\x65')(chr(7569 - 7452) + '\x74' + chr(102) + '\x2d' + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def yfmcYc1f1fmv(PmE5_h409JAA, NoZxuO7wjArS):
PmE5_h409JAA = EVVKPun88TqM(PmE5_h409JAA, nzTpIcepk0o8('\060' + chr(7315 - 7204) + chr(0b110001), 0b1000))
assert roI3spqORKae(PmE5_h409JAA, roI3spqORKae(ES5oEprVxulp(b'\xd3h\xb3z\xa8\xaa\xc7\xba\xec\xce\xa7\xcf'), chr(100) + '\x65' + chr(0b111110 + 0o45) + chr(111) + '\x64' + chr(0b1100101))(chr(9538 - 9421) + chr(116) + chr(0b1100110) + chr(0b1101 + 0o40) + '\x38'))[nzTpIcepk0o8(chr(0b1101 + 0o43) + chr(111) + chr(0b110000), 8)] <= NoZxuO7wjArS + nzTpIcepk0o8(chr(0b110000) + chr(9425 - 9314) + chr(49), 8), roI3spqORKae(ES5oEprVxulp(b'\xd6n\xa7V\xf4\xfa\x91\xdb\xc4\xec\xf2\xcb\x0cy_\x9f}\xd5\x0c\xec\xdd\x8e\xe7\x03\x91\xf4\x0c\xdc\xf6'), chr(0b1010111 + 0o15) + chr(0b1100101) + chr(8833 - 8734) + '\x6f' + '\144' + '\x65')('\165' + chr(5388 - 5272) + '\146' + chr(0b11010 + 0o23) + chr(0b111000))
if roI3spqORKae(PmE5_h409JAA, roI3spqORKae(ES5oEprVxulp(b'\xd3h\xb3z\xa8\xaa\xc7\xba\xec\xce\xa7\xcf'), chr(6106 - 6006) + '\145' + chr(0b1100011) + '\157' + chr(0b10010 + 0o122) + '\145')(chr(0b1110101) + '\164' + chr(7519 - 7417) + chr(783 - 738) + chr(0b111000)))[nzTpIcepk0o8(chr(0b10011 + 0o35) + chr(0b1101111) + chr(794 - 746), 8)] < NoZxuO7wjArS + nzTpIcepk0o8(chr(2298 - 2250) + chr(0b1101111) + chr(0b110001), 8):
NIv4q21tgWSo = nDF4gVNx0u9Q.UmwwEp7MzR6q(NoZxuO7wjArS + nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110001), 8), dtype=PmE5_h409JAA.RcX9bbuOzh5L)
NIv4q21tgWSo[:PmE5_h409JAA.lhbM092AFW8f[nzTpIcepk0o8(chr(0b11000 + 0o30) + chr(0b1001100 + 0o43) + chr(2304 - 2256), 8)]] = PmE5_h409JAA
PmE5_h409JAA = NIv4q21tgWSo
o8wB6rLEskY2 = (NoZxuO7wjArS + nzTpIcepk0o8(chr(0b11 + 0o55) + chr(0b1101110 + 0o1) + chr(0b110001), 8)) // nzTpIcepk0o8(chr(1103 - 1055) + chr(10495 - 10384) + chr(0b110001 + 0o1), 0b1000)
NoZxuO7wjArS = o8wB6rLEskY2 * nzTpIcepk0o8(chr(0b10100 + 0o34) + chr(111) + chr(50), 8)
WgZUEOuIyTUO = PmE5_h409JAA[:o8wB6rLEskY2] + PmE5_h409JAA[o8wB6rLEskY2:NoZxuO7wjArS][::-nzTpIcepk0o8('\060' + chr(111) + chr(0b110001), 8)]
return WgZUEOuIyTUO |
cggh/scikit-allel | allel/stats/sf.py | fold_joint_sfs | def fold_joint_sfs(s, n1, n2):
"""Fold a joint site frequency spectrum.
Parameters
----------
s : array_like, int, shape (m_chromosomes, n_chromosomes)
Joint site frequency spectrum.
n1, n2 : int, optional
The total number of chromosomes called in each population.
Returns
-------
joint_sfs_folded : ndarray, int
Folded joint site frequency spectrum.
"""
# check inputs
s = asarray_ndim(s, 2)
assert s.shape[0] <= n1 + 1, 'invalid number of chromosomes'
assert s.shape[1] <= n2 + 1, 'invalid number of chromosomes'
# need to check s has all entries up to m
if s.shape[0] < n1 + 1:
sm = np.zeros((n1 + 1, s.shape[1]), dtype=s.dtype)
sm[:s.shape[0]] = s
s = sm
# need to check s has all entries up to n
if s.shape[1] < n2 + 1:
sn = np.zeros((s.shape[0], n2 + 1), dtype=s.dtype)
sn[:, :s.shape[1]] = s
s = sn
# fold
mf = (n1 + 1) // 2
nf = (n2 + 1) // 2
n1 = mf * 2
n2 = nf * 2
o = (s[:mf, :nf] + # top left
s[mf:n1, :nf][::-1] + # top right
s[:mf, nf:n2][:, ::-1] + # bottom left
s[mf:n1, nf:n2][::-1, ::-1]) # bottom right
return o | python | def fold_joint_sfs(s, n1, n2):
"""Fold a joint site frequency spectrum.
Parameters
----------
s : array_like, int, shape (m_chromosomes, n_chromosomes)
Joint site frequency spectrum.
n1, n2 : int, optional
The total number of chromosomes called in each population.
Returns
-------
joint_sfs_folded : ndarray, int
Folded joint site frequency spectrum.
"""
# check inputs
s = asarray_ndim(s, 2)
assert s.shape[0] <= n1 + 1, 'invalid number of chromosomes'
assert s.shape[1] <= n2 + 1, 'invalid number of chromosomes'
# need to check s has all entries up to m
if s.shape[0] < n1 + 1:
sm = np.zeros((n1 + 1, s.shape[1]), dtype=s.dtype)
sm[:s.shape[0]] = s
s = sm
# need to check s has all entries up to n
if s.shape[1] < n2 + 1:
sn = np.zeros((s.shape[0], n2 + 1), dtype=s.dtype)
sn[:, :s.shape[1]] = s
s = sn
# fold
mf = (n1 + 1) // 2
nf = (n2 + 1) // 2
n1 = mf * 2
n2 = nf * 2
o = (s[:mf, :nf] + # top left
s[mf:n1, :nf][::-1] + # top right
s[:mf, nf:n2][:, ::-1] + # bottom left
s[mf:n1, nf:n2][::-1, ::-1]) # bottom right
return o | [
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... | Fold a joint site frequency spectrum.
Parameters
----------
s : array_like, int, shape (m_chromosomes, n_chromosomes)
Joint site frequency spectrum.
n1, n2 : int, optional
The total number of chromosomes called in each population.
Returns
-------
joint_sfs_folded : ndarray, int
Folded joint site frequency spectrum. | [
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"spectrum",
"."
] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/stats/sf.py#L428-L472 | train | Fold a joint site frequency spectrum. | 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(50) + chr(0b1011 + 0o52) + chr(0b1101 + 0o47), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(10394 - 10283) + chr(730 - 679) + chr(0b110011) + chr(0b10111 + 0o37), 44919 - 44911), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110010) + chr(0b110101) + chr(0b110100), 8), nzTpIcepk0o8('\x30' + chr(111) + '\x32' + chr(951 - 899) + '\x31', ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(0b10111 + 0o37) + '\060', ord("\x08")), nzTpIcepk0o8(chr(2151 - 2103) + chr(0b1101111) + '\062' + chr(54) + chr(0b10000 + 0o46), 0b1000), nzTpIcepk0o8('\060' + chr(111) + '\x32' + chr(3005 - 2950) + chr(2613 - 2559), 0b1000), nzTpIcepk0o8(chr(1752 - 1704) + chr(111) + chr(1039 - 989) + chr(54), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1001010 + 0o45) + chr(2657 - 2604) + chr(0b110001), 20125 - 20117), nzTpIcepk0o8(chr(0b1100 + 0o44) + chr(0b1101101 + 0o2) + chr(700 - 650) + chr(0b10001 + 0o43) + chr(49), 8), nzTpIcepk0o8(chr(656 - 608) + '\157' + chr(1525 - 1474) + '\x32' + chr(0b100110 + 0o12), 26485 - 26477), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x34' + '\063', 0b1000), nzTpIcepk0o8(chr(0b100001 + 0o17) + '\x6f' + chr(54) + chr(0b110000), 8), nzTpIcepk0o8('\x30' + chr(10188 - 10077) + chr(0b100001 + 0o20) + '\062' + chr(0b100110 + 0o15), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(55), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(0b10110 + 0o35) + '\060' + chr(49), ord("\x08")), nzTpIcepk0o8(chr(2127 - 2079) + chr(0b110011 + 0o74) + chr(0b10101 + 0o35) + chr(0b1001 + 0o56) + chr(0b110011), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(50) + '\067' + chr(827 - 779), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + '\x32' + '\x30' + chr(1105 - 1057), 63717 - 63709), nzTpIcepk0o8(chr(48) + chr(111) + '\x31' + chr(0b110011) + chr(54), 0b1000), nzTpIcepk0o8(chr(0b100001 + 0o17) + chr(0b1100100 + 0o13) + chr(1268 - 1219) + chr(1549 - 1496) + '\062', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\062' + '\065', 0b1000), nzTpIcepk0o8(chr(2185 - 2137) + '\x6f' + chr(0b11111 + 0o22) + chr(0b110010) + '\065', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(9169 - 9058) + chr(2076 - 2027) + chr(1740 - 1690) + '\065', 8), nzTpIcepk0o8(chr(48) + chr(0b1010010 + 0o35) + '\061' + chr(51) + chr(55), 0b1000), nzTpIcepk0o8(chr(0b10011 + 0o35) + chr(11146 - 11035) + '\x33' + chr(51) + '\x35', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\061' + chr(792 - 743) + '\060', 0o10), nzTpIcepk0o8(chr(519 - 471) + chr(0b1100111 + 0o10) + chr(0b10111 + 0o33) + '\061' + '\x31', 24135 - 24127), nzTpIcepk0o8(chr(48) + chr(111) + chr(381 - 330) + '\x31' + '\062', ord("\x08")), nzTpIcepk0o8(chr(0b100 + 0o54) + chr(0b1101111) + '\x32' + chr(0b110000) + '\067', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1000101 + 0o52) + chr(0b110111) + '\x35', 0o10), nzTpIcepk0o8(chr(0b100001 + 0o17) + chr(0b10100 + 0o133) + chr(0b101000 + 0o12) + chr(0b110110) + '\062', 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(890 - 841) + chr(0b11110 + 0o26) + chr(53), ord("\x08")), nzTpIcepk0o8(chr(0b11100 + 0o24) + chr(111) + chr(51) + chr(52) + chr(50), 40726 - 40718), nzTpIcepk0o8(chr(0b1111 + 0o41) + chr(0b1001011 + 0o44) + chr(51) + chr(51) + chr(0b110101), 8), nzTpIcepk0o8(chr(0b1 + 0o57) + '\x6f' + chr(51) + chr(0b110 + 0o52) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1001101 + 0o42) + '\061' + chr(0b110011), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b110110 + 0o71) + chr(0b1010 + 0o53) + chr(0b110011), ord("\x08")), nzTpIcepk0o8(chr(147 - 99) + chr(5698 - 5587) + '\x32' + chr(0b110010) + chr(51), 30676 - 30668), nzTpIcepk0o8('\x30' + '\x6f' + chr(1036 - 985) + '\x37' + chr(0b111 + 0o52), 59799 - 59791)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(1680 - 1632) + chr(3675 - 3564) + chr(1956 - 1903) + chr(464 - 416), 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x82'), chr(8714 - 8614) + chr(0b111110 + 0o47) + '\x63' + chr(0b1101111) + chr(100) + '\x65')(chr(117) + chr(0b1110100) + chr(0b1100110) + '\055' + chr(3136 - 3080)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def eCfD3JloQORi(PmE5_h409JAA, YYJGqULB4ite, vX1Eq0k9zbZq):
PmE5_h409JAA = EVVKPun88TqM(PmE5_h409JAA, nzTpIcepk0o8(chr(1726 - 1678) + chr(0b1010101 + 0o32) + chr(1311 - 1261), ord("\x08")))
assert roI3spqORKae(PmE5_h409JAA, roI3spqORKae(ES5oEprVxulp(b'\xc0\xb6\xce\xec\x00\x8f\x8cWo\xf6\xe8E'), chr(2344 - 2244) + chr(0b1000010 + 0o43) + chr(0b111110 + 0o45) + chr(0b110000 + 0o77) + '\x64' + chr(0b1100101))(chr(0b1110101) + chr(0b1101010 + 0o12) + '\x66' + '\055' + chr(0b111000)))[nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x30', 39009 - 39001)] <= YYJGqULB4ite + nzTpIcepk0o8(chr(0b110000) + chr(0b0 + 0o157) + chr(0b100010 + 0o17), ord("\x08")), roI3spqORKae(ES5oEprVxulp(b"\xc5\xb0\xda\xc0\\\xdf\xda6G\xd4\xbdAU!'\xae\xdd\x98\xe36\x18z8:,\xb2%\xec\xb9"), chr(333 - 233) + chr(0b1100101) + chr(0b10110 + 0o115) + '\157' + chr(5216 - 5116) + '\145')(chr(0b1001010 + 0o53) + chr(0b1001110 + 0o46) + '\x66' + chr(0b10111 + 0o26) + '\x38')
assert roI3spqORKae(PmE5_h409JAA, roI3spqORKae(ES5oEprVxulp(b'\xc0\xb6\xce\xec\x00\x8f\x8cWo\xf6\xe8E'), chr(9596 - 9496) + chr(6513 - 6412) + '\x63' + chr(0b1101111) + chr(0b111011 + 0o51) + chr(7379 - 7278))('\x75' + '\x74' + '\x66' + chr(0b100101 + 0o10) + chr(0b111000)))[nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b1010 + 0o47), 8)] <= vX1Eq0k9zbZq + nzTpIcepk0o8(chr(48) + chr(111) + chr(2312 - 2263), 8), roI3spqORKae(ES5oEprVxulp(b"\xc5\xb0\xda\xc0\\\xdf\xda6G\xd4\xbdAU!'\xae\xdd\x98\xe36\x18z8:,\xb2%\xec\xb9"), chr(8504 - 8404) + chr(4667 - 4566) + chr(99) + chr(1550 - 1439) + chr(6799 - 6699) + chr(2315 - 2214))('\x75' + '\164' + '\x66' + chr(947 - 902) + chr(0b111000))
if roI3spqORKae(PmE5_h409JAA, roI3spqORKae(ES5oEprVxulp(b'\xc0\xb6\xce\xec\x00\x8f\x8cWo\xf6\xe8E'), chr(100) + chr(101) + chr(0b1100011) + '\x6f' + chr(100) + chr(0b1100101))('\165' + chr(116) + chr(102) + chr(472 - 427) + '\x38'))[nzTpIcepk0o8('\060' + chr(0b1101111) + chr(48), 8)] < YYJGqULB4ite + nzTpIcepk0o8(chr(0b100111 + 0o11) + chr(0b1101111) + '\061', 8):
miZza6ggsjTu = nDF4gVNx0u9Q.UmwwEp7MzR6q((YYJGqULB4ite + nzTpIcepk0o8(chr(217 - 169) + '\x6f' + chr(0b11111 + 0o22), 8), PmE5_h409JAA.lhbM092AFW8f[nzTpIcepk0o8(chr(316 - 268) + '\x6f' + '\x31', 8)]), dtype=PmE5_h409JAA.RcX9bbuOzh5L)
miZza6ggsjTu[:PmE5_h409JAA.lhbM092AFW8f[nzTpIcepk0o8('\060' + '\157' + chr(48), 8)]] = PmE5_h409JAA
PmE5_h409JAA = miZza6ggsjTu
if roI3spqORKae(PmE5_h409JAA, roI3spqORKae(ES5oEprVxulp(b'\xc0\xb6\xce\xec\x00\x8f\x8cWo\xf6\xe8E'), chr(0b1100100) + '\145' + chr(0b10101 + 0o116) + chr(9478 - 9367) + chr(0b10011 + 0o121) + '\145')(chr(877 - 760) + chr(116) + chr(0b1100110) + '\x2d' + chr(2723 - 2667)))[nzTpIcepk0o8(chr(0b101000 + 0o10) + chr(111) + '\x31', 8)] < vX1Eq0k9zbZq + nzTpIcepk0o8(chr(0b100000 + 0o20) + '\157' + chr(0b1000 + 0o51), 8):
NIv4q21tgWSo = nDF4gVNx0u9Q.UmwwEp7MzR6q((PmE5_h409JAA.lhbM092AFW8f[nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x30', 8)], vX1Eq0k9zbZq + nzTpIcepk0o8(chr(993 - 945) + '\157' + chr(188 - 139), 8)), dtype=PmE5_h409JAA.RcX9bbuOzh5L)
NIv4q21tgWSo[:, :PmE5_h409JAA.lhbM092AFW8f[nzTpIcepk0o8(chr(0b101010 + 0o6) + '\157' + '\061', 8)]] = PmE5_h409JAA
PmE5_h409JAA = NIv4q21tgWSo
eSpQ3s64hKLx = (YYJGqULB4ite + nzTpIcepk0o8(chr(971 - 923) + chr(4439 - 4328) + '\061', 8)) // nzTpIcepk0o8(chr(48) + '\157' + '\x32', 8)
o8wB6rLEskY2 = (vX1Eq0k9zbZq + nzTpIcepk0o8(chr(1883 - 1835) + chr(111) + '\061', 8)) // nzTpIcepk0o8('\x30' + chr(111) + chr(888 - 838), 8)
YYJGqULB4ite = eSpQ3s64hKLx * nzTpIcepk0o8('\x30' + '\157' + chr(50), 8)
vX1Eq0k9zbZq = o8wB6rLEskY2 * nzTpIcepk0o8('\x30' + '\x6f' + '\062', 8)
WgZUEOuIyTUO = PmE5_h409JAA[:eSpQ3s64hKLx, :o8wB6rLEskY2] + PmE5_h409JAA[eSpQ3s64hKLx:YYJGqULB4ite, :o8wB6rLEskY2][::-nzTpIcepk0o8('\060' + '\x6f' + chr(0b100101 + 0o14), 8)] + PmE5_h409JAA[:eSpQ3s64hKLx, o8wB6rLEskY2:vX1Eq0k9zbZq][:, ::-nzTpIcepk0o8(chr(0b10100 + 0o34) + chr(5524 - 5413) + '\x31', 8)] + PmE5_h409JAA[eSpQ3s64hKLx:YYJGqULB4ite, o8wB6rLEskY2:vX1Eq0k9zbZq][::-nzTpIcepk0o8('\060' + '\x6f' + chr(49), 8), ::-nzTpIcepk0o8('\x30' + '\157' + chr(1011 - 962), 8)]
return WgZUEOuIyTUO |
cggh/scikit-allel | allel/stats/sf.py | plot_sfs | def plot_sfs(s, yscale='log', bins=None, n=None,
clip_endpoints=True, label=None, plot_kwargs=None,
ax=None):
"""Plot a site frequency spectrum.
Parameters
----------
s : array_like, int, shape (n_chromosomes,)
Site frequency spectrum.
yscale : string, optional
Y axis scale.
bins : int or array_like, int, optional
Allele count bins.
n : int, optional
Number of chromosomes sampled. If provided, X axis will be plotted
as allele frequency, otherwise as allele count.
clip_endpoints : bool, optional
If True, do not plot first and last values from frequency spectrum.
label : string, optional
Label for data series in plot.
plot_kwargs : dict-like
Additional keyword arguments, passed through to ax.plot().
ax : axes, optional
Axes on which to draw. If not provided, a new figure will be created.
Returns
-------
ax : axes
The axes on which the plot was drawn.
"""
import matplotlib.pyplot as plt
import scipy
# check inputs
s = asarray_ndim(s, 1)
# setup axes
if ax is None:
fig, ax = plt.subplots()
# setup data
if bins is None:
if clip_endpoints:
x = np.arange(1, s.shape[0]-1)
y = s[1:-1]
else:
x = np.arange(s.shape[0])
y = s
else:
if clip_endpoints:
y, b, _ = scipy.stats.binned_statistic(
np.arange(1, s.shape[0]-1),
values=s[1:-1],
bins=bins,
statistic='sum')
else:
y, b, _ = scipy.stats.binned_statistic(
np.arange(s.shape[0]),
values=s,
bins=bins,
statistic='sum')
# use bin midpoints for plotting
x = (b[:-1] + b[1:]) / 2
if n:
# convert allele counts to allele frequencies
x = x / n
ax.set_xlabel('derived allele frequency')
else:
ax.set_xlabel('derived allele count')
# do plotting
if plot_kwargs is None:
plot_kwargs = dict()
ax.plot(x, y, label=label, **plot_kwargs)
# tidy
ax.set_yscale(yscale)
ax.set_ylabel('site frequency')
ax.autoscale(axis='x', tight=True)
return ax | python | def plot_sfs(s, yscale='log', bins=None, n=None,
clip_endpoints=True, label=None, plot_kwargs=None,
ax=None):
"""Plot a site frequency spectrum.
Parameters
----------
s : array_like, int, shape (n_chromosomes,)
Site frequency spectrum.
yscale : string, optional
Y axis scale.
bins : int or array_like, int, optional
Allele count bins.
n : int, optional
Number of chromosomes sampled. If provided, X axis will be plotted
as allele frequency, otherwise as allele count.
clip_endpoints : bool, optional
If True, do not plot first and last values from frequency spectrum.
label : string, optional
Label for data series in plot.
plot_kwargs : dict-like
Additional keyword arguments, passed through to ax.plot().
ax : axes, optional
Axes on which to draw. If not provided, a new figure will be created.
Returns
-------
ax : axes
The axes on which the plot was drawn.
"""
import matplotlib.pyplot as plt
import scipy
# check inputs
s = asarray_ndim(s, 1)
# setup axes
if ax is None:
fig, ax = plt.subplots()
# setup data
if bins is None:
if clip_endpoints:
x = np.arange(1, s.shape[0]-1)
y = s[1:-1]
else:
x = np.arange(s.shape[0])
y = s
else:
if clip_endpoints:
y, b, _ = scipy.stats.binned_statistic(
np.arange(1, s.shape[0]-1),
values=s[1:-1],
bins=bins,
statistic='sum')
else:
y, b, _ = scipy.stats.binned_statistic(
np.arange(s.shape[0]),
values=s,
bins=bins,
statistic='sum')
# use bin midpoints for plotting
x = (b[:-1] + b[1:]) / 2
if n:
# convert allele counts to allele frequencies
x = x / n
ax.set_xlabel('derived allele frequency')
else:
ax.set_xlabel('derived allele count')
# do plotting
if plot_kwargs is None:
plot_kwargs = dict()
ax.plot(x, y, label=label, **plot_kwargs)
# tidy
ax.set_yscale(yscale)
ax.set_ylabel('site frequency')
ax.autoscale(axis='x', tight=True)
return ax | [
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... | Plot a site frequency spectrum.
Parameters
----------
s : array_like, int, shape (n_chromosomes,)
Site frequency spectrum.
yscale : string, optional
Y axis scale.
bins : int or array_like, int, optional
Allele count bins.
n : int, optional
Number of chromosomes sampled. If provided, X axis will be plotted
as allele frequency, otherwise as allele count.
clip_endpoints : bool, optional
If True, do not plot first and last values from frequency spectrum.
label : string, optional
Label for data series in plot.
plot_kwargs : dict-like
Additional keyword arguments, passed through to ax.plot().
ax : axes, optional
Axes on which to draw. If not provided, a new figure will be created.
Returns
-------
ax : axes
The axes on which the plot was drawn. | [
"Plot",
"a",
"site",
"frequency",
"spectrum",
"."
] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/stats/sf.py#L475-L558 | train | Plots a site frequency spectrum. | 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) + '\064' + '\066', 0o10), nzTpIcepk0o8(chr(0b10000 + 0o40) + chr(111) + chr(51) + chr(2137 - 2084), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x31' + chr(55) + chr(2410 - 2356), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + '\062' + '\064' + '\x32', 0b1000), nzTpIcepk0o8('\x30' + chr(11112 - 11001) + chr(0b11110 + 0o23) + chr(0b110110) + '\067', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(1066 - 1017) + '\x31' + chr(1888 - 1836), 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(0b1010 + 0o47) + '\067' + chr(55), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1011 + 0o144) + chr(50) + chr(0b110011) + chr(55), 0b1000), nzTpIcepk0o8(chr(0b1011 + 0o45) + '\157' + chr(2050 - 2000) + chr(0b101100 + 0o4) + '\x37', 0o10), nzTpIcepk0o8(chr(48) + chr(9328 - 9217) + chr(53) + chr(50), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110011) + chr(48) + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b100111 + 0o110) + chr(1943 - 1892) + '\061' + chr(53), 0o10), nzTpIcepk0o8(chr(2070 - 2022) + '\157' + chr(0b10001 + 0o41) + chr(2298 - 2243) + chr(50), 58435 - 58427), nzTpIcepk0o8(chr(48) + chr(111) + '\x32' + chr(0b101011 + 0o13) + '\064', 15409 - 15401), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\064', 4134 - 4126), nzTpIcepk0o8(chr(48) + chr(111) + '\061' + '\060' + '\064', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b111011 + 0o64) + chr(0b11 + 0o57) + chr(50) + '\x31', 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110010) + chr(0b11110 + 0o30), 48977 - 48969), nzTpIcepk0o8(chr(0b110000) + chr(0b1001000 + 0o47) + chr(0b10011 + 0o36) + chr(0b110001) + '\x32', 24026 - 24018), nzTpIcepk0o8(chr(1603 - 1555) + chr(3260 - 3149) + '\064' + chr(0b100000 + 0o25), 42734 - 42726), nzTpIcepk0o8('\060' + '\x6f' + chr(51) + chr(0b101101 + 0o11) + '\x36', 61786 - 61778), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(50) + '\060', 0b1000), nzTpIcepk0o8('\x30' + chr(7874 - 7763) + chr(2350 - 2301) + '\x33' + chr(0b110001), 0b1000), nzTpIcepk0o8(chr(0b101001 + 0o7) + chr(0b1101111) + chr(2282 - 2231) + '\x31' + '\x34', 24726 - 24718), nzTpIcepk0o8(chr(48) + '\x6f' + chr(51) + chr(49) + '\063', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b100101 + 0o112) + '\x32' + chr(54) + chr(0b110111), 43387 - 43379), nzTpIcepk0o8(chr(0b10111 + 0o31) + chr(0b1101111) + '\063' + chr(811 - 760) + chr(53), 53751 - 53743), nzTpIcepk0o8(chr(48) + '\157' + chr(263 - 214) + chr(2485 - 2435) + chr(48), 0o10), nzTpIcepk0o8('\060' + chr(0b111011 + 0o64) + '\x31' + '\x36' + chr(0b100 + 0o62), 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(0b10001 + 0o41) + chr(0b110000) + chr(365 - 314), 0o10), nzTpIcepk0o8('\x30' + chr(0b100 + 0o153) + chr(0b11110 + 0o24) + '\x31', 800 - 792), nzTpIcepk0o8(chr(154 - 106) + chr(111) + chr(0b11100 + 0o26) + chr(0b110111) + chr(49), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(239 - 189) + '\061' + chr(0b110111), 3993 - 3985), nzTpIcepk0o8(chr(0b100101 + 0o13) + chr(638 - 527) + chr(0b10011 + 0o40) + '\062' + chr(53), 0b1000), nzTpIcepk0o8(chr(463 - 415) + '\157' + chr(964 - 912) + '\066', 8), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110000 + 0o3) + chr(51) + chr(1457 - 1408), 20723 - 20715), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110010) + '\x34' + chr(431 - 379), ord("\x08")), nzTpIcepk0o8(chr(2000 - 1952) + chr(0b1101111) + chr(1192 - 1143) + '\x30' + '\063', 0o10), nzTpIcepk0o8('\060' + '\x6f' + '\x31' + chr(51) + '\062', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1100110 + 0o11) + chr(51) + '\062' + chr(0b110000), 51951 - 51943)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + '\x6f' + '\x35' + chr(0b10110 + 0o32), 41315 - 41307)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x08'), chr(100) + '\x65' + chr(104 - 5) + '\x6f' + chr(0b1100100) + chr(9635 - 9534))(chr(0b11011 + 0o132) + chr(116) + chr(0b1001000 + 0o36) + '\055' + chr(0b11010 + 0o36)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def oQgu9rZcOS2h(PmE5_h409JAA, YlnxpOvv9Uzx=roI3spqORKae(ES5oEprVxulp(b'Jr\x19'), chr(100) + chr(0b1100101) + '\143' + '\157' + chr(0b1100001 + 0o3) + chr(101))('\x75' + chr(4672 - 4556) + chr(102) + chr(45) + '\070'), LfioTTi_I2sD=None, NoZxuO7wjArS=None, vSrEUdiJz6WM=nzTpIcepk0o8('\060' + chr(111) + chr(357 - 308), 7115 - 7107), OkDIn6t2Cke6=None, svwoYs1fJDLp=None, ZtB7KOLCW2Hk=None):
(Z7HGgmIyegqz,) = (roI3spqORKae(rFFUeiYWzOhx(roI3spqORKae(ES5oEprVxulp(b'K|\n\xd2\x1b#\x0b\xf3\xeeH\xec\xbd\xc3\xc4h+\xe5'), '\144' + chr(7458 - 7357) + chr(7990 - 7891) + chr(0b1101111) + chr(0b1100100) + chr(101))('\165' + '\x74' + chr(102) + '\x2d' + chr(56)), roI3spqORKae(ES5oEprVxulp(b'Vd\x0e\xce\x188'), chr(100) + '\145' + chr(0b1100010 + 0o1) + chr(0b1101111) + chr(0b1011010 + 0o12) + chr(101))(chr(6510 - 6393) + chr(5656 - 5540) + '\146' + chr(1864 - 1819) + chr(0b111000))), roI3spqORKae(ES5oEprVxulp(b'Vd\x0e\xce\x188'), '\x64' + chr(0b100110 + 0o77) + '\143' + chr(0b1101111) + '\x64' + '\x65')(chr(11937 - 11820) + chr(9731 - 9615) + chr(4759 - 4657) + chr(72 - 27) + chr(56))),)
(wnoNUOmKe_M_,) = (zGgTE_CdZfvi(roI3spqORKae(ES5oEprVxulp(b'U~\x17\xd2\x0e'), chr(0b1000 + 0o134) + '\145' + chr(0b1100011) + chr(8171 - 8060) + '\x64' + chr(0b1100101))(chr(5711 - 5594) + '\164' + chr(102) + chr(45) + '\x38')),)
PmE5_h409JAA = EVVKPun88TqM(PmE5_h409JAA, nzTpIcepk0o8('\060' + chr(9475 - 9364) + '\x31', 8))
if ZtB7KOLCW2Hk is None:
(ux0XlXMUdKbX, ZtB7KOLCW2Hk) = Z7HGgmIyegqz.subplots()
if LfioTTi_I2sD is None:
if vSrEUdiJz6WM:
bI5jsQ9OkQtj = nDF4gVNx0u9Q.chmI_GMU_sEi(nzTpIcepk0o8('\x30' + chr(9477 - 9366) + chr(0b100101 + 0o14), 8), PmE5_h409JAA.lhbM092AFW8f[nzTpIcepk0o8(chr(48) + '\157' + '\060', 0o10)] - nzTpIcepk0o8(chr(1493 - 1445) + chr(0b1010001 + 0o36) + chr(473 - 424), 8))
Fi3yzxctM1zW = PmE5_h409JAA[nzTpIcepk0o8(chr(0b110000) + '\157' + chr(1567 - 1518), 8):-nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(2305 - 2256), 8)]
else:
bI5jsQ9OkQtj = nDF4gVNx0u9Q.chmI_GMU_sEi(PmE5_h409JAA.lhbM092AFW8f[nzTpIcepk0o8(chr(300 - 252) + chr(0b1011110 + 0o21) + chr(48), 8)])
Fi3yzxctM1zW = PmE5_h409JAA
else:
if vSrEUdiJz6WM:
(Fi3yzxctM1zW, xFDEVQn5qSdh, zIqcgNgQ9U6F) = wnoNUOmKe_M_.stats.binned_statistic(nDF4gVNx0u9Q.chmI_GMU_sEi(nzTpIcepk0o8('\x30' + chr(0b10111 + 0o130) + '\061', 8), PmE5_h409JAA.lhbM092AFW8f[nzTpIcepk0o8('\x30' + '\x6f' + chr(48), 8)] - nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x31', 8)), values=PmE5_h409JAA[nzTpIcepk0o8(chr(319 - 271) + chr(10721 - 10610) + chr(2023 - 1974), 8):-nzTpIcepk0o8(chr(0b110000) + chr(202 - 91) + chr(2360 - 2311), 8)], bins=LfioTTi_I2sD, statistic=roI3spqORKae(ES5oEprVxulp(b'Uh\x13'), chr(0b1011100 + 0o10) + chr(5150 - 5049) + chr(99) + chr(0b1000101 + 0o52) + chr(0b1100100) + chr(0b1011001 + 0o14))(chr(0b101100 + 0o111) + chr(0b1100111 + 0o15) + chr(0b1001011 + 0o33) + chr(45) + chr(394 - 338)))
else:
(Fi3yzxctM1zW, xFDEVQn5qSdh, zIqcgNgQ9U6F) = wnoNUOmKe_M_.stats.binned_statistic(nDF4gVNx0u9Q.chmI_GMU_sEi(PmE5_h409JAA.lhbM092AFW8f[nzTpIcepk0o8('\060' + chr(0b1100101 + 0o12) + '\x30', 8)]), values=PmE5_h409JAA, bins=LfioTTi_I2sD, statistic=roI3spqORKae(ES5oEprVxulp(b'Uh\x13'), chr(100) + chr(0b1100101) + chr(453 - 354) + chr(0b1101 + 0o142) + '\x64' + chr(0b1100101))(chr(4607 - 4490) + '\x74' + chr(7568 - 7466) + chr(668 - 623) + chr(463 - 407)))
bI5jsQ9OkQtj = (xFDEVQn5qSdh[:-nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110001), 8)] + xFDEVQn5qSdh[nzTpIcepk0o8(chr(0b1111 + 0o41) + '\x6f' + chr(1409 - 1360), 8):]) / nzTpIcepk0o8(chr(607 - 559) + '\157' + '\062', ord("\x08"))
if NoZxuO7wjArS:
bI5jsQ9OkQtj = bI5jsQ9OkQtj / NoZxuO7wjArS
roI3spqORKae(ZtB7KOLCW2Hk, roI3spqORKae(ES5oEprVxulp(b'Ux\n\xfd\x0f \x1e\xfd\xe2F'), '\x64' + chr(0b110110 + 0o57) + chr(0b1010111 + 0o14) + '\x6f' + chr(100) + chr(0b101001 + 0o74))(chr(0b10011 + 0o142) + chr(0b1110100) + chr(102) + '\x2d' + chr(0b100000 + 0o30)))(roI3spqORKae(ES5oEprVxulp(b'Bx\x0c\xcb\x01)\x1b\xbf\xe6F\xae\xa8\xd6\xd1$"\xe3s;P\x93~:\xb5'), '\x64' + chr(0b1011101 + 0o10) + chr(6936 - 6837) + '\x6f' + chr(0b11011 + 0o111) + chr(0b1011001 + 0o14))(chr(0b1101011 + 0o12) + chr(116) + chr(0b1100110) + '\055' + chr(0b111 + 0o61)))
else:
roI3spqORKae(ZtB7KOLCW2Hk, roI3spqORKae(ES5oEprVxulp(b'Ux\n\xfd\x0f \x1e\xfd\xe2F'), chr(0b1011001 + 0o13) + chr(0b1100 + 0o131) + chr(99) + chr(2227 - 2116) + chr(0b1100100) + chr(0b11010 + 0o113))(chr(0b1110101) + chr(0b1110100) + '\146' + '\x2d' + '\x38'))(roI3spqORKae(ES5oEprVxulp(b"Bx\x0c\xcb\x01)\x1b\xbf\xe6F\xae\xa8\xd6\xd1$'\xfec$Q"), chr(100) + '\145' + chr(0b10101 + 0o116) + chr(640 - 529) + '\144' + chr(6149 - 6048))(chr(117) + chr(4277 - 4161) + chr(0b1001100 + 0o32) + chr(811 - 766) + chr(56)))
if svwoYs1fJDLp is None:
svwoYs1fJDLp = znjnJWK64FDT()
roI3spqORKae(ZtB7KOLCW2Hk, roI3spqORKae(ES5oEprVxulp(b'Vq\x11\xd6'), chr(5392 - 5292) + chr(5715 - 5614) + chr(3433 - 3334) + chr(111) + chr(3083 - 2983) + '\x65')('\x75' + '\164' + chr(0b1001000 + 0o36) + chr(0b101101) + chr(341 - 285)))(bI5jsQ9OkQtj, Fi3yzxctM1zW, label=OkDIn6t2Cke6, **svwoYs1fJDLp)
roI3spqORKae(ZtB7KOLCW2Hk, roI3spqORKae(ES5oEprVxulp(b'Ux\n\xfd\x0e?\x1c\xfe\xebO'), chr(0b1100100) + chr(0b1100101) + '\143' + chr(4378 - 4267) + chr(100) + '\145')(chr(117) + chr(0b1110100) + '\x66' + '\055' + '\x38'))(YlnxpOvv9Uzx)
roI3spqORKae(ZtB7KOLCW2Hk, roI3spqORKae(ES5oEprVxulp(b'Ux\n\xfd\x0e \x1e\xfd\xe2F'), chr(100) + '\145' + chr(99) + chr(111) + chr(2093 - 1993) + chr(0b100101 + 0o100))(chr(9055 - 8938) + '\164' + '\146' + '\x2d' + '\070'))(roI3spqORKae(ES5oEprVxulp(b'Ut\n\xc7W*\r\xfa\xf6_\xa7\xa3\xd9\xcd'), '\x64' + chr(3472 - 3371) + '\143' + '\157' + '\144' + '\145')('\165' + chr(0b10011 + 0o141) + chr(0b1001101 + 0o31) + chr(683 - 638) + '\070'))
roI3spqORKae(ZtB7KOLCW2Hk, roI3spqORKae(ES5oEprVxulp(b'Gh\n\xcd\x04/\x1e\xf3\xe2'), '\144' + chr(0b1100101) + '\x63' + chr(111) + chr(0b1100100) + chr(0b1100101))('\x75' + chr(0b1001110 + 0o46) + chr(102) + '\055' + chr(0b111000)))(axis=roI3spqORKae(ES5oEprVxulp(b'^'), chr(0b111000 + 0o54) + chr(9934 - 9833) + chr(1344 - 1245) + chr(0b1101111) + chr(0b1100100) + chr(0b111 + 0o136))('\165' + '\164' + '\146' + chr(45) + chr(0b111000)), tight=nzTpIcepk0o8(chr(0b110000) + chr(0b1000010 + 0o55) + chr(49), 8))
return ZtB7KOLCW2Hk |
cggh/scikit-allel | allel/stats/sf.py | plot_sfs_folded | def plot_sfs_folded(*args, **kwargs):
"""Plot a folded site frequency spectrum.
Parameters
----------
s : array_like, int, shape (n_chromosomes/2,)
Site frequency spectrum.
yscale : string, optional
Y axis scale.
bins : int or array_like, int, optional
Allele count bins.
n : int, optional
Number of chromosomes sampled. If provided, X axis will be plotted
as allele frequency, otherwise as allele count.
clip_endpoints : bool, optional
If True, do not plot first and last values from frequency spectrum.
label : string, optional
Label for data series in plot.
plot_kwargs : dict-like
Additional keyword arguments, passed through to ax.plot().
ax : axes, optional
Axes on which to draw. If not provided, a new figure will be created.
Returns
-------
ax : axes
The axes on which the plot was drawn.
"""
ax = plot_sfs(*args, **kwargs)
n = kwargs.get('n', None)
if n:
ax.set_xlabel('minor allele frequency')
else:
ax.set_xlabel('minor allele count')
return ax | python | def plot_sfs_folded(*args, **kwargs):
"""Plot a folded site frequency spectrum.
Parameters
----------
s : array_like, int, shape (n_chromosomes/2,)
Site frequency spectrum.
yscale : string, optional
Y axis scale.
bins : int or array_like, int, optional
Allele count bins.
n : int, optional
Number of chromosomes sampled. If provided, X axis will be plotted
as allele frequency, otherwise as allele count.
clip_endpoints : bool, optional
If True, do not plot first and last values from frequency spectrum.
label : string, optional
Label for data series in plot.
plot_kwargs : dict-like
Additional keyword arguments, passed through to ax.plot().
ax : axes, optional
Axes on which to draw. If not provided, a new figure will be created.
Returns
-------
ax : axes
The axes on which the plot was drawn.
"""
ax = plot_sfs(*args, **kwargs)
n = kwargs.get('n', None)
if n:
ax.set_xlabel('minor allele frequency')
else:
ax.set_xlabel('minor allele count')
return ax | [
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Site frequency spectrum.
yscale : string, optional
Y axis scale.
bins : int or array_like, int, optional
Allele count bins.
n : int, optional
Number of chromosomes sampled. If provided, X axis will be plotted
as allele frequency, otherwise as allele count.
clip_endpoints : bool, optional
If True, do not plot first and last values from frequency spectrum.
label : string, optional
Label for data series in plot.
plot_kwargs : dict-like
Additional keyword arguments, passed through to ax.plot().
ax : axes, optional
Axes on which to draw. If not provided, a new figure will be created.
Returns
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ax : axes
The axes on which the plot was drawn. | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/stats/sf.py#L562-L598 | train | Plot a folded site frequency spectrum. | 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(1319 - 1271) + chr(0b110110 + 0o71) + chr(51) + chr(0b10101 + 0o40) + '\065', 36518 - 36510), nzTpIcepk0o8('\060' + '\x6f' + '\063' + chr(0b101010 + 0o6) + chr(1036 - 981), 0o10), nzTpIcepk0o8(chr(0b100100 + 0o14) + chr(111) + chr(0b110001) + chr(0b110111), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b11 + 0o57) + '\x30' + chr(0b101100 + 0o7), ord("\x08")), nzTpIcepk0o8(chr(0b1010 + 0o46) + chr(111) + chr(1664 - 1610) + chr(1744 - 1693), 0o10), nzTpIcepk0o8(chr(2284 - 2236) + chr(0b1101111) + chr(0b110111) + chr(0b1000 + 0o55), 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(217 - 167) + chr(2185 - 2137) + '\x31', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b0 + 0o157) + '\061' + chr(0b110100), 16249 - 16241), nzTpIcepk0o8('\060' + chr(111) + '\062' + '\x36' + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(0b10011 + 0o35) + chr(0b1101111) + chr(812 - 763) + chr(49) + chr(0b110100), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b110100 + 0o73) + '\067' + chr(0b100100 + 0o14), ord("\x08")), nzTpIcepk0o8(chr(1066 - 1018) + '\x6f' + chr(0b110001) + chr(0b110000 + 0o6) + chr(126 - 76), ord("\x08")), nzTpIcepk0o8(chr(0b100010 + 0o16) + chr(111) + '\063' + '\x36' + '\066', 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(1447 - 1397) + chr(1491 - 1436) + '\x35', ord("\x08")), nzTpIcepk0o8(chr(0b11110 + 0o22) + chr(111) + '\x36' + '\x37', 0o10), nzTpIcepk0o8('\x30' + chr(111) + '\061' + chr(0b111 + 0o54) + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(0b101110 + 0o2) + chr(0b1101111) + chr(0b101010 + 0o10) + '\063', 65082 - 65074), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110010) + chr(0b11110 + 0o22) + chr(2013 - 1964), 8), nzTpIcepk0o8(chr(48) + '\x6f' + '\x33' + chr(0b110011) + '\x33', 42873 - 42865), nzTpIcepk0o8(chr(1884 - 1836) + chr(0b100001 + 0o116) + chr(1795 - 1744) + chr(0b110001 + 0o4) + chr(1498 - 1447), 0o10), nzTpIcepk0o8('\060' + chr(111) + '\x32' + chr(0b100111 + 0o12) + chr(53), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(0b110111) + '\x33', 0o10), nzTpIcepk0o8(chr(0b101001 + 0o7) + chr(0b10100 + 0o133) + chr(2151 - 2101) + chr(0b110011) + chr(0b110000), 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(0b110001) + chr(0b110100) + '\x35', 0b1000), nzTpIcepk0o8(chr(0b1011 + 0o45) + '\x6f' + chr(50) + chr(0b110010) + chr(861 - 811), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(310 - 261) + chr(0b110011) + chr(1452 - 1402), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(857 - 808) + '\062' + '\x34', ord("\x08")), nzTpIcepk0o8(chr(0b111 + 0o51) + chr(0b10 + 0o155) + chr(0b101101 + 0o4) + chr(1064 - 1011) + chr(0b1011 + 0o53), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(49) + chr(0b110101) + chr(0b110100), 0o10), nzTpIcepk0o8(chr(0b100001 + 0o17) + chr(0b1101111) + chr(0b110011) + chr(1740 - 1690) + chr(1381 - 1333), ord("\x08")), nzTpIcepk0o8(chr(214 - 166) + '\x6f' + '\x32' + chr(55) + chr(2266 - 2214), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + '\061' + '\066' + '\x30', 0b1000), nzTpIcepk0o8(chr(882 - 834) + '\x6f' + chr(0b1000 + 0o52) + '\x31' + '\062', 0o10), nzTpIcepk0o8(chr(0b100111 + 0o11) + chr(0b0 + 0o157) + chr(51) + chr(49) + chr(0b110000 + 0o2), 56545 - 56537), nzTpIcepk0o8(chr(0b11000 + 0o30) + '\157' + chr(0b110011) + '\065' + chr(1374 - 1324), 0o10), nzTpIcepk0o8(chr(48) + chr(1048 - 937) + '\x32' + '\065' + '\x33', 51546 - 51538), nzTpIcepk0o8(chr(488 - 440) + chr(0b100110 + 0o111) + '\064' + '\064', 54488 - 54480), nzTpIcepk0o8('\x30' + chr(6526 - 6415) + chr(710 - 661) + chr(0b100111 + 0o15) + '\x35', 8), nzTpIcepk0o8(chr(0b1 + 0o57) + chr(971 - 860) + chr(1361 - 1311) + chr(0b110100) + chr(0b110100 + 0o3), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b10101 + 0o132) + '\x31' + chr(0b110011) + chr(52), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + chr(0b1010100 + 0o33) + chr(53) + chr(0b10100 + 0o34), 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xc3'), chr(6654 - 6554) + '\x65' + chr(0b110111 + 0o54) + chr(0b1101111) + chr(5524 - 5424) + chr(0b11 + 0o142))(chr(0b101101 + 0o110) + chr(0b1110100) + '\146' + chr(45) + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def yl6ZKE2dxiFE(*eemPYp2vtTSr, **q5n0sHDDTy90):
ZtB7KOLCW2Hk = oQgu9rZcOS2h(*eemPYp2vtTSr, **q5n0sHDDTy90)
NoZxuO7wjArS = q5n0sHDDTy90.GUKetu4xaGsJ(roI3spqORKae(ES5oEprVxulp(b'\x83'), chr(100) + chr(0b1100101) + chr(99) + chr(0b1100011 + 0o14) + chr(5727 - 5627) + chr(4278 - 4177))('\x75' + chr(0b1110100) + chr(7663 - 7561) + chr(157 - 112) + chr(188 - 132)), None)
if NoZxuO7wjArS:
roI3spqORKae(ZtB7KOLCW2Hk, roI3spqORKae(ES5oEprVxulp(b'\x9e\xa2{\xdcKQ\xe0n\xd0 '), chr(0b1100100) + chr(101) + chr(0b10010 + 0o121) + '\157' + '\144' + '\145')(chr(1299 - 1182) + chr(0b1100101 + 0o17) + chr(0b1100110) + '\x2d' + chr(164 - 108)))(roI3spqORKae(ES5oEprVxulp(b'\x80\xaea\xecA\x1d\xe0`\xd9)T\x17\xd6\xdbE:b\xf4\xbe\x85\xeeB'), '\x64' + chr(3545 - 3444) + chr(0b1100011) + chr(0b1101111) + chr(100) + chr(0b1001101 + 0o30))(chr(0b1011000 + 0o35) + chr(7582 - 7466) + '\x66' + '\x2d' + chr(2775 - 2719)))
else:
roI3spqORKae(ZtB7KOLCW2Hk, roI3spqORKae(ES5oEprVxulp(b'\x9e\xa2{\xdcKQ\xe0n\xd0 '), chr(0b100011 + 0o101) + chr(0b1100101) + chr(99) + '\157' + chr(6053 - 5953) + chr(0b100011 + 0o102))(chr(0b1110101) + '\164' + chr(102) + chr(45) + '\070'))(roI3spqORKae(ES5oEprVxulp(b'\x80\xaea\xecA\x1d\xe0`\xd9)T\x17\xd6\xdeX*}\xf5'), chr(9387 - 9287) + chr(9003 - 8902) + chr(5972 - 5873) + chr(0b1000010 + 0o55) + chr(0b1100100) + '\145')(chr(0b1110101) + chr(0b1110100) + chr(0b110100 + 0o62) + '\055' + chr(56)))
return ZtB7KOLCW2Hk |
cggh/scikit-allel | allel/stats/sf.py | plot_sfs_scaled | def plot_sfs_scaled(*args, **kwargs):
"""Plot a scaled site frequency spectrum.
Parameters
----------
s : array_like, int, shape (n_chromosomes,)
Site frequency spectrum.
yscale : string, optional
Y axis scale.
bins : int or array_like, int, optional
Allele count bins.
n : int, optional
Number of chromosomes sampled. If provided, X axis will be plotted
as allele frequency, otherwise as allele count.
clip_endpoints : bool, optional
If True, do not plot first and last values from frequency spectrum.
label : string, optional
Label for data series in plot.
plot_kwargs : dict-like
Additional keyword arguments, passed through to ax.plot().
ax : axes, optional
Axes on which to draw. If not provided, a new figure will be created.
Returns
-------
ax : axes
The axes on which the plot was drawn.
"""
kwargs.setdefault('yscale', 'linear')
ax = plot_sfs(*args, **kwargs)
ax.set_ylabel('scaled site frequency')
return ax | python | def plot_sfs_scaled(*args, **kwargs):
"""Plot a scaled site frequency spectrum.
Parameters
----------
s : array_like, int, shape (n_chromosomes,)
Site frequency spectrum.
yscale : string, optional
Y axis scale.
bins : int or array_like, int, optional
Allele count bins.
n : int, optional
Number of chromosomes sampled. If provided, X axis will be plotted
as allele frequency, otherwise as allele count.
clip_endpoints : bool, optional
If True, do not plot first and last values from frequency spectrum.
label : string, optional
Label for data series in plot.
plot_kwargs : dict-like
Additional keyword arguments, passed through to ax.plot().
ax : axes, optional
Axes on which to draw. If not provided, a new figure will be created.
Returns
-------
ax : axes
The axes on which the plot was drawn.
"""
kwargs.setdefault('yscale', 'linear')
ax = plot_sfs(*args, **kwargs)
ax.set_ylabel('scaled site frequency')
return ax | [
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... | Plot a scaled site frequency spectrum.
Parameters
----------
s : array_like, int, shape (n_chromosomes,)
Site frequency spectrum.
yscale : string, optional
Y axis scale.
bins : int or array_like, int, optional
Allele count bins.
n : int, optional
Number of chromosomes sampled. If provided, X axis will be plotted
as allele frequency, otherwise as allele count.
clip_endpoints : bool, optional
If True, do not plot first and last values from frequency spectrum.
label : string, optional
Label for data series in plot.
plot_kwargs : dict-like
Additional keyword arguments, passed through to ax.plot().
ax : axes, optional
Axes on which to draw. If not provided, a new figure will be created.
Returns
-------
ax : axes
The axes on which the plot was drawn. | [
"Plot",
"a",
"scaled",
"site",
"frequency",
"spectrum",
"."
] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/stats/sf.py#L602-L634 | train | Plot a scaled site frequency spectrum. | 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(1812 - 1763) + chr(0b101010 + 0o12), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(0b11000 + 0o33) + '\066' + chr(863 - 813), ord("\x08")), nzTpIcepk0o8(chr(878 - 830) + chr(111) + chr(51) + '\067' + chr(55), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + '\063' + chr(0b110011) + chr(331 - 279), 2231 - 2223), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x32' + '\065' + chr(0b110010), 0b1000), nzTpIcepk0o8(chr(1255 - 1207) + '\157' + chr(0b100101 + 0o22) + '\x30', 0o10), nzTpIcepk0o8(chr(0b1000 + 0o50) + '\157' + '\061' + chr(0b101010 + 0o11) + '\x37', 0o10), nzTpIcepk0o8(chr(0b101011 + 0o5) + chr(111) + '\x31' + chr(0b110100) + chr(0b110100), 35401 - 35393), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110010) + chr(73 - 21) + chr(0b110101), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b111 + 0o56) + chr(0b110101), 17551 - 17543), nzTpIcepk0o8('\x30' + '\157' + chr(49) + chr(54), 33290 - 33282), nzTpIcepk0o8(chr(48) + '\157' + chr(1947 - 1893) + '\065', 0b1000), nzTpIcepk0o8(chr(48) + chr(7393 - 7282) + chr(0b1011 + 0o46) + chr(49) + chr(0b110111), 51312 - 51304), nzTpIcepk0o8('\x30' + chr(111) + chr(0b1101 + 0o46) + '\x30' + chr(53), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(743 - 694) + '\x36' + chr(1746 - 1693), 21971 - 21963), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110010) + '\065' + chr(608 - 558), 8), nzTpIcepk0o8(chr(567 - 519) + chr(4292 - 4181) + chr(0b100110 + 0o14) + '\x35' + chr(0b110001), 13484 - 13476), nzTpIcepk0o8('\060' + '\157' + chr(0b100111 + 0o14) + chr(0b110111) + chr(52), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101000 + 0o7) + '\x32' + chr(1596 - 1544) + chr(0b110010 + 0o0), 0o10), nzTpIcepk0o8(chr(1633 - 1585) + '\x6f' + chr(1343 - 1293) + '\063' + chr(51), 0b1000), nzTpIcepk0o8('\x30' + chr(594 - 483) + '\x32' + chr(890 - 842), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(1335 - 1285) + chr(138 - 90) + chr(0b101101 + 0o6), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b101100 + 0o103) + chr(846 - 796) + '\x34' + chr(54), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b101000 + 0o11) + chr(0b1000 + 0o53) + chr(896 - 848), 23328 - 23320), nzTpIcepk0o8(chr(0b0 + 0o60) + chr(2255 - 2144) + chr(49) + '\063' + chr(2363 - 2312), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1011111 + 0o20) + chr(1086 - 1033) + '\065', 8), nzTpIcepk0o8('\x30' + chr(6172 - 6061) + '\x32' + chr(1973 - 1919), 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b1110 + 0o43) + chr(968 - 916) + '\x30', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(51) + chr(1409 - 1355) + chr(130 - 76), 0b1000), nzTpIcepk0o8(chr(2087 - 2039) + chr(111) + '\063' + chr(0b110010) + '\x33', 0o10), nzTpIcepk0o8('\060' + chr(5550 - 5439) + '\061' + chr(1312 - 1259) + chr(0b11000 + 0o35), ord("\x08")), nzTpIcepk0o8('\x30' + chr(11882 - 11771) + chr(52) + chr(50), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110001) + chr(0b110111) + '\061', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x33' + chr(0b110100) + chr(0b100101 + 0o17), 31268 - 31260), nzTpIcepk0o8('\x30' + chr(5173 - 5062) + chr(51) + chr(54) + chr(1120 - 1071), ord("\x08")), nzTpIcepk0o8(chr(0b11100 + 0o24) + chr(111) + '\x33' + '\x33' + chr(1158 - 1106), 8), nzTpIcepk0o8(chr(0b10010 + 0o36) + chr(111) + chr(117 - 66) + chr(0b1 + 0o64), 32205 - 32197), nzTpIcepk0o8(chr(48) + '\x6f' + '\064' + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(1538 - 1487) + chr(0b100000 + 0o23) + '\x32', 30901 - 30893), nzTpIcepk0o8('\060' + chr(3018 - 2907) + chr(1633 - 1583) + '\x33' + '\x30', 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(2263 - 2215) + chr(111) + chr(0b110101) + chr(0b110000), 61328 - 61320)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'"'), '\144' + chr(101) + '\143' + chr(111) + chr(0b1010001 + 0o23) + chr(0b1100101))(chr(0b10101 + 0o140) + '\x74' + chr(7080 - 6978) + chr(0b101101) + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def StW7W51buBpB(*eemPYp2vtTSr, **q5n0sHDDTy90):
roI3spqORKae(q5n0sHDDTy90, roI3spqORKae(ES5oEprVxulp(b'v\x97\xcf\x96\xe7M\x14]\xd7BYf'), chr(0b1100100) + chr(1765 - 1664) + '\x63' + chr(111) + chr(3231 - 3131) + '\145')(chr(0b1110101) + chr(116) + chr(0b1100110) + chr(1323 - 1278) + chr(0b11111 + 0o31)))(roI3spqORKae(ES5oEprVxulp(b'u\x81\x9c\xbd\xc6]'), chr(100) + chr(101) + chr(7769 - 7670) + chr(10580 - 10469) + chr(0b1100100) + chr(0b1100101))(chr(117) + chr(0b1110100) + '\x66' + chr(1980 - 1935) + '\x38'), roI3spqORKae(ES5oEprVxulp(b'`\x9b\x91\xb9\xcbJ'), '\x64' + chr(0b1100101) + chr(99) + chr(0b1101111) + '\x64' + chr(3111 - 3010))(chr(1636 - 1519) + '\164' + chr(0b1001001 + 0o35) + '\055' + chr(56)))
ZtB7KOLCW2Hk = oQgu9rZcOS2h(*eemPYp2vtTSr, **q5n0sHDDTy90)
roI3spqORKae(ZtB7KOLCW2Hk, roI3spqORKae(ES5oEprVxulp(b'\x7f\x97\x8b\x83\xd3T>\x06\xc0A'), '\x64' + chr(0b1000010 + 0o43) + chr(0b1010001 + 0o22) + '\157' + chr(3582 - 3482) + chr(0b101111 + 0o66))('\x75' + chr(0b1100011 + 0o21) + chr(10051 - 9949) + chr(0b101101) + chr(0b111000)))(roI3spqORKae(ES5oEprVxulp(b'\x7f\x91\x9e\xb0\xcf\\\x7f\x17\xccYk\x15)\xb7\x10\xdb\xdc\x99\xcc\xf8i'), chr(8444 - 8344) + '\x65' + chr(0b1100011) + chr(0b1101111) + '\144' + chr(0b1000100 + 0o41))('\x75' + chr(0b1110100) + chr(0b1100110) + chr(1646 - 1601) + chr(2467 - 2411)))
return ZtB7KOLCW2Hk |
cggh/scikit-allel | allel/stats/sf.py | plot_sfs_folded_scaled | def plot_sfs_folded_scaled(*args, **kwargs):
"""Plot a folded scaled site frequency spectrum.
Parameters
----------
s : array_like, int, shape (n_chromosomes/2,)
Site frequency spectrum.
yscale : string, optional
Y axis scale.
bins : int or array_like, int, optional
Allele count bins.
n : int, optional
Number of chromosomes sampled. If provided, X axis will be plotted
as allele frequency, otherwise as allele count.
clip_endpoints : bool, optional
If True, do not plot first and last values from frequency spectrum.
label : string, optional
Label for data series in plot.
plot_kwargs : dict-like
Additional keyword arguments, passed through to ax.plot().
ax : axes, optional
Axes on which to draw. If not provided, a new figure will be created.
Returns
-------
ax : axes
The axes on which the plot was drawn.
"""
kwargs.setdefault('yscale', 'linear')
ax = plot_sfs_folded(*args, **kwargs)
ax.set_ylabel('scaled site frequency')
n = kwargs.get('n', None)
if n:
ax.set_xlabel('minor allele frequency')
else:
ax.set_xlabel('minor allele count')
return ax | python | def plot_sfs_folded_scaled(*args, **kwargs):
"""Plot a folded scaled site frequency spectrum.
Parameters
----------
s : array_like, int, shape (n_chromosomes/2,)
Site frequency spectrum.
yscale : string, optional
Y axis scale.
bins : int or array_like, int, optional
Allele count bins.
n : int, optional
Number of chromosomes sampled. If provided, X axis will be plotted
as allele frequency, otherwise as allele count.
clip_endpoints : bool, optional
If True, do not plot first and last values from frequency spectrum.
label : string, optional
Label for data series in plot.
plot_kwargs : dict-like
Additional keyword arguments, passed through to ax.plot().
ax : axes, optional
Axes on which to draw. If not provided, a new figure will be created.
Returns
-------
ax : axes
The axes on which the plot was drawn.
"""
kwargs.setdefault('yscale', 'linear')
ax = plot_sfs_folded(*args, **kwargs)
ax.set_ylabel('scaled site frequency')
n = kwargs.get('n', None)
if n:
ax.set_xlabel('minor allele frequency')
else:
ax.set_xlabel('minor allele count')
return ax | [
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Parameters
----------
s : array_like, int, shape (n_chromosomes/2,)
Site frequency spectrum.
yscale : string, optional
Y axis scale.
bins : int or array_like, int, optional
Allele count bins.
n : int, optional
Number of chromosomes sampled. If provided, X axis will be plotted
as allele frequency, otherwise as allele count.
clip_endpoints : bool, optional
If True, do not plot first and last values from frequency spectrum.
label : string, optional
Label for data series in plot.
plot_kwargs : dict-like
Additional keyword arguments, passed through to ax.plot().
ax : axes, optional
Axes on which to draw. If not provided, a new figure will be created.
Returns
-------
ax : axes
The axes on which the plot was drawn. | [
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"spectrum",
"."
] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/stats/sf.py#L638-L675 | train | Plots a folded scaled site frequency spectrum. | 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(226 - 178) + chr(11121 - 11010) + '\x36' + chr(48), 0o10), nzTpIcepk0o8(chr(227 - 179) + chr(9468 - 9357) + chr(632 - 583) + '\066' + chr(2080 - 2028), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\062' + '\x31' + chr(51), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(50) + chr(0b110000) + '\x36', 0b1000), nzTpIcepk0o8(chr(0b1101 + 0o43) + chr(111) + '\062' + chr(0b1001 + 0o47), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110011) + '\x34' + '\061', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(1990 - 1935) + '\x30', 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110011) + chr(0b10011 + 0o43) + chr(0b110001), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110001) + '\064', 4540 - 4532), nzTpIcepk0o8(chr(699 - 651) + chr(111) + chr(50) + '\066' + chr(1329 - 1281), 63096 - 63088), nzTpIcepk0o8('\060' + '\x6f' + chr(49), 58239 - 58231), nzTpIcepk0o8(chr(0b11010 + 0o26) + chr(111) + chr(0b110011) + '\x32' + chr(0b110100), 49695 - 49687), nzTpIcepk0o8(chr(48) + '\x6f' + chr(49) + chr(874 - 820), 17633 - 17625), nzTpIcepk0o8(chr(1887 - 1839) + chr(111) + '\062' + chr(653 - 598) + '\063', 61650 - 61642), nzTpIcepk0o8('\x30' + chr(0b10000 + 0o137) + chr(0b110010) + chr(0b110111) + chr(2838 - 2784), 31643 - 31635), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x33' + '\060' + chr(51), 43604 - 43596), nzTpIcepk0o8(chr(1354 - 1306) + '\157' + chr(0b110010) + '\x31' + chr(0b10111 + 0o37), 0b1000), nzTpIcepk0o8(chr(0b10111 + 0o31) + '\157' + chr(2171 - 2121) + '\x31' + chr(0b110001), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(1679 - 1626) + '\x36', 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(0b101010 + 0o11) + chr(0b0 + 0o60) + chr(123 - 73), 0o10), nzTpIcepk0o8(chr(48) + chr(10307 - 10196) + chr(0b1000 + 0o55) + chr(0b110010), 0o10), nzTpIcepk0o8('\x30' + chr(7050 - 6939) + '\x33' + '\x34' + chr(154 - 100), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(1963 - 1913) + '\065' + chr(49), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110001) + chr(0b11001 + 0o27) + chr(49), 22005 - 21997), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x31' + chr(1435 - 1384) + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(2406 - 2295) + '\063' + '\x32' + chr(0b101 + 0o62), 0b1000), nzTpIcepk0o8(chr(1936 - 1888) + chr(111) + chr(0b11 + 0o62) + chr(2531 - 2476), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(1125 - 1074) + chr(0b110011) + '\062', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(1120 - 1009) + '\x32' + chr(0b110100) + chr(0b110100 + 0o0), 0b1000), nzTpIcepk0o8(chr(48) + chr(8827 - 8716) + chr(0b101100 + 0o5) + '\x30' + chr(0b110000), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + '\x33' + chr(2617 - 2564) + chr(52), ord("\x08")), nzTpIcepk0o8(chr(0b1101 + 0o43) + chr(0b1101111) + '\x32' + chr(49) + '\x37', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b11 + 0o56) + chr(2236 - 2186) + '\x34', 60570 - 60562), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x33' + chr(1087 - 1037) + '\064', 8), nzTpIcepk0o8(chr(48) + chr(3141 - 3030) + chr(662 - 609) + chr(55), 8), nzTpIcepk0o8('\060' + chr(111) + '\x35' + chr(0b110100), 0b1000), nzTpIcepk0o8('\060' + chr(8968 - 8857) + chr(51) + '\063' + chr(1634 - 1581), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110001) + chr(0b110100) + '\066', 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110001) + chr(0b110000) + chr(0b10111 + 0o31), 8), nzTpIcepk0o8('\060' + '\x6f' + chr(50) + chr(52) + chr(0b110111), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + chr(0b1100111 + 0o10) + '\065' + chr(1283 - 1235), 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x1e'), chr(0b1100100) + chr(9276 - 9175) + chr(0b1100011) + chr(111) + '\x64' + chr(0b101100 + 0o71))(chr(13132 - 13015) + '\x74' + '\146' + chr(1571 - 1526) + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def YqyWlDCXkKNP(*eemPYp2vtTSr, **q5n0sHDDTy90):
roI3spqORKae(q5n0sHDDTy90, roI3spqORKae(ES5oEprVxulp(b'J\x11\xbb\xcc]\x94s\xc8~\xdfV\x87'), '\144' + '\x65' + chr(0b1100011) + chr(0b1101111) + '\x64' + '\145')(chr(0b101 + 0o160) + chr(116) + chr(0b1100110) + '\x2d' + '\x38'))(roI3spqORKae(ES5oEprVxulp(b'I\x07\xe8\xe7|\x84'), '\x64' + '\145' + chr(0b1100010 + 0o1) + chr(173 - 62) + chr(0b1001101 + 0o27) + chr(0b1000110 + 0o37))(chr(0b111001 + 0o74) + '\x74' + chr(9274 - 9172) + chr(0b101101) + chr(0b111000 + 0o0)), roI3spqORKae(ES5oEprVxulp(b'\\\x1d\xe5\xe3q\x93'), chr(100) + chr(9903 - 9802) + chr(2982 - 2883) + '\x6f' + '\144' + chr(0b1100101))(chr(0b1110000 + 0o5) + chr(0b10110 + 0o136) + '\x66' + chr(0b101101) + '\070'))
ZtB7KOLCW2Hk = yl6ZKE2dxiFE(*eemPYp2vtTSr, **q5n0sHDDTy90)
roI3spqORKae(ZtB7KOLCW2Hk, roI3spqORKae(ES5oEprVxulp(b'C\x11\xff\xd9i\x8dY\x93i\xdc'), chr(0b1100100) + chr(0b100001 + 0o104) + chr(99) + chr(0b1000100 + 0o53) + '\x64' + '\145')('\x75' + '\x74' + chr(0b1011001 + 0o15) + '\055' + chr(2187 - 2131)))(roI3spqORKae(ES5oEprVxulp(b'C\x17\xea\xeau\x85\x18\x82e\xc4d\xf4h\xc9\xdb\xb2\xfb\xec@\xa1S'), chr(0b1100100) + '\145' + chr(3614 - 3515) + chr(1738 - 1627) + '\144' + chr(101))('\x75' + chr(0b1110100) + chr(0b1100110) + chr(0b100011 + 0o12) + '\x38'))
NoZxuO7wjArS = q5n0sHDDTy90.GUKetu4xaGsJ(roI3spqORKae(ES5oEprVxulp(b'^'), chr(100) + '\145' + chr(0b0 + 0o143) + chr(2547 - 2436) + chr(0b1100100) + chr(3798 - 3697))(chr(0b1111 + 0o146) + '\x74' + chr(0b1100110) + chr(0b101101) + '\070'), None)
if NoZxuO7wjArS:
roI3spqORKae(ZtB7KOLCW2Hk, roI3spqORKae(ES5oEprVxulp(b'C\x11\xff\xd9h\x8dY\x93i\xdc'), chr(0b1100100) + chr(0b1100101) + chr(0b1100011) + '\x6f' + '\x64' + chr(0b1100101))(chr(0b10000 + 0o145) + '\164' + '\x66' + chr(497 - 452) + chr(0b111000)))(roI3spqORKae(ES5oEprVxulp(b']\x1d\xe5\xe9b\xc1Y\x9d`\xd5m\xb1.\xdd\xcc\xa6\xff\xfcK\xacI\x9f'), chr(212 - 112) + chr(0b1100101) + chr(99) + chr(357 - 246) + chr(795 - 695) + chr(0b1100101))('\165' + chr(0b1110100 + 0o0) + chr(0b10 + 0o144) + chr(0b101101) + chr(56)))
else:
roI3spqORKae(ZtB7KOLCW2Hk, roI3spqORKae(ES5oEprVxulp(b'C\x11\xff\xd9h\x8dY\x93i\xdc'), '\144' + chr(0b1100101) + chr(99) + '\157' + chr(100) + '\145')(chr(117) + '\x74' + chr(0b111101 + 0o51) + chr(0b101001 + 0o4) + '\070'))(roI3spqORKae(ES5oEprVxulp(b']\x1d\xe5\xe9b\xc1Y\x9d`\xd5m\xb1.\xd8\xd1\xb6\xe0\xfd'), chr(100) + chr(0b1100101) + '\x63' + '\x6f' + '\144' + '\x65')('\x75' + '\x74' + chr(0b1100110) + '\055' + chr(0b111000)))
return ZtB7KOLCW2Hk |
cggh/scikit-allel | allel/stats/sf.py | plot_joint_sfs | def plot_joint_sfs(s, ax=None, imshow_kwargs=None):
"""Plot a joint site frequency spectrum.
Parameters
----------
s : array_like, int, shape (n_chromosomes_pop1, n_chromosomes_pop2)
Joint site frequency spectrum.
ax : axes, optional
Axes on which to draw. If not provided, a new figure will be created.
imshow_kwargs : dict-like
Additional keyword arguments, passed through to ax.imshow().
Returns
-------
ax : axes
The axes on which the plot was drawn.
"""
import matplotlib.pyplot as plt
from matplotlib.colors import LogNorm
# check inputs
s = asarray_ndim(s, 2)
# setup axes
if ax is None:
w = plt.rcParams['figure.figsize'][0]
fig, ax = plt.subplots(figsize=(w, w))
# set plotting defaults
if imshow_kwargs is None:
imshow_kwargs = dict()
imshow_kwargs.setdefault('cmap', 'jet')
imshow_kwargs.setdefault('interpolation', 'none')
imshow_kwargs.setdefault('aspect', 'auto')
imshow_kwargs.setdefault('norm', LogNorm())
# plot data
ax.imshow(s.T, **imshow_kwargs)
# tidy
ax.invert_yaxis()
ax.set_xlabel('derived allele count (population 1)')
ax.set_ylabel('derived allele count (population 2)')
return ax | python | def plot_joint_sfs(s, ax=None, imshow_kwargs=None):
"""Plot a joint site frequency spectrum.
Parameters
----------
s : array_like, int, shape (n_chromosomes_pop1, n_chromosomes_pop2)
Joint site frequency spectrum.
ax : axes, optional
Axes on which to draw. If not provided, a new figure will be created.
imshow_kwargs : dict-like
Additional keyword arguments, passed through to ax.imshow().
Returns
-------
ax : axes
The axes on which the plot was drawn.
"""
import matplotlib.pyplot as plt
from matplotlib.colors import LogNorm
# check inputs
s = asarray_ndim(s, 2)
# setup axes
if ax is None:
w = plt.rcParams['figure.figsize'][0]
fig, ax = plt.subplots(figsize=(w, w))
# set plotting defaults
if imshow_kwargs is None:
imshow_kwargs = dict()
imshow_kwargs.setdefault('cmap', 'jet')
imshow_kwargs.setdefault('interpolation', 'none')
imshow_kwargs.setdefault('aspect', 'auto')
imshow_kwargs.setdefault('norm', LogNorm())
# plot data
ax.imshow(s.T, **imshow_kwargs)
# tidy
ax.invert_yaxis()
ax.set_xlabel('derived allele count (population 1)')
ax.set_ylabel('derived allele count (population 2)')
return ax | [
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... | Plot a joint site frequency spectrum.
Parameters
----------
s : array_like, int, shape (n_chromosomes_pop1, n_chromosomes_pop2)
Joint site frequency spectrum.
ax : axes, optional
Axes on which to draw. If not provided, a new figure will be created.
imshow_kwargs : dict-like
Additional keyword arguments, passed through to ax.imshow().
Returns
-------
ax : axes
The axes on which the plot was drawn. | [
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"spectrum",
"."
] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/stats/sf.py#L678-L724 | train | Plots a joint site frequency spectrum. | 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(0b100100 + 0o14) + '\x6f' + chr(643 - 592) + chr(0b101000 + 0o15), 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(0b110001) + '\x31' + '\062', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1010100 + 0o33) + '\067' + chr(2732 - 2677), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(1908 - 1859) + chr(49) + chr(232 - 181), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(239 - 190) + '\x33' + chr(48), 6674 - 6666), nzTpIcepk0o8('\x30' + '\x6f' + '\x32' + chr(0b10011 + 0o44) + chr(54), 8634 - 8626), nzTpIcepk0o8(chr(199 - 151) + chr(0b1101111) + '\x35' + chr(573 - 519), 21963 - 21955), nzTpIcepk0o8('\060' + chr(111) + chr(0b110101) + '\x34', ord("\x08")), nzTpIcepk0o8(chr(1566 - 1518) + chr(111) + chr(0b110011) + chr(53) + '\066', 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(1282 - 1231) + chr(0b111 + 0o60) + chr(0b110110), 0b1000), nzTpIcepk0o8(chr(666 - 618) + chr(0b1101111) + '\x31' + chr(2556 - 2505) + chr(54), 0b1000), nzTpIcepk0o8(chr(2111 - 2063) + '\157' + '\061' + '\x31' + chr(0b110000), 0b1000), nzTpIcepk0o8(chr(0b101000 + 0o10) + chr(936 - 825) + '\x33' + '\x32' + chr(271 - 221), 33752 - 33744), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(50) + chr(0b10010 + 0o42), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110011) + '\061' + '\065', 21266 - 21258), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\063' + chr(0b110100) + chr(0b110100), 0o10), nzTpIcepk0o8(chr(48) + chr(9817 - 9706) + chr(1513 - 1463) + '\067' + '\061', 60825 - 60817), nzTpIcepk0o8(chr(48) + chr(111) + '\061' + chr(0b110001) + '\065', 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(50) + chr(0b1001 + 0o56) + chr(51), 61233 - 61225), nzTpIcepk0o8(chr(0b1 + 0o57) + chr(111) + '\063' + chr(48) + chr(55), 0b1000), nzTpIcepk0o8(chr(724 - 676) + chr(0b100101 + 0o112) + chr(51) + chr(1996 - 1945), 28295 - 28287), nzTpIcepk0o8(chr(223 - 175) + chr(111) + '\x31' + chr(79 - 29) + chr(101 - 49), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(1557 - 1507) + '\x31' + '\x35', 18077 - 18069), nzTpIcepk0o8('\060' + chr(2301 - 2190) + chr(0b110011) + chr(0b110101) + chr(0b101011 + 0o7), 31715 - 31707), nzTpIcepk0o8(chr(0b11101 + 0o23) + chr(10409 - 10298) + '\062' + '\060', 0b1000), nzTpIcepk0o8(chr(1172 - 1124) + chr(111) + chr(0b110001) + chr(0b110011) + chr(1191 - 1141), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + '\x33' + '\060' + '\x35', 12330 - 12322), nzTpIcepk0o8(chr(1160 - 1112) + chr(0b1101111) + '\x31' + '\064' + chr(0b110111), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + chr(0b1101 + 0o44) + chr(0b110001) + '\062', 8), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b100000 + 0o22) + chr(0b100011 + 0o24) + chr(0b110000), 0o10), nzTpIcepk0o8(chr(0b1 + 0o57) + chr(0b11001 + 0o126) + '\062' + '\061' + chr(53), 8), nzTpIcepk0o8('\x30' + '\x6f' + chr(49) + chr(0b110000) + '\065', 62070 - 62062), nzTpIcepk0o8('\060' + chr(0b1001 + 0o146) + '\x33' + chr(0b100000 + 0o25) + chr(50), 8), nzTpIcepk0o8(chr(0b11 + 0o55) + chr(0b101 + 0o152) + '\x36' + chr(1097 - 1049), 22053 - 22045), nzTpIcepk0o8('\x30' + chr(111) + chr(61 - 12) + '\x31' + '\x33', 8), nzTpIcepk0o8(chr(48) + '\x6f' + chr(51) + chr(54) + '\064', 26304 - 26296), nzTpIcepk0o8('\060' + chr(0b1011 + 0o144) + chr(49) + chr(0b110110) + chr(2280 - 2226), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b11101 + 0o122) + chr(1992 - 1942) + chr(0b110111) + chr(0b110001), 8), nzTpIcepk0o8(chr(48) + '\157' + '\x31' + chr(0b110011) + '\064', 0o10), nzTpIcepk0o8('\x30' + chr(11876 - 11765) + chr(0b110100) + chr(55), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + chr(4312 - 4201) + chr(53) + chr(0b101001 + 0o7), ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'3'), chr(0b1100100) + chr(0b1100101) + '\143' + '\x6f' + chr(0b1100100) + chr(0b1100101))(chr(117) + '\x74' + '\x66' + chr(0b101101) + chr(0b11111 + 0o31)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def NO6u6bXPW1Ss(PmE5_h409JAA, ZtB7KOLCW2Hk=None, TbyqRkDRVs9Z=None):
(Z7HGgmIyegqz,) = (roI3spqORKae(rFFUeiYWzOhx(roI3spqORKae(ES5oEprVxulp(b'p+K;4\xd1Z@\x87\x9cp8\xabd\xa1\x8b\xcd'), '\x64' + '\x65' + chr(0b1100011) + chr(0b1101111) + '\144' + chr(0b1011010 + 0o13))(chr(7697 - 7580) + '\164' + chr(102) + chr(0b100110 + 0o7) + chr(56)), roI3spqORKae(ES5oEprVxulp(b"m3O'7\xca"), chr(0b1100100) + chr(0b110 + 0o137) + '\143' + chr(0b1101010 + 0o5) + chr(0b1100100) + chr(0b11001 + 0o114))(chr(6958 - 6841) + '\x74' + '\x66' + chr(0b101 + 0o50) + chr(0b111000))), roI3spqORKae(ES5oEprVxulp(b"m3O'7\xca"), '\x64' + '\145' + chr(99) + chr(0b1101111) + '\144' + chr(5395 - 5294))('\165' + '\164' + chr(5388 - 5286) + chr(45) + chr(0b101010 + 0o16))),)
(qwCYnYsW1FGm,) = (roI3spqORKae(roI3spqORKae(rFFUeiYWzOhx(roI3spqORKae(ES5oEprVxulp(b'p+K;4\xd1Z@\x87\x9cp+\xbdx\xa2\x96\xca'), chr(0b1100100) + '\x65' + chr(99) + '\157' + '\144' + '\x65')(chr(117) + '\x74' + chr(0b101111 + 0o67) + chr(45) + chr(0b1111 + 0o51)), roI3spqORKae(ES5oEprVxulp(b'Q%X\x057\xccC'), '\144' + chr(0b11111 + 0o106) + chr(99) + '\x6f' + chr(0b1100100) + chr(101))(chr(117) + chr(0b1110100) + chr(4972 - 4870) + '\055' + chr(0b111000))), roI3spqORKae(ES5oEprVxulp(b'~%S$*\xcd'), chr(100) + chr(101) + chr(6949 - 6850) + chr(0b1100010 + 0o15) + '\x64' + chr(0b1000110 + 0o37))('\x75' + '\164' + chr(0b1100110) + chr(1317 - 1272) + chr(3040 - 2984))), roI3spqORKae(ES5oEprVxulp(b'Q%X\x057\xccC'), '\144' + chr(0b111011 + 0o52) + chr(99) + chr(0b1101111) + chr(2198 - 2098) + chr(0b1100101 + 0o0))('\165' + '\164' + chr(0b1100110) + '\x2d' + chr(0b111000))),)
PmE5_h409JAA = EVVKPun88TqM(PmE5_h409JAA, nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b100000 + 0o22), 0b1000))
if ZtB7KOLCW2Hk is None:
sm7_CLmeWGR7 = Z7HGgmIyegqz.Arpwt0FOuO5L[roI3spqORKae(ES5oEprVxulp(b'{#X>*\xdb\x00J\x87\x99-!\xa8q'), '\x64' + '\145' + '\x63' + '\157' + '\144' + '\145')(chr(0b1000000 + 0o65) + chr(0b101000 + 0o114) + chr(0b1100110) + chr(0b101101) + chr(1529 - 1473))][nzTpIcepk0o8(chr(0b110000) + chr(0b111011 + 0o64) + chr(672 - 624), 0o10)]
(ux0XlXMUdKbX, ZtB7KOLCW2Hk) = Z7HGgmIyegqz.subplots(figsize=(sm7_CLmeWGR7, sm7_CLmeWGR7))
if TbyqRkDRVs9Z is None:
TbyqRkDRVs9Z = znjnJWK64FDT()
roI3spqORKae(TbyqRkDRVs9Z, roI3spqORKae(ES5oEprVxulp(b'g/\x0f\x01\x15\xcbe\x15\x9c\x91\t\x1b'), '\x64' + chr(0b10000 + 0o125) + '\143' + chr(0b110110 + 0o71) + chr(100) + chr(0b1100101))(chr(0b1100110 + 0o17) + '\x74' + chr(5505 - 5403) + '\x2d' + chr(0b10 + 0o66)))(roI3spqORKae(ES5oEprVxulp(b"~'^;"), chr(0b1100100) + chr(0b100010 + 0o103) + chr(99) + '\157' + chr(0b11011 + 0o111) + chr(0b10101 + 0o120))(chr(0b1110101) + chr(0b1110100) + '\146' + chr(0b101101) + '\070'), roI3spqORKae(ES5oEprVxulp(b'w/K'), chr(4444 - 4344) + chr(8475 - 8374) + '\x63' + '\157' + chr(0b1100100) + '\x65')(chr(0b1010000 + 0o45) + '\164' + chr(0b1100101 + 0o1) + chr(45) + chr(0b111000)))
roI3spqORKae(TbyqRkDRVs9Z, roI3spqORKae(ES5oEprVxulp(b'g/\x0f\x01\x15\xcbe\x15\x9c\x91\t\x1b'), chr(1207 - 1107) + chr(0b1100101) + chr(0b100001 + 0o102) + '\157' + chr(0b1100100) + chr(101))('\165' + chr(0b1110100) + chr(8446 - 8344) + chr(45) + chr(0b111000 + 0o0)))(roI3spqORKae(ES5oEprVxulp(b"t$K.*\xceA@\x8f\x8a7'\xbc"), '\x64' + chr(7219 - 7118) + '\143' + chr(0b1100000 + 0o17) + chr(0b11 + 0o141) + chr(0b1100101))(chr(2308 - 2191) + chr(2444 - 2328) + chr(0b100011 + 0o103) + chr(0b1100 + 0o41) + '\x38'), roI3spqORKae(ES5oEprVxulp(b's%Q.'), chr(0b1100100) + chr(6055 - 5954) + '\143' + '\157' + '\x64' + '\145')('\x75' + chr(0b1001010 + 0o52) + chr(102) + chr(0b101101) + chr(56)))
roI3spqORKae(TbyqRkDRVs9Z, roI3spqORKae(ES5oEprVxulp(b'g/\x0f\x01\x15\xcbe\x15\x9c\x91\t\x1b'), chr(7544 - 7444) + '\x65' + chr(0b1100011) + '\157' + '\144' + chr(0b1100101))(chr(0b100110 + 0o117) + chr(0b100101 + 0o117) + '\x66' + '\x2d' + chr(0b111000)))(roI3spqORKae(ES5oEprVxulp(b'|9O.;\xca'), '\x64' + chr(101) + chr(0b1100011) + '\157' + chr(7358 - 7258) + '\x65')(chr(117) + chr(0b101001 + 0o113) + chr(9576 - 9474) + '\055' + chr(0b111000)), roI3spqORKae(ES5oEprVxulp(b'|?K$'), chr(0b100010 + 0o102) + chr(101) + '\x63' + '\x6f' + '\x64' + '\x65')(chr(0b110100 + 0o101) + chr(2635 - 2519) + chr(2569 - 2467) + chr(0b100011 + 0o12) + '\070'))
roI3spqORKae(TbyqRkDRVs9Z, roI3spqORKae(ES5oEprVxulp(b'g/\x0f\x01\x15\xcbe\x15\x9c\x91\t\x1b'), chr(0b1100100) + chr(2865 - 2764) + '\143' + chr(3671 - 3560) + '\144' + chr(101))('\165' + chr(6503 - 6387) + '\146' + chr(45) + chr(0b111000)))(roI3spqORKae(ES5oEprVxulp(b's%M&'), chr(0b1100100) + chr(0b1100101) + '\x63' + chr(0b1101111) + '\x64' + '\x65')(chr(244 - 127) + chr(116) + '\x66' + chr(392 - 347) + '\x38'), qwCYnYsW1FGm())
roI3spqORKae(ZtB7KOLCW2Hk, roI3spqORKae(ES5oEprVxulp(b"t'L#7\xc9"), chr(100) + '\145' + chr(5254 - 5155) + '\x6f' + '\144' + chr(101))(chr(0b1110101) + chr(116) + chr(5524 - 5422) + chr(0b11000 + 0o25) + '\x38'))(roI3spqORKae(PmE5_h409JAA, roI3spqORKae(ES5oEprVxulp(b'u;\t\x13\x1d\x8aqb\x86\x9ah\x1a'), '\x64' + chr(101) + chr(161 - 62) + chr(0b10010 + 0o135) + chr(100) + chr(3243 - 3142))(chr(117) + chr(8531 - 8415) + '\x66' + '\x2d' + chr(0b111000))), **TbyqRkDRVs9Z)
roI3spqORKae(ZtB7KOLCW2Hk, roI3spqORKae(ES5oEprVxulp(b't$I.*\xcaqU\x8f\x867;'), chr(100) + '\145' + chr(99) + chr(0b1011010 + 0o25) + chr(100) + chr(4669 - 4568))(chr(0b11111 + 0o126) + chr(9897 - 9781) + chr(0b1100110) + '\x2d' + chr(0b111000)))()
roI3spqORKae(ZtB7KOLCW2Hk, roI3spqORKae(ES5oEprVxulp(b'n/K\x14 \xd2ON\x8b\x92'), chr(0b1001110 + 0o26) + chr(0b1010111 + 0o16) + chr(6765 - 6666) + chr(310 - 199) + chr(0b10101 + 0o117) + '\x65')(chr(0b1010001 + 0o44) + '\x74' + chr(0b1010000 + 0o26) + chr(45) + chr(489 - 433)))(roI3spqORKae(ES5oEprVxulp(b'y/M".\xdbJ\x0c\x8f\x922-\xbeq\xed\x87\xd68\xd5\xb3;|\xfd\x85`/\xa9\x06>\xd1\xe2+\xca\x01b'), chr(0b1100100) + '\145' + chr(0b1100011) + chr(0b1101111) + chr(0b1100100) + chr(0b111111 + 0o46))('\165' + chr(11537 - 11421) + chr(8257 - 8155) + '\x2d' + '\x38'))
roI3spqORKae(ZtB7KOLCW2Hk, roI3spqORKae(ES5oEprVxulp(b'n/K\x14!\xd2ON\x8b\x92'), chr(0b101 + 0o137) + chr(138 - 37) + chr(99) + '\x6f' + '\144' + chr(0b1011101 + 0o10))('\x75' + '\x74' + chr(8223 - 8121) + chr(0b101101) + chr(56)))(roI3spqORKae(ES5oEprVxulp(b'y/M".\xdbJ\x0c\x8f\x922-\xbeq\xed\x87\xd68\xd5\xb3;|\xfd\x85`/\xa9\x06>\xd1\xe2+\xca\x02b'), '\144' + chr(101) + chr(99) + chr(11062 - 10951) + chr(100) + chr(0b1100101))('\x75' + chr(0b101 + 0o157) + '\146' + chr(0b101101) + chr(0b1110 + 0o52)))
return ZtB7KOLCW2Hk |
cggh/scikit-allel | allel/stats/sf.py | plot_joint_sfs_folded | def plot_joint_sfs_folded(*args, **kwargs):
"""Plot a joint site frequency spectrum.
Parameters
----------
s : array_like, int, shape (n_chromosomes_pop1/2, n_chromosomes_pop2/2)
Joint site frequency spectrum.
ax : axes, optional
Axes on which to draw. If not provided, a new figure will be created.
imshow_kwargs : dict-like
Additional keyword arguments, passed through to ax.imshow().
Returns
-------
ax : axes
The axes on which the plot was drawn.
"""
ax = plot_joint_sfs(*args, **kwargs)
ax.set_xlabel('minor allele count (population 1)')
ax.set_ylabel('minor allele count (population 2)')
return ax | python | def plot_joint_sfs_folded(*args, **kwargs):
"""Plot a joint site frequency spectrum.
Parameters
----------
s : array_like, int, shape (n_chromosomes_pop1/2, n_chromosomes_pop2/2)
Joint site frequency spectrum.
ax : axes, optional
Axes on which to draw. If not provided, a new figure will be created.
imshow_kwargs : dict-like
Additional keyword arguments, passed through to ax.imshow().
Returns
-------
ax : axes
The axes on which the plot was drawn.
"""
ax = plot_joint_sfs(*args, **kwargs)
ax.set_xlabel('minor allele count (population 1)')
ax.set_ylabel('minor allele count (population 2)')
return ax | [
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"set_ylab... | Plot a joint site frequency spectrum.
Parameters
----------
s : array_like, int, shape (n_chromosomes_pop1/2, n_chromosomes_pop2/2)
Joint site frequency spectrum.
ax : axes, optional
Axes on which to draw. If not provided, a new figure will be created.
imshow_kwargs : dict-like
Additional keyword arguments, passed through to ax.imshow().
Returns
-------
ax : axes
The axes on which the plot was drawn. | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/stats/sf.py#L728-L749 | train | Plots a joint site frequency spectrum folded in the order of the population 1 and 2. | 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(0b1100011 + 0o14) + chr(0b101 + 0o56) + chr(0b110000) + '\064', 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110111) + chr(50), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(49) + chr(50) + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(0b11010 + 0o26) + chr(0b1101111) + chr(48), 9583 - 9575), nzTpIcepk0o8(chr(0b110000) + chr(4228 - 4117) + chr(0b110110) + chr(2117 - 2067), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110101), 0o10), nzTpIcepk0o8(chr(349 - 301) + chr(0b1101111) + chr(1745 - 1696) + chr(52) + '\067', 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110011) + chr(48), 6116 - 6108), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x33' + chr(48) + chr(0b11110 + 0o26), 8), nzTpIcepk0o8('\x30' + chr(111) + '\061' + chr(387 - 339), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(4803 - 4692) + '\061' + chr(0b11000 + 0o33) + '\062', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b11101 + 0o122) + chr(0b110010) + chr(0b1 + 0o63) + chr(1738 - 1689), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\064' + chr(0b1000 + 0o53), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110001) + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(644 - 596) + chr(111) + chr(0b11010 + 0o27) + chr(0b11001 + 0o36) + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(0b11000 + 0o30) + chr(5300 - 5189) + chr(0b110010) + chr(53) + chr(51), ord("\x08")), nzTpIcepk0o8(chr(946 - 898) + chr(10911 - 10800) + chr(940 - 891) + '\x37' + chr(399 - 350), 6542 - 6534), nzTpIcepk0o8('\x30' + chr(111) + chr(0b101100 + 0o6) + chr(54) + chr(53), 0b1000), nzTpIcepk0o8('\060' + chr(5097 - 4986) + chr(50) + '\x35' + chr(113 - 64), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b11101 + 0o26) + chr(0b110011 + 0o1) + chr(1102 - 1049), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(1908 - 1857) + '\067', ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(51) + '\066', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x32' + chr(0b110101) + chr(55), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b11101 + 0o25) + chr(0b100111 + 0o13) + chr(55), 14130 - 14122), nzTpIcepk0o8(chr(463 - 415) + chr(4319 - 4208) + '\x31' + chr(1640 - 1589) + chr(54), ord("\x08")), nzTpIcepk0o8(chr(755 - 707) + '\157' + '\x32' + chr(52) + chr(1365 - 1311), 37066 - 37058), nzTpIcepk0o8(chr(0b101011 + 0o5) + chr(0b101010 + 0o105) + chr(0b110001) + chr(0b100110 + 0o21) + chr(52), ord("\x08")), nzTpIcepk0o8(chr(0b101111 + 0o1) + chr(0b1101111) + chr(49) + '\061' + '\060', 28595 - 28587), nzTpIcepk0o8(chr(1029 - 981) + '\x6f' + '\061' + chr(0b101 + 0o54) + chr(0b110001), 22611 - 22603), nzTpIcepk0o8(chr(48) + '\x6f' + '\x31' + chr(0b110010) + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(0b100100 + 0o14) + chr(0b1101111) + chr(826 - 771) + chr(2236 - 2188), 58134 - 58126), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x31' + '\062' + chr(263 - 213), 8), nzTpIcepk0o8(chr(0b10 + 0o56) + chr(111) + '\063' + '\x33' + '\x35', ord("\x08")), nzTpIcepk0o8(chr(1089 - 1041) + chr(0b1101111) + chr(50) + chr(0b110111) + chr(0b110001), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(729 - 618) + chr(0b10000 + 0o41) + chr(53) + chr(50), 0b1000), nzTpIcepk0o8('\x30' + chr(111) + '\x32' + chr(0b100 + 0o55) + chr(0b110011), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + '\061' + '\067' + chr(0b101010 + 0o13), 8), nzTpIcepk0o8(chr(1331 - 1283) + chr(2459 - 2348) + '\061' + chr(52) + chr(536 - 488), 0b1000), nzTpIcepk0o8(chr(48) + chr(2736 - 2625) + chr(0b1101 + 0o46) + chr(0b10011 + 0o35) + chr(52), 8), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(1358 - 1309) + chr(49) + chr(55), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + chr(111) + chr(1060 - 1007) + chr(48), 24107 - 24099)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xea'), chr(0b1100100) + '\145' + '\143' + chr(111) + '\144' + '\x65')(chr(0b1101001 + 0o14) + '\164' + chr(0b1100110) + chr(0b11000 + 0o25) + chr(0b101101 + 0o13)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def GLjTLYJQ9Gri(*eemPYp2vtTSr, **q5n0sHDDTy90):
ZtB7KOLCW2Hk = NO6u6bXPW1Ss(*eemPYp2vtTSr, **q5n0sHDDTy90)
roI3spqORKae(ZtB7KOLCW2Hk, roI3spqORKae(ES5oEprVxulp(b'\xb7_#_Ji\x06z\xa1d'), chr(0b100101 + 0o77) + '\145' + chr(0b1100011) + chr(111) + chr(100) + chr(0b110100 + 0o61))('\165' + '\164' + chr(0b1 + 0o145) + chr(45) + chr(71 - 15)))(roI3spqORKae(ES5oEprVxulp(b'\xa9S9o@%\x06t\xa8m6\xc4\x03l\x12\xde\x17\xc1\x89\xcdoq\xdf\xe22\xc7\x08!&<\x18c\xf4'), chr(0b111101 + 0o47) + '\145' + chr(99) + '\157' + '\x64' + chr(0b1100 + 0o131))('\165' + '\x74' + chr(102) + '\055' + chr(0b110111 + 0o1)))
roI3spqORKae(ZtB7KOLCW2Hk, roI3spqORKae(ES5oEprVxulp(b'\xb7_#_Ki\x06z\xa1d'), '\144' + '\x65' + chr(0b1100011) + '\x6f' + chr(0b1100010 + 0o2) + chr(1839 - 1738))(chr(0b11010 + 0o133) + chr(0b1001 + 0o153) + chr(0b11100 + 0o112) + chr(1894 - 1849) + '\070'))(roI3spqORKae(ES5oEprVxulp(b'\xa9S9o@%\x06t\xa8m6\xc4\x03l\x12\xde\x17\xc1\x89\xcdoq\xdf\xe22\xc7\x08!&<\x18`\xf4'), '\144' + '\145' + '\x63' + chr(111) + chr(7045 - 6945) + chr(101))(chr(0b1110101) + chr(4600 - 4484) + '\x66' + chr(45) + '\070'))
return ZtB7KOLCW2Hk |
cggh/scikit-allel | allel/stats/sf.py | plot_joint_sfs_scaled | def plot_joint_sfs_scaled(*args, **kwargs):
"""Plot a scaled joint site frequency spectrum.
Parameters
----------
s : array_like, int, shape (n_chromosomes_pop1, n_chromosomes_pop2)
Joint site frequency spectrum.
ax : axes, optional
Axes on which to draw. If not provided, a new figure will be created.
imshow_kwargs : dict-like
Additional keyword arguments, passed through to ax.imshow().
Returns
-------
ax : axes
The axes on which the plot was drawn.
"""
imshow_kwargs = kwargs.get('imshow_kwargs', dict())
imshow_kwargs.setdefault('norm', None)
kwargs['imshow_kwargs'] = imshow_kwargs
ax = plot_joint_sfs(*args, **kwargs)
return ax | python | def plot_joint_sfs_scaled(*args, **kwargs):
"""Plot a scaled joint site frequency spectrum.
Parameters
----------
s : array_like, int, shape (n_chromosomes_pop1, n_chromosomes_pop2)
Joint site frequency spectrum.
ax : axes, optional
Axes on which to draw. If not provided, a new figure will be created.
imshow_kwargs : dict-like
Additional keyword arguments, passed through to ax.imshow().
Returns
-------
ax : axes
The axes on which the plot was drawn.
"""
imshow_kwargs = kwargs.get('imshow_kwargs', dict())
imshow_kwargs.setdefault('norm', None)
kwargs['imshow_kwargs'] = imshow_kwargs
ax = plot_joint_sfs(*args, **kwargs)
return ax | [
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Parameters
----------
s : array_like, int, shape (n_chromosomes_pop1, n_chromosomes_pop2)
Joint site frequency spectrum.
ax : axes, optional
Axes on which to draw. If not provided, a new figure will be created.
imshow_kwargs : dict-like
Additional keyword arguments, passed through to ax.imshow().
Returns
-------
ax : axes
The axes on which the plot was drawn. | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/stats/sf.py#L753-L775 | train | Plot a scaled joint site frequency spectrum. | 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) + chr(111) + chr(0b101000 + 0o16) + chr(53), 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b1100 + 0o46) + chr(0b110100) + chr(429 - 376), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b1101 + 0o44) + chr(0b1010 + 0o54) + chr(54), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(1249 - 1198) + chr(999 - 945) + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(944 - 833) + chr(49) + chr(584 - 530) + chr(0b110000 + 0o1), 33837 - 33829), nzTpIcepk0o8('\060' + '\157' + '\063' + chr(2394 - 2341), 0b1000), nzTpIcepk0o8(chr(956 - 908) + chr(0b1101111) + chr(178 - 127) + chr(0b1110 + 0o42) + chr(2028 - 1973), 0b1000), nzTpIcepk0o8(chr(0b100010 + 0o16) + chr(0b1101111) + chr(1460 - 1411) + '\067' + '\x32', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1010001 + 0o36) + chr(2172 - 2123) + chr(0b110111) + '\060', ord("\x08")), nzTpIcepk0o8(chr(0b110000 + 0o0) + chr(0b1101111) + '\x32' + chr(0b110111) + chr(0b100001 + 0o22), 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(0b110001) + chr(50) + '\062', 0b1000), nzTpIcepk0o8('\060' + '\157' + '\x33' + chr(48) + '\063', ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110011) + chr(0b100010 + 0o22) + chr(0b1001 + 0o56), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(2757 - 2646) + '\x31' + '\x37' + chr(1979 - 1924), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(2001 - 1946) + '\066', 516 - 508), nzTpIcepk0o8(chr(48) + '\x6f' + '\x33', 0o10), nzTpIcepk0o8('\060' + '\157' + '\064' + chr(0b110011 + 0o2), 37363 - 37355), nzTpIcepk0o8(chr(0b11110 + 0o22) + chr(0b1101111) + '\063' + chr(50), ord("\x08")), nzTpIcepk0o8(chr(0b11 + 0o55) + chr(12228 - 12117) + '\x33' + '\x34' + chr(0b10011 + 0o42), 0o10), nzTpIcepk0o8(chr(48) + chr(0b11011 + 0o124) + chr(49) + chr(783 - 732) + '\062', 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + '\x36' + chr(0b1101 + 0o50), 8), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(744 - 694) + chr(0b101010 + 0o10), 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(55) + chr(50), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b11000 + 0o127) + chr(49) + chr(1024 - 976), 41159 - 41151), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(404 - 354) + chr(0b11100 + 0o32) + chr(51), 43239 - 43231), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110001) + '\x34' + chr(0b1101 + 0o44), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x31' + chr(0b110000 + 0o7) + chr(0b10000 + 0o45), 54514 - 54506), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(51) + '\x37' + chr(0b110011), 35495 - 35487), nzTpIcepk0o8(chr(0b110000) + chr(10159 - 10048) + '\x33' + chr(0b110001) + chr(0b100111 + 0o12), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(1762 - 1708) + chr(789 - 741), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(580 - 531) + chr(50) + chr(0b110101 + 0o0), 15264 - 15256), nzTpIcepk0o8(chr(0b11010 + 0o26) + chr(0b111 + 0o150) + chr(0b110011) + '\x33', 64633 - 64625), nzTpIcepk0o8(chr(0b110 + 0o52) + chr(11257 - 11146) + chr(745 - 695) + chr(0b110000) + chr(53), 10345 - 10337), nzTpIcepk0o8(chr(0b1 + 0o57) + chr(111) + '\x31' + chr(0b101010 + 0o13) + chr(52), 654 - 646), nzTpIcepk0o8('\x30' + chr(111) + chr(2189 - 2138) + chr(55) + '\065', 0b1000), nzTpIcepk0o8('\x30' + chr(2099 - 1988) + chr(0b100100 + 0o15) + '\063' + chr(1236 - 1181), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(52) + chr(1272 - 1218), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1111 + 0o140) + chr(0b11111 + 0o24) + chr(50) + chr(52), 0o10), nzTpIcepk0o8('\060' + '\x6f' + '\x33' + '\067' + '\x32', 23572 - 23564), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x31' + chr(0b110100) + chr(0b110111), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b10100 + 0o41) + '\x30', 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x1b'), '\144' + '\x65' + '\x63' + chr(0b1101111) + chr(0b10001 + 0o123) + chr(0b1100101))(chr(0b10111 + 0o136) + '\164' + chr(102) + chr(0b101101) + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def w_kVbsli3acp(*eemPYp2vtTSr, **q5n0sHDDTy90):
TbyqRkDRVs9Z = q5n0sHDDTy90.GUKetu4xaGsJ(roI3spqORKae(ES5oEprVxulp(b'\\\xc8\x05\x9c\x1ej\x98\x11\x0f\xda \xa4\x94'), chr(0b1100100) + '\x65' + chr(160 - 61) + chr(0b1101111) + chr(0b1100100) + chr(0b1100101))(chr(0b1011110 + 0o27) + chr(3682 - 3566) + chr(0b1100110) + '\055' + '\070'), znjnJWK64FDT())
roI3spqORKae(TbyqRkDRVs9Z, roI3spqORKae(ES5oEprVxulp(b'O\xc0F\xbe<h\x8cC\n\xd4\x05\x90'), '\x64' + '\x65' + '\x63' + '\157' + chr(0b1100100) + chr(0b10100 + 0o121))('\x75' + chr(3167 - 3051) + chr(102) + '\055' + chr(1896 - 1840)))(roI3spqORKae(ES5oEprVxulp(b'[\xca\x04\x99'), chr(0b101 + 0o137) + chr(2474 - 2373) + chr(0b1100011) + chr(0b1101111) + '\x64' + chr(101))(chr(0b1110101) + chr(116) + chr(762 - 660) + chr(0b101101) + chr(0b110011 + 0o5)), None)
q5n0sHDDTy90[roI3spqORKae(ES5oEprVxulp(b'\\\xc8\x05\x9c\x1ej\x98\x11\x0f\xda \xa4\x94'), chr(0b1100100 + 0o0) + chr(1705 - 1604) + chr(0b1010110 + 0o15) + chr(111) + chr(0b1001101 + 0o27) + '\145')('\165' + '\164' + chr(0b1010110 + 0o20) + '\055' + '\070')] = TbyqRkDRVs9Z
ZtB7KOLCW2Hk = NO6u6bXPW1Ss(*eemPYp2vtTSr, **q5n0sHDDTy90)
return ZtB7KOLCW2Hk |
cggh/scikit-allel | allel/stats/sf.py | plot_joint_sfs_folded_scaled | def plot_joint_sfs_folded_scaled(*args, **kwargs):
"""Plot a scaled folded joint site frequency spectrum.
Parameters
----------
s : array_like, int, shape (n_chromosomes_pop1/2, n_chromosomes_pop2/2)
Joint site frequency spectrum.
ax : axes, optional
Axes on which to draw. If not provided, a new figure will be created.
imshow_kwargs : dict-like
Additional keyword arguments, passed through to ax.imshow().
Returns
-------
ax : axes
The axes on which the plot was drawn.
"""
imshow_kwargs = kwargs.get('imshow_kwargs', dict())
imshow_kwargs.setdefault('norm', None)
kwargs['imshow_kwargs'] = imshow_kwargs
ax = plot_joint_sfs_folded(*args, **kwargs)
ax.set_xlabel('minor allele count (population 1)')
ax.set_ylabel('minor allele count (population 2)')
return ax | python | def plot_joint_sfs_folded_scaled(*args, **kwargs):
"""Plot a scaled folded joint site frequency spectrum.
Parameters
----------
s : array_like, int, shape (n_chromosomes_pop1/2, n_chromosomes_pop2/2)
Joint site frequency spectrum.
ax : axes, optional
Axes on which to draw. If not provided, a new figure will be created.
imshow_kwargs : dict-like
Additional keyword arguments, passed through to ax.imshow().
Returns
-------
ax : axes
The axes on which the plot was drawn.
"""
imshow_kwargs = kwargs.get('imshow_kwargs', dict())
imshow_kwargs.setdefault('norm', None)
kwargs['imshow_kwargs'] = imshow_kwargs
ax = plot_joint_sfs_folded(*args, **kwargs)
ax.set_xlabel('minor allele count (population 1)')
ax.set_ylabel('minor allele count (population 2)')
return ax | [
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Parameters
----------
s : array_like, int, shape (n_chromosomes_pop1/2, n_chromosomes_pop2/2)
Joint site frequency spectrum.
ax : axes, optional
Axes on which to draw. If not provided, a new figure will be created.
imshow_kwargs : dict-like
Additional keyword arguments, passed through to ax.imshow().
Returns
-------
ax : axes
The axes on which the plot was drawn. | [
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"spectrum",
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/stats/sf.py#L779-L803 | train | Plot a scaled folded joint site frequency spectrum. | 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(0b10100 + 0o34) + '\x6f' + chr(1023 - 973) + chr(1295 - 1242) + '\066', 0o10), nzTpIcepk0o8(chr(95 - 47) + chr(111) + chr(0b101100 + 0o5) + '\065' + '\x37', 21260 - 21252), nzTpIcepk0o8('\x30' + '\157' + chr(0b110011) + chr(0b110111), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + '\x37' + chr(1355 - 1300), ord("\x08")), nzTpIcepk0o8(chr(1095 - 1047) + '\x6f' + chr(0b110011) + chr(1483 - 1432) + '\x34', 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110011) + '\x30' + '\x37', 0b1000), nzTpIcepk0o8(chr(0b1001 + 0o47) + '\157' + chr(0b110010) + '\x36' + chr(0b11101 + 0o27), 44596 - 44588), nzTpIcepk0o8('\060' + chr(0b1001000 + 0o47) + chr(50) + chr(0b110000 + 0o2) + chr(52), ord("\x08")), nzTpIcepk0o8(chr(0b100110 + 0o12) + chr(111) + '\x34' + chr(51), 51894 - 51886), nzTpIcepk0o8('\060' + '\x6f' + '\x37' + chr(716 - 664), 50636 - 50628), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x32' + '\x37' + chr(0b1011 + 0o47), 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(318 - 268) + '\x32' + chr(0b110011), 57290 - 57282), nzTpIcepk0o8('\x30' + chr(0b1101001 + 0o6) + chr(55) + '\064', 8), nzTpIcepk0o8(chr(0b11010 + 0o26) + chr(11747 - 11636) + '\063' + chr(0b110001) + chr(2534 - 2481), ord("\x08")), nzTpIcepk0o8('\x30' + chr(4324 - 4213) + chr(0b110110) + chr(50), 28610 - 28602), nzTpIcepk0o8('\x30' + '\157' + chr(0b101001 + 0o11) + chr(51) + '\063', 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b11100 + 0o27) + chr(50) + '\066', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\063' + chr(50) + chr(54), 8), nzTpIcepk0o8(chr(48) + '\157' + chr(50) + '\x35' + '\x35', ord("\x08")), nzTpIcepk0o8(chr(418 - 370) + chr(0b111001 + 0o66) + '\x31' + chr(796 - 744) + '\x35', 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(334 - 284) + chr(0b110011) + '\062', 6837 - 6829), nzTpIcepk0o8('\060' + chr(111) + chr(0b100010 + 0o22), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(51) + '\x30' + '\x30', 0o10), nzTpIcepk0o8(chr(0b0 + 0o60) + chr(0b1101111) + '\065' + chr(0b100101 + 0o22), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + '\x32' + chr(0b110000) + '\x37', 1141 - 1133), nzTpIcepk0o8(chr(48) + '\x6f' + chr(53) + chr(50), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(50) + chr(0b110110) + chr(0b110000), 0b1000), nzTpIcepk0o8(chr(1601 - 1553) + chr(111) + chr(51) + '\064' + chr(49), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + '\x35' + chr(53), 0o10), nzTpIcepk0o8(chr(54 - 6) + chr(0b1101111) + chr(49) + chr(51) + chr(0b11011 + 0o34), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + '\063' + chr(0b110100 + 0o3) + chr(0b110000), 61618 - 61610), nzTpIcepk0o8('\x30' + chr(0b100000 + 0o117) + '\x33' + chr(0b110101) + '\061', 0o10), nzTpIcepk0o8('\060' + chr(111) + '\061' + chr(0b110011) + chr(2344 - 2293), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(51) + '\062' + '\x36', 8), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b10101 + 0o35) + '\x34' + chr(0b101 + 0o56), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b101100 + 0o103) + chr(0b10110 + 0o34) + '\060' + chr(0b110100), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(50) + chr(574 - 521) + chr(49), 26838 - 26830), nzTpIcepk0o8('\060' + '\157' + chr(49) + '\x36', 22101 - 22093), nzTpIcepk0o8(chr(862 - 814) + '\x6f' + chr(1810 - 1760) + chr(0b110000) + '\x37', 8), nzTpIcepk0o8(chr(48) + '\x6f' + chr(50) + chr(0b11 + 0o57) + chr(1210 - 1161), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(1442 - 1394) + chr(111) + chr(261 - 208) + chr(48), 13434 - 13426)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x80'), chr(100) + chr(0b1010 + 0o133) + '\143' + chr(0b1101111) + chr(0b1010000 + 0o24) + chr(101))('\x75' + chr(0b0 + 0o164) + '\x66' + chr(260 - 215) + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def LEImeY7kHJIG(*eemPYp2vtTSr, **q5n0sHDDTy90):
TbyqRkDRVs9Z = q5n0sHDDTy90.GUKetu4xaGsJ(roI3spqORKae(ES5oEprVxulp(b'\xc7\x02lW\xb3\xb0\xeb\xffT]\xc8\xf4O'), chr(8886 - 8786) + chr(101) + chr(3803 - 3704) + chr(0b1101111) + chr(3185 - 3085) + chr(0b110111 + 0o56))(chr(11843 - 11726) + chr(3690 - 3574) + chr(0b1001111 + 0o27) + chr(1485 - 1440) + chr(56)), znjnJWK64FDT())
roI3spqORKae(TbyqRkDRVs9Z, roI3spqORKae(ES5oEprVxulp(b'\xd4\n/u\x91\xb2\xff\xadQS\xed\xc0'), chr(100) + chr(6158 - 6057) + chr(0b1100011) + '\x6f' + chr(0b100110 + 0o76) + chr(9856 - 9755))(chr(117) + chr(0b1110100) + chr(9351 - 9249) + chr(1802 - 1757) + chr(56)))(roI3spqORKae(ES5oEprVxulp(b'\xc0\x00mR'), chr(0b1100100) + chr(0b1100101) + '\x63' + '\x6f' + chr(3662 - 3562) + '\145')(chr(0b1001111 + 0o46) + '\164' + '\x66' + chr(45) + chr(0b111000)), None)
q5n0sHDDTy90[roI3spqORKae(ES5oEprVxulp(b'\xc7\x02lW\xb3\xb0\xeb\xffT]\xc8\xf4O'), chr(4373 - 4273) + '\145' + chr(0b1100011) + chr(111) + '\144' + chr(8677 - 8576))(chr(117) + chr(0b10111 + 0o135) + chr(0b100110 + 0o100) + '\x2d' + chr(0b111000))] = TbyqRkDRVs9Z
ZtB7KOLCW2Hk = GLjTLYJQ9Gri(*eemPYp2vtTSr, **q5n0sHDDTy90)
roI3spqORKae(ZtB7KOLCW2Hk, roI3spqORKae(ES5oEprVxulp(b'\xdd\nk`\xa4\xab\xd5\xf6FP'), '\x64' + chr(101) + chr(5121 - 5022) + chr(0b1001100 + 0o43) + chr(100) + chr(101))(chr(0b1010011 + 0o42) + '\164' + '\146' + '\x2d' + '\070'))(roI3spqORKae(ES5oEprVxulp(b'\xc3\x06qP\xae\xe7\xd5\xf8OY\xd6\xf6\x1c\xae]\xee\xb8\xa2\x8dM\xeak\xb0Z\xebK\xc4\x88B1\xd8\xd8r'), chr(100) + chr(855 - 754) + chr(4843 - 4744) + chr(0b1101111) + '\144' + '\145')('\165' + chr(0b1110100) + chr(0b1100110) + '\x2d' + chr(0b111000)))
roI3spqORKae(ZtB7KOLCW2Hk, roI3spqORKae(ES5oEprVxulp(b'\xdd\nk`\xa5\xab\xd5\xf6FP'), chr(3783 - 3683) + '\145' + chr(0b110010 + 0o61) + chr(7538 - 7427) + chr(0b1010111 + 0o15) + '\145')('\x75' + chr(3636 - 3520) + '\146' + chr(0b10010 + 0o33) + chr(56)))(roI3spqORKae(ES5oEprVxulp(b'\xc3\x06qP\xae\xe7\xd5\xf8OY\xd6\xf6\x1c\xae]\xee\xb8\xa2\x8dM\xeak\xb0Z\xebK\xc4\x88B1\xd8\xdbr'), '\144' + chr(8075 - 7974) + chr(0b1100011) + chr(1999 - 1888) + '\x64' + chr(101))('\x75' + chr(0b1001110 + 0o46) + chr(9265 - 9163) + '\055' + chr(1604 - 1548)))
return ZtB7KOLCW2Hk |
cggh/scikit-allel | allel/compat.py | memoryview_safe | def memoryview_safe(x):
"""Make array safe to run in a Cython memoryview-based kernel. These
kernels typically break down with the error ``ValueError: buffer source
array is read-only`` when running in dask distributed.
See Also
--------
https://github.com/dask/distributed/issues/1978
https://github.com/cggh/scikit-allel/issues/206
"""
if not x.flags.writeable:
if not x.flags.owndata:
x = x.copy(order='A')
x.setflags(write=True)
return x | python | def memoryview_safe(x):
"""Make array safe to run in a Cython memoryview-based kernel. These
kernels typically break down with the error ``ValueError: buffer source
array is read-only`` when running in dask distributed.
See Also
--------
https://github.com/dask/distributed/issues/1978
https://github.com/cggh/scikit-allel/issues/206
"""
if not x.flags.writeable:
if not x.flags.owndata:
x = x.copy(order='A')
x.setflags(write=True)
return x | [
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See Also
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https://github.com/dask/distributed/issues/1978
https://github.com/cggh/scikit-allel/issues/206 | [
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"when... | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/compat.py#L51-L66 | train | Make array safe to run in a Cython memoryview - based kernel. | 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(0b11000 + 0o127) + chr(0b100111 + 0o12) + chr(216 - 162) + '\x32', 0b1000), nzTpIcepk0o8('\060' + chr(0b110111 + 0o70) + chr(53) + chr(0b10100 + 0o36), 49758 - 49750), nzTpIcepk0o8(chr(48) + '\x6f' + chr(51) + chr(1574 - 1525) + chr(1380 - 1327), 0o10), nzTpIcepk0o8(chr(1963 - 1915) + '\157' + chr(0b110001 + 0o2) + '\066' + '\065', 63857 - 63849), nzTpIcepk0o8(chr(48) + '\157' + chr(0b10110 + 0o34) + '\067', 0o10), nzTpIcepk0o8('\060' + '\157' + chr(0b110011) + '\x32' + chr(0b110101), 0o10), nzTpIcepk0o8(chr(528 - 480) + chr(111) + '\063' + '\063' + '\x32', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1001111 + 0o40) + chr(0b110010) + chr(1594 - 1545), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(54) + chr(0b100100 + 0o16), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(51) + '\x30' + chr(0b110100), 18007 - 17999), nzTpIcepk0o8(chr(0b110000) + chr(12026 - 11915) + chr(402 - 351) + '\061', 26285 - 26277), nzTpIcepk0o8('\060' + '\157' + chr(0b10011 + 0o37) + chr(1745 - 1693), 0b1000), nzTpIcepk0o8('\060' + chr(0b1100 + 0o143) + chr(0b100111 + 0o15) + chr(634 - 580), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x32' + '\x36' + '\062', 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x31', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(553 - 503) + '\x30' + chr(970 - 920), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + '\061' + chr(0b111 + 0o53) + chr(1156 - 1107), 44547 - 44539), nzTpIcepk0o8(chr(48) + '\x6f' + '\062' + chr(0b110111) + '\065', 0o10), nzTpIcepk0o8(chr(0b10100 + 0o34) + chr(0b1101111) + chr(0b110001) + chr(54) + '\x31', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(12212 - 12101) + chr(0b101101 + 0o12) + chr(609 - 557), 0b1000), nzTpIcepk0o8(chr(0b110 + 0o52) + chr(111) + '\063' + '\x37' + '\060', 0o10), nzTpIcepk0o8('\060' + chr(111) + '\x33' + chr(49), 8), nzTpIcepk0o8('\x30' + '\x6f' + '\062' + chr(0b100011 + 0o15) + chr(0b110000), 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(0b110010) + chr(0b110010) + '\067', 27099 - 27091), nzTpIcepk0o8(chr(247 - 199) + chr(11857 - 11746) + '\063' + '\x32' + '\x36', 18397 - 18389), nzTpIcepk0o8('\060' + chr(0b101 + 0o152) + chr(49) + chr(54) + chr(0b110100), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + chr(0b10011 + 0o37) + chr(48), 0o10), nzTpIcepk0o8(chr(1296 - 1248) + chr(0b111000 + 0o67) + chr(290 - 240) + chr(2934 - 2879) + chr(1948 - 1899), ord("\x08")), nzTpIcepk0o8(chr(1832 - 1784) + '\157' + chr(0b110111), 54058 - 54050), nzTpIcepk0o8(chr(48) + chr(111) + chr(49) + chr(0b10110 + 0o33) + chr(2202 - 2149), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b11110 + 0o31) + '\x30', 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(512 - 462) + '\061' + chr(777 - 729), 0b1000), nzTpIcepk0o8(chr(798 - 750) + chr(111) + chr(49) + '\067' + '\066', 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(50) + chr(54) + chr(0b110010), 8), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x31' + chr(1474 - 1424) + chr(965 - 915), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\061' + chr(0b110101) + '\061', 0o10), nzTpIcepk0o8('\060' + chr(2949 - 2838) + chr(53) + '\x30', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x31' + chr(52) + '\x33', 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(404 - 353) + chr(0b110110) + '\063', 23094 - 23086), nzTpIcepk0o8(chr(0b101110 + 0o2) + chr(894 - 783) + chr(242 - 193) + '\x30' + '\061', 58437 - 58429)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + '\157' + '\x35' + chr(48), 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\\'), '\144' + chr(0b1100101) + chr(0b1100011) + '\x6f' + '\144' + '\145')('\x75' + chr(0b1010 + 0o152) + '\146' + chr(0b100011 + 0o12) + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def ygMIbkSSXS59(bI5jsQ9OkQtj):
if not roI3spqORKae(bI5jsQ9OkQtj.flags, roI3spqORKae(ES5oEprVxulp(b'%M\x87\xb3v\x9a\x8bvt\xf1LB'), chr(100) + chr(5198 - 5097) + chr(0b100111 + 0o74) + chr(0b110100 + 0o73) + chr(100) + '\x65')(chr(0b1110101) + '\164' + chr(0b101010 + 0o74) + chr(0b101101) + chr(0b100000 + 0o30))):
if not roI3spqORKae(bI5jsQ9OkQtj.flags, roI3spqORKae(ES5oEprVxulp(b'\x1d]\xa3\x91v\xa1\xbb'), chr(100) + '\145' + '\143' + chr(10046 - 9935) + '\x64' + '\x65')(chr(0b1110101) + '\164' + '\146' + '\x2d' + chr(56))):
bI5jsQ9OkQtj = bI5jsQ9OkQtj.copy(order=roI3spqORKae(ES5oEprVxulp(b'3'), chr(0b1100100) + '\x65' + chr(0b1010110 + 0o15) + chr(111) + chr(0b1100100) + '\x65')('\165' + chr(0b1110100) + chr(102) + chr(0b100111 + 0o6) + chr(0b110100 + 0o4)))
roI3spqORKae(bI5jsQ9OkQtj, roI3spqORKae(ES5oEprVxulp(b'\x01O\xb9\x93{\xb4\xbdb'), chr(100) + '\x65' + chr(0b1101 + 0o126) + chr(111) + chr(0b11100 + 0o110) + '\145')(chr(0b1110101) + chr(116) + chr(0b111111 + 0o47) + chr(0b101101) + chr(56)))(write=nzTpIcepk0o8(chr(48) + chr(0b1100010 + 0o15) + chr(0b110001), 8))
return bI5jsQ9OkQtj |
cggh/scikit-allel | allel/io/vcf_read.py | _prep_fields_param | def _prep_fields_param(fields):
"""Prepare the `fields` parameter, and determine whether or not to store samples."""
store_samples = False
if fields is None:
# add samples by default
return True, None
if isinstance(fields, str):
fields = [fields]
else:
fields = list(fields)
if 'samples' in fields:
fields.remove('samples')
store_samples = True
elif '*' in fields:
store_samples = True
return store_samples, fields | python | def _prep_fields_param(fields):
"""Prepare the `fields` parameter, and determine whether or not to store samples."""
store_samples = False
if fields is None:
# add samples by default
return True, None
if isinstance(fields, str):
fields = [fields]
else:
fields = list(fields)
if 'samples' in fields:
fields.remove('samples')
store_samples = True
elif '*' in fields:
store_samples = True
return store_samples, fields | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/io/vcf_read.py#L51-L71 | train | Prepare the fields parameter and determine whether or not to store samples. | 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) + '\x31' + '\063', 0b1000), nzTpIcepk0o8('\060' + '\157' + '\x33' + '\063' + chr(0b110001), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(2798 - 2743) + chr(1025 - 977), 51030 - 51022), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b101011 + 0o6) + '\066' + chr(53 - 3), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + '\061' + chr(53) + chr(0b10100 + 0o43), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\061' + '\064' + chr(0b110011 + 0o4), 11996 - 11988), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b100000 + 0o23) + chr(48) + chr(0b100111 + 0o20), 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110001) + chr(51) + chr(0b101001 + 0o16), 12067 - 12059), nzTpIcepk0o8(chr(0b110000) + chr(6340 - 6229) + chr(50) + chr(48) + chr(54), 0b1000), nzTpIcepk0o8(chr(1389 - 1341) + chr(5532 - 5421) + chr(50) + chr(0b101011 + 0o14) + chr(0b110110), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1011101 + 0o22) + chr(0b10000 + 0o41) + chr(953 - 900), 0b1000), nzTpIcepk0o8(chr(1145 - 1097) + chr(0b1101111) + chr(0b110011) + '\x34' + chr(0b110110), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\061' + chr(1925 - 1876) + '\063', 58977 - 58969), nzTpIcepk0o8('\060' + '\x6f' + chr(51) + '\x34' + chr(0b11110 + 0o30), 8), nzTpIcepk0o8('\060' + '\157' + chr(1882 - 1828) + chr(0b10010 + 0o37), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110001) + chr(0b110101) + chr(2333 - 2278), 8), nzTpIcepk0o8('\060' + chr(6905 - 6794) + '\062' + chr(0b110100) + '\x36', 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(49) + '\x34', 0b1000), nzTpIcepk0o8('\060' + '\157' + '\062' + '\x34' + '\062', 0o10), nzTpIcepk0o8(chr(0b100011 + 0o15) + chr(111) + chr(0b11101 + 0o30) + '\x32', 0o10), nzTpIcepk0o8(chr(0b10001 + 0o37) + '\x6f' + chr(54) + chr(0b110001 + 0o6), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x33' + '\066' + '\062', 0b1000), nzTpIcepk0o8(chr(478 - 430) + chr(2051 - 1940) + '\061' + '\066' + chr(1301 - 1250), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(49) + chr(844 - 789), 3041 - 3033), nzTpIcepk0o8(chr(0b1011 + 0o45) + chr(0b1101111) + '\x36' + chr(0b110010), 56204 - 56196), nzTpIcepk0o8('\x30' + '\157' + '\x31' + '\x36' + chr(198 - 144), ord("\x08")), nzTpIcepk0o8(chr(2098 - 2050) + chr(111) + chr(0b110001 + 0o0) + '\x34' + chr(0b110010), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(50) + '\062', 0o10), nzTpIcepk0o8('\x30' + chr(12067 - 11956) + '\x36', ord("\x08")), nzTpIcepk0o8(chr(0b10111 + 0o31) + chr(2454 - 2343) + chr(0b110001) + '\x32' + chr(54), 0o10), nzTpIcepk0o8(chr(48) + '\157' + '\062' + chr(0b110101) + '\x33', 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(49) + chr(302 - 253) + '\065', 0b1000), nzTpIcepk0o8(chr(0b11100 + 0o24) + '\x6f' + chr(0b110011) + chr(791 - 739), 0b1000), nzTpIcepk0o8('\x30' + '\157' + '\062' + chr(0b110111) + chr(0b110110), 8), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(50) + chr(0b11111 + 0o30) + '\x34', 57556 - 57548), nzTpIcepk0o8(chr(1626 - 1578) + '\x6f' + chr(0b110010) + chr(51) + chr(0b110101), 0o10), nzTpIcepk0o8(chr(48) + chr(5682 - 5571) + chr(0b110001 + 0o2) + '\064' + '\x31', ord("\x08")), nzTpIcepk0o8(chr(0b11111 + 0o21) + chr(7896 - 7785) + chr(2474 - 2424) + '\063' + chr(840 - 786), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b110100 + 0o73) + '\067' + '\x36', ord("\x08")), nzTpIcepk0o8('\x30' + chr(11802 - 11691) + chr(0b110011 + 0o2) + chr(0b1011 + 0o51), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + chr(7478 - 7367) + chr(0b110101) + '\060', ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'%'), chr(0b1100100) + '\x65' + chr(0b1100011) + chr(0b1001101 + 0o42) + '\x64' + chr(101))('\x75' + '\164' + chr(0b111010 + 0o54) + chr(0b11011 + 0o22) + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def VUIwV6a3wMvG(ZXDdzgbdtBfz):
a6mfQSAdDiNA = nzTpIcepk0o8(chr(0b110000) + chr(10741 - 10630) + '\x30', 0o10)
if ZXDdzgbdtBfz is None:
return (nzTpIcepk0o8(chr(0b110000) + chr(0b1000100 + 0o53) + '\061', 0o10), None)
if suIjIS24Zkqw(ZXDdzgbdtBfz, N9zlRy29S1SS):
ZXDdzgbdtBfz = [ZXDdzgbdtBfz]
else:
ZXDdzgbdtBfz = H4NoA26ON7iG(ZXDdzgbdtBfz)
if roI3spqORKae(ES5oEprVxulp(b'x\xb8U\x02\x03\x02\xb4'), chr(4332 - 4232) + chr(0b11 + 0o142) + chr(0b1100011) + chr(4198 - 4087) + chr(0b111110 + 0o46) + chr(0b1100101))(chr(0b0 + 0o165) + '\x74' + chr(0b110010 + 0o64) + '\055' + '\070') in ZXDdzgbdtBfz:
roI3spqORKae(ZXDdzgbdtBfz, roI3spqORKae(ES5oEprVxulp(b"{\x94T'\x07\x03\xf5\x15\xeb\xf5L\xa3"), chr(0b101100 + 0o70) + '\x65' + chr(0b1100011) + chr(0b1101111) + '\x64' + chr(0b1000101 + 0o40))(chr(117) + chr(0b1101111 + 0o5) + chr(6811 - 6709) + '\x2d' + chr(0b101001 + 0o17)))(roI3spqORKae(ES5oEprVxulp(b'x\xb8U\x02\x03\x02\xb4'), chr(0b1100100) + '\x65' + chr(7804 - 7705) + chr(0b1101111) + chr(5325 - 5225) + chr(0b100010 + 0o103))(chr(6957 - 6840) + '\164' + chr(9534 - 9432) + chr(0b101101) + chr(146 - 90)))
a6mfQSAdDiNA = nzTpIcepk0o8(chr(0b11 + 0o55) + chr(111) + '\061', 8)
elif roI3spqORKae(ES5oEprVxulp(b'!'), chr(100) + chr(4900 - 4799) + chr(99) + '\157' + chr(0b1100100) + chr(0b1100101))('\x75' + chr(0b1110100) + chr(0b1100110) + '\055' + chr(0b110 + 0o62)) in ZXDdzgbdtBfz:
a6mfQSAdDiNA = nzTpIcepk0o8('\060' + '\157' + '\061', 8)
return (a6mfQSAdDiNA, ZXDdzgbdtBfz) |
cggh/scikit-allel | allel/io/vcf_read.py | _chunk_iter_progress | def _chunk_iter_progress(it, log, prefix):
"""Wrap a chunk iterator for progress logging."""
n_variants = 0
before_all = time.time()
before_chunk = before_all
for chunk, chunk_length, chrom, pos in it:
after_chunk = time.time()
elapsed_chunk = after_chunk - before_chunk
elapsed = after_chunk - before_all
n_variants += chunk_length
chrom = text_type(chrom, 'utf8')
message = (
'%s %s rows in %.2fs; chunk in %.2fs (%s rows/s)' %
(prefix, n_variants, elapsed, elapsed_chunk,
int(chunk_length // elapsed_chunk))
)
if chrom:
message += '; %s:%s' % (chrom, pos)
print(message, file=log)
log.flush()
yield chunk, chunk_length, chrom, pos
before_chunk = after_chunk
after_all = time.time()
elapsed = after_all - before_all
print('%s all done (%s rows/s)' %
(prefix, int(n_variants // elapsed)), file=log)
log.flush() | python | def _chunk_iter_progress(it, log, prefix):
"""Wrap a chunk iterator for progress logging."""
n_variants = 0
before_all = time.time()
before_chunk = before_all
for chunk, chunk_length, chrom, pos in it:
after_chunk = time.time()
elapsed_chunk = after_chunk - before_chunk
elapsed = after_chunk - before_all
n_variants += chunk_length
chrom = text_type(chrom, 'utf8')
message = (
'%s %s rows in %.2fs; chunk in %.2fs (%s rows/s)' %
(prefix, n_variants, elapsed, elapsed_chunk,
int(chunk_length // elapsed_chunk))
)
if chrom:
message += '; %s:%s' % (chrom, pos)
print(message, file=log)
log.flush()
yield chunk, chunk_length, chrom, pos
before_chunk = after_chunk
after_all = time.time()
elapsed = after_all - before_all
print('%s all done (%s rows/s)' %
(prefix, int(n_variants // elapsed)), file=log)
log.flush() | [
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"logging",
"."
] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/io/vcf_read.py#L74-L100 | train | Wrap a chunk iterator for progress logging. | 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(0b10 + 0o63) + chr(53), 27140 - 27132), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(1618 - 1567) + chr(0b1 + 0o63) + chr(0b110 + 0o54), 12002 - 11994), nzTpIcepk0o8(chr(0b1 + 0o57) + '\157' + chr(49) + chr(53) + '\x31', 0o10), nzTpIcepk0o8('\x30' + chr(6163 - 6052) + '\x32' + chr(0b1001 + 0o56), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(54) + '\x33', 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110011) + '\x31' + chr(0b101101 + 0o7), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110011) + chr(53) + chr(853 - 804), 0o10), nzTpIcepk0o8('\x30' + chr(0b11100 + 0o123) + chr(50) + '\065' + '\062', ord("\x08")), nzTpIcepk0o8(chr(1984 - 1936) + '\157' + '\063' + chr(54) + chr(49), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\067' + chr(0b110100), 27079 - 27071), nzTpIcepk0o8('\060' + chr(9979 - 9868) + '\x35' + chr(0b110011 + 0o0), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110011) + chr(51), 42922 - 42914), nzTpIcepk0o8(chr(1507 - 1459) + '\x6f' + chr(0b1001 + 0o52) + '\062' + chr(1314 - 1260), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110010) + '\x34', 64048 - 64040), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b100001 + 0o20) + '\067' + '\x35', 0o10), nzTpIcepk0o8(chr(0b100010 + 0o16) + '\x6f' + chr(0b110010) + chr(528 - 475) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b101011 + 0o6) + chr(50) + chr(0b110010), 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(0b1110 + 0o43) + '\061' + chr(53), 0o10), nzTpIcepk0o8('\060' + chr(0b1011010 + 0o25) + chr(1277 - 1227) + '\x36' + '\065', 64866 - 64858), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(2167 - 2117) + chr(2320 - 2266) + '\x32', 0o10), nzTpIcepk0o8(chr(0b110000 + 0o0) + chr(0b1101111) + chr(0b110001) + '\063' + chr(50), 2553 - 2545), nzTpIcepk0o8('\060' + '\157' + '\x33' + chr(1340 - 1292) + chr(0b110001), 31172 - 31164), nzTpIcepk0o8(chr(0b10 + 0o56) + chr(0b1101111) + chr(0b110010) + '\067' + chr(0b110100), 0o10), nzTpIcepk0o8('\x30' + chr(111) + '\063' + '\x32' + chr(49), 16437 - 16429), nzTpIcepk0o8('\x30' + chr(1374 - 1263) + chr(51) + chr(0b100100 + 0o20) + chr(0b100000 + 0o23), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(0b110001) + '\x35', 36040 - 36032), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110001) + chr(0b10101 + 0o34) + chr(0b110010), ord("\x08")), nzTpIcepk0o8('\x30' + chr(2357 - 2246) + chr(0b110001 + 0o1) + '\064' + chr(0b100111 + 0o17), ord("\x08")), nzTpIcepk0o8('\060' + chr(1485 - 1374) + chr(1818 - 1764) + '\064', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1011011 + 0o24) + chr(0b110011) + chr(1843 - 1795) + '\065', 41950 - 41942), nzTpIcepk0o8(chr(48) + chr(11918 - 11807) + '\x32' + '\x30' + '\063', 22225 - 22217), nzTpIcepk0o8(chr(0b110000) + chr(0b10111 + 0o130) + chr(99 - 49) + chr(55) + chr(51), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + '\x31' + chr(0b10001 + 0o43) + chr(0b110110), ord("\x08")), nzTpIcepk0o8(chr(1901 - 1853) + chr(0b111100 + 0o63) + chr(1614 - 1563) + chr(48), 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(0b1 + 0o65) + chr(0b110011), 8), nzTpIcepk0o8(chr(979 - 931) + chr(111) + chr(0b110001) + chr(428 - 380) + chr(0b100011 + 0o20), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110001) + chr(0b100011 + 0o20) + chr(0b110110), 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(49) + chr(49) + '\x30', 30614 - 30606), nzTpIcepk0o8(chr(48) + chr(0b111101 + 0o62) + chr(0b101101 + 0o12) + '\x31', ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b10111 + 0o34) + chr(52), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b10001 + 0o44) + chr(0b11100 + 0o24), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x03'), chr(100) + chr(101) + chr(0b100110 + 0o75) + chr(111) + '\x64' + chr(6157 - 6056))(chr(0b1110101) + chr(116) + '\146' + '\055' + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def _Inj3jb7axrv(NOukaRmWFG1j, lmiGj7TonZgV, ZJwZgaHE72Po):
J_Nfjz8pWxyQ = nzTpIcepk0o8(chr(0b11011 + 0o25) + chr(2495 - 2384) + '\060', 14462 - 14454)
inOVLOw0BaMq = oprIvDIRQyCb.oprIvDIRQyCb()
IHQqaZX08WiY = inOVLOw0BaMq
for (WckxBx1Uqdpm, Rv_V5730xaZB, fW0_QlhvSEii, IGIA_fu6MbaO) in NOukaRmWFG1j:
h_l2eq4di7ij = oprIvDIRQyCb.oprIvDIRQyCb()
kItb_JFLiVpN = h_l2eq4di7ij - IHQqaZX08WiY
GCI4bClrnjBQ = h_l2eq4di7ij - inOVLOw0BaMq
J_Nfjz8pWxyQ += Rv_V5730xaZB
fW0_QlhvSEii = H8p5T_wwctMA(fW0_QlhvSEii, roI3spqORKae(ES5oEprVxulp(b'X\x96\x0f/'), '\144' + '\x65' + chr(99) + '\157' + chr(100) + '\x65')('\165' + chr(0b1110100) + chr(0b1100110) + chr(0b101101) + chr(1726 - 1670)))
FksNMH1w_ns6 = roI3spqORKae(ES5oEprVxulp(b'\x08\x91I2@\xec\x9b\xc5\x86O\x0br\xb84X\x82`+\xc6\x89z\xa2\xd4\xa4\x8dfj\xcfZ\xe5\xa6\x95T~@cvmJ<_\x8d\x1ed\x1c\xbf\xc0'), chr(0b1001101 + 0o27) + '\145' + chr(0b1100011) + chr(4705 - 4594) + chr(0b101111 + 0o65) + chr(0b1100101))('\x75' + '\164' + chr(6138 - 6036) + chr(0b101101) + chr(0b111000)) % (ZJwZgaHE72Po, J_Nfjz8pWxyQ, GCI4bClrnjBQ, kItb_JFLiVpN, nzTpIcepk0o8(Rv_V5730xaZB // kItb_JFLiVpN))
if fW0_QlhvSEii:
FksNMH1w_ns6 += roI3spqORKae(ES5oEprVxulp(b'\x16\xc2Ld\t\xe9\x9a'), chr(100) + chr(0b111110 + 0o47) + chr(0b1001011 + 0o30) + chr(0b1101111) + chr(0b1100100) + '\x65')('\165' + '\164' + chr(0b1100110) + chr(45) + chr(0b11100 + 0o34)) % (fW0_QlhvSEii, IGIA_fu6MbaO)
v8jsMqaYV6U2(FksNMH1w_ns6, file=lmiGj7TonZgV)
roI3spqORKae(lmiGj7TonZgV, roI3spqORKae(ES5oEprVxulp(b'F\xb5\x19nq\xbe\xbf\xfd\xb3LX^'), '\x64' + chr(6603 - 6502) + '\143' + chr(111) + chr(739 - 639) + '\145')(chr(0b100 + 0o161) + '\x74' + '\x66' + chr(817 - 772) + chr(0b111000)))()
yield (WckxBx1Uqdpm, Rv_V5730xaZB, fW0_QlhvSEii, IGIA_fu6MbaO)
IHQqaZX08WiY = h_l2eq4di7ij
K2H4YXSyY4BR = oprIvDIRQyCb.oprIvDIRQyCb()
GCI4bClrnjBQ = K2H4YXSyY4BR - inOVLOw0BaMq
v8jsMqaYV6U2(roI3spqORKae(ES5oEprVxulp(b'\x08\x91Iv_\xa0\xc9\xce\x9eRN;\xfe1\x0e\x8c "\xc2\xc1u\xb2\x95'), '\x64' + chr(0b100101 + 0o100) + chr(0b1100011) + chr(0b1000001 + 0o56) + chr(4907 - 4807) + chr(101))('\165' + chr(0b1110100) + '\x66' + '\x2d' + chr(0b111000)) % (ZJwZgaHE72Po, nzTpIcepk0o8(J_Nfjz8pWxyQ // GCI4bClrnjBQ)), file=lmiGj7TonZgV)
roI3spqORKae(lmiGj7TonZgV, roI3spqORKae(ES5oEprVxulp(b'F\xb5\x19nq\xbe\xbf\xfd\xb3LX^'), '\x64' + '\x65' + '\143' + chr(0b1011111 + 0o20) + '\144' + chr(0b111001 + 0o54))(chr(7944 - 7827) + chr(0b1110100) + '\146' + chr(0b101101) + '\070'))() |
cggh/scikit-allel | allel/io/vcf_read.py | read_vcf | def read_vcf(input,
fields=None,
exclude_fields=None,
rename_fields=None,
types=None,
numbers=None,
alt_number=DEFAULT_ALT_NUMBER,
fills=None,
region=None,
tabix='tabix',
samples=None,
transformers=None,
buffer_size=DEFAULT_BUFFER_SIZE,
chunk_length=DEFAULT_CHUNK_LENGTH,
log=None):
"""Read data from a VCF file into NumPy arrays.
.. versionchanged:: 1.12.0
Now returns None if no variants are found in the VCF file or matching the
requested region.
Parameters
----------
input : string or file-like
{input}
fields : list of strings, optional
{fields}
exclude_fields : list of strings, optional
{exclude_fields}
rename_fields : dict[str -> str], optional
{rename_fields}
types : dict, optional
{types}
numbers : dict, optional
{numbers}
alt_number : int, optional
{alt_number}
fills : dict, optional
{fills}
region : string, optional
{region}
tabix : string, optional
{tabix}
samples : list of strings
{samples}
transformers : list of transformer objects, optional
{transformers}
buffer_size : int, optional
{buffer_size}
chunk_length : int, optional
{chunk_length}
log : file-like, optional
{log}
Returns
-------
data : dict[str, ndarray]
A dictionary holding arrays, or None if no variants were found.
"""
# samples requested?
# noinspection PyTypeChecker
store_samples, fields = _prep_fields_param(fields)
# setup
fields, samples, headers, it = iter_vcf_chunks(
input=input, fields=fields, exclude_fields=exclude_fields, types=types,
numbers=numbers, alt_number=alt_number, buffer_size=buffer_size,
chunk_length=chunk_length, fills=fills, region=region, tabix=tabix,
samples=samples, transformers=transformers
)
# handle field renaming
if rename_fields:
rename_fields, it = _do_rename(it, fields=fields,
rename_fields=rename_fields,
headers=headers)
# setup progress logging
if log is not None:
it = _chunk_iter_progress(it, log, prefix='[read_vcf]')
# read all chunks into a list
chunks = [d[0] for d in it]
if chunks:
# setup output
output = dict()
if len(samples) > 0 and store_samples:
output['samples'] = samples
# find array keys
keys = sorted(chunks[0].keys())
# concatenate chunks
for k in keys:
output[k] = np.concatenate([chunk[k] for chunk in chunks], axis=0)
else:
output = None
return output | python | def read_vcf(input,
fields=None,
exclude_fields=None,
rename_fields=None,
types=None,
numbers=None,
alt_number=DEFAULT_ALT_NUMBER,
fills=None,
region=None,
tabix='tabix',
samples=None,
transformers=None,
buffer_size=DEFAULT_BUFFER_SIZE,
chunk_length=DEFAULT_CHUNK_LENGTH,
log=None):
"""Read data from a VCF file into NumPy arrays.
.. versionchanged:: 1.12.0
Now returns None if no variants are found in the VCF file or matching the
requested region.
Parameters
----------
input : string or file-like
{input}
fields : list of strings, optional
{fields}
exclude_fields : list of strings, optional
{exclude_fields}
rename_fields : dict[str -> str], optional
{rename_fields}
types : dict, optional
{types}
numbers : dict, optional
{numbers}
alt_number : int, optional
{alt_number}
fills : dict, optional
{fills}
region : string, optional
{region}
tabix : string, optional
{tabix}
samples : list of strings
{samples}
transformers : list of transformer objects, optional
{transformers}
buffer_size : int, optional
{buffer_size}
chunk_length : int, optional
{chunk_length}
log : file-like, optional
{log}
Returns
-------
data : dict[str, ndarray]
A dictionary holding arrays, or None if no variants were found.
"""
# samples requested?
# noinspection PyTypeChecker
store_samples, fields = _prep_fields_param(fields)
# setup
fields, samples, headers, it = iter_vcf_chunks(
input=input, fields=fields, exclude_fields=exclude_fields, types=types,
numbers=numbers, alt_number=alt_number, buffer_size=buffer_size,
chunk_length=chunk_length, fills=fills, region=region, tabix=tabix,
samples=samples, transformers=transformers
)
# handle field renaming
if rename_fields:
rename_fields, it = _do_rename(it, fields=fields,
rename_fields=rename_fields,
headers=headers)
# setup progress logging
if log is not None:
it = _chunk_iter_progress(it, log, prefix='[read_vcf]')
# read all chunks into a list
chunks = [d[0] for d in it]
if chunks:
# setup output
output = dict()
if len(samples) > 0 and store_samples:
output['samples'] = samples
# find array keys
keys = sorted(chunks[0].keys())
# concatenate chunks
for k in keys:
output[k] = np.concatenate([chunk[k] for chunk in chunks], axis=0)
else:
output = None
return output | [
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.. versionchanged:: 1.12.0
Now returns None if no variants are found in the VCF file or matching the
requested region.
Parameters
----------
input : string or file-like
{input}
fields : list of strings, optional
{fields}
exclude_fields : list of strings, optional
{exclude_fields}
rename_fields : dict[str -> str], optional
{rename_fields}
types : dict, optional
{types}
numbers : dict, optional
{numbers}
alt_number : int, optional
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fills : dict, optional
{fills}
region : string, optional
{region}
tabix : string, optional
{tabix}
samples : list of strings
{samples}
transformers : list of transformer objects, optional
{transformers}
buffer_size : int, optional
{buffer_size}
chunk_length : int, optional
{chunk_length}
log : file-like, optional
{log}
Returns
-------
data : dict[str, ndarray]
A dictionary holding arrays, or None if no variants were found. | [
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"arrays",
"."
] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/io/vcf_read.py#L240-L345 | train | Read data from a VCF file into NumPy arrays. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x31' + '\x36' + '\063', 0o10), nzTpIcepk0o8('\x30' + chr(364 - 253) + chr(247 - 197) + '\064' + '\063', 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + '\063' + chr(51) + chr(49), 0o10), nzTpIcepk0o8('\x30' + chr(0b1001010 + 0o45) + '\x33' + '\x33' + chr(0b110101), 0o10), nzTpIcepk0o8(chr(48) + chr(0b10010 + 0o135) + '\x32' + chr(0b110111) + chr(0b110 + 0o53), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\063' + chr(0b10 + 0o57) + chr(1324 - 1275), 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(55) + chr(0b110001), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110001) + chr(0b10001 + 0o40) + chr(55), 47598 - 47590), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x32' + chr(0b100111 + 0o11) + '\060', 38296 - 38288), nzTpIcepk0o8('\x30' + chr(10364 - 10253) + chr(51), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x33' + chr(50) + chr(55), 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110011) + chr(0b110000) + chr(49), 0b1000), nzTpIcepk0o8('\060' + chr(0b11100 + 0o123) + chr(1904 - 1855) + '\x37' + chr(0b110011), 0o10), nzTpIcepk0o8(chr(971 - 923) + chr(0b1011100 + 0o23) + chr(51) + chr(0b10010 + 0o42) + chr(48), 0o10), nzTpIcepk0o8('\x30' + chr(0b10000 + 0o137) + chr(0b110001) + chr(53) + chr(50), ord("\x08")), nzTpIcepk0o8(chr(0b10100 + 0o34) + '\x6f' + chr(0b100101 + 0o14) + '\061' + chr(52), 10162 - 10154), nzTpIcepk0o8('\060' + '\x6f' + chr(50) + '\x33' + '\x36', 5835 - 5827), nzTpIcepk0o8(chr(0b11011 + 0o25) + chr(0b1101111) + chr(0b110001) + chr(51) + '\061', 38967 - 38959), nzTpIcepk0o8('\060' + '\x6f' + chr(0b0 + 0o66) + chr(50), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\064' + chr(48), 0o10), nzTpIcepk0o8(chr(1547 - 1499) + '\x6f' + chr(49) + '\061' + chr(2367 - 2317), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(49) + chr(594 - 542), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b10111 + 0o34) + chr(52) + chr(51), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(1207 - 1096) + chr(0b110000 + 0o1) + chr(53) + chr(0b10011 + 0o40), 0o10), nzTpIcepk0o8(chr(48) + chr(0b11001 + 0o126) + chr(0b11 + 0o60) + chr(54) + chr(1742 - 1687), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\063' + chr(55) + chr(48), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1010011 + 0o34) + chr(0b110010) + chr(53) + chr(0b11110 + 0o30), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(50) + '\x30' + '\x34', 0b1000), nzTpIcepk0o8(chr(1438 - 1390) + chr(0b10100 + 0o133) + chr(0b0 + 0o63) + chr(0b1111 + 0o50) + chr(0b110110), 59484 - 59476), nzTpIcepk0o8('\x30' + chr(644 - 533) + chr(0b11111 + 0o22) + chr(0b101001 + 0o10) + chr(55), 8), nzTpIcepk0o8(chr(48) + chr(0b1001100 + 0o43) + '\x37' + chr(2482 - 2427), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x32' + chr(55) + chr(244 - 189), 0b1000), nzTpIcepk0o8(chr(0b10010 + 0o36) + chr(111) + chr(143 - 89) + chr(886 - 832), 0o10), nzTpIcepk0o8(chr(0b1000 + 0o50) + '\157' + chr(293 - 242) + chr(0b10100 + 0o36), ord("\x08")), nzTpIcepk0o8(chr(326 - 278) + '\x6f' + '\061' + '\x31' + chr(0b110100), 8), nzTpIcepk0o8(chr(48) + '\157' + '\062' + chr(50), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(51) + '\x37' + chr(2013 - 1964), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(690 - 641) + chr(53), 0o10), nzTpIcepk0o8(chr(0b101011 + 0o5) + chr(0b1101111) + '\x33' + chr(48) + chr(2188 - 2133), ord("\x08")), nzTpIcepk0o8('\x30' + chr(2078 - 1967) + '\x32' + '\062' + chr(52), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(789 - 736) + chr(0b1010 + 0o46), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b']'), chr(0b10001 + 0o123) + chr(101) + chr(0b1100011) + '\157' + chr(0b1100100) + chr(101))('\x75' + chr(0b1011100 + 0o30) + chr(0b1100110) + '\055' + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def dJcAjb1PAC11(QnTXOd5N96r1, ZXDdzgbdtBfz=None, m7febIoEHkQl=None, X719Kkz4Qu_5=None, DzfuqSe6qH0o=None, vlxREQkYI3ar=None, ylss10JPIXgG=VtSJAdWbO3vK, tZ41UfIgDZkG=None, SiTpDn8thAb3=None, zDhdJKI1a4t1=roI3spqORKae(ES5oEprVxulp(b'\x07\xc2\xbb\xb4\xc1'), '\144' + '\x65' + '\x63' + '\x6f' + '\x64' + chr(101))(chr(0b1110101) + chr(0b1110100) + '\x66' + chr(0b1001 + 0o44) + chr(1721 - 1665)), BSbljhMZAGaC=None, AllcsXRtujK_=None, hG3E2obYFZMl=OFzsXuzIcuuU, Rv_V5730xaZB=rhI5nb3QnemL, lmiGj7TonZgV=None):
(a6mfQSAdDiNA, ZXDdzgbdtBfz) = VUIwV6a3wMvG(ZXDdzgbdtBfz)
(ZXDdzgbdtBfz, BSbljhMZAGaC, UyworZfslHjc, NOukaRmWFG1j) = v5AmWdIIYZEI(input=QnTXOd5N96r1, fields=ZXDdzgbdtBfz, exclude_fields=m7febIoEHkQl, types=DzfuqSe6qH0o, numbers=vlxREQkYI3ar, alt_number=ylss10JPIXgG, buffer_size=hG3E2obYFZMl, chunk_length=Rv_V5730xaZB, fills=tZ41UfIgDZkG, region=SiTpDn8thAb3, tabix=zDhdJKI1a4t1, samples=BSbljhMZAGaC, transformers=AllcsXRtujK_)
if X719Kkz4Qu_5:
(X719Kkz4Qu_5, NOukaRmWFG1j) = VIBhxIrT_PjM(NOukaRmWFG1j, fields=ZXDdzgbdtBfz, rename_fields=X719Kkz4Qu_5, headers=UyworZfslHjc)
if lmiGj7TonZgV is not None:
NOukaRmWFG1j = _Inj3jb7axrv(NOukaRmWFG1j, lmiGj7TonZgV, prefix=roI3spqORKae(ES5oEprVxulp(b'(\xd1\xbc\xbc\xdd\x96O,\xe6^'), chr(0b1000010 + 0o42) + '\145' + '\143' + chr(4372 - 4261) + chr(0b1100100) + '\145')(chr(0b1001000 + 0o55) + '\164' + chr(2920 - 2818) + chr(45) + chr(56)))
oZNsnwnkWZSh = [vPPlOXQgR3SM[nzTpIcepk0o8('\x30' + chr(111) + '\060', ord("\x08"))] for vPPlOXQgR3SM in NOukaRmWFG1j]
if oZNsnwnkWZSh:
toKQXlEvBKaK = znjnJWK64FDT()
if ftfygxgFas5X(BSbljhMZAGaC) > nzTpIcepk0o8(chr(1192 - 1144) + chr(111) + chr(48), 8) and a6mfQSAdDiNA:
toKQXlEvBKaK[roI3spqORKae(ES5oEprVxulp(b'\x00\xc2\xb4\xad\xd5\xacJ'), '\x64' + chr(101) + chr(0b1100011) + '\157' + '\144' + '\145')(chr(117) + '\x74' + chr(102) + chr(127 - 82) + chr(0b101001 + 0o17))] = BSbljhMZAGaC
HOp0ZjSPeQln = V3OlOVg98A85(oZNsnwnkWZSh[nzTpIcepk0o8(chr(48) + chr(0b1000110 + 0o51) + chr(0b110000), 8)].keys())
for B6UAF1zReOyJ in HOp0ZjSPeQln:
toKQXlEvBKaK[B6UAF1zReOyJ] = nDF4gVNx0u9Q.concatenate([WckxBx1Uqdpm[B6UAF1zReOyJ] for WckxBx1Uqdpm in oZNsnwnkWZSh], axis=nzTpIcepk0o8('\060' + '\157' + chr(0b110000), 8))
else:
toKQXlEvBKaK = None
return toKQXlEvBKaK |
cggh/scikit-allel | allel/io/vcf_read.py | vcf_to_npz | def vcf_to_npz(input, output,
compressed=True,
overwrite=False,
fields=None,
exclude_fields=None,
rename_fields=None,
types=None,
numbers=None,
alt_number=DEFAULT_ALT_NUMBER,
fills=None,
region=None,
tabix=True,
samples=None,
transformers=None,
buffer_size=DEFAULT_BUFFER_SIZE,
chunk_length=DEFAULT_CHUNK_LENGTH,
log=None):
"""Read data from a VCF file into NumPy arrays and save as a .npz file.
.. versionchanged:: 1.12.0
Now will not create any output file if no variants are found in the VCF file or
matching the requested region.
Parameters
----------
input : string
{input}
output : string
{output}
compressed : bool, optional
If True (default), save with compression.
overwrite : bool, optional
{overwrite}
fields : list of strings, optional
{fields}
exclude_fields : list of strings, optional
{exclude_fields}
rename_fields : dict[str -> str], optional
{rename_fields}
types : dict, optional
{types}
numbers : dict, optional
{numbers}
alt_number : int, optional
{alt_number}
fills : dict, optional
{fills}
region : string, optional
{region}
tabix : string, optional
{tabix}
samples : list of strings
{samples}
transformers : list of transformer objects, optional
{transformers}
buffer_size : int, optional
{buffer_size}
chunk_length : int, optional
{chunk_length}
log : file-like, optional
{log}
"""
# guard condition
if not overwrite and os.path.exists(output):
raise ValueError('file exists at path %r; use overwrite=True to replace' % output)
# read all data into memory
data = read_vcf(
input=input, fields=fields, exclude_fields=exclude_fields,
rename_fields=rename_fields, types=types, numbers=numbers,
alt_number=alt_number, buffer_size=buffer_size, chunk_length=chunk_length,
log=log, fills=fills, region=region, tabix=tabix, samples=samples,
transformers=transformers
)
if data is None:
# no data, bail out
return
# setup save function
if compressed:
savez = np.savez_compressed
else:
savez = np.savez
# save as npz
savez(output, **data) | python | def vcf_to_npz(input, output,
compressed=True,
overwrite=False,
fields=None,
exclude_fields=None,
rename_fields=None,
types=None,
numbers=None,
alt_number=DEFAULT_ALT_NUMBER,
fills=None,
region=None,
tabix=True,
samples=None,
transformers=None,
buffer_size=DEFAULT_BUFFER_SIZE,
chunk_length=DEFAULT_CHUNK_LENGTH,
log=None):
"""Read data from a VCF file into NumPy arrays and save as a .npz file.
.. versionchanged:: 1.12.0
Now will not create any output file if no variants are found in the VCF file or
matching the requested region.
Parameters
----------
input : string
{input}
output : string
{output}
compressed : bool, optional
If True (default), save with compression.
overwrite : bool, optional
{overwrite}
fields : list of strings, optional
{fields}
exclude_fields : list of strings, optional
{exclude_fields}
rename_fields : dict[str -> str], optional
{rename_fields}
types : dict, optional
{types}
numbers : dict, optional
{numbers}
alt_number : int, optional
{alt_number}
fills : dict, optional
{fills}
region : string, optional
{region}
tabix : string, optional
{tabix}
samples : list of strings
{samples}
transformers : list of transformer objects, optional
{transformers}
buffer_size : int, optional
{buffer_size}
chunk_length : int, optional
{chunk_length}
log : file-like, optional
{log}
"""
# guard condition
if not overwrite and os.path.exists(output):
raise ValueError('file exists at path %r; use overwrite=True to replace' % output)
# read all data into memory
data = read_vcf(
input=input, fields=fields, exclude_fields=exclude_fields,
rename_fields=rename_fields, types=types, numbers=numbers,
alt_number=alt_number, buffer_size=buffer_size, chunk_length=chunk_length,
log=log, fills=fills, region=region, tabix=tabix, samples=samples,
transformers=transformers
)
if data is None:
# no data, bail out
return
# setup save function
if compressed:
savez = np.savez_compressed
else:
savez = np.savez
# save as npz
savez(output, **data) | [
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"numbers"... | Read data from a VCF file into NumPy arrays and save as a .npz file.
.. versionchanged:: 1.12.0
Now will not create any output file if no variants are found in the VCF file or
matching the requested region.
Parameters
----------
input : string
{input}
output : string
{output}
compressed : bool, optional
If True (default), save with compression.
overwrite : bool, optional
{overwrite}
fields : list of strings, optional
{fields}
exclude_fields : list of strings, optional
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rename_fields : dict[str -> str], optional
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region : string, optional
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tabix : string, optional
{tabix}
samples : list of strings
{samples}
transformers : list of transformer objects, optional
{transformers}
buffer_size : int, optional
{buffer_size}
chunk_length : int, optional
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{log} | [
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"file",
"."
] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/io/vcf_read.py#L375-L463 | train | Read data from a VCF file into NumPy arrays and save as a. npz 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' + '\x6f' + '\x30', 52172 - 52164), nzTpIcepk0o8(chr(0b110000) + chr(3725 - 3614) + '\063' + chr(0b110111) + chr(877 - 824), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + '\x32', 0o10), nzTpIcepk0o8('\060' + chr(11940 - 11829) + chr(50) + '\060' + '\062', 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(50) + chr(0b110110) + chr(51), ord("\x08")), nzTpIcepk0o8('\x30' + chr(8160 - 8049) + chr(1753 - 1704) + '\061' + chr(0b101001 + 0o12), 0o10), nzTpIcepk0o8(chr(323 - 275) + '\157' + chr(51) + '\060', 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b10101 + 0o36) + chr(52) + chr(53), 0o10), nzTpIcepk0o8(chr(0b100011 + 0o15) + chr(4085 - 3974) + chr(50) + '\060' + chr(55), 0b1000), nzTpIcepk0o8(chr(0b1 + 0o57) + chr(111) + '\x31' + '\064' + chr(2022 - 1967), 2278 - 2270), nzTpIcepk0o8(chr(0b110000) + chr(6662 - 6551) + '\x33' + '\x35' + chr(0b110001), 10173 - 10165), nzTpIcepk0o8(chr(0b110 + 0o52) + '\157' + chr(0b11101 + 0o24) + '\x31' + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(0b111 + 0o51) + '\157' + chr(51) + '\065' + chr(53), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b101010 + 0o10) + chr(52) + '\065', 57958 - 57950), nzTpIcepk0o8(chr(833 - 785) + '\157' + chr(51) + chr(0b110001) + chr(0b10 + 0o64), 0b1000), nzTpIcepk0o8(chr(1110 - 1062) + '\x6f' + '\x31' + chr(53) + chr(0b110101), 0o10), nzTpIcepk0o8('\x30' + '\157' + '\x32' + chr(987 - 937) + '\061', 44068 - 44060), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110011) + chr(0b110101), 25904 - 25896), nzTpIcepk0o8('\x30' + chr(0b10100 + 0o133) + chr(0b110001) + chr(1643 - 1589), 0o10), nzTpIcepk0o8('\060' + chr(0b1000 + 0o147) + chr(50) + chr(0b10010 + 0o44) + chr(52), 27123 - 27115), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b1000 + 0o52) + chr(0b10 + 0o60) + '\x30', 0o10), nzTpIcepk0o8(chr(0b10110 + 0o32) + '\157' + '\062' + chr(0b110010) + chr(2316 - 2262), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b100110 + 0o111) + chr(49) + chr(0b110001), 2965 - 2957), nzTpIcepk0o8(chr(0b110000) + chr(9482 - 9371) + chr(159 - 109) + chr(0b110 + 0o60) + chr(0b100000 + 0o22), 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(1878 - 1828) + chr(50) + chr(49), 8), nzTpIcepk0o8(chr(575 - 527) + chr(111) + chr(50), 8), nzTpIcepk0o8(chr(48) + chr(0b1101001 + 0o6) + chr(0b1010 + 0o47) + chr(51) + chr(568 - 519), 57656 - 57648), nzTpIcepk0o8(chr(48) + chr(12044 - 11933) + chr(0b100110 + 0o14) + chr(0b110111) + chr(0b110100), 0o10), nzTpIcepk0o8(chr(0b110000 + 0o0) + chr(111) + chr(50) + chr(0b100101 + 0o13) + chr(50), 8), nzTpIcepk0o8('\x30' + '\157' + chr(0b110001), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + '\066' + '\x35', 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(0b10011 + 0o37) + chr(48) + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x32' + chr(54) + chr(215 - 167), ord("\x08")), nzTpIcepk0o8(chr(0b101010 + 0o6) + chr(0b1100010 + 0o15) + chr(49) + '\x35' + '\x33', 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(0b100000 + 0o22) + chr(0b110100) + '\067', 0o10), nzTpIcepk0o8('\x30' + chr(0b111101 + 0o62) + chr(0b110001) + chr(1144 - 1096) + '\061', 0b1000), nzTpIcepk0o8(chr(48) + '\157' + '\063' + chr(0b101010 + 0o7) + chr(2775 - 2720), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(593 - 542) + chr(0b110011) + '\066', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(49) + '\x34' + '\x34', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110011) + chr(997 - 943) + '\x37', 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(9131 - 9020) + chr(0b110101) + chr(48), ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'.'), chr(0b111110 + 0o46) + chr(9216 - 9115) + chr(99) + '\157' + '\x64' + chr(101))(chr(0b1010010 + 0o43) + chr(0b1110100) + '\146' + chr(0b101010 + 0o3) + chr(0b100110 + 0o22)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def kx7ibUEstj2S(QnTXOd5N96r1, toKQXlEvBKaK, jDmXwRv7MD8b=nzTpIcepk0o8(chr(1177 - 1129) + chr(111) + chr(0b110001), 8), JewFVgkSGnBd=nzTpIcepk0o8(chr(48) + '\x6f' + chr(929 - 881), 8), ZXDdzgbdtBfz=None, m7febIoEHkQl=None, X719Kkz4Qu_5=None, DzfuqSe6qH0o=None, vlxREQkYI3ar=None, ylss10JPIXgG=VtSJAdWbO3vK, tZ41UfIgDZkG=None, SiTpDn8thAb3=None, zDhdJKI1a4t1=nzTpIcepk0o8(chr(975 - 927) + chr(111) + '\x31', 8), BSbljhMZAGaC=None, AllcsXRtujK_=None, hG3E2obYFZMl=OFzsXuzIcuuU, Rv_V5730xaZB=rhI5nb3QnemL, lmiGj7TonZgV=None):
if not JewFVgkSGnBd and roI3spqORKae(aHUqKstZLeS6.path, roI3spqORKae(ES5oEprVxulp(b'z\xaeK\xfb\xdd\x1bm\xa0\xf1\x0b\xb8|'), '\144' + '\x65' + chr(99) + '\x6f' + chr(0b1010000 + 0o24) + chr(9943 - 9842))('\165' + chr(0b1110100) + chr(8697 - 8595) + chr(1169 - 1124) + chr(0b11 + 0o65)))(toKQXlEvBKaK):
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'f\x94n\xe7\x93.`\x8c\xf4\x13\x9ah\x8c\xd1\xee\x1d\xf0if\x94\xb5\xe42\x92\xe4q<\x9c\xedwP\xf1\xc7\x19\xce5\xaa\xe30\x85u\x98"\xf6\xdckj\x80\xf7\x0b\x88+\x88'), chr(4095 - 3995) + chr(0b1100101) + chr(4828 - 4729) + chr(0b110111 + 0o70) + '\144' + '\x65')(chr(0b1111 + 0o146) + '\164' + '\146' + chr(0b101101) + chr(627 - 571)) % toKQXlEvBKaK)
FfKOThdpoDTb = dJcAjb1PAC11(input=QnTXOd5N96r1, fields=ZXDdzgbdtBfz, exclude_fields=m7febIoEHkQl, rename_fields=X719Kkz4Qu_5, types=DzfuqSe6qH0o, numbers=vlxREQkYI3ar, alt_number=ylss10JPIXgG, buffer_size=hG3E2obYFZMl, chunk_length=Rv_V5730xaZB, log=lmiGj7TonZgV, fills=tZ41UfIgDZkG, region=SiTpDn8thAb3, tabix=zDhdJKI1a4t1, samples=BSbljhMZAGaC, transformers=AllcsXRtujK_)
if FfKOThdpoDTb is None:
return
if jDmXwRv7MD8b:
FEs9i6EwoWJD = nDF4gVNx0u9Q.savez_compressed
else:
FEs9i6EwoWJD = nDF4gVNx0u9Q.savez
FEs9i6EwoWJD(toKQXlEvBKaK, **FfKOThdpoDTb) |
cggh/scikit-allel | allel/io/vcf_read.py | vcf_to_hdf5 | def vcf_to_hdf5(input, output,
group='/',
compression='gzip',
compression_opts=1,
shuffle=False,
overwrite=False,
vlen=True,
fields=None,
exclude_fields=None,
rename_fields=None,
types=None,
numbers=None,
alt_number=DEFAULT_ALT_NUMBER,
fills=None,
region=None,
tabix='tabix',
samples=None,
transformers=None,
buffer_size=DEFAULT_BUFFER_SIZE,
chunk_length=DEFAULT_CHUNK_LENGTH,
chunk_width=DEFAULT_CHUNK_WIDTH,
log=None):
"""Read data from a VCF file and load into an HDF5 file.
.. versionchanged:: 1.12.0
Now will not create any output file if no variants are found in the VCF file or
matching the requested region.
Parameters
----------
input : string
{input}
output : string
{output}
group : string
Group within destination HDF5 file to store data in.
compression : string
Compression algorithm, e.g., 'gzip' (default).
compression_opts : int
Compression level, e.g., 1 (default).
shuffle : bool
Use byte shuffling, which may improve compression (default is False).
overwrite : bool
{overwrite}
vlen : bool
If True, store variable length strings. Note that there is considerable storage
overhead for variable length strings in HDF5, and leaving this option as True (
default) may lead to large file sizes. If False, all strings will be stored in
the HDF5 file as fixed length strings, even if they are specified as 'object'
type. In this case, the string length for any field with 'object' type will be
determined based on the maximum length of strings found in the first chunk,
and this may cause values to be truncated if longer values are found in later
chunks. To avoid truncation and large file sizes, manually set the type for all
string fields to an explicit fixed length string type, e.g., 'S10' for a field
where you know at most 10 characters are required.
fields : list of strings, optional
{fields}
exclude_fields : list of strings, optional
{exclude_fields}
rename_fields : dict[str -> str], optional
{rename_fields}
types : dict, optional
{types}
numbers : dict, optional
{numbers}
alt_number : int, optional
{alt_number}
fills : dict, optional
{fills}
region : string, optional
{region}
tabix : string, optional
{tabix}
samples : list of strings
{samples}
transformers : list of transformer objects, optional
{transformers}
buffer_size : int, optional
{buffer_size}
chunk_length : int, optional
{chunk_length}
chunk_width : int, optional
{chunk_width}
log : file-like, optional
{log}
"""
import h5py
# samples requested?
# noinspection PyTypeChecker
store_samples, fields = _prep_fields_param(fields)
# setup chunk iterator
fields, samples, headers, it = iter_vcf_chunks(
input, fields=fields, exclude_fields=exclude_fields, types=types,
numbers=numbers, alt_number=alt_number, buffer_size=buffer_size,
chunk_length=chunk_length, fills=fills, region=region, tabix=tabix,
samples=samples, transformers=transformers
)
# handle field renaming
if rename_fields:
rename_fields, it = _do_rename(it, fields=fields,
rename_fields=rename_fields,
headers=headers)
# setup progress logging
if log is not None:
it = _chunk_iter_progress(it, log, prefix='[vcf_to_hdf5]')
# read first chunk
try:
chunk, _, _, _ = next(it)
except StopIteration:
# no data, bail out
return
with h5py.File(output, mode='a') as h5f:
# obtain root group that data will be stored into
root = h5f.require_group(group)
if len(samples) > 0 and store_samples:
# store samples
name = 'samples'
if name in root:
if overwrite:
del root[name]
else:
raise ValueError(
'dataset exists at path %r; use overwrite=True to replace' % name)
if samples.dtype.kind == 'O':
if vlen:
t = h5py.special_dtype(vlen=str)
else:
samples = samples.astype('S')
t = samples.dtype
else:
t = samples.dtype
root.create_dataset(name, data=samples, chunks=None, dtype=t)
# setup datasets
# noinspection PyTypeChecker
keys = _hdf5_setup_datasets(
chunk=chunk, root=root, chunk_length=chunk_length, chunk_width=chunk_width,
compression=compression, compression_opts=compression_opts, shuffle=shuffle,
overwrite=overwrite, headers=headers, vlen=vlen
)
# store first chunk
_hdf5_store_chunk(root, keys, chunk, vlen)
# store remaining chunks
for chunk, _, _, _ in it:
_hdf5_store_chunk(root, keys, chunk, vlen) | python | def vcf_to_hdf5(input, output,
group='/',
compression='gzip',
compression_opts=1,
shuffle=False,
overwrite=False,
vlen=True,
fields=None,
exclude_fields=None,
rename_fields=None,
types=None,
numbers=None,
alt_number=DEFAULT_ALT_NUMBER,
fills=None,
region=None,
tabix='tabix',
samples=None,
transformers=None,
buffer_size=DEFAULT_BUFFER_SIZE,
chunk_length=DEFAULT_CHUNK_LENGTH,
chunk_width=DEFAULT_CHUNK_WIDTH,
log=None):
"""Read data from a VCF file and load into an HDF5 file.
.. versionchanged:: 1.12.0
Now will not create any output file if no variants are found in the VCF file or
matching the requested region.
Parameters
----------
input : string
{input}
output : string
{output}
group : string
Group within destination HDF5 file to store data in.
compression : string
Compression algorithm, e.g., 'gzip' (default).
compression_opts : int
Compression level, e.g., 1 (default).
shuffle : bool
Use byte shuffling, which may improve compression (default is False).
overwrite : bool
{overwrite}
vlen : bool
If True, store variable length strings. Note that there is considerable storage
overhead for variable length strings in HDF5, and leaving this option as True (
default) may lead to large file sizes. If False, all strings will be stored in
the HDF5 file as fixed length strings, even if they are specified as 'object'
type. In this case, the string length for any field with 'object' type will be
determined based on the maximum length of strings found in the first chunk,
and this may cause values to be truncated if longer values are found in later
chunks. To avoid truncation and large file sizes, manually set the type for all
string fields to an explicit fixed length string type, e.g., 'S10' for a field
where you know at most 10 characters are required.
fields : list of strings, optional
{fields}
exclude_fields : list of strings, optional
{exclude_fields}
rename_fields : dict[str -> str], optional
{rename_fields}
types : dict, optional
{types}
numbers : dict, optional
{numbers}
alt_number : int, optional
{alt_number}
fills : dict, optional
{fills}
region : string, optional
{region}
tabix : string, optional
{tabix}
samples : list of strings
{samples}
transformers : list of transformer objects, optional
{transformers}
buffer_size : int, optional
{buffer_size}
chunk_length : int, optional
{chunk_length}
chunk_width : int, optional
{chunk_width}
log : file-like, optional
{log}
"""
import h5py
# samples requested?
# noinspection PyTypeChecker
store_samples, fields = _prep_fields_param(fields)
# setup chunk iterator
fields, samples, headers, it = iter_vcf_chunks(
input, fields=fields, exclude_fields=exclude_fields, types=types,
numbers=numbers, alt_number=alt_number, buffer_size=buffer_size,
chunk_length=chunk_length, fills=fills, region=region, tabix=tabix,
samples=samples, transformers=transformers
)
# handle field renaming
if rename_fields:
rename_fields, it = _do_rename(it, fields=fields,
rename_fields=rename_fields,
headers=headers)
# setup progress logging
if log is not None:
it = _chunk_iter_progress(it, log, prefix='[vcf_to_hdf5]')
# read first chunk
try:
chunk, _, _, _ = next(it)
except StopIteration:
# no data, bail out
return
with h5py.File(output, mode='a') as h5f:
# obtain root group that data will be stored into
root = h5f.require_group(group)
if len(samples) > 0 and store_samples:
# store samples
name = 'samples'
if name in root:
if overwrite:
del root[name]
else:
raise ValueError(
'dataset exists at path %r; use overwrite=True to replace' % name)
if samples.dtype.kind == 'O':
if vlen:
t = h5py.special_dtype(vlen=str)
else:
samples = samples.astype('S')
t = samples.dtype
else:
t = samples.dtype
root.create_dataset(name, data=samples, chunks=None, dtype=t)
# setup datasets
# noinspection PyTypeChecker
keys = _hdf5_setup_datasets(
chunk=chunk, root=root, chunk_length=chunk_length, chunk_width=chunk_width,
compression=compression, compression_opts=compression_opts, shuffle=shuffle,
overwrite=overwrite, headers=headers, vlen=vlen
)
# store first chunk
_hdf5_store_chunk(root, keys, chunk, vlen)
# store remaining chunks
for chunk, _, _, _ in it:
_hdf5_store_chunk(root, keys, chunk, vlen) | [
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"=... | Read data from a VCF file and load into an HDF5 file.
.. versionchanged:: 1.12.0
Now will not create any output file if no variants are found in the VCF file or
matching the requested region.
Parameters
----------
input : string
{input}
output : string
{output}
group : string
Group within destination HDF5 file to store data in.
compression : string
Compression algorithm, e.g., 'gzip' (default).
compression_opts : int
Compression level, e.g., 1 (default).
shuffle : bool
Use byte shuffling, which may improve compression (default is False).
overwrite : bool
{overwrite}
vlen : bool
If True, store variable length strings. Note that there is considerable storage
overhead for variable length strings in HDF5, and leaving this option as True (
default) may lead to large file sizes. If False, all strings will be stored in
the HDF5 file as fixed length strings, even if they are specified as 'object'
type. In this case, the string length for any field with 'object' type will be
determined based on the maximum length of strings found in the first chunk,
and this may cause values to be truncated if longer values are found in later
chunks. To avoid truncation and large file sizes, manually set the type for all
string fields to an explicit fixed length string type, e.g., 'S10' for a field
where you know at most 10 characters are required.
fields : list of strings, optional
{fields}
exclude_fields : list of strings, optional
{exclude_fields}
rename_fields : dict[str -> str], optional
{rename_fields}
types : dict, optional
{types}
numbers : dict, optional
{numbers}
alt_number : int, optional
{alt_number}
fills : dict, optional
{fills}
region : string, optional
{region}
tabix : string, optional
{tabix}
samples : list of strings
{samples}
transformers : list of transformer objects, optional
{transformers}
buffer_size : int, optional
{buffer_size}
chunk_length : int, optional
{chunk_length}
chunk_width : int, optional
{chunk_width}
log : file-like, optional
{log} | [
"Read",
"data",
"from",
"a",
"VCF",
"file",
"and",
"load",
"into",
"an",
"HDF5",
"file",
"."
] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/io/vcf_read.py#L600-L757 | train | Read data from a VCF file and store it into an HDF5 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('\060' + chr(0b1101111) + chr(0b110001) + '\x35' + '\x31', 0o10), nzTpIcepk0o8(chr(545 - 497) + '\157' + '\x36' + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1011011 + 0o24) + chr(50) + chr(0b101001 + 0o13) + chr(50), 50968 - 50960), nzTpIcepk0o8(chr(48) + chr(0b1011 + 0o144) + '\x32' + chr(0b110100), 0o10), nzTpIcepk0o8('\x30' + chr(4769 - 4658) + chr(144 - 90) + chr(868 - 815), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(2080 - 2025) + chr(1057 - 1006), 0o10), nzTpIcepk0o8('\060' + '\x6f' + '\x32' + chr(54) + '\x32', 44677 - 44669), nzTpIcepk0o8(chr(1269 - 1221) + '\157' + chr(0b100010 + 0o17) + chr(0b101010 + 0o7) + chr(50), 11342 - 11334), nzTpIcepk0o8(chr(0b11001 + 0o27) + chr(0b1101111) + chr(0b110011) + chr(50) + chr(1076 - 1026), 0o10), nzTpIcepk0o8(chr(0b11 + 0o55) + chr(8536 - 8425) + chr(0b1011 + 0o50) + chr(0b110001) + chr(0b100110 + 0o13), 22498 - 22490), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110010) + chr(688 - 633), 57986 - 57978), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(1111 - 1061) + chr(0b110100) + '\x36', 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(51) + '\x35' + chr(0b100011 + 0o16), 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110011) + chr(0b101 + 0o61) + '\x34', 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110010) + chr(51) + '\x32', 0o10), nzTpIcepk0o8(chr(48) + chr(6707 - 6596) + chr(0b110010 + 0o0) + chr(0b110 + 0o54) + chr(0b11010 + 0o34), 0b1000), nzTpIcepk0o8(chr(0b1111 + 0o41) + '\x6f' + '\062' + chr(0b101110 + 0o4) + chr(0b10 + 0o61), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b0 + 0o61) + chr(0b101000 + 0o15), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(2087 - 2038) + '\067' + '\x35', 0b1000), nzTpIcepk0o8('\060' + chr(0b110001 + 0o76) + chr(51) + chr(0b110011) + chr(0b10110 + 0o41), 0o10), nzTpIcepk0o8('\x30' + chr(654 - 543) + chr(754 - 703) + chr(0b110000) + chr(0b110000), 9942 - 9934), nzTpIcepk0o8(chr(48) + chr(0b1001011 + 0o44) + chr(51) + chr(0b110000) + chr(1756 - 1707), 0o10), nzTpIcepk0o8(chr(0b11001 + 0o27) + '\157' + '\x32' + '\065' + '\x33', 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(0b110010) + '\064' + chr(670 - 615), 0o10), nzTpIcepk0o8(chr(254 - 206) + chr(0b1101001 + 0o6) + chr(1175 - 1126) + '\x31' + '\065', 28194 - 28186), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\063' + chr(52) + chr(0b110100 + 0o1), 26035 - 26027), nzTpIcepk0o8('\x30' + chr(111) + '\061' + chr(50) + '\x34', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b100 + 0o55) + chr(0b110111) + '\065', 8), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b10000 + 0o42) + chr(54) + chr(54), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(51) + chr(0b110000) + chr(0b110110), ord("\x08")), nzTpIcepk0o8(chr(0b101001 + 0o7) + chr(0b111100 + 0o63) + chr(0b110011) + chr(2813 - 2759) + '\065', ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + '\x31' + chr(0b11010 + 0o35) + chr(52), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b1000 + 0o52) + '\x36' + chr(2735 - 2681), 8), nzTpIcepk0o8(chr(1034 - 986) + chr(111) + '\062' + chr(525 - 473) + chr(0b110001), 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(1272 - 1217) + chr(139 - 90), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(366 - 316) + chr(55) + chr(54), 19842 - 19834), nzTpIcepk0o8('\x30' + '\157' + chr(1987 - 1938) + '\x34', 0o10), nzTpIcepk0o8(chr(0b11110 + 0o22) + chr(0b11111 + 0o120) + chr(402 - 352) + chr(53) + chr(55), 58329 - 58321), nzTpIcepk0o8(chr(0b11 + 0o55) + chr(6964 - 6853) + '\x33' + chr(51) + '\062', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b1 + 0o62) + chr(0b101111 + 0o6) + chr(0b1 + 0o65), 46746 - 46738)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(180 - 132) + '\x6f' + chr(53) + chr(2082 - 2034), 23835 - 23827)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'G'), chr(9265 - 9165) + chr(0b1100101) + chr(0b1001110 + 0o25) + chr(0b1101111) + '\144' + '\145')('\165' + chr(0b1110100) + chr(0b1001011 + 0o33) + '\x2d' + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def nemRBLEvuMiC(QnTXOd5N96r1, toKQXlEvBKaK, F9lJ8RbIonqb=roI3spqORKae(ES5oEprVxulp(b'F'), chr(0b1100100) + chr(6759 - 6658) + chr(99) + chr(0b1101111) + chr(0b1100100) + chr(9496 - 9395))(chr(117) + '\x74' + '\x66' + chr(74 - 29) + '\x38'), fMBaJ20ka8As=roI3spqORKae(ES5oEprVxulp(b'\x0eI\xcbd'), '\144' + '\x65' + chr(8264 - 8165) + chr(0b1101111) + chr(0b101111 + 0o65) + chr(0b1111 + 0o126))(chr(2525 - 2408) + chr(0b1000011 + 0o61) + chr(0b1100110) + '\x2d' + chr(56)), EIyuImofeDqy=nzTpIcepk0o8(chr(0b10011 + 0o35) + '\x6f' + '\x31', 0b1000), dZZw4QwP4vMc=nzTpIcepk0o8('\060' + chr(111) + chr(48), 18062 - 18054), JewFVgkSGnBd=nzTpIcepk0o8('\x30' + '\157' + chr(1620 - 1572), 8), slJqodU33FPg=nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(1499 - 1450), 8), ZXDdzgbdtBfz=None, m7febIoEHkQl=None, X719Kkz4Qu_5=None, DzfuqSe6qH0o=None, vlxREQkYI3ar=None, ylss10JPIXgG=VtSJAdWbO3vK, tZ41UfIgDZkG=None, SiTpDn8thAb3=None, zDhdJKI1a4t1=roI3spqORKae(ES5oEprVxulp(b'\x1dR\xc0}M'), chr(100) + '\145' + '\143' + '\x6f' + chr(2179 - 2079) + chr(0b1100101))('\x75' + chr(116) + '\146' + chr(0b100011 + 0o12) + chr(56)), BSbljhMZAGaC=None, AllcsXRtujK_=None, hG3E2obYFZMl=OFzsXuzIcuuU, Rv_V5730xaZB=rhI5nb3QnemL, ZEziWnPUF0VV=WNgVXP95IpJ3, lmiGj7TonZgV=None):
(RqFza2bfJyrc,) = (zGgTE_CdZfvi(roI3spqORKae(ES5oEprVxulp(b'\x01\x06\xd2m'), chr(0b1100100) + '\145' + chr(0b101111 + 0o64) + '\157' + chr(0b1100100) + chr(101))(chr(0b1101100 + 0o11) + '\164' + '\x66' + chr(530 - 485) + '\x38')),)
(a6mfQSAdDiNA, ZXDdzgbdtBfz) = VUIwV6a3wMvG(ZXDdzgbdtBfz)
(ZXDdzgbdtBfz, BSbljhMZAGaC, UyworZfslHjc, NOukaRmWFG1j) = v5AmWdIIYZEI(QnTXOd5N96r1, fields=ZXDdzgbdtBfz, exclude_fields=m7febIoEHkQl, types=DzfuqSe6qH0o, numbers=vlxREQkYI3ar, alt_number=ylss10JPIXgG, buffer_size=hG3E2obYFZMl, chunk_length=Rv_V5730xaZB, fills=tZ41UfIgDZkG, region=SiTpDn8thAb3, tabix=zDhdJKI1a4t1, samples=BSbljhMZAGaC, transformers=AllcsXRtujK_)
if X719Kkz4Qu_5:
(X719Kkz4Qu_5, NOukaRmWFG1j) = VIBhxIrT_PjM(NOukaRmWFG1j, fields=ZXDdzgbdtBfz, rename_fields=X719Kkz4Qu_5, headers=UyworZfslHjc)
if lmiGj7TonZgV is not None:
NOukaRmWFG1j = _Inj3jb7axrv(NOukaRmWFG1j, lmiGj7TonZgV, prefix=roI3spqORKae(ES5oEprVxulp(b'2E\xc1rjO\xdd\x15\xba\xadq\x93\xb4'), '\x64' + chr(101) + chr(0b1001010 + 0o31) + chr(10185 - 10074) + chr(0b1100100) + chr(101))(chr(0b1001011 + 0o52) + chr(10674 - 10558) + chr(0b1100000 + 0o6) + '\055' + chr(2399 - 2343)))
try:
(WckxBx1Uqdpm, zIqcgNgQ9U6F, zIqcgNgQ9U6F, zIqcgNgQ9U6F) = ltB3XhPy2rYf(NOukaRmWFG1j)
except ZOdpVDJPWn4I:
return
with roI3spqORKae(RqFza2bfJyrc, roI3spqORKae(ES5oEprVxulp(b'/Z\xceq'), chr(976 - 876) + chr(0b1100101) + chr(0b1100011) + chr(0b101 + 0o152) + '\144' + '\x65')('\x75' + chr(0b1110 + 0o146) + '\x66' + chr(0b100110 + 0o7) + chr(1046 - 990)))(toKQXlEvBKaK, mode=roI3spqORKae(ES5oEprVxulp(b'\x08'), chr(2970 - 2870) + chr(101) + chr(0b1100011) + '\157' + chr(0b100000 + 0o104) + '\145')('\x75' + chr(0b1110100) + chr(1425 - 1323) + chr(45) + '\x38')) as uqjdddtgqsHt:
kF9CWBi2ucGu = uqjdddtgqsHt.require_group(F9lJ8RbIonqb)
if ftfygxgFas5X(BSbljhMZAGaC) > nzTpIcepk0o8(chr(0b1010 + 0o46) + chr(11368 - 11257) + chr(0b110000), 8) and a6mfQSAdDiNA:
SLVB2BPA_mIe = roI3spqORKae(ES5oEprVxulp(b'\x1aR\xcfdY^\xc1'), chr(0b110001 + 0o63) + chr(0b1100101) + chr(99) + chr(2627 - 2516) + chr(7395 - 7295) + '\x65')(chr(0b1110101) + '\x74' + '\x66' + chr(0b11011 + 0o22) + chr(56))
if SLVB2BPA_mIe in kF9CWBi2ucGu:
if JewFVgkSGnBd:
del kF9CWBi2ucGu[SLVB2BPA_mIe]
else:
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'\rR\xd6uF^\xc6j\xb7\xb1~\xd5\x9d\x87\xba\xf7\xe7-\r\xbe\xb4\xa9\x8b\x82?\xdet\x08\xc5\xa3\xd5\x13\xc0\xc4K\xc9~\xc6\xae\x8bTg\xd0aP\x1b\xc6%\xf2\xbbr\xd6\x85\x95\xf9\xf3'), '\144' + chr(289 - 188) + chr(0b1000 + 0o133) + '\x6f' + chr(7271 - 7171) + chr(2990 - 2889))(chr(117) + chr(116) + chr(0b1100110) + chr(0b101101) + '\070') % SLVB2BPA_mIe)
if roI3spqORKae(BSbljhMZAGaC.dtype, roI3spqORKae(ES5oEprVxulp(b'<R\xd8R\x01\t\x84(\xa7\x8br\xf5'), '\x64' + chr(0b11110 + 0o107) + '\143' + chr(0b1000110 + 0o51) + chr(0b1100100) + '\145')('\x75' + chr(0b1110100) + chr(0b1001001 + 0o35) + chr(0b101101) + chr(0b111000))) == roI3spqORKae(ES5oEprVxulp(b'&'), chr(0b111111 + 0o45) + chr(1082 - 981) + chr(0b101101 + 0o66) + chr(6127 - 6016) + chr(100) + '\145')('\x75' + chr(10548 - 10432) + '\146' + chr(1741 - 1696) + '\x38'):
if slJqodU33FPg:
h3Vc_4wxEbgd = RqFza2bfJyrc.special_dtype(vlen=N9zlRy29S1SS)
else:
BSbljhMZAGaC = BSbljhMZAGaC.xqAChpcBkssb(roI3spqORKae(ES5oEprVxulp(b':'), chr(0b1100100) + chr(101) + chr(0b1100011) + chr(111) + chr(0b10 + 0o142) + chr(101))(chr(0b1000100 + 0o61) + chr(3329 - 3213) + chr(0b111000 + 0o56) + chr(0b11000 + 0o25) + chr(56)))
h3Vc_4wxEbgd = BSbljhMZAGaC.RcX9bbuOzh5L
else:
h3Vc_4wxEbgd = BSbljhMZAGaC.RcX9bbuOzh5L
roI3spqORKae(kF9CWBi2ucGu, roI3spqORKae(ES5oEprVxulp(b'\nA\xc7uA^\xed.\xb3\xbdv\xd5\x8c\x80'), chr(576 - 476) + '\145' + chr(99) + chr(111) + chr(5445 - 5345) + chr(1066 - 965))('\x75' + chr(3098 - 2982) + chr(102) + chr(0b100100 + 0o11) + '\x38'))(SLVB2BPA_mIe, data=BSbljhMZAGaC, chunks=None, dtype=h3Vc_4wxEbgd)
HOp0ZjSPeQln = VKUVwFnHx5vV(chunk=WckxBx1Uqdpm, root=kF9CWBi2ucGu, chunk_length=Rv_V5730xaZB, chunk_width=ZEziWnPUF0VV, compression=fMBaJ20ka8As, compression_opts=EIyuImofeDqy, shuffle=dZZw4QwP4vMc, overwrite=JewFVgkSGnBd, headers=UyworZfslHjc, vlen=slJqodU33FPg)
tyLqitWY7I6o(kF9CWBi2ucGu, HOp0ZjSPeQln, WckxBx1Uqdpm, slJqodU33FPg)
for (WckxBx1Uqdpm, zIqcgNgQ9U6F, zIqcgNgQ9U6F, zIqcgNgQ9U6F) in NOukaRmWFG1j:
tyLqitWY7I6o(kF9CWBi2ucGu, HOp0ZjSPeQln, WckxBx1Uqdpm, slJqodU33FPg) |
cggh/scikit-allel | allel/io/vcf_read.py | vcf_to_zarr | def vcf_to_zarr(input, output,
group='/',
compressor='default',
overwrite=False,
fields=None,
exclude_fields=None,
rename_fields=None,
types=None,
numbers=None,
alt_number=DEFAULT_ALT_NUMBER,
fills=None,
region=None,
tabix='tabix',
samples=None,
transformers=None,
buffer_size=DEFAULT_BUFFER_SIZE,
chunk_length=DEFAULT_CHUNK_LENGTH,
chunk_width=DEFAULT_CHUNK_WIDTH,
log=None):
"""Read data from a VCF file and load into a Zarr on-disk store.
.. versionchanged:: 1.12.0
Now will not create any output files if no variants are found in the VCF file or
matching the requested region.
Parameters
----------
input : string
{input}
output : string
{output}
group : string
Group within destination Zarr hierarchy to store data in.
compressor : compressor
Compression algorithm, e.g., zarr.Blosc(cname='zstd', clevel=1, shuffle=1).
overwrite : bool
{overwrite}
fields : list of strings, optional
{fields}
exclude_fields : list of strings, optional
{exclude_fields}
rename_fields : dict[str -> str], optional
{rename_fields}
types : dict, optional
{types}
numbers : dict, optional
{numbers}
alt_number : int, optional
{alt_number}
fills : dict, optional
{fills}
region : string, optional
{region}
tabix : string, optional
{tabix}
samples : list of strings
{samples}
transformers : list of transformer objects, optional
{transformers}
buffer_size : int, optional
{buffer_size}
chunk_length : int, optional
{chunk_length}
chunk_width : int, optional
{chunk_width}
log : file-like, optional
{log}
"""
import zarr
# samples requested?
# noinspection PyTypeChecker
store_samples, fields = _prep_fields_param(fields)
# setup chunk iterator
fields, samples, headers, it = iter_vcf_chunks(
input, fields=fields, exclude_fields=exclude_fields, types=types,
numbers=numbers, alt_number=alt_number, buffer_size=buffer_size,
chunk_length=chunk_length, fills=fills, region=region, tabix=tabix,
samples=samples, transformers=transformers
)
# handle field renaming
if rename_fields:
rename_fields, it = _do_rename(it, fields=fields,
rename_fields=rename_fields,
headers=headers)
# check for any case-insensitive duplicate fields
# https://github.com/cggh/scikit-allel/issues/215
ci_field_index = defaultdict(list)
for f in fields:
if rename_fields:
f = rename_fields.get(f, f)
ci_field_index[f.lower()].append(f)
for k, v in ci_field_index.items():
if len(v) > 1:
msg = textwrap.fill(
'Found two or more fields with the same name when compared '
'case-insensitive: {!r}; this is not supported because it causes '
'problems on platforms with a case-insensitive file system, which is '
'usually the default on Windows and Mac OS. Please rename fields so they '
'are distinct under a case-insensitive comparison via the '
'rename_fields argument.'.format(v), width=80)
raise ValueError(msg)
# setup progress logging
if log is not None:
it = _chunk_iter_progress(it, log, prefix='[vcf_to_zarr]')
# read first chunk
try:
chunk, _, _, _ = next(it)
except StopIteration:
# no data, bail out
return
# open root group
root = zarr.open_group(output, mode='a', path=group)
if len(samples) > 0 and store_samples:
# store samples
if samples.dtype.kind == 'O':
if PY2:
dtype = 'unicode'
else:
dtype = 'str'
else:
dtype = samples.dtype
root.create_dataset('samples', data=samples, compressor=None, overwrite=overwrite,
dtype=dtype)
# setup datasets
# noinspection PyTypeChecker
keys = _zarr_setup_datasets(
chunk, root=root, chunk_length=chunk_length, chunk_width=chunk_width,
compressor=compressor, overwrite=overwrite, headers=headers
)
# store first chunk
_zarr_store_chunk(root, keys, chunk)
# store remaining chunks
for chunk, _, _, _ in it:
_zarr_store_chunk(root, keys, chunk) | python | def vcf_to_zarr(input, output,
group='/',
compressor='default',
overwrite=False,
fields=None,
exclude_fields=None,
rename_fields=None,
types=None,
numbers=None,
alt_number=DEFAULT_ALT_NUMBER,
fills=None,
region=None,
tabix='tabix',
samples=None,
transformers=None,
buffer_size=DEFAULT_BUFFER_SIZE,
chunk_length=DEFAULT_CHUNK_LENGTH,
chunk_width=DEFAULT_CHUNK_WIDTH,
log=None):
"""Read data from a VCF file and load into a Zarr on-disk store.
.. versionchanged:: 1.12.0
Now will not create any output files if no variants are found in the VCF file or
matching the requested region.
Parameters
----------
input : string
{input}
output : string
{output}
group : string
Group within destination Zarr hierarchy to store data in.
compressor : compressor
Compression algorithm, e.g., zarr.Blosc(cname='zstd', clevel=1, shuffle=1).
overwrite : bool
{overwrite}
fields : list of strings, optional
{fields}
exclude_fields : list of strings, optional
{exclude_fields}
rename_fields : dict[str -> str], optional
{rename_fields}
types : dict, optional
{types}
numbers : dict, optional
{numbers}
alt_number : int, optional
{alt_number}
fills : dict, optional
{fills}
region : string, optional
{region}
tabix : string, optional
{tabix}
samples : list of strings
{samples}
transformers : list of transformer objects, optional
{transformers}
buffer_size : int, optional
{buffer_size}
chunk_length : int, optional
{chunk_length}
chunk_width : int, optional
{chunk_width}
log : file-like, optional
{log}
"""
import zarr
# samples requested?
# noinspection PyTypeChecker
store_samples, fields = _prep_fields_param(fields)
# setup chunk iterator
fields, samples, headers, it = iter_vcf_chunks(
input, fields=fields, exclude_fields=exclude_fields, types=types,
numbers=numbers, alt_number=alt_number, buffer_size=buffer_size,
chunk_length=chunk_length, fills=fills, region=region, tabix=tabix,
samples=samples, transformers=transformers
)
# handle field renaming
if rename_fields:
rename_fields, it = _do_rename(it, fields=fields,
rename_fields=rename_fields,
headers=headers)
# check for any case-insensitive duplicate fields
# https://github.com/cggh/scikit-allel/issues/215
ci_field_index = defaultdict(list)
for f in fields:
if rename_fields:
f = rename_fields.get(f, f)
ci_field_index[f.lower()].append(f)
for k, v in ci_field_index.items():
if len(v) > 1:
msg = textwrap.fill(
'Found two or more fields with the same name when compared '
'case-insensitive: {!r}; this is not supported because it causes '
'problems on platforms with a case-insensitive file system, which is '
'usually the default on Windows and Mac OS. Please rename fields so they '
'are distinct under a case-insensitive comparison via the '
'rename_fields argument.'.format(v), width=80)
raise ValueError(msg)
# setup progress logging
if log is not None:
it = _chunk_iter_progress(it, log, prefix='[vcf_to_zarr]')
# read first chunk
try:
chunk, _, _, _ = next(it)
except StopIteration:
# no data, bail out
return
# open root group
root = zarr.open_group(output, mode='a', path=group)
if len(samples) > 0 and store_samples:
# store samples
if samples.dtype.kind == 'O':
if PY2:
dtype = 'unicode'
else:
dtype = 'str'
else:
dtype = samples.dtype
root.create_dataset('samples', data=samples, compressor=None, overwrite=overwrite,
dtype=dtype)
# setup datasets
# noinspection PyTypeChecker
keys = _zarr_setup_datasets(
chunk, root=root, chunk_length=chunk_length, chunk_width=chunk_width,
compressor=compressor, overwrite=overwrite, headers=headers
)
# store first chunk
_zarr_store_chunk(root, keys, chunk)
# store remaining chunks
for chunk, _, _, _ in it:
_zarr_store_chunk(root, keys, chunk) | [
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.. versionchanged:: 1.12.0
Now will not create any output files if no variants are found in the VCF file or
matching the requested region.
Parameters
----------
input : string
{input}
output : string
{output}
group : string
Group within destination Zarr hierarchy to store data in.
compressor : compressor
Compression algorithm, e.g., zarr.Blosc(cname='zstd', clevel=1, shuffle=1).
overwrite : bool
{overwrite}
fields : list of strings, optional
{fields}
exclude_fields : list of strings, optional
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types : dict, optional
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numbers : dict, optional
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alt_number : int, optional
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fills : dict, optional
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region : string, optional
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tabix : string, optional
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samples : list of strings
{samples}
transformers : list of transformer objects, optional
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"."
] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/io/vcf_read.py#L846-L993 | train | Read data from a VCF file and load into a Zarr on - disk store. | 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(1742 - 1694) + '\157' + chr(49) + chr(1927 - 1874) + chr(1879 - 1830), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1100000 + 0o17) + chr(1642 - 1588) + chr(0b110111), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(0b10 + 0o60) + chr(51) + chr(50), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1000100 + 0o53) + '\061' + chr(0b1011 + 0o47) + '\061', ord("\x08")), nzTpIcepk0o8(chr(0b100001 + 0o17) + chr(0b1101111) + chr(0b110010 + 0o0) + chr(360 - 309) + chr(0b101001 + 0o16), 9825 - 9817), nzTpIcepk0o8(chr(153 - 105) + chr(0b1101111) + '\x32' + '\060', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\063' + '\x32' + chr(49), 19981 - 19973), nzTpIcepk0o8('\060' + '\x6f' + '\063' + '\x31', 53134 - 53126), nzTpIcepk0o8('\x30' + '\x6f' + chr(296 - 247) + chr(2097 - 2047) + chr(50), 2516 - 2508), nzTpIcepk0o8(chr(2151 - 2103) + '\157' + chr(1272 - 1223) + chr(55) + '\x36', ord("\x08")), nzTpIcepk0o8(chr(617 - 569) + '\x6f' + chr(50) + chr(0b110001) + '\061', ord("\x08")), nzTpIcepk0o8('\x30' + chr(3026 - 2915) + '\063' + chr(0b10100 + 0o35) + '\x31', 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x33' + chr(0b10101 + 0o34) + '\065', 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b10011 + 0o40) + '\x30' + '\060', 0b1000), nzTpIcepk0o8(chr(196 - 148) + chr(12126 - 12015) + chr(50) + '\x37' + '\067', 0o10), nzTpIcepk0o8(chr(1219 - 1171) + chr(0b1101111) + chr(0b110001) + chr(0b11100 + 0o30) + chr(0b10 + 0o64), 0o10), nzTpIcepk0o8(chr(0b10 + 0o56) + '\157' + chr(0b110010) + chr(49), 0b1000), nzTpIcepk0o8('\060' + chr(0b1100101 + 0o12) + chr(1287 - 1238) + chr(54) + '\x33', 998 - 990), nzTpIcepk0o8(chr(225 - 177) + chr(0b1000 + 0o147) + '\063' + '\x34' + '\063', ord("\x08")), nzTpIcepk0o8(chr(1551 - 1503) + chr(0b1100010 + 0o15) + chr(51) + chr(0b110001) + '\060', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b100111 + 0o110) + chr(51) + chr(55) + chr(2510 - 2457), 0o10), nzTpIcepk0o8(chr(0b110000 + 0o0) + '\157' + chr(51) + chr(0b10 + 0o62), 0b1000), nzTpIcepk0o8(chr(251 - 203) + '\157' + chr(51) + chr(0b110111) + '\066', 0b1000), nzTpIcepk0o8(chr(971 - 923) + chr(111) + chr(0b10 + 0o65) + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(418 - 370) + chr(4336 - 4225) + chr(0b11010 + 0o31) + chr(0b110000 + 0o1) + '\061', 8), nzTpIcepk0o8('\x30' + chr(12083 - 11972) + '\063' + '\061' + chr(0b101011 + 0o6), 8), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(49) + chr(50) + '\x33', 61325 - 61317), nzTpIcepk0o8(chr(952 - 904) + chr(2244 - 2133) + chr(1204 - 1155) + chr(0b110100 + 0o0) + chr(0b100010 + 0o25), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(53) + '\x35', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(52) + chr(52), 0o10), nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(614 - 503) + '\062' + chr(0b110011) + chr(49), 35833 - 35825), nzTpIcepk0o8('\060' + chr(111) + '\x31' + chr(0b110111) + chr(0b110110), 8), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b1100 + 0o47) + '\061' + chr(131 - 79), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(2566 - 2515) + chr(0b11 + 0o62) + '\062', 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(1079 - 1030) + '\064' + chr(1221 - 1168), 51291 - 51283), nzTpIcepk0o8(chr(0b100000 + 0o20) + chr(0b1101111) + chr(145 - 95) + chr(502 - 453) + chr(0b110110), 0b1000), nzTpIcepk0o8('\x30' + chr(1591 - 1480) + chr(50) + chr(0b1111 + 0o50) + chr(0b110001), 0o10), nzTpIcepk0o8('\x30' + chr(0b110 + 0o151) + '\063' + '\062' + chr(0b100010 + 0o21), 0o10), nzTpIcepk0o8(chr(0b100111 + 0o11) + chr(0b1101111 + 0o0) + chr(50) + '\061' + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(633 - 585) + '\157' + '\x32' + '\064' + '\065', 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x35' + '\060', 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'G'), chr(100) + chr(0b1100101) + chr(0b1100011) + chr(0b11101 + 0o122) + chr(8908 - 8808) + chr(0b1001011 + 0o32))('\x75' + chr(10036 - 9920) + chr(0b1100110) + '\055' + chr(0b10010 + 0o46)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def dGTZ4XU_i2QR(QnTXOd5N96r1, toKQXlEvBKaK, F9lJ8RbIonqb=roI3spqORKae(ES5oEprVxulp(b'F'), '\144' + chr(452 - 351) + '\143' + chr(111) + '\144' + '\145')(chr(5222 - 5105) + '\x74' + chr(496 - 394) + chr(45) + chr(0b111000 + 0o0)), vYSmt4Hy2weS=roI3spqORKae(ES5oEprVxulp(b'\rR\xfc0\xea|\xa5'), '\144' + chr(375 - 274) + chr(99) + chr(111) + '\x64' + '\145')('\x75' + chr(0b1110010 + 0o2) + '\x66' + '\x2d' + chr(2703 - 2647)), JewFVgkSGnBd=nzTpIcepk0o8('\060' + '\157' + chr(0b110000), 0o10), ZXDdzgbdtBfz=None, m7febIoEHkQl=None, X719Kkz4Qu_5=None, DzfuqSe6qH0o=None, vlxREQkYI3ar=None, ylss10JPIXgG=VtSJAdWbO3vK, tZ41UfIgDZkG=None, SiTpDn8thAb3=None, zDhdJKI1a4t1=roI3spqORKae(ES5oEprVxulp(b'\x1dV\xf88\xe7'), '\x64' + '\x65' + chr(99) + chr(111) + chr(0b10000 + 0o124) + '\x65')('\165' + chr(0b1011111 + 0o25) + '\x66' + '\x2d' + chr(0b111 + 0o61)), BSbljhMZAGaC=None, AllcsXRtujK_=None, hG3E2obYFZMl=OFzsXuzIcuuU, Rv_V5730xaZB=rhI5nb3QnemL, ZEziWnPUF0VV=WNgVXP95IpJ3, lmiGj7TonZgV=None):
(JGLr9WXztTvP,) = (zGgTE_CdZfvi(roI3spqORKae(ES5oEprVxulp(b'\x13V\xe8#'), chr(100) + '\x65' + chr(0b101111 + 0o64) + chr(0b1101111) + chr(0b1100100) + '\x65')(chr(5586 - 5469) + '\x74' + '\x66' + chr(0b101101) + chr(2991 - 2935))),)
(a6mfQSAdDiNA, ZXDdzgbdtBfz) = VUIwV6a3wMvG(ZXDdzgbdtBfz)
(ZXDdzgbdtBfz, BSbljhMZAGaC, UyworZfslHjc, NOukaRmWFG1j) = v5AmWdIIYZEI(QnTXOd5N96r1, fields=ZXDdzgbdtBfz, exclude_fields=m7febIoEHkQl, types=DzfuqSe6qH0o, numbers=vlxREQkYI3ar, alt_number=ylss10JPIXgG, buffer_size=hG3E2obYFZMl, chunk_length=Rv_V5730xaZB, fills=tZ41UfIgDZkG, region=SiTpDn8thAb3, tabix=zDhdJKI1a4t1, samples=BSbljhMZAGaC, transformers=AllcsXRtujK_)
if X719Kkz4Qu_5:
(X719Kkz4Qu_5, NOukaRmWFG1j) = VIBhxIrT_PjM(NOukaRmWFG1j, fields=ZXDdzgbdtBfz, rename_fields=X719Kkz4Qu_5, headers=UyworZfslHjc)
VUMAfReIS7gY = mM1QxhFYKsbc(H4NoA26ON7iG)
for _R8IKF5IwAfX in ZXDdzgbdtBfz:
if X719Kkz4Qu_5:
_R8IKF5IwAfX = X719Kkz4Qu_5.GUKetu4xaGsJ(_R8IKF5IwAfX, _R8IKF5IwAfX)
roI3spqORKae(VUMAfReIS7gY[_R8IKF5IwAfX.lower()], roI3spqORKae(ES5oEprVxulp(b'!c\xc9e\xe7w\x96v8\x11\xdc\xfc'), '\144' + chr(101) + chr(0b101011 + 0o70) + chr(111) + chr(0b101011 + 0o71) + chr(0b1000000 + 0o45))(chr(0b1100 + 0o151) + chr(0b1100110 + 0o16) + chr(0b101100 + 0o72) + '\x2d' + chr(929 - 873)))(_R8IKF5IwAfX)
for (B6UAF1zReOyJ, r7AA1pbLjb44) in roI3spqORKae(VUMAfReIS7gY, roI3spqORKae(ES5oEprVxulp(b'0h\xf4\x1f\xdaj\x99-a\x08\xd1\xa0'), '\x64' + '\x65' + '\x63' + chr(5380 - 5269) + chr(0b1010110 + 0o16) + '\145')(chr(117) + chr(7207 - 7091) + chr(0b101100 + 0o72) + chr(1029 - 984) + chr(0b111000)))():
if ftfygxgFas5X(r7AA1pbLjb44) > nzTpIcepk0o8(chr(0b100 + 0o54) + chr(111) + chr(0b110001), ord("\x08")):
sldzbHve8G1S = uYu3mQtEJax0.pPmkLCVA328e(roI3spqORKae(ES5oEprVxulp(b"/X\xef?\xfb0\xa5n=^\xe6\xbb\xed\xad\xd0\x14tS\x85\xa1\x98p\x9aO\xe9\xbe:\x13E\x04\xed\x16\xa9\xca\x16\xef\xd4\xb6\xaa\xcb\x08Z\xffq\xe8x\xb4wr\x1d\xe6\xa4\xbd\xa1\xcd\x03uS\x80\xa9\x8ey\xd3U\xa7\xba6\t^M\xed\x17\xba\x8f_\xae\xc2\xf2\xf8\xd8R\x17\xee9\xf6c\xf1p!^\xe7\xa6\xb9\xe0\xcc\x13a\x03\x8c\xba\x89y\x9a\x1c\xab\xac0\x06XW\xfc^\xa5\x9eE\xed\xd8\xa6\xf9\xc0\x1a\x17\xea#\xf0r\xbd|?\r\xa9\xa6\xa3\xe0\xcf\np\x07\x85\xa7\x8fq\x8d\x1c\xbe\xa0'\x0f\rE\xb9\x1d\xad\x99\x00\xa3\xd0\xbd\xf9\xc0\x07D\xf3%\xf6f\xb494\x17\xe5\xac\xed\xb3\xc6\x15e\x16\x8e\xe4\xddk\x96U\xaa\xa1s\x0e^\x04\xec\r\xb9\x8b\t\xe2\xc0\xf3\xfe\xcd\x0c\x17\xfe4\xf9q\xa4u&^\xe6\xa7\xed\x97\xd6\x08u\x1c\x94\xbb\xdd}\x90X\xe9\x842\x04\rk\xcaP\xec\xba\t\xeb\xd8\xa0\xef\x85\x1bR\xf40\xf2u\xf1\x7f;\x1b\xe5\xad\xbe\xe0\xcc\t1\x07\x8b\xad\x84<\x9fN\xac\xe97\x0e^P\xf0\x10\xaf\x9eE\xfb\xd7\xb7\xef\xd7IV\xba2\xfec\xb44;\x10\xfa\xac\xa3\xb3\xd6\x12x\x05\x86\xe8\x9es\x93L\xa8\xbb:\x14BJ\xb9\x08\xa5\x8bE\xfa\xd1\xb6\xaa\xd7\x0cY\xfb<\xfaO\xb7p7\x12\xed\xba\xed\xa1\xcd\x01d\x1e\x86\xa6\x892"), chr(0b1100100) + chr(101) + chr(8076 - 7977) + '\x6f' + chr(0b11011 + 0o111) + chr(0b1100101))('\x75' + chr(11798 - 11682) + chr(0b1011010 + 0o14) + '\x2d' + '\x38').q33KG3foQ_CJ(r7AA1pbLjb44), width=nzTpIcepk0o8(chr(48) + '\x6f' + chr(49) + '\x32' + chr(0b101010 + 0o6), 0b1000))
raise WbNHlDKpyPtQ(sldzbHve8G1S)
if lmiGj7TonZgV is not None:
NOukaRmWFG1j = _Inj3jb7axrv(NOukaRmWFG1j, lmiGj7TonZgV, prefix=roI3spqORKae(ES5oEprVxulp(b'2A\xf97\xc0d\xbeF(\x1f\xfb\xbb\x90'), chr(5822 - 5722) + '\x65' + chr(99) + '\x6f' + chr(100) + '\x65')(chr(13005 - 12888) + chr(9743 - 9627) + chr(102) + '\055' + chr(0b111000)))
try:
(WckxBx1Uqdpm, zIqcgNgQ9U6F, zIqcgNgQ9U6F, zIqcgNgQ9U6F) = ltB3XhPy2rYf(NOukaRmWFG1j)
except ZOdpVDJPWn4I:
return
kF9CWBi2ucGu = JGLr9WXztTvP.open_group(toKQXlEvBKaK, mode=roI3spqORKae(ES5oEprVxulp(b'\x08'), '\144' + chr(4026 - 3925) + chr(99) + chr(6375 - 6264) + chr(0b1100100) + chr(8005 - 7904))('\165' + chr(116) + '\x66' + '\055' + chr(0b10 + 0o66)), path=F9lJ8RbIonqb)
if ftfygxgFas5X(BSbljhMZAGaC) > nzTpIcepk0o8(chr(1202 - 1154) + '\x6f' + '\x30', 8) and a6mfQSAdDiNA:
if roI3spqORKae(BSbljhMZAGaC.dtype, roI3spqORKae(ES5oEprVxulp(b'<V\xe0\x17\xab"\xe7{\'<\xec\x9a'), chr(0b1011010 + 0o12) + chr(0b1100101) + chr(2395 - 2296) + '\157' + '\144' + chr(0b11001 + 0o114))('\165' + '\164' + chr(102) + '\x2d' + chr(56))) == roI3spqORKae(ES5oEprVxulp(b'&'), chr(100) + chr(0b111111 + 0o46) + chr(5128 - 5029) + '\157' + chr(100) + chr(0b1010000 + 0o25))('\165' + '\164' + chr(0b11011 + 0o113) + chr(0b1 + 0o54) + '\x38'):
if rd1Zt5ggQ4Ye:
RcX9bbuOzh5L = roI3spqORKae(ES5oEprVxulp(b'\x1cY\xf32\xf0t\xb4'), chr(3593 - 3493) + chr(7389 - 7288) + '\143' + chr(0b1101111) + chr(0b1000100 + 0o40) + chr(0b1100101))('\x75' + '\x74' + chr(102) + '\x2d' + chr(0b1010 + 0o56))
else:
RcX9bbuOzh5L = roI3spqORKae(ES5oEprVxulp(b'\x1aC\xe8'), '\x64' + chr(9325 - 9224) + '\143' + '\x6f' + '\x64' + chr(101))(chr(117) + '\164' + '\x66' + chr(0b101101) + chr(2421 - 2365))
else:
RcX9bbuOzh5L = BSbljhMZAGaC.RcX9bbuOzh5L
roI3spqORKae(kF9CWBi2ucGu, roI3spqORKae(ES5oEprVxulp(b'\nE\xff0\xebu\x8e}3\n\xe8\xba\xa8\xb4'), chr(2475 - 2375) + '\145' + chr(99) + chr(7318 - 7207) + chr(100) + chr(101))('\165' + chr(0b1110100) + chr(0b1010000 + 0o26) + chr(45) + chr(56)))(roI3spqORKae(ES5oEprVxulp(b'\x1aV\xf7!\xf3u\xa2'), '\144' + chr(0b1100101) + '\143' + chr(111) + chr(0b1100 + 0o130) + '\145')(chr(0b1110101) + chr(116) + chr(4671 - 4569) + chr(45) + chr(0b111000)), data=BSbljhMZAGaC, compressor=None, overwrite=JewFVgkSGnBd, dtype=RcX9bbuOzh5L)
HOp0ZjSPeQln = bAkrEFzPBN36(WckxBx1Uqdpm, root=kF9CWBi2ucGu, chunk_length=Rv_V5730xaZB, chunk_width=ZEziWnPUF0VV, compressor=vYSmt4Hy2weS, overwrite=JewFVgkSGnBd, headers=UyworZfslHjc)
_D28b2RgY94r(kF9CWBi2ucGu, HOp0ZjSPeQln, WckxBx1Uqdpm)
for (WckxBx1Uqdpm, zIqcgNgQ9U6F, zIqcgNgQ9U6F, zIqcgNgQ9U6F) in NOukaRmWFG1j:
_D28b2RgY94r(kF9CWBi2ucGu, HOp0ZjSPeQln, WckxBx1Uqdpm) |
cggh/scikit-allel | allel/io/vcf_read.py | iter_vcf_chunks | def iter_vcf_chunks(input,
fields=None,
exclude_fields=None,
types=None,
numbers=None,
alt_number=DEFAULT_ALT_NUMBER,
fills=None,
region=None,
tabix='tabix',
samples=None,
transformers=None,
buffer_size=DEFAULT_BUFFER_SIZE,
chunk_length=DEFAULT_CHUNK_LENGTH):
"""Iterate over chunks of data from a VCF file as NumPy arrays.
Parameters
----------
input : string
{input}
fields : list of strings, optional
{fields}
exclude_fields : list of strings, optional
{exclude_fields}
types : dict, optional
{types}
numbers : dict, optional
{numbers}
alt_number : int, optional
{alt_number}
fills : dict, optional
{fills}
region : string, optional
{region}
tabix : string, optional
{tabix}
samples : list of strings
{samples}
transformers : list of transformer objects, optional
{transformers}
buffer_size : int, optional
{buffer_size}
chunk_length : int, optional
{chunk_length}
Returns
-------
fields : list of strings
Normalised names of fields that will be extracted.
samples : ndarray
Samples for which data will be extracted.
headers : VCFHeaders
Tuple of metadata extracted from VCF headers.
it : iterator
Chunk iterator.
"""
# setup commmon keyword args
kwds = dict(fields=fields, exclude_fields=exclude_fields, types=types,
numbers=numbers, alt_number=alt_number, chunk_length=chunk_length,
fills=fills, samples=samples, region=region)
# setup input stream
stream = _setup_input_stream(input=input, region=region, tabix=tabix,
buffer_size=buffer_size)
# setup iterator
fields, samples, headers, it = _iter_vcf_stream(stream, **kwds)
# setup transformers
if transformers is not None:
# API flexibility
if not isinstance(transformers, (list, tuple)):
transformers = [transformers]
for trans in transformers:
fields = trans.transform_fields(fields)
it = _chunk_iter_transform(it, transformers)
return fields, samples, headers, it | python | def iter_vcf_chunks(input,
fields=None,
exclude_fields=None,
types=None,
numbers=None,
alt_number=DEFAULT_ALT_NUMBER,
fills=None,
region=None,
tabix='tabix',
samples=None,
transformers=None,
buffer_size=DEFAULT_BUFFER_SIZE,
chunk_length=DEFAULT_CHUNK_LENGTH):
"""Iterate over chunks of data from a VCF file as NumPy arrays.
Parameters
----------
input : string
{input}
fields : list of strings, optional
{fields}
exclude_fields : list of strings, optional
{exclude_fields}
types : dict, optional
{types}
numbers : dict, optional
{numbers}
alt_number : int, optional
{alt_number}
fills : dict, optional
{fills}
region : string, optional
{region}
tabix : string, optional
{tabix}
samples : list of strings
{samples}
transformers : list of transformer objects, optional
{transformers}
buffer_size : int, optional
{buffer_size}
chunk_length : int, optional
{chunk_length}
Returns
-------
fields : list of strings
Normalised names of fields that will be extracted.
samples : ndarray
Samples for which data will be extracted.
headers : VCFHeaders
Tuple of metadata extracted from VCF headers.
it : iterator
Chunk iterator.
"""
# setup commmon keyword args
kwds = dict(fields=fields, exclude_fields=exclude_fields, types=types,
numbers=numbers, alt_number=alt_number, chunk_length=chunk_length,
fills=fills, samples=samples, region=region)
# setup input stream
stream = _setup_input_stream(input=input, region=region, tabix=tabix,
buffer_size=buffer_size)
# setup iterator
fields, samples, headers, it = _iter_vcf_stream(stream, **kwds)
# setup transformers
if transformers is not None:
# API flexibility
if not isinstance(transformers, (list, tuple)):
transformers = [transformers]
for trans in transformers:
fields = trans.transform_fields(fields)
it = _chunk_iter_transform(it, transformers)
return fields, samples, headers, it | [
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{buffer_size}
chunk_length : int, optional
{chunk_length}
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-------
fields : list of strings
Normalised names of fields that will be extracted.
samples : ndarray
Samples for which data will be extracted.
headers : VCFHeaders
Tuple of metadata extracted from VCF headers.
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ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(726 - 678) + chr(111) + '\061' + chr(1665 - 1617), 0b1000), nzTpIcepk0o8(chr(0b101000 + 0o10) + '\x6f' + '\x33' + '\x36' + chr(54), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1100101 + 0o12) + chr(0b1 + 0o60) + chr(48) + '\x32', 35898 - 35890), nzTpIcepk0o8(chr(0b11110 + 0o22) + chr(0b1101111) + chr(0b110010) + '\x36' + chr(53), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(0b101101 + 0o6) + chr(0b110010 + 0o0) + chr(0b11001 + 0o36), 2805 - 2797), nzTpIcepk0o8(chr(0b110000) + chr(0b100001 + 0o116) + '\x33' + chr(0b11000 + 0o32), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(0b10011 + 0o37) + chr(48) + chr(0b101011 + 0o6), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\061', 42854 - 42846), nzTpIcepk0o8(chr(48) + '\x6f' + chr(1075 - 1026) + chr(51) + chr(0b100111 + 0o12), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(7815 - 7704) + chr(0b110011) + chr(1370 - 1318) + '\x36', 36191 - 36183), nzTpIcepk0o8(chr(0b101101 + 0o3) + '\x6f' + '\x31' + '\064' + '\x30', ord("\x08")), nzTpIcepk0o8(chr(0b111 + 0o51) + chr(111) + chr(0b110011) + chr(0b11001 + 0o36) + '\x34', 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(1372 - 1321) + chr(0b1101 + 0o45) + chr(0b110001), 21165 - 21157), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\063' + chr(51) + '\x31', 15320 - 15312), nzTpIcepk0o8('\x30' + chr(111) + chr(0b101011 + 0o7) + chr(0b1001 + 0o50) + '\066', 22927 - 22919), nzTpIcepk0o8(chr(0b100110 + 0o12) + chr(0b1101111) + '\066' + '\x30', 0o10), nzTpIcepk0o8(chr(48) + chr(0b111110 + 0o61) + chr(51) + chr(0b110101) + chr(371 - 320), 50301 - 50293), nzTpIcepk0o8(chr(48) + chr(111) + '\x37' + chr(2375 - 2320), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(54) + '\x37', 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x33' + chr(0b110010) + '\062', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101000 + 0o7) + chr(0b110011) + '\060' + '\066', 0b1000), nzTpIcepk0o8(chr(48) + chr(313 - 202) + chr(0b110010) + chr(0b110110) + '\060', 12867 - 12859), nzTpIcepk0o8(chr(48) + chr(0b1000010 + 0o55) + chr(0b0 + 0o62) + chr(0b110011) + '\063', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(294 - 183) + '\x33' + chr(55) + '\x37', 65020 - 65012), nzTpIcepk0o8(chr(0b1011 + 0o45) + '\157' + '\062' + chr(53) + '\x35', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b11101 + 0o122) + chr(2869 - 2815) + chr(868 - 813), 8), nzTpIcepk0o8('\060' + chr(0b1001001 + 0o46) + chr(51) + chr(0b100000 + 0o27) + chr(0b110000 + 0o1), 25216 - 25208), nzTpIcepk0o8('\x30' + chr(111) + '\063' + '\x33' + chr(55), 0b1000), nzTpIcepk0o8(chr(0b101010 + 0o6) + chr(9224 - 9113) + '\061' + chr(53) + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(0b100010 + 0o16) + chr(6870 - 6759) + chr(1315 - 1262) + '\067', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(1206 - 1095) + chr(2172 - 2123) + '\066' + chr(2342 - 2292), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(51) + chr(2473 - 2420) + chr(53), 39897 - 39889), nzTpIcepk0o8(chr(48) + chr(1937 - 1826) + chr(0b111 + 0o54) + chr(0b110010) + chr(53), ord("\x08")), nzTpIcepk0o8(chr(0b11011 + 0o25) + '\157' + '\x33' + chr(0b110111) + '\x37', 8), nzTpIcepk0o8(chr(537 - 489) + '\157' + '\x35' + '\060', 5259 - 5251), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110010) + '\x33', 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(50) + chr(51) + chr(0b100110 + 0o14), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x36' + chr(0b100011 + 0o16), 0b1000), nzTpIcepk0o8(chr(327 - 279) + '\x6f' + chr(50) + chr(1263 - 1211), 0b1000), nzTpIcepk0o8('\x30' + '\157' + '\062' + '\065' + chr(0b110000), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b10001 + 0o37) + '\157' + '\065' + chr(0b110000), 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'&'), chr(0b1100100) + '\145' + '\x63' + chr(1217 - 1106) + chr(0b1100100) + '\x65')(chr(0b10000 + 0o145) + '\x74' + '\x66' + chr(0b101101) + chr(398 - 342)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def v5AmWdIIYZEI(QnTXOd5N96r1, ZXDdzgbdtBfz=None, m7febIoEHkQl=None, DzfuqSe6qH0o=None, vlxREQkYI3ar=None, ylss10JPIXgG=VtSJAdWbO3vK, tZ41UfIgDZkG=None, SiTpDn8thAb3=None, zDhdJKI1a4t1=roI3spqORKae(ES5oEprVxulp(b'|\x97 \xdc\xaf'), '\x64' + chr(0b1110 + 0o127) + chr(574 - 475) + '\x6f' + chr(0b1010011 + 0o21) + '\145')(chr(117) + chr(0b1110100) + chr(537 - 435) + '\x2d' + chr(56)), BSbljhMZAGaC=None, AllcsXRtujK_=None, hG3E2obYFZMl=OFzsXuzIcuuU, Rv_V5730xaZB=rhI5nb3QnemL):
TRoKXhn8KxPi = znjnJWK64FDT(fields=ZXDdzgbdtBfz, exclude_fields=m7febIoEHkQl, types=DzfuqSe6qH0o, numbers=vlxREQkYI3ar, alt_number=ylss10JPIXgG, chunk_length=Rv_V5730xaZB, fills=tZ41UfIgDZkG, samples=BSbljhMZAGaC, region=SiTpDn8thAb3)
ztC3O2ZXmsJr = qxK6ER2ses38(input=QnTXOd5N96r1, region=SiTpDn8thAb3, tabix=zDhdJKI1a4t1, buffer_size=hG3E2obYFZMl)
(ZXDdzgbdtBfz, BSbljhMZAGaC, UyworZfslHjc, NOukaRmWFG1j) = WmOIfyYROrb_(ztC3O2ZXmsJr, **TRoKXhn8KxPi)
if AllcsXRtujK_ is not None:
if not suIjIS24Zkqw(AllcsXRtujK_, (H4NoA26ON7iG, nfNqtJL5aRaY)):
AllcsXRtujK_ = [AllcsXRtujK_]
for LfvO36Vo32Xq in AllcsXRtujK_:
ZXDdzgbdtBfz = LfvO36Vo32Xq.transform_fields(ZXDdzgbdtBfz)
NOukaRmWFG1j = YI7CU1gJUdQz(NOukaRmWFG1j, AllcsXRtujK_)
return (ZXDdzgbdtBfz, BSbljhMZAGaC, UyworZfslHjc, NOukaRmWFG1j) |
cggh/scikit-allel | allel/io/vcf_read.py | vcf_to_dataframe | def vcf_to_dataframe(input,
fields=None,
exclude_fields=None,
types=None,
numbers=None,
alt_number=DEFAULT_ALT_NUMBER,
fills=None,
region=None,
tabix='tabix',
transformers=None,
buffer_size=DEFAULT_BUFFER_SIZE,
chunk_length=DEFAULT_CHUNK_LENGTH,
log=None):
"""Read data from a VCF file into a pandas DataFrame.
Parameters
----------
input : string
{input}
fields : list of strings, optional
{fields}
exclude_fields : list of strings, optional
{exclude_fields}
types : dict, optional
{types}
numbers : dict, optional
{numbers}
alt_number : int, optional
{alt_number}
fills : dict, optional
{fills}
region : string, optional
{region}
tabix : string, optional
{tabix}
transformers : list of transformer objects, optional
{transformers}
buffer_size : int, optional
{buffer_size}
chunk_length : int, optional
{chunk_length}
log : file-like, optional
{log}
Returns
-------
df : pandas.DataFrame
"""
import pandas
# samples requested?
# noinspection PyTypeChecker
_, fields = _prep_fields_param(fields)
# setup
fields, _, _, it = iter_vcf_chunks(
input=input, fields=fields, exclude_fields=exclude_fields, types=types,
numbers=numbers, alt_number=alt_number, buffer_size=buffer_size,
chunk_length=chunk_length, fills=fills, region=region, tabix=tabix, samples=[],
transformers=transformers
)
# setup progress logging
if log is not None:
it = _chunk_iter_progress(it, log, prefix='[vcf_to_dataframe]')
# read all chunks into a list
chunks = [d[0] for d in it]
# setup output
output = None
if chunks:
# concatenate chunks
output = pandas.concat([_chunk_to_dataframe(fields, chunk)
for chunk in chunks])
return output | python | def vcf_to_dataframe(input,
fields=None,
exclude_fields=None,
types=None,
numbers=None,
alt_number=DEFAULT_ALT_NUMBER,
fills=None,
region=None,
tabix='tabix',
transformers=None,
buffer_size=DEFAULT_BUFFER_SIZE,
chunk_length=DEFAULT_CHUNK_LENGTH,
log=None):
"""Read data from a VCF file into a pandas DataFrame.
Parameters
----------
input : string
{input}
fields : list of strings, optional
{fields}
exclude_fields : list of strings, optional
{exclude_fields}
types : dict, optional
{types}
numbers : dict, optional
{numbers}
alt_number : int, optional
{alt_number}
fills : dict, optional
{fills}
region : string, optional
{region}
tabix : string, optional
{tabix}
transformers : list of transformer objects, optional
{transformers}
buffer_size : int, optional
{buffer_size}
chunk_length : int, optional
{chunk_length}
log : file-like, optional
{log}
Returns
-------
df : pandas.DataFrame
"""
import pandas
# samples requested?
# noinspection PyTypeChecker
_, fields = _prep_fields_param(fields)
# setup
fields, _, _, it = iter_vcf_chunks(
input=input, fields=fields, exclude_fields=exclude_fields, types=types,
numbers=numbers, alt_number=alt_number, buffer_size=buffer_size,
chunk_length=chunk_length, fills=fills, region=region, tabix=tabix, samples=[],
transformers=transformers
)
# setup progress logging
if log is not None:
it = _chunk_iter_progress(it, log, prefix='[vcf_to_dataframe]')
# read all chunks into a list
chunks = [d[0] for d in it]
# setup output
output = None
if chunks:
# concatenate chunks
output = pandas.concat([_chunk_to_dataframe(fields, chunk)
for chunk in chunks])
return output | [
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... | Read data from a VCF file into a pandas DataFrame.
Parameters
----------
input : string
{input}
fields : list of strings, optional
{fields}
exclude_fields : list of strings, optional
{exclude_fields}
types : dict, optional
{types}
numbers : dict, optional
{numbers}
alt_number : int, optional
{alt_number}
fills : dict, optional
{fills}
region : string, optional
{region}
tabix : string, optional
{tabix}
transformers : list of transformer objects, optional
{transformers}
buffer_size : int, optional
{buffer_size}
chunk_length : int, optional
{chunk_length}
log : file-like, optional
{log}
Returns
-------
df : pandas.DataFrame | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/io/vcf_read.py#L1801-L1881 | train | Read data from 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(0b100010 + 0o16) + chr(0b1001101 + 0o42) + '\x33' + chr(566 - 516) + chr(1272 - 1218), 0b1000), nzTpIcepk0o8(chr(0b10111 + 0o31) + chr(11577 - 11466) + chr(0b100 + 0o57) + chr(50) + chr(0b110010), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(50) + '\x37' + '\x35', 0o10), nzTpIcepk0o8(chr(0b10011 + 0o35) + chr(866 - 755) + '\061' + chr(1006 - 952) + chr(1664 - 1610), 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(0b101100 + 0o5) + chr(2316 - 2265) + chr(343 - 290), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1000100 + 0o53) + chr(49) + chr(50) + chr(51), 46069 - 46061), nzTpIcepk0o8('\x30' + chr(111) + '\x32' + '\x37' + chr(0b110100), 0o10), nzTpIcepk0o8(chr(0b100110 + 0o12) + chr(0b0 + 0o157) + chr(0b110000 + 0o4) + chr(0b110100), 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(0b10100 + 0o35) + '\x35' + chr(535 - 487), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(1243 - 1193) + chr(0b101101 + 0o7) + chr(0b110000), 0b1000), nzTpIcepk0o8(chr(0b1110 + 0o42) + chr(2960 - 2849) + chr(51) + chr(0b110101) + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(1290 - 1242) + '\157' + '\x32' + '\064' + '\062', 0o10), nzTpIcepk0o8(chr(0b10010 + 0o36) + '\157' + '\x31' + '\x37' + chr(0b110000), 0o10), nzTpIcepk0o8(chr(48) + chr(0b100001 + 0o116) + chr(50) + chr(1406 - 1353) + chr(1832 - 1783), 0b1000), nzTpIcepk0o8(chr(1286 - 1238) + '\x6f' + chr(0b11 + 0o60) + chr(0b110101) + chr(0b11110 + 0o23), 40173 - 40165), nzTpIcepk0o8(chr(0b100010 + 0o16) + chr(0b1101 + 0o142) + chr(0b110010) + chr(2695 - 2643) + '\x37', ord("\x08")), nzTpIcepk0o8(chr(363 - 315) + '\x6f' + chr(51) + '\x30' + chr(0b11000 + 0o34), 64819 - 64811), nzTpIcepk0o8('\060' + chr(111) + chr(438 - 388) + chr(55) + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(0b10011 + 0o35) + chr(0b1101010 + 0o5) + chr(442 - 392) + '\x33' + chr(1534 - 1480), 27328 - 27320), nzTpIcepk0o8('\060' + chr(0b1 + 0o156) + '\x31' + '\x37' + chr(319 - 270), 59072 - 59064), nzTpIcepk0o8(chr(48) + chr(1245 - 1134) + chr(0b11101 + 0o31) + chr(0b101000 + 0o10), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1011110 + 0o21) + chr(0b110000 + 0o3) + chr(1828 - 1780) + chr(0b110110), 0b1000), nzTpIcepk0o8(chr(0b100111 + 0o11) + '\x6f' + chr(52) + '\x37', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x32' + '\x32' + chr(49), 688 - 680), nzTpIcepk0o8(chr(1852 - 1804) + chr(0b11111 + 0o120) + '\061' + chr(1819 - 1765) + '\x35', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x37', 0b1000), nzTpIcepk0o8(chr(0b11000 + 0o30) + '\x6f' + '\x32' + chr(2008 - 1960) + chr(51), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\062' + chr(0b11101 + 0o31) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + '\x33' + '\064' + '\067', 27413 - 27405), nzTpIcepk0o8(chr(0b110000) + chr(0b11010 + 0o125) + chr(154 - 103) + '\066' + chr(0b10110 + 0o32), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110010) + chr(571 - 516), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(51) + chr(389 - 334) + chr(0b110101), 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(1803 - 1753) + chr(0b110001 + 0o3) + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(1739 - 1691) + '\x6f' + '\063' + chr(0b11010 + 0o26) + chr(54), 8), nzTpIcepk0o8('\x30' + chr(111) + chr(2835 - 2780), 8), nzTpIcepk0o8('\x30' + chr(4649 - 4538) + '\x32' + '\067', 8), nzTpIcepk0o8('\060' + '\157' + chr(0b110101), 0o10), nzTpIcepk0o8(chr(0b0 + 0o60) + chr(0b11000 + 0o127) + chr(0b110001) + '\062' + chr(0b110100), 0o10), nzTpIcepk0o8(chr(721 - 673) + '\x6f' + '\061' + chr(2567 - 2513) + chr(0b110001), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + '\x32' + chr(49) + chr(0b110001), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + chr(4703 - 4592) + chr(0b10100 + 0o41) + '\x30', 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xf8'), chr(0b110110 + 0o56) + '\145' + chr(99) + '\157' + chr(0b10001 + 0o123) + chr(0b1010 + 0o133))(chr(117) + chr(0b1110100) + '\146' + '\055' + chr(2775 - 2719)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def yNatpt70d4Iw(QnTXOd5N96r1, ZXDdzgbdtBfz=None, m7febIoEHkQl=None, DzfuqSe6qH0o=None, vlxREQkYI3ar=None, ylss10JPIXgG=VtSJAdWbO3vK, tZ41UfIgDZkG=None, SiTpDn8thAb3=None, zDhdJKI1a4t1=roI3spqORKae(ES5oEprVxulp(b'\xa2\xb3\xdf\x1f%'), '\x64' + '\145' + '\x63' + chr(9420 - 9309) + chr(100) + '\145')('\165' + chr(116) + chr(0b10111 + 0o117) + chr(255 - 210) + chr(507 - 451)), AllcsXRtujK_=None, hG3E2obYFZMl=OFzsXuzIcuuU, Rv_V5730xaZB=rhI5nb3QnemL, lmiGj7TonZgV=None):
(DlW31l1chrSA,) = (zGgTE_CdZfvi(roI3spqORKae(ES5oEprVxulp(b'\xa6\xb3\xd3\x12< '), chr(0b11011 + 0o111) + chr(1952 - 1851) + chr(0b1100010 + 0o1) + '\157' + chr(100) + chr(101))(chr(8426 - 8309) + '\x74' + '\146' + '\x2d' + chr(832 - 776))),)
(zIqcgNgQ9U6F, ZXDdzgbdtBfz) = VUIwV6a3wMvG(ZXDdzgbdtBfz)
(ZXDdzgbdtBfz, zIqcgNgQ9U6F, zIqcgNgQ9U6F, NOukaRmWFG1j) = v5AmWdIIYZEI(input=QnTXOd5N96r1, fields=ZXDdzgbdtBfz, exclude_fields=m7febIoEHkQl, types=DzfuqSe6qH0o, numbers=vlxREQkYI3ar, alt_number=ylss10JPIXgG, buffer_size=hG3E2obYFZMl, chunk_length=Rv_V5730xaZB, fills=tZ41UfIgDZkG, region=SiTpDn8thAb3, tabix=zDhdJKI1a4t1, samples=[], transformers=AllcsXRtujK_)
if lmiGj7TonZgV is not None:
NOukaRmWFG1j = _Inj3jb7axrv(NOukaRmWFG1j, lmiGj7TonZgV, prefix=roI3spqORKae(ES5oEprVxulp(b"\x8d\xa4\xde\x10\x02'\xd3{\x0c\xc1\x9e\xc3\x1e\xdb\x88\xca\xa1\xe6"), chr(0b1100100) + chr(0b1100101) + chr(0b1100011) + chr(111) + '\144' + chr(101))(chr(117) + chr(868 - 752) + chr(0b1001000 + 0o36) + '\055' + chr(1791 - 1735)))
oZNsnwnkWZSh = [vPPlOXQgR3SM[nzTpIcepk0o8('\060' + chr(0b111000 + 0o67) + chr(48), ord("\x08"))] for vPPlOXQgR3SM in NOukaRmWFG1j]
toKQXlEvBKaK = None
if oZNsnwnkWZSh:
toKQXlEvBKaK = DlW31l1chrSA.concat([y2tU0XZjykBo(ZXDdzgbdtBfz, WckxBx1Uqdpm) for WckxBx1Uqdpm in oZNsnwnkWZSh])
return toKQXlEvBKaK |
cggh/scikit-allel | allel/io/vcf_read.py | vcf_to_csv | def vcf_to_csv(input, output,
fields=None,
exclude_fields=None,
types=None,
numbers=None,
alt_number=DEFAULT_ALT_NUMBER,
fills=None,
region=None,
tabix='tabix',
transformers=None,
buffer_size=DEFAULT_BUFFER_SIZE,
chunk_length=DEFAULT_CHUNK_LENGTH,
log=None,
**kwargs):
r"""Read data from a VCF file and write out to a comma-separated values (CSV) file.
Parameters
----------
input : string
{input}
output : string
{output}
fields : list of strings, optional
{fields}
exclude_fields : list of strings, optional
{exclude_fields}
types : dict, optional
{types}
numbers : dict, optional
{numbers}
alt_number : int, optional
{alt_number}
fills : dict, optional
{fills}
region : string, optional
{region}
tabix : string, optional
{tabix}
transformers : list of transformer objects, optional
{transformers}
buffer_size : int, optional
{buffer_size}
chunk_length : int, optional
{chunk_length}
log : file-like, optional
{log}
kwargs : keyword arguments
All remaining keyword arguments are passed through to pandas.DataFrame.to_csv().
E.g., to write a tab-delimited file, provide `sep='\t'`.
"""
# samples requested?
# noinspection PyTypeChecker
_, fields = _prep_fields_param(fields)
# setup
fields, _, _, it = iter_vcf_chunks(
input=input, fields=fields, exclude_fields=exclude_fields, types=types,
numbers=numbers, alt_number=alt_number, buffer_size=buffer_size,
chunk_length=chunk_length, fills=fills, region=region, tabix=tabix, samples=[],
transformers=transformers
)
# setup progress logging
if log is not None:
it = _chunk_iter_progress(it, log, prefix='[vcf_to_csv]')
kwargs['index'] = False
for i, (chunk, _, _, _) in enumerate(it):
df = _chunk_to_dataframe(fields, chunk)
if i == 0:
kwargs['header'] = True
kwargs['mode'] = 'w'
else:
kwargs['header'] = False
kwargs['mode'] = 'a'
df.to_csv(output, **kwargs) | python | def vcf_to_csv(input, output,
fields=None,
exclude_fields=None,
types=None,
numbers=None,
alt_number=DEFAULT_ALT_NUMBER,
fills=None,
region=None,
tabix='tabix',
transformers=None,
buffer_size=DEFAULT_BUFFER_SIZE,
chunk_length=DEFAULT_CHUNK_LENGTH,
log=None,
**kwargs):
r"""Read data from a VCF file and write out to a comma-separated values (CSV) file.
Parameters
----------
input : string
{input}
output : string
{output}
fields : list of strings, optional
{fields}
exclude_fields : list of strings, optional
{exclude_fields}
types : dict, optional
{types}
numbers : dict, optional
{numbers}
alt_number : int, optional
{alt_number}
fills : dict, optional
{fills}
region : string, optional
{region}
tabix : string, optional
{tabix}
transformers : list of transformer objects, optional
{transformers}
buffer_size : int, optional
{buffer_size}
chunk_length : int, optional
{chunk_length}
log : file-like, optional
{log}
kwargs : keyword arguments
All remaining keyword arguments are passed through to pandas.DataFrame.to_csv().
E.g., to write a tab-delimited file, provide `sep='\t'`.
"""
# samples requested?
# noinspection PyTypeChecker
_, fields = _prep_fields_param(fields)
# setup
fields, _, _, it = iter_vcf_chunks(
input=input, fields=fields, exclude_fields=exclude_fields, types=types,
numbers=numbers, alt_number=alt_number, buffer_size=buffer_size,
chunk_length=chunk_length, fills=fills, region=region, tabix=tabix, samples=[],
transformers=transformers
)
# setup progress logging
if log is not None:
it = _chunk_iter_progress(it, log, prefix='[vcf_to_csv]')
kwargs['index'] = False
for i, (chunk, _, _, _) in enumerate(it):
df = _chunk_to_dataframe(fields, chunk)
if i == 0:
kwargs['header'] = True
kwargs['mode'] = 'w'
else:
kwargs['header'] = False
kwargs['mode'] = 'a'
df.to_csv(output, **kwargs) | [
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Parameters
----------
input : string
{input}
output : string
{output}
fields : list of strings, optional
{fields}
exclude_fields : list of strings, optional
{exclude_fields}
types : dict, optional
{types}
numbers : dict, optional
{numbers}
alt_number : int, optional
{alt_number}
fills : dict, optional
{fills}
region : string, optional
{region}
tabix : string, optional
{tabix}
transformers : list of transformer objects, optional
{transformers}
buffer_size : int, optional
{buffer_size}
chunk_length : int, optional
{chunk_length}
log : file-like, optional
{log}
kwargs : keyword arguments
All remaining keyword arguments are passed through to pandas.DataFrame.to_csv().
E.g., to write a tab-delimited file, provide `sep='\t'`. | [
"r",
"Read",
"data",
"from",
"a",
"VCF",
"file",
"and",
"write",
"out",
"to",
"a",
"comma",
"-",
"separated",
"values",
"(",
"CSV",
")",
"file",
"."
] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/io/vcf_read.py#L1902-L1979 | train | r Read data from a VCF file and write out to a comma - separated CSV file. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(521 - 473) + '\157' + chr(0b1100 + 0o45) + chr(0b110101) + '\064', 0b1000), nzTpIcepk0o8(chr(0b1000 + 0o50) + chr(0b1101111) + chr(1782 - 1731) + chr(0b110000) + chr(0b110001 + 0o5), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(49) + chr(1667 - 1614), 0b1000), nzTpIcepk0o8('\x30' + chr(8928 - 8817) + chr(0b110001) + chr(1823 - 1773) + '\x36', 0b1000), nzTpIcepk0o8(chr(1766 - 1718) + chr(111) + '\x37' + chr(0b110110), ord("\x08")), nzTpIcepk0o8('\x30' + chr(7826 - 7715) + '\061' + chr(55) + '\x30', ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(2818 - 2763) + '\x34', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(7695 - 7584) + chr(0b110001) + chr(0b110001) + chr(51), ord("\x08")), nzTpIcepk0o8(chr(1589 - 1541) + '\157' + chr(330 - 281) + '\x33' + chr(582 - 532), 43989 - 43981), nzTpIcepk0o8('\060' + chr(0b110111 + 0o70) + '\x32' + '\x34' + chr(0b100010 + 0o24), 0b1000), nzTpIcepk0o8(chr(0b10001 + 0o37) + chr(0b1101111) + chr(1948 - 1899) + chr(55) + chr(0b110011), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110011) + '\x34' + chr(948 - 900), 0b1000), nzTpIcepk0o8('\x30' + chr(111) + '\x33' + chr(50) + chr(0b1110 + 0o50), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(10566 - 10455) + chr(0b10010 + 0o40) + chr(0b1111 + 0o42) + '\065', 0o10), nzTpIcepk0o8(chr(1277 - 1229) + chr(111) + '\x31' + chr(0b11111 + 0o24) + '\x37', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(1572 - 1521) + chr(0b101111 + 0o4) + '\x30', 0o10), nzTpIcepk0o8('\060' + '\157' + chr(1715 - 1666) + '\x36' + '\x34', 0o10), nzTpIcepk0o8(chr(48) + chr(0b10010 + 0o135) + '\x32' + '\x31', 9074 - 9066), nzTpIcepk0o8(chr(0b110000) + chr(11807 - 11696) + chr(293 - 242) + chr(487 - 436) + chr(0b10010 + 0o41), 4706 - 4698), nzTpIcepk0o8('\x30' + chr(7588 - 7477) + chr(51) + chr(0b110100) + chr(0b11100 + 0o30), 39149 - 39141), nzTpIcepk0o8(chr(1222 - 1174) + chr(4759 - 4648) + chr(49) + chr(0b11100 + 0o30), 48836 - 48828), nzTpIcepk0o8(chr(810 - 762) + chr(111) + chr(1838 - 1789) + '\x35' + '\x34', 8), nzTpIcepk0o8(chr(0b100000 + 0o20) + '\x6f' + chr(0b110011) + chr(0b110011) + chr(0b101011 + 0o10), 8), nzTpIcepk0o8(chr(0b11010 + 0o26) + chr(0b1110 + 0o141) + '\061' + '\067' + chr(0b0 + 0o63), 8), nzTpIcepk0o8(chr(0b110000) + chr(0b1100 + 0o143) + '\x31' + chr(54) + '\062', 3051 - 3043), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(51) + '\x30' + '\x37', 0o10), nzTpIcepk0o8(chr(1957 - 1909) + '\157' + '\x32' + chr(0b110010) + chr(54), 0o10), nzTpIcepk0o8(chr(0b10011 + 0o35) + chr(0b1101111) + '\x32' + chr(0b110001) + chr(0b1001 + 0o52), 0o10), nzTpIcepk0o8('\x30' + chr(8415 - 8304) + '\x31' + '\x34' + '\064', 0b1000), nzTpIcepk0o8(chr(771 - 723) + chr(0b111010 + 0o65) + chr(1910 - 1859) + '\066' + chr(0b110001), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1000110 + 0o51) + chr(50) + '\x37', 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(0b11010 + 0o30) + chr(0b101111 + 0o2), 8), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(1033 - 984) + '\x30' + chr(0b110100), 34104 - 34096), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(50) + chr(0b10000 + 0o44), 0o10), nzTpIcepk0o8('\x30' + chr(4465 - 4354) + chr(0b110010) + chr(166 - 117) + '\x32', 53895 - 53887), nzTpIcepk0o8(chr(1298 - 1250) + chr(0b1100010 + 0o15) + '\062' + chr(0b110011) + chr(1935 - 1882), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + '\063' + chr(2091 - 2038) + '\065', 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(766 - 715) + '\x32' + chr(2651 - 2597), 8), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x33' + '\063' + chr(0b11001 + 0o33), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110001) + chr(0b110011 + 0o4) + '\066', 58209 - 58201)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(2091 - 2038) + chr(0b100001 + 0o17), 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'B'), chr(0b110101 + 0o57) + chr(0b11010 + 0o113) + chr(527 - 428) + chr(0b1010011 + 0o34) + '\144' + chr(0b1011001 + 0o14))(chr(10335 - 10218) + chr(0b1110100) + chr(0b1100110) + chr(1304 - 1259) + chr(1304 - 1248)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def w6uhXQg6hqjS(QnTXOd5N96r1, toKQXlEvBKaK, ZXDdzgbdtBfz=None, m7febIoEHkQl=None, DzfuqSe6qH0o=None, vlxREQkYI3ar=None, ylss10JPIXgG=VtSJAdWbO3vK, tZ41UfIgDZkG=None, SiTpDn8thAb3=None, zDhdJKI1a4t1=roI3spqORKae(ES5oEprVxulp(b'\x18\xa7o?F'), '\144' + chr(0b1010011 + 0o22) + chr(99) + chr(6628 - 6517) + chr(0b1100100) + '\145')('\x75' + '\164' + '\146' + chr(0b101101) + chr(0b111000)), AllcsXRtujK_=None, hG3E2obYFZMl=OFzsXuzIcuuU, Rv_V5730xaZB=rhI5nb3QnemL, lmiGj7TonZgV=None, **q5n0sHDDTy90):
(zIqcgNgQ9U6F, ZXDdzgbdtBfz) = VUIwV6a3wMvG(ZXDdzgbdtBfz)
(ZXDdzgbdtBfz, zIqcgNgQ9U6F, zIqcgNgQ9U6F, NOukaRmWFG1j) = v5AmWdIIYZEI(input=QnTXOd5N96r1, fields=ZXDdzgbdtBfz, exclude_fields=m7febIoEHkQl, types=DzfuqSe6qH0o, numbers=vlxREQkYI3ar, alt_number=ylss10JPIXgG, buffer_size=hG3E2obYFZMl, chunk_length=Rv_V5730xaZB, fills=tZ41UfIgDZkG, region=SiTpDn8thAb3, tabix=zDhdJKI1a4t1, samples=[], transformers=AllcsXRtujK_)
if lmiGj7TonZgV is not None:
NOukaRmWFG1j = _Inj3jb7axrv(NOukaRmWFG1j, lmiGj7TonZgV, prefix=roI3spqORKae(ES5oEprVxulp(b'7\xb0n0a\x0cS\x149\xd5\r\xbd'), chr(0b11101 + 0o107) + '\145' + chr(0b10010 + 0o121) + '\x6f' + '\144' + chr(101))(chr(0b101 + 0o160) + chr(668 - 552) + '\x66' + chr(752 - 707) + chr(0b111000)))
q5n0sHDDTy90[roI3spqORKae(ES5oEprVxulp(b'\x05\xa8i3F'), chr(0b1100100) + chr(8384 - 8283) + chr(0b1100011) + chr(0b1101111) + '\x64' + chr(2382 - 2281))(chr(9780 - 9663) + chr(0b1110100) + chr(0b1100110) + '\055' + chr(56))] = nzTpIcepk0o8('\x30' + chr(9471 - 9360) + chr(0b101010 + 0o6), 0o10)
for (ZlbFMSG8gCoF, (WckxBx1Uqdpm, zIqcgNgQ9U6F, zIqcgNgQ9U6F, zIqcgNgQ9U6F)) in _kV_Bomx8PZ4(NOukaRmWFG1j):
jpOn8DNZxbbx = y2tU0XZjykBo(ZXDdzgbdtBfz, WckxBx1Uqdpm)
if ZlbFMSG8gCoF == nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x30', 8):
q5n0sHDDTy90[roI3spqORKae(ES5oEprVxulp(b'\x04\xa3l2[\n'), chr(0b1100100) + chr(1038 - 937) + '\143' + '\x6f' + chr(0b1100100) + chr(0b111001 + 0o54))(chr(6912 - 6795) + chr(7184 - 7068) + '\146' + chr(0b101101) + chr(56))] = nzTpIcepk0o8('\060' + chr(414 - 303) + chr(49), ord("\x08"))
q5n0sHDDTy90[roI3spqORKae(ES5oEprVxulp(b'\x01\xa9i3'), '\144' + chr(0b1100101) + chr(4368 - 4269) + '\x6f' + '\x64' + chr(101))(chr(0b1110000 + 0o5) + '\x74' + '\x66' + chr(0b100111 + 0o6) + chr(246 - 190))] = roI3spqORKae(ES5oEprVxulp(b'\x1b'), '\144' + chr(5312 - 5211) + chr(99) + '\157' + chr(3907 - 3807) + '\x65')(chr(3144 - 3027) + chr(0b10101 + 0o137) + '\146' + chr(0b100001 + 0o14) + '\070')
else:
q5n0sHDDTy90[roI3spqORKae(ES5oEprVxulp(b'\x04\xa3l2[\n'), chr(0b1100100) + chr(1970 - 1869) + '\143' + chr(0b1101111) + chr(9836 - 9736) + '\145')('\x75' + '\x74' + chr(0b101010 + 0o74) + chr(0b1010 + 0o43) + chr(56))] = nzTpIcepk0o8('\x30' + chr(4529 - 4418) + chr(0b110000), 8)
q5n0sHDDTy90[roI3spqORKae(ES5oEprVxulp(b'\x01\xa9i3'), chr(0b110101 + 0o57) + chr(0b110111 + 0o56) + '\143' + '\157' + chr(100) + chr(101))(chr(0b1100 + 0o151) + chr(0b1110100) + '\x66' + chr(0b101101) + chr(0b111000))] = roI3spqORKae(ES5oEprVxulp(b'\r'), chr(0b1011101 + 0o7) + chr(5431 - 5330) + '\143' + chr(0b1101111) + '\144' + chr(0b1100101))(chr(0b1011 + 0o152) + '\164' + chr(0b1100110) + chr(45) + '\x38')
roI3spqORKae(jpOn8DNZxbbx, roI3spqORKae(ES5oEprVxulp(b'\x18\xa9R5M\x0e'), chr(0b111011 + 0o51) + chr(101) + '\143' + chr(0b1101111) + chr(100) + chr(0b1010110 + 0o17))('\x75' + chr(10764 - 10648) + '\146' + chr(0b101101) + chr(56)))(toKQXlEvBKaK, **q5n0sHDDTy90) |
cggh/scikit-allel | allel/io/vcf_read.py | vcf_to_recarray | def vcf_to_recarray(input,
fields=None,
exclude_fields=None,
types=None,
numbers=None,
alt_number=DEFAULT_ALT_NUMBER,
fills=None,
region=None,
tabix='tabix',
transformers=None,
buffer_size=DEFAULT_BUFFER_SIZE,
chunk_length=DEFAULT_CHUNK_LENGTH,
log=None):
"""Read data from a VCF file into a NumPy recarray.
Parameters
----------
input : string
{input}
fields : list of strings, optional
{fields}
exclude_fields : list of strings, optional
{exclude_fields}
types : dict, optional
{types}
numbers : dict, optional
{numbers}
alt_number : int, optional
{alt_number}
fills : dict, optional
{fills}
region : string, optional
{region}
tabix : string, optional
{tabix}
transformers : list of transformer objects, optional
{transformers}
buffer_size : int, optional
{buffer_size}
chunk_length : int, optional
{chunk_length}
log : file-like, optional
{log}
Returns
-------
ra : np.rec.array
"""
# samples requested?
# noinspection PyTypeChecker
_, fields = _prep_fields_param(fields)
# setup chunk iterator
# N.B., set samples to empty list so we don't get any calldata fields
fields, _, _, it = iter_vcf_chunks(
input=input, fields=fields, exclude_fields=exclude_fields, types=types,
numbers=numbers, alt_number=alt_number, buffer_size=buffer_size,
chunk_length=chunk_length, fills=fills, region=region, tabix=tabix, samples=[],
transformers=transformers
)
# setup progress logging
if log is not None:
it = _chunk_iter_progress(it, log, prefix='[vcf_to_recarray]')
# read all chunks into a list
chunks = [d[0] for d in it]
# setup output
output = None
if chunks:
# concatenate chunks
output = np.concatenate([_chunk_to_recarray(fields, chunk) for chunk in chunks])
return output | python | def vcf_to_recarray(input,
fields=None,
exclude_fields=None,
types=None,
numbers=None,
alt_number=DEFAULT_ALT_NUMBER,
fills=None,
region=None,
tabix='tabix',
transformers=None,
buffer_size=DEFAULT_BUFFER_SIZE,
chunk_length=DEFAULT_CHUNK_LENGTH,
log=None):
"""Read data from a VCF file into a NumPy recarray.
Parameters
----------
input : string
{input}
fields : list of strings, optional
{fields}
exclude_fields : list of strings, optional
{exclude_fields}
types : dict, optional
{types}
numbers : dict, optional
{numbers}
alt_number : int, optional
{alt_number}
fills : dict, optional
{fills}
region : string, optional
{region}
tabix : string, optional
{tabix}
transformers : list of transformer objects, optional
{transformers}
buffer_size : int, optional
{buffer_size}
chunk_length : int, optional
{chunk_length}
log : file-like, optional
{log}
Returns
-------
ra : np.rec.array
"""
# samples requested?
# noinspection PyTypeChecker
_, fields = _prep_fields_param(fields)
# setup chunk iterator
# N.B., set samples to empty list so we don't get any calldata fields
fields, _, _, it = iter_vcf_chunks(
input=input, fields=fields, exclude_fields=exclude_fields, types=types,
numbers=numbers, alt_number=alt_number, buffer_size=buffer_size,
chunk_length=chunk_length, fills=fills, region=region, tabix=tabix, samples=[],
transformers=transformers
)
# setup progress logging
if log is not None:
it = _chunk_iter_progress(it, log, prefix='[vcf_to_recarray]')
# read all chunks into a list
chunks = [d[0] for d in it]
# setup output
output = None
if chunks:
# concatenate chunks
output = np.concatenate([_chunk_to_recarray(fields, chunk) for chunk in chunks])
return output | [
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"... | Read data from a VCF file into a NumPy recarray.
Parameters
----------
input : string
{input}
fields : list of strings, optional
{fields}
exclude_fields : list of strings, optional
{exclude_fields}
types : dict, optional
{types}
numbers : dict, optional
{numbers}
alt_number : int, optional
{alt_number}
fills : dict, optional
{fills}
region : string, optional
{region}
tabix : string, optional
{tabix}
transformers : list of transformer objects, optional
{transformers}
buffer_size : int, optional
{buffer_size}
chunk_length : int, optional
{chunk_length}
log : file-like, optional
{log}
Returns
-------
ra : np.rec.array | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/io/vcf_read.py#L2020-L2098 | train | Read data from a VCF file into a NumPy recarray. | 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' + '\x33' + '\x30' + '\x33', 42396 - 42388), nzTpIcepk0o8('\060' + '\x6f' + chr(51) + chr(83 - 32) + chr(0b101000 + 0o16), 10722 - 10714), nzTpIcepk0o8('\060' + chr(111) + chr(0b110011) + chr(0b110010) + chr(0b110101), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + '\061' + chr(0b11000 + 0o33) + '\x31', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(49) + '\062' + '\065', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1111 + 0o140) + chr(0b110001) + chr(0b1010 + 0o52) + chr(0b111 + 0o53), 30309 - 30301), nzTpIcepk0o8(chr(0b101000 + 0o10) + chr(111) + '\x32' + chr(54), 0b1000), nzTpIcepk0o8(chr(0b11100 + 0o24) + chr(111) + chr(0b110100) + '\x37', 0b1000), nzTpIcepk0o8('\060' + chr(111) + '\x33' + chr(0b110111) + '\066', ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + '\x33' + chr(0b11100 + 0o32) + chr(0b110100), 0b1000), nzTpIcepk0o8('\x30' + '\157' + '\x31' + chr(0b10011 + 0o36), 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110010) + chr(0b110101) + chr(50), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110001) + chr(49) + chr(0b10100 + 0o42), 23060 - 23052), nzTpIcepk0o8('\x30' + '\x6f' + chr(583 - 533) + chr(0b10011 + 0o41) + '\x32', 0o10), nzTpIcepk0o8(chr(2093 - 2045) + chr(111) + chr(2264 - 2213) + chr(49) + chr(1040 - 989), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + '\062' + chr(0b10011 + 0o41) + chr(50), 8), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(51) + chr(0b110000) + chr(2056 - 2005), 8), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x31' + '\x35' + chr(111 - 60), ord("\x08")), nzTpIcepk0o8(chr(743 - 695) + '\x6f' + '\x36' + chr(0b1 + 0o64), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110010 + 0o1) + chr(2245 - 2193), 0b1000), nzTpIcepk0o8(chr(0b1010 + 0o46) + chr(111) + chr(0b11110 + 0o25) + chr(0b101100 + 0o6) + chr(0b110100), 48279 - 48271), nzTpIcepk0o8(chr(242 - 194) + '\157' + '\x33' + chr(0b10110 + 0o34) + chr(0b101101 + 0o4), 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110011) + chr(55) + chr(911 - 857), 8), nzTpIcepk0o8(chr(48) + '\157' + chr(151 - 101) + chr(0b10 + 0o56) + chr(49), 39627 - 39619), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x36' + '\063', 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b101100 + 0o11) + chr(1531 - 1483), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + '\x32' + '\x32' + chr(0b1110 + 0o51), ord("\x08")), nzTpIcepk0o8(chr(1481 - 1433) + '\157' + '\x31' + chr(53) + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(12112 - 12001) + chr(0b101010 + 0o10) + chr(0b0 + 0o66) + chr(2570 - 2516), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1100010 + 0o15) + chr(1046 - 992) + chr(640 - 588), 49255 - 49247), nzTpIcepk0o8('\x30' + chr(3806 - 3695) + chr(51) + chr(50) + '\065', 8), nzTpIcepk0o8(chr(1757 - 1709) + chr(1987 - 1876) + chr(0b110011) + chr(0b1100 + 0o51) + chr(2260 - 2209), 0b1000), nzTpIcepk0o8(chr(535 - 487) + chr(0b100001 + 0o116) + chr(53) + chr(755 - 700), 49002 - 48994), nzTpIcepk0o8('\060' + chr(9482 - 9371) + chr(50) + chr(2180 - 2125) + '\x34', 17909 - 17901), nzTpIcepk0o8('\x30' + chr(111) + chr(0b10000 + 0o43) + '\x31' + chr(2370 - 2321), 0o10), nzTpIcepk0o8(chr(2122 - 2074) + chr(111) + chr(0b1100 + 0o45) + chr(0b10000 + 0o44) + chr(0b110110), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(9830 - 9719) + chr(49) + '\064' + '\x34', ord("\x08")), nzTpIcepk0o8(chr(1939 - 1891) + chr(0b1101111) + '\x31' + chr(0b110010) + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(588 - 537) + chr(0b110111) + chr(0b101101 + 0o5), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110001) + chr(0b110001) + '\066', 8)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(0b1100100 + 0o13) + chr(53) + '\x30', 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xed'), chr(1125 - 1025) + chr(5566 - 5465) + chr(0b1100011) + chr(111) + '\144' + chr(0b1100101))('\165' + chr(0b1000100 + 0o60) + '\146' + chr(972 - 927) + chr(2790 - 2734)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def NwKQcXhe51xS(QnTXOd5N96r1, ZXDdzgbdtBfz=None, m7febIoEHkQl=None, DzfuqSe6qH0o=None, vlxREQkYI3ar=None, ylss10JPIXgG=VtSJAdWbO3vK, tZ41UfIgDZkG=None, SiTpDn8thAb3=None, zDhdJKI1a4t1=roI3spqORKae(ES5oEprVxulp(b'\xb7\xbf\xb70-'), chr(100) + chr(101) + chr(0b1100011) + chr(6298 - 6187) + chr(6333 - 6233) + chr(101))('\x75' + '\164' + chr(2812 - 2710) + chr(45) + chr(56)), AllcsXRtujK_=None, hG3E2obYFZMl=OFzsXuzIcuuU, Rv_V5730xaZB=rhI5nb3QnemL, lmiGj7TonZgV=None):
(zIqcgNgQ9U6F, ZXDdzgbdtBfz) = VUIwV6a3wMvG(ZXDdzgbdtBfz)
(ZXDdzgbdtBfz, zIqcgNgQ9U6F, zIqcgNgQ9U6F, NOukaRmWFG1j) = v5AmWdIIYZEI(input=QnTXOd5N96r1, fields=ZXDdzgbdtBfz, exclude_fields=m7febIoEHkQl, types=DzfuqSe6qH0o, numbers=vlxREQkYI3ar, alt_number=ylss10JPIXgG, buffer_size=hG3E2obYFZMl, chunk_length=Rv_V5730xaZB, fills=tZ41UfIgDZkG, region=SiTpDn8thAb3, tabix=zDhdJKI1a4t1, samples=[], transformers=AllcsXRtujK_)
if lmiGj7TonZgV is not None:
NOukaRmWFG1j = _Inj3jb7axrv(NOukaRmWFG1j, lmiGj7TonZgV, prefix=roI3spqORKae(ES5oEprVxulp(b'\x98\xa8\xb6?\n\x16yx\x8c\x91j\xcb<\xd0\xaa\xdb\x9e'), chr(0b1100100) + '\x65' + chr(0b1100011) + '\157' + chr(100) + chr(0b1100101))('\165' + chr(13416 - 13300) + chr(102) + chr(0b101101) + chr(1273 - 1217)))
oZNsnwnkWZSh = [vPPlOXQgR3SM[nzTpIcepk0o8('\060' + chr(4715 - 4604) + '\x30', 0b1000)] for vPPlOXQgR3SM in NOukaRmWFG1j]
toKQXlEvBKaK = None
if oZNsnwnkWZSh:
toKQXlEvBKaK = nDF4gVNx0u9Q.concatenate([Dicm7mpcb7wf(ZXDdzgbdtBfz, WckxBx1Uqdpm) for WckxBx1Uqdpm in oZNsnwnkWZSh])
return toKQXlEvBKaK |
cggh/scikit-allel | allel/io/fasta.py | write_fasta | def write_fasta(path, sequences, names, mode='w', width=80):
"""Write nucleotide sequences stored as numpy arrays to a FASTA file.
Parameters
----------
path : string
File path.
sequences : sequence of arrays
One or more ndarrays of dtype 'S1' containing the sequences.
names : sequence of strings
Names of the sequences.
mode : string, optional
Use 'a' to append to an existing file.
width : int, optional
Maximum line width.
"""
# check inputs
if isinstance(sequences, np.ndarray):
# single sequence
sequences = [sequences]
names = [names]
if len(sequences) != len(names):
raise ValueError('must provide the same number of sequences and names')
for sequence in sequences:
if sequence.dtype != np.dtype('S1'):
raise ValueError('expected S1 dtype, found %r' % sequence.dtype)
# force binary mode
mode = 'ab' if 'a' in mode else 'wb'
# write to file
with open(path, mode=mode) as fasta:
for name, sequence in zip(names, sequences):
# force bytes
if isinstance(name, text_type):
name = name.encode('ascii')
header = b'>' + name + b'\n'
fasta.write(header)
for i in range(0, sequence.size, width):
line = sequence[i:i+width].tostring() + b'\n'
fasta.write(line) | python | def write_fasta(path, sequences, names, mode='w', width=80):
"""Write nucleotide sequences stored as numpy arrays to a FASTA file.
Parameters
----------
path : string
File path.
sequences : sequence of arrays
One or more ndarrays of dtype 'S1' containing the sequences.
names : sequence of strings
Names of the sequences.
mode : string, optional
Use 'a' to append to an existing file.
width : int, optional
Maximum line width.
"""
# check inputs
if isinstance(sequences, np.ndarray):
# single sequence
sequences = [sequences]
names = [names]
if len(sequences) != len(names):
raise ValueError('must provide the same number of sequences and names')
for sequence in sequences:
if sequence.dtype != np.dtype('S1'):
raise ValueError('expected S1 dtype, found %r' % sequence.dtype)
# force binary mode
mode = 'ab' if 'a' in mode else 'wb'
# write to file
with open(path, mode=mode) as fasta:
for name, sequence in zip(names, sequences):
# force bytes
if isinstance(name, text_type):
name = name.encode('ascii')
header = b'>' + name + b'\n'
fasta.write(header)
for i in range(0, sequence.size, width):
line = sequence[i:i+width].tostring() + b'\n'
fasta.write(line) | [
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File path.
sequences : sequence of arrays
One or more ndarrays of dtype 'S1' containing the sequences.
names : sequence of strings
Names of the sequences.
mode : string, optional
Use 'a' to append to an existing file.
width : int, optional
Maximum line width. | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/io/fasta.py#L11-L54 | train | Write nucleotide sequences stored as numpy arrays to a FASTA file. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(48) + chr(2214 - 2103) + chr(49) + chr(49) + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x35' + chr(0b1011 + 0o46), 52272 - 52264), nzTpIcepk0o8(chr(1675 - 1627) + chr(0b1101111) + chr(51) + chr(1235 - 1180) + chr(0b10011 + 0o41), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + '\x33' + '\064' + '\x36', 36414 - 36406), nzTpIcepk0o8(chr(874 - 826) + chr(111) + '\x33' + '\064' + chr(840 - 788), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(839 - 788) + chr(0b11 + 0o57) + '\x36', 56406 - 56398), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(50) + chr(0b110000), 52714 - 52706), nzTpIcepk0o8(chr(0b11111 + 0o21) + chr(6035 - 5924) + chr(0b100110 + 0o14) + chr(0b110011 + 0o2) + '\063', 0o10), nzTpIcepk0o8('\060' + chr(2207 - 2096) + chr(51) + '\067' + '\066', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1011110 + 0o21) + chr(0b11101 + 0o25) + chr(0b110101) + '\x34', 0b1000), nzTpIcepk0o8(chr(868 - 820) + '\x6f' + chr(2295 - 2246) + '\x34', 0b1000), nzTpIcepk0o8(chr(329 - 281) + chr(1548 - 1437) + chr(0b110111 + 0o0) + chr(1222 - 1173), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(1350 - 1299) + chr(0b110010) + chr(0b110010), 0b1000), nzTpIcepk0o8(chr(1830 - 1782) + chr(0b1011010 + 0o25) + chr(1698 - 1647) + '\x37' + '\060', 0b1000), nzTpIcepk0o8(chr(1785 - 1737) + chr(111) + chr(1913 - 1862) + chr(0b110011) + '\067', 0o10), nzTpIcepk0o8(chr(1868 - 1820) + chr(0b1101111) + chr(0b11111 + 0o22) + chr(2452 - 2397) + '\062', 0o10), nzTpIcepk0o8(chr(0b1 + 0o57) + chr(0b1101111) + chr(0b110010) + '\065', 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110111) + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b101111 + 0o100) + chr(0b1000 + 0o54) + chr(51), 0b1000), nzTpIcepk0o8('\060' + chr(4544 - 4433) + chr(0b110011) + chr(0b100111 + 0o20) + '\x31', 64883 - 64875), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x32' + '\061', 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b100111 + 0o13) + chr(0b101010 + 0o12) + '\x31', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101100 + 0o3) + chr(0b100100 + 0o16) + '\x34' + '\x35', 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110001) + chr(0b101101 + 0o11) + chr(0b110111), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b101001 + 0o10) + '\x31' + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110011) + chr(0b10100 + 0o43) + chr(0b101010 + 0o15), 0o10), nzTpIcepk0o8(chr(48) + chr(5335 - 5224) + chr(2531 - 2480) + '\062' + chr(0b110010), 8), nzTpIcepk0o8('\x30' + '\x6f' + '\061' + chr(55) + '\060', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + '\062' + '\062' + chr(0b10011 + 0o42), ord("\x08")), nzTpIcepk0o8('\060' + chr(11095 - 10984) + chr(0b110011) + '\x31' + chr(0b100010 + 0o20), 0b1000), nzTpIcepk0o8(chr(1377 - 1329) + '\157' + '\x33' + chr(0b110111) + '\066', 8), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110011) + chr(51), 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(0b110001) + '\064' + chr(0b110110), 19015 - 19007), nzTpIcepk0o8(chr(582 - 534) + chr(0b1100000 + 0o17) + chr(0b110011) + chr(49) + '\x33', 34607 - 34599), nzTpIcepk0o8(chr(241 - 193) + '\157' + '\063' + '\063' + chr(0b101000 + 0o16), 36948 - 36940), nzTpIcepk0o8(chr(48) + '\157' + chr(50) + chr(0b110000) + '\x36', 0b1000), nzTpIcepk0o8(chr(0b1111 + 0o41) + '\x6f' + chr(50) + chr(0b11100 + 0o31) + chr(53), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + '\x31' + '\x34' + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x32' + chr(981 - 928) + chr(54), 56362 - 56354), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\062' + chr(2147 - 2098) + chr(0b101011 + 0o6), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + '\157' + chr(53) + chr(0b11 + 0o55), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'c'), '\144' + chr(611 - 510) + chr(99) + chr(111) + '\x64' + chr(0b1100101))('\x75' + '\164' + chr(102) + '\x2d' + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def ROYi2PwyMhWh(_pSYqrosNb95, BBlgUX_QmYPa, TMMrjsiU6eED, bmJ7SvuZE3jD=roI3spqORKae(ES5oEprVxulp(b':'), '\x64' + chr(5585 - 5484) + chr(6535 - 6436) + chr(0b1000001 + 0o56) + chr(0b11000 + 0o114) + '\145')(chr(5681 - 5564) + '\x74' + chr(102) + chr(0b101101) + chr(56)), dH3vcKdvgBu0=nzTpIcepk0o8('\060' + chr(111) + chr(49) + chr(0b100 + 0o56) + '\x30', ord("\x08"))):
if suIjIS24Zkqw(BBlgUX_QmYPa, roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'#M\x9d\x94\x96\xb7i'), chr(7943 - 7843) + chr(1443 - 1342) + chr(0b1100011) + chr(0b1101111) + '\x64' + chr(101))(chr(0b1110101) + chr(7971 - 7855) + chr(102) + chr(45) + chr(56)))):
BBlgUX_QmYPa = [BBlgUX_QmYPa]
TMMrjsiU6eED = [TMMrjsiU6eED]
if ftfygxgFas5X(BBlgUX_QmYPa) != ftfygxgFas5X(TMMrjsiU6eED):
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b' \\\x8f\x92\xc4\xa6b\xc4\x88\xc5h\\\xf2\x8c\xb7\x1f5KB\x94t\x81\xcb\x02!\x9d\xb7\n\xb5\xa5\x98;\x15\xae\xaf\xf3\xc8\x0b\xcd\xec>\t\x9d\x88\x80\xf6~\xca\x93\xc9\x7f'), chr(0b1100100) + chr(101) + chr(6223 - 6124) + '\157' + '\144' + '\x65')(chr(0b1110101) + chr(116) + chr(102) + '\055' + chr(0b111000)))
for AaFeo0lw34C3 in BBlgUX_QmYPa:
if roI3spqORKae(AaFeo0lw34C3, roI3spqORKae(ES5oEprVxulp(b'\x1fJ\xa4\xdf\x86\xb4e\xe4\x84\xc49u'), '\144' + '\x65' + chr(6529 - 6430) + chr(0b1000011 + 0o54) + '\144' + chr(101))(chr(0b1110101) + chr(10789 - 10673) + '\x66' + chr(0b10001 + 0o34) + chr(56))) != roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'\x1fJ\xa4\xdf\x86\xb4e\xe4\x84\xc49u'), chr(5142 - 5042) + '\145' + chr(0b100001 + 0o102) + '\x6f' + chr(0b110000 + 0o64) + chr(0b1100101))(chr(0b1110101) + chr(116) + '\x66' + chr(45) + '\x38'))(roI3spqORKae(ES5oEprVxulp(b'\x1e\x18'), chr(0b110100 + 0o60) + chr(0b111001 + 0o54) + chr(99) + chr(0b1101111) + '\144' + chr(0b1100101))('\165' + '\x74' + '\x66' + chr(45) + chr(56))):
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'(Q\x8c\x83\x87\xa2u\xcf\xde\xff=\x19\xb6\x8c\xa6\np\x14\x03\x9f~\xd4\xcb\x13l\xda\xa0'), chr(0b110 + 0o136) + '\145' + '\x63' + '\x6f' + chr(3617 - 3517) + '\x65')(chr(8452 - 8335) + chr(0b1110100) + chr(5458 - 5356) + chr(0b101010 + 0o3) + chr(0b111000)) % roI3spqORKae(AaFeo0lw34C3, roI3spqORKae(ES5oEprVxulp(b'\x1fJ\xa4\xdf\x86\xb4e\xe4\x84\xc49u'), chr(0b110100 + 0o60) + chr(101) + chr(0b1100011) + '\157' + chr(0b1100100) + chr(5283 - 5182))(chr(6767 - 6650) + chr(10640 - 10524) + chr(0b1100110 + 0o0) + chr(0b100 + 0o51) + chr(0b10100 + 0o44))))
bmJ7SvuZE3jD = roI3spqORKae(ES5oEprVxulp(b',K'), chr(0b1100100) + chr(0b1100101) + chr(0b1001 + 0o132) + chr(0b1101111) + '\144' + '\x65')(chr(117) + chr(116) + '\146' + '\x2d' + chr(0b111000)) if roI3spqORKae(ES5oEprVxulp(b','), '\x64' + chr(101) + chr(0b111110 + 0o45) + chr(0b1101111) + '\x64' + chr(0b1100101))('\165' + chr(0b1110100) + '\x66' + chr(1747 - 1702) + chr(3049 - 2993)) in bmJ7SvuZE3jD else roI3spqORKae(ES5oEprVxulp(b':K'), chr(0b1110 + 0o126) + '\x65' + chr(8087 - 7988) + '\157' + chr(0b1100100) + chr(0b1100100 + 0o1))(chr(0b1110101) + '\164' + chr(102) + '\x2d' + chr(0b111000))
with DnU3Rq9N5ala(_pSYqrosNb95, mode=bmJ7SvuZE3jD) as _BUp4xuDxHpk:
for (SLVB2BPA_mIe, AaFeo0lw34C3) in TxMFWa_Xzviv(TMMrjsiU6eED, BBlgUX_QmYPa):
if suIjIS24Zkqw(SLVB2BPA_mIe, H8p5T_wwctMA):
SLVB2BPA_mIe = SLVB2BPA_mIe.YqIaRFfeo4Ha(roI3spqORKae(ES5oEprVxulp(b',Z\x9f\x8f\x8d'), chr(0b1100100) + chr(4171 - 4070) + chr(0b1100 + 0o127) + chr(111) + '\x64' + chr(0b11011 + 0o112))(chr(0b1110101) + chr(0b101 + 0o157) + chr(0b1100110) + chr(0b101101) + '\x38'))
jkp_M8Pp8CIt = ES5oEprVxulp(b's') + SLVB2BPA_mIe + ES5oEprVxulp(b'G')
roI3spqORKae(_BUp4xuDxHpk, roI3spqORKae(ES5oEprVxulp(b' E\xcc\x8e\x8c\xa6f\x9a\xb2\xdc}\x0b'), chr(0b11010 + 0o112) + chr(0b1100101) + chr(99) + chr(111) + chr(0b1100100) + chr(0b1011010 + 0o13))(chr(0b1110101) + chr(116) + '\146' + chr(312 - 267) + chr(0b111000)))(jkp_M8Pp8CIt)
for ZlbFMSG8gCoF in bbT2xIe5pzk7(nzTpIcepk0o8('\060' + '\157' + '\060', 0o10), roI3spqORKae(AaFeo0lw34C3, roI3spqORKae(ES5oEprVxulp(b'(\x18\xb4\x94\xae\xb7A\xe3\xbf\xefbU'), chr(0b11111 + 0o105) + chr(0b101101 + 0o70) + chr(99) + chr(7727 - 7616) + '\x64' + chr(101))(chr(0b1101011 + 0o12) + '\x74' + chr(5540 - 5438) + chr(0b101101) + chr(0b11 + 0o65))), dH3vcKdvgBu0):
ffiOpFBWGmZU = AaFeo0lw34C3[ZlbFMSG8gCoF:ZlbFMSG8gCoF + dH3vcKdvgBu0].tostring() + ES5oEprVxulp(b'G')
roI3spqORKae(_BUp4xuDxHpk, roI3spqORKae(ES5oEprVxulp(b' E\xcc\x8e\x8c\xa6f\x9a\xb2\xdc}\x0b'), chr(0b1100100) + chr(0b1001110 + 0o27) + chr(3221 - 3122) + chr(111) + '\144' + '\145')('\165' + '\x74' + chr(102) + chr(1232 - 1187) + '\070'))(ffiOpFBWGmZU) |
cggh/scikit-allel | allel/stats/hw.py | heterozygosity_observed | def heterozygosity_observed(g, fill=np.nan):
"""Calculate the rate of observed heterozygosity for each variant.
Parameters
----------
g : array_like, int, shape (n_variants, n_samples, ploidy)
Genotype array.
fill : float, optional
Use this value for variants where all calls are missing.
Returns
-------
ho : ndarray, float, shape (n_variants,)
Observed heterozygosity
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 0], [0, 0]],
... [[0, 0], [0, 1], [1, 1]],
... [[0, 0], [1, 1], [2, 2]],
... [[1, 1], [1, 2], [-1, -1]]])
>>> allel.heterozygosity_observed(g)
array([0. , 0.33333333, 0. , 0.5 ])
"""
# check inputs
if not hasattr(g, 'count_het') or not hasattr(g, 'count_called'):
g = GenotypeArray(g, copy=False)
# count hets
n_het = np.asarray(g.count_het(axis=1))
n_called = np.asarray(g.count_called(axis=1))
# calculate rate of observed heterozygosity, accounting for variants
# where all calls are missing
with ignore_invalid():
ho = np.where(n_called > 0, n_het / n_called, fill)
return ho | python | def heterozygosity_observed(g, fill=np.nan):
"""Calculate the rate of observed heterozygosity for each variant.
Parameters
----------
g : array_like, int, shape (n_variants, n_samples, ploidy)
Genotype array.
fill : float, optional
Use this value for variants where all calls are missing.
Returns
-------
ho : ndarray, float, shape (n_variants,)
Observed heterozygosity
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 0], [0, 0]],
... [[0, 0], [0, 1], [1, 1]],
... [[0, 0], [1, 1], [2, 2]],
... [[1, 1], [1, 2], [-1, -1]]])
>>> allel.heterozygosity_observed(g)
array([0. , 0.33333333, 0. , 0.5 ])
"""
# check inputs
if not hasattr(g, 'count_het') or not hasattr(g, 'count_called'):
g = GenotypeArray(g, copy=False)
# count hets
n_het = np.asarray(g.count_het(axis=1))
n_called = np.asarray(g.count_called(axis=1))
# calculate rate of observed heterozygosity, accounting for variants
# where all calls are missing
with ignore_invalid():
ho = np.where(n_called > 0, n_het / n_called, fill)
return ho | [
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Parameters
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g : array_like, int, shape (n_variants, n_samples, ploidy)
Genotype array.
fill : float, optional
Use this value for variants where all calls are missing.
Returns
-------
ho : ndarray, float, shape (n_variants,)
Observed heterozygosity
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 0], [0, 0]],
... [[0, 0], [0, 1], [1, 1]],
... [[0, 0], [1, 1], [2, 2]],
... [[1, 1], [1, 2], [-1, -1]]])
>>> allel.heterozygosity_observed(g)
array([0. , 0.33333333, 0. , 0.5 ]) | [
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ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(48) + '\157' + chr(49) + chr(51) + '\x36', 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(978 - 928) + '\060', 0b1000), nzTpIcepk0o8(chr(0b11100 + 0o24) + chr(111) + chr(51) + chr(0b1011 + 0o50) + chr(53), 18685 - 18677), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(1992 - 1942) + chr(0b11110 + 0o30) + '\x35', 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\062' + chr(0b110110) + chr(0b110001 + 0o0), 0b1000), nzTpIcepk0o8(chr(0b10011 + 0o35) + '\157' + '\061' + '\064' + chr(119 - 68), 0o10), nzTpIcepk0o8(chr(1184 - 1136) + '\157' + chr(0b10101 + 0o36) + chr(1907 - 1858), 53145 - 53137), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(2288 - 2235) + chr(0b110001), 64990 - 64982), nzTpIcepk0o8('\x30' + '\x6f' + '\x33' + chr(0b1110 + 0o42) + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(0b1011 + 0o45) + chr(111) + chr(2330 - 2281) + '\064' + '\060', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(49) + '\062' + '\065', 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(49) + '\065' + chr(2420 - 2370), ord("\x08")), nzTpIcepk0o8(chr(0b10101 + 0o33) + '\x6f' + chr(51) + chr(1757 - 1705) + '\067', 0o10), nzTpIcepk0o8(chr(0b101110 + 0o2) + chr(7022 - 6911) + chr(0b110010) + chr(2201 - 2152) + chr(303 - 251), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(51) + chr(0b110011) + '\x34', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(3567 - 3456) + chr(0b110001) + '\x37' + '\x30', ord("\x08")), nzTpIcepk0o8(chr(0b0 + 0o60) + chr(0b1101111) + chr(49) + chr(0b110110) + chr(48), 0o10), nzTpIcepk0o8(chr(838 - 790) + chr(0b1001100 + 0o43) + chr(0b110001) + chr(0b110111), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + '\x33' + '\x32' + chr(0b101 + 0o54), 0b1000), nzTpIcepk0o8(chr(0b101111 + 0o1) + '\157' + chr(49) + chr(0b110101) + chr(49), 0b1000), nzTpIcepk0o8(chr(0b1110 + 0o42) + chr(0b1101111) + chr(0b110010) + chr(53) + '\x35', 61275 - 61267), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x33' + chr(54) + '\x30', 0b1000), nzTpIcepk0o8(chr(1158 - 1110) + chr(111) + chr(2250 - 2200) + chr(52) + chr(1577 - 1528), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b10101 + 0o132) + chr(0b110011) + '\060' + chr(0b110101), 0o10), nzTpIcepk0o8(chr(195 - 147) + chr(111) + chr(0b110010) + chr(0b110100) + chr(957 - 908), 8), nzTpIcepk0o8(chr(48) + '\157' + chr(0b10111 + 0o33) + '\x34' + chr(0b110001), 8), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x33' + chr(0b101110 + 0o3) + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\062' + chr(0b110000) + chr(48), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110001) + '\066' + chr(2472 - 2419), 37474 - 37466), nzTpIcepk0o8('\x30' + chr(2162 - 2051) + chr(0b101101 + 0o10) + '\x36', 27281 - 27273), nzTpIcepk0o8('\060' + chr(0b1000111 + 0o50) + chr(2380 - 2331) + chr(49) + chr(0b1000 + 0o54), 2362 - 2354), nzTpIcepk0o8('\060' + chr(11732 - 11621) + chr(49) + chr(52) + chr(49), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(7307 - 7196) + chr(0b0 + 0o65), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(2312 - 2262) + '\x33' + '\061', ord("\x08")), nzTpIcepk0o8(chr(0b11 + 0o55) + chr(6959 - 6848) + chr(1729 - 1679) + chr(1826 - 1777) + chr(0b110011), 0o10), nzTpIcepk0o8(chr(68 - 20) + chr(0b1100111 + 0o10) + '\062' + '\x31' + '\x31', 0b1000), nzTpIcepk0o8('\060' + chr(111) + '\x37' + chr(1132 - 1084), 0o10), nzTpIcepk0o8(chr(933 - 885) + chr(111) + chr(0b110001) + '\062' + chr(0b11011 + 0o26), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + '\063' + '\065' + '\063', 0o10), nzTpIcepk0o8(chr(964 - 916) + chr(0b1011010 + 0o25) + chr(52) + '\x35', 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + '\x6f' + chr(2785 - 2732) + chr(0b110000), 41708 - 41700)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'p'), chr(100) + chr(0b1100101) + '\x63' + chr(111) + chr(0b1100100) + chr(101))(chr(117) + chr(116) + chr(0b1100110) + '\x2d' + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def EiWVYWFIDWx0(KQq7Z9J63zv1, pPmkLCVA328e=roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'0q\xb3'), '\144' + chr(101) + '\x63' + chr(0b110110 + 0o71) + chr(9725 - 9625) + chr(0b11100 + 0o111))(chr(0b1110101) + chr(116) + chr(102) + chr(0b10000 + 0o35) + chr(0b0 + 0o70)))):
if not dRKdVnHPFq7C(KQq7Z9J63zv1, roI3spqORKae(ES5oEprVxulp(b'=\x7f\xa8\xdb\xc5<qL\xb0'), chr(0b110001 + 0o63) + chr(390 - 289) + chr(0b1010110 + 0o15) + chr(0b1101111) + chr(100) + '\x65')(chr(0b1110101) + chr(0b1110100) + chr(0b1100110) + '\x2d' + chr(0b101001 + 0o17))) or not dRKdVnHPFq7C(KQq7Z9J63zv1, roI3spqORKae(ES5oEprVxulp(b'=\x7f\xa8\xdb\xc5<zH\xa8\x0c0\x0e'), '\x64' + '\x65' + '\143' + chr(111) + '\144' + chr(8308 - 8207))(chr(0b1110101) + '\x74' + chr(0b1100110) + chr(0b101001 + 0o4) + chr(0b10101 + 0o43))):
KQq7Z9J63zv1 = kkrDeTnxPwnD(KQq7Z9J63zv1, copy=nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110000), 0b1000))
medeWsy_CPZH = nDF4gVNx0u9Q.asarray(KQq7Z9J63zv1.count_het(axis=nzTpIcepk0o8(chr(48) + '\157' + chr(0b100110 + 0o13), 40298 - 40290)))
MdoSoOCiIpLb = nDF4gVNx0u9Q.asarray(KQq7Z9J63zv1.count_called(axis=nzTpIcepk0o8(chr(48) + chr(0b101000 + 0o107) + chr(49), 8)))
with riuxP2ykwrwf():
iP_fLynJjbnV = nDF4gVNx0u9Q.xWH4M7K6Qbd3(MdoSoOCiIpLb > nzTpIcepk0o8(chr(0b110000) + chr(4746 - 4635) + '\060', 8), medeWsy_CPZH / MdoSoOCiIpLb, pPmkLCVA328e)
return iP_fLynJjbnV |
cggh/scikit-allel | allel/stats/hw.py | heterozygosity_expected | def heterozygosity_expected(af, ploidy, fill=np.nan):
"""Calculate the expected rate of heterozygosity for each variant
under Hardy-Weinberg equilibrium.
Parameters
----------
af : array_like, float, shape (n_variants, n_alleles)
Allele frequencies array.
ploidy : int
Sample ploidy.
fill : float, optional
Use this value for variants where allele frequencies do not sum to 1.
Returns
-------
he : ndarray, float, shape (n_variants,)
Expected heterozygosity
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 0], [0, 0]],
... [[0, 0], [0, 1], [1, 1]],
... [[0, 0], [1, 1], [2, 2]],
... [[1, 1], [1, 2], [-1, -1]]])
>>> af = g.count_alleles().to_frequencies()
>>> allel.heterozygosity_expected(af, ploidy=2)
array([0. , 0.5 , 0.66666667, 0.375 ])
"""
# check inputs
af = asarray_ndim(af, 2)
# calculate expected heterozygosity
out = 1 - np.sum(np.power(af, ploidy), axis=1)
# fill values where allele frequencies could not be calculated
af_sum = np.sum(af, axis=1)
with ignore_invalid():
out[(af_sum < 1) | np.isnan(af_sum)] = fill
return out | python | def heterozygosity_expected(af, ploidy, fill=np.nan):
"""Calculate the expected rate of heterozygosity for each variant
under Hardy-Weinberg equilibrium.
Parameters
----------
af : array_like, float, shape (n_variants, n_alleles)
Allele frequencies array.
ploidy : int
Sample ploidy.
fill : float, optional
Use this value for variants where allele frequencies do not sum to 1.
Returns
-------
he : ndarray, float, shape (n_variants,)
Expected heterozygosity
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 0], [0, 0]],
... [[0, 0], [0, 1], [1, 1]],
... [[0, 0], [1, 1], [2, 2]],
... [[1, 1], [1, 2], [-1, -1]]])
>>> af = g.count_alleles().to_frequencies()
>>> allel.heterozygosity_expected(af, ploidy=2)
array([0. , 0.5 , 0.66666667, 0.375 ])
"""
# check inputs
af = asarray_ndim(af, 2)
# calculate expected heterozygosity
out = 1 - np.sum(np.power(af, ploidy), axis=1)
# fill values where allele frequencies could not be calculated
af_sum = np.sum(af, axis=1)
with ignore_invalid():
out[(af_sum < 1) | np.isnan(af_sum)] = fill
return out | [
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Parameters
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af : array_like, float, shape (n_variants, n_alleles)
Allele frequencies array.
ploidy : int
Sample ploidy.
fill : float, optional
Use this value for variants where allele frequencies do not sum to 1.
Returns
-------
he : ndarray, float, shape (n_variants,)
Expected heterozygosity
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 0], [0, 0]],
... [[0, 0], [0, 1], [1, 1]],
... [[0, 0], [1, 1], [2, 2]],
... [[1, 1], [1, 2], [-1, -1]]])
>>> af = g.count_alleles().to_frequencies()
>>> allel.heterozygosity_expected(af, ploidy=2)
array([0. , 0.5 , 0.66666667, 0.375 ]) | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/stats/hw.py#L58-L103 | train | Calculate the expected heterozygosity for each variant
under Hardy - Weinberg equilibrium. | 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(10245 - 10134) + chr(0b110011) + '\x37' + chr(0b110011), 0o10), nzTpIcepk0o8(chr(391 - 343) + chr(0b10000 + 0o137) + chr(0b10101 + 0o37) + chr(55), 0b1000), nzTpIcepk0o8('\x30' + chr(3090 - 2979) + '\063' + chr(49) + '\x33', 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(49) + '\066' + chr(0b110000), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1111 + 0o140) + chr(1461 - 1412) + '\060' + chr(1905 - 1850), 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(0b101111 + 0o4) + chr(51) + chr(2213 - 2165), ord("\x08")), nzTpIcepk0o8(chr(1546 - 1498) + '\157' + chr(52) + '\x32', 40465 - 40457), nzTpIcepk0o8(chr(0b11101 + 0o23) + '\x6f' + '\x33' + chr(0b110100) + chr(0b110101), 53642 - 53634), nzTpIcepk0o8(chr(0b10000 + 0o40) + chr(0b1101111) + chr(0b110111) + chr(2556 - 2505), 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(1811 - 1761) + chr(0b110101) + chr(0b110000), 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(2153 - 2102) + '\061' + chr(0b110100), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(50) + '\x33' + chr(54), 43191 - 43183), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110010) + '\061' + '\060', 0o10), nzTpIcepk0o8(chr(1846 - 1798) + chr(8323 - 8212) + chr(0b110011) + chr(49) + chr(2064 - 2013), 8), nzTpIcepk0o8(chr(0b110000) + chr(10264 - 10153) + chr(51) + chr(591 - 540) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(1839 - 1791) + '\x6f' + chr(49) + '\066' + '\065', ord("\x08")), nzTpIcepk0o8('\x30' + chr(11055 - 10944) + chr(0b110001) + chr(52) + '\060', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(1952 - 1841) + chr(2005 - 1954) + chr(655 - 604) + '\067', 63292 - 63284), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110001) + chr(1903 - 1853) + '\060', 22278 - 22270), nzTpIcepk0o8(chr(0b100000 + 0o20) + chr(0b1101111) + chr(0b110010) + chr(1061 - 1013) + chr(54), 19064 - 19056), nzTpIcepk0o8(chr(2089 - 2041) + '\157' + chr(0b110010) + '\x35' + chr(55), 62344 - 62336), nzTpIcepk0o8('\060' + chr(4840 - 4729) + chr(49) + '\x37' + chr(0b110100), 52217 - 52209), nzTpIcepk0o8('\x30' + chr(1742 - 1631) + '\061' + chr(0b1101 + 0o46) + chr(51), 28659 - 28651), nzTpIcepk0o8('\060' + '\157' + chr(0b11110 + 0o30) + chr(54), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + '\063' + '\x36', 0b1000), nzTpIcepk0o8(chr(1737 - 1689) + chr(6034 - 5923) + chr(0b100001 + 0o21) + '\x35' + chr(0b110000), 8), nzTpIcepk0o8(chr(0b11 + 0o55) + '\157' + '\063' + '\x35' + chr(106 - 58), 0o10), nzTpIcepk0o8(chr(0b11100 + 0o24) + chr(8322 - 8211) + chr(0b1110 + 0o50) + '\060', ord("\x08")), nzTpIcepk0o8(chr(1364 - 1316) + chr(0b1101001 + 0o6) + '\x33' + chr(0b110100) + chr(48), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(49) + chr(0b110110) + chr(55), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b10010 + 0o135) + '\x37' + chr(51), 8), nzTpIcepk0o8('\060' + '\x6f' + '\063' + '\060' + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b10 + 0o61) + '\063' + chr(787 - 735), 8), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110010) + chr(0b110100) + '\x35', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(6707 - 6596) + chr(0b110111), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(49) + '\061' + chr(0b110010), 0b1000), nzTpIcepk0o8(chr(0b101111 + 0o1) + '\157' + chr(1070 - 1021) + chr(49) + '\x37', 0b1000), nzTpIcepk0o8(chr(1470 - 1422) + '\157' + chr(50) + chr(0b110111) + chr(50), 0b1000), nzTpIcepk0o8(chr(2032 - 1984) + chr(111) + '\061' + '\065' + chr(0b110010), 22511 - 22503), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x37', 8)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + '\x6f' + '\x35' + chr(0b110000), ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xd5'), chr(0b10001 + 0o123) + chr(6843 - 6742) + '\x63' + chr(111) + '\x64' + '\x65')(chr(0b101111 + 0o106) + chr(0b101001 + 0o113) + chr(0b1010 + 0o134) + chr(0b101101) + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def HNgng4gbWbeY(l9mZkaAlpJU1, QEldLunXvDJ_, pPmkLCVA328e=roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'\x95F\xa5'), chr(100) + chr(0b1000111 + 0o36) + '\143' + chr(7364 - 7253) + '\144' + '\145')(chr(10646 - 10529) + chr(0b1110100) + chr(0b10011 + 0o123) + '\x2d' + '\070'))):
l9mZkaAlpJU1 = EVVKPun88TqM(l9mZkaAlpJU1, nzTpIcepk0o8(chr(875 - 827) + chr(111) + chr(50), 0b1000))
VwOu8WkJ9cpc = nzTpIcepk0o8(chr(0b11101 + 0o23) + chr(0b1011110 + 0o21) + chr(1209 - 1160), ord("\x08")) - nDF4gVNx0u9Q.oclC8DLjA_lV(nDF4gVNx0u9Q.power(l9mZkaAlpJU1, QEldLunXvDJ_), axis=nzTpIcepk0o8('\060' + chr(111) + chr(244 - 195), 8))
VpXYECK9DV5t = nDF4gVNx0u9Q.oclC8DLjA_lV(l9mZkaAlpJU1, axis=nzTpIcepk0o8(chr(0b110000) + chr(0b1101010 + 0o5) + chr(49), 8))
with riuxP2ykwrwf():
VwOu8WkJ9cpc[(VpXYECK9DV5t < nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110001), 8)) | nDF4gVNx0u9Q.w1q0TwtATQ6X(VpXYECK9DV5t)] = pPmkLCVA328e
return VwOu8WkJ9cpc |
cggh/scikit-allel | allel/stats/hw.py | inbreeding_coefficient | def inbreeding_coefficient(g, fill=np.nan):
"""Calculate the inbreeding coefficient for each variant.
Parameters
----------
g : array_like, int, shape (n_variants, n_samples, ploidy)
Genotype array.
fill : float, optional
Use this value for variants where the expected heterozygosity is
zero.
Returns
-------
f : ndarray, float, shape (n_variants,)
Inbreeding coefficient.
Notes
-----
The inbreeding coefficient is calculated as *1 - (Ho/He)* where *Ho* is
the observed heterozygosity and *He* is the expected heterozygosity.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 0], [0, 0]],
... [[0, 0], [0, 1], [1, 1]],
... [[0, 0], [1, 1], [2, 2]],
... [[1, 1], [1, 2], [-1, -1]]])
>>> allel.inbreeding_coefficient(g)
array([ nan, 0.33333333, 1. , -0.33333333])
"""
# check inputs
if not hasattr(g, 'count_het') or not hasattr(g, 'count_called'):
g = GenotypeArray(g, copy=False)
# calculate observed and expected heterozygosity
ho = heterozygosity_observed(g)
af = g.count_alleles().to_frequencies()
he = heterozygosity_expected(af, ploidy=g.shape[-1], fill=0)
# calculate inbreeding coefficient, accounting for variants with no
# expected heterozygosity
with ignore_invalid():
f = np.where(he > 0, 1 - (ho / he), fill)
return f | python | def inbreeding_coefficient(g, fill=np.nan):
"""Calculate the inbreeding coefficient for each variant.
Parameters
----------
g : array_like, int, shape (n_variants, n_samples, ploidy)
Genotype array.
fill : float, optional
Use this value for variants where the expected heterozygosity is
zero.
Returns
-------
f : ndarray, float, shape (n_variants,)
Inbreeding coefficient.
Notes
-----
The inbreeding coefficient is calculated as *1 - (Ho/He)* where *Ho* is
the observed heterozygosity and *He* is the expected heterozygosity.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 0], [0, 0]],
... [[0, 0], [0, 1], [1, 1]],
... [[0, 0], [1, 1], [2, 2]],
... [[1, 1], [1, 2], [-1, -1]]])
>>> allel.inbreeding_coefficient(g)
array([ nan, 0.33333333, 1. , -0.33333333])
"""
# check inputs
if not hasattr(g, 'count_het') or not hasattr(g, 'count_called'):
g = GenotypeArray(g, copy=False)
# calculate observed and expected heterozygosity
ho = heterozygosity_observed(g)
af = g.count_alleles().to_frequencies()
he = heterozygosity_expected(af, ploidy=g.shape[-1], fill=0)
# calculate inbreeding coefficient, accounting for variants with no
# expected heterozygosity
with ignore_invalid():
f = np.where(he > 0, 1 - (ho / he), fill)
return f | [
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Parameters
----------
g : array_like, int, shape (n_variants, n_samples, ploidy)
Genotype array.
fill : float, optional
Use this value for variants where the expected heterozygosity is
zero.
Returns
-------
f : ndarray, float, shape (n_variants,)
Inbreeding coefficient.
Notes
-----
The inbreeding coefficient is calculated as *1 - (Ho/He)* where *Ho* is
the observed heterozygosity and *He* is the expected heterozygosity.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 0], [0, 0]],
... [[0, 0], [0, 1], [1, 1]],
... [[0, 0], [1, 1], [2, 2]],
... [[1, 1], [1, 2], [-1, -1]]])
>>> allel.inbreeding_coefficient(g)
array([ nan, 0.33333333, 1. , -0.33333333]) | [
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"variant",
"."
] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/stats/hw.py#L106-L157 | train | Calculate the inbreeding coefficient for each variant in the hierarchy. | 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(1237 - 1187) + chr(55), 0b1000), nzTpIcepk0o8(chr(1520 - 1472) + '\x6f' + '\061' + '\061' + '\x37', ord("\x08")), nzTpIcepk0o8(chr(0b111 + 0o51) + chr(111) + chr(0b110001) + '\067' + chr(1380 - 1326), 7704 - 7696), nzTpIcepk0o8(chr(0b110000) + chr(0b101101 + 0o102) + '\x32' + chr(52) + '\061', 0o10), nzTpIcepk0o8(chr(0b11010 + 0o26) + chr(0b1101111) + '\x30', 0o10), nzTpIcepk0o8('\x30' + '\157' + '\x31' + chr(0b110010) + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(0b110000 + 0o0) + '\x6f' + chr(381 - 330) + chr(0b110111) + chr(681 - 633), 0o10), nzTpIcepk0o8('\060' + chr(7700 - 7589) + chr(841 - 790) + chr(0b101100 + 0o13), 59211 - 59203), nzTpIcepk0o8('\060' + chr(0b1010110 + 0o31) + chr(0b100011 + 0o16) + chr(0b110000) + '\x30', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1011 + 0o144) + chr(0b110011) + chr(0b110001) + chr(55), 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110001) + '\x32', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b110110 + 0o71) + chr(2320 - 2270) + chr(52), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(212 - 162) + chr(492 - 441) + chr(0b10 + 0o57), 0b1000), nzTpIcepk0o8(chr(0b101111 + 0o1) + '\157' + chr(0b11010 + 0o31) + chr(0b11110 + 0o24) + '\060', 0b1000), nzTpIcepk0o8(chr(48) + chr(2349 - 2238) + '\063' + chr(1864 - 1810) + chr(0b1 + 0o61), ord("\x08")), nzTpIcepk0o8(chr(350 - 302) + chr(0b100010 + 0o115) + chr(0b1 + 0o61) + chr(50) + chr(52), 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(1146 - 1096) + chr(0b110101) + chr(1271 - 1222), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(0b0 + 0o61) + chr(0b110101 + 0o1) + chr(54), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(705 - 651) + '\x30', 0o10), nzTpIcepk0o8(chr(1294 - 1246) + '\157' + chr(0b110010) + '\x37' + chr(484 - 431), 43663 - 43655), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(724 - 674) + chr(0b1111 + 0o44) + chr(0b110101), 24920 - 24912), nzTpIcepk0o8('\060' + '\157' + chr(49) + chr(50) + chr(53), 8), nzTpIcepk0o8(chr(1637 - 1589) + '\157' + chr(0b110010) + chr(0b110111) + '\x36', ord("\x08")), nzTpIcepk0o8(chr(0b10111 + 0o31) + chr(0b1010100 + 0o33) + chr(0b100100 + 0o15) + chr(0b110101) + chr(0b11001 + 0o36), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b10011 + 0o36) + '\066' + chr(0b110010), 44195 - 44187), nzTpIcepk0o8(chr(410 - 362) + chr(111) + '\x31' + '\x31' + chr(0b0 + 0o62), 0o10), nzTpIcepk0o8(chr(526 - 478) + '\157' + chr(52) + chr(577 - 527), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110011) + chr(824 - 770) + chr(0b11011 + 0o33), 0o10), nzTpIcepk0o8('\060' + chr(4675 - 4564) + chr(0b101 + 0o54) + '\x35', 0b1000), nzTpIcepk0o8('\060' + '\x6f' + '\064' + '\x33', 11671 - 11663), nzTpIcepk0o8(chr(1804 - 1756) + chr(6565 - 6454) + chr(0b11000 + 0o32) + chr(0b1010 + 0o51) + '\064', ord("\x08")), nzTpIcepk0o8(chr(0b110 + 0o52) + chr(0b111110 + 0o61) + chr(0b1000 + 0o53) + chr(0b110001) + chr(54), ord("\x08")), nzTpIcepk0o8('\060' + chr(1173 - 1062) + chr(0b110010) + '\067' + chr(494 - 439), 50257 - 50249), nzTpIcepk0o8(chr(48) + chr(2831 - 2720) + '\063' + chr(0b110111) + chr(0b101001 + 0o10), 0o10), nzTpIcepk0o8(chr(942 - 894) + chr(11699 - 11588) + '\063' + chr(55) + '\065', 0b1000), nzTpIcepk0o8(chr(251 - 203) + chr(3875 - 3764) + chr(50) + chr(53) + chr(2892 - 2838), 51787 - 51779), nzTpIcepk0o8('\x30' + '\x6f' + chr(752 - 701) + chr(0b100000 + 0o27) + chr(0b11100 + 0o31), 8), nzTpIcepk0o8(chr(0b110000) + chr(0b11010 + 0o125) + chr(0b110001) + chr(0b110100) + chr(54), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + '\063' + chr(0b1010 + 0o46), 35052 - 35044), nzTpIcepk0o8('\x30' + chr(3178 - 3067) + chr(53), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(1147 - 1099) + chr(0b1101111) + chr(380 - 327) + chr(0b110000), 4375 - 4367)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'9'), chr(0b110011 + 0o61) + chr(101) + '\x63' + chr(0b1101111) + chr(0b1100100) + '\x65')(chr(117) + chr(116) + chr(667 - 565) + '\055' + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def rfyn55uBXwPX(KQq7Z9J63zv1, pPmkLCVA328e=roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'y.\x10'), chr(0b1100100) + chr(0b1100010 + 0o3) + chr(2248 - 2149) + chr(0b1101111) + chr(0b1011111 + 0o5) + chr(6614 - 6513))('\165' + '\x74' + chr(0b101001 + 0o75) + '\055' + chr(0b100000 + 0o30)))):
if not dRKdVnHPFq7C(KQq7Z9J63zv1, roI3spqORKae(ES5oEprVxulp(b't \x0b\xcft\n\x90z4'), '\144' + chr(9055 - 8954) + '\143' + '\157' + '\x64' + chr(0b1100101))(chr(0b1110101) + '\164' + '\146' + chr(45) + chr(56))) or not dRKdVnHPFq7C(KQq7Z9J63zv1, roI3spqORKae(ES5oEprVxulp(b't \x0b\xcft\n\x9b~,\xa3op'), chr(0b1100100) + chr(1089 - 988) + '\x63' + '\157' + '\144' + chr(0b1100101))(chr(0b110100 + 0o101) + '\x74' + chr(0b1100110) + chr(840 - 795) + chr(56))):
KQq7Z9J63zv1 = kkrDeTnxPwnD(KQq7Z9J63zv1, copy=nzTpIcepk0o8('\x30' + chr(6077 - 5966) + chr(0b110000), 8))
iP_fLynJjbnV = EiWVYWFIDWx0(KQq7Z9J63zv1)
l9mZkaAlpJU1 = KQq7Z9J63zv1.count_alleles().to_frequencies()
JAJ2qK7L8U3L = HNgng4gbWbeY(l9mZkaAlpJU1, ploidy=KQq7Z9J63zv1.lhbM092AFW8f[-nzTpIcepk0o8(chr(48) + '\x6f' + chr(49), ord("\x08"))], fill=nzTpIcepk0o8(chr(1017 - 969) + chr(111) + chr(48), 8))
with riuxP2ykwrwf():
_R8IKF5IwAfX = nDF4gVNx0u9Q.xWH4M7K6Qbd3(JAJ2qK7L8U3L > nzTpIcepk0o8(chr(48) + '\157' + '\x30', 8), nzTpIcepk0o8(chr(0b100 + 0o54) + chr(0b1101111) + chr(0b110001), 8) - iP_fLynJjbnV / JAJ2qK7L8U3L, pPmkLCVA328e)
return _R8IKF5IwAfX |
cggh/scikit-allel | allel/stats/mendel.py | mendel_errors | def mendel_errors(parent_genotypes, progeny_genotypes):
"""Locate genotype calls not consistent with Mendelian transmission of
alleles.
Parameters
----------
parent_genotypes : array_like, int, shape (n_variants, 2, 2)
Genotype calls for the two parents.
progeny_genotypes : array_like, int, shape (n_variants, n_progeny, 2)
Genotype calls for the progeny.
Returns
-------
me : ndarray, int, shape (n_variants, n_progeny)
Count of Mendel errors for each progeny genotype call.
Examples
--------
The following are all consistent with Mendelian transmission. Note that a
value of 0 is returned for missing calls::
>>> import allel
>>> import numpy as np
>>> genotypes = np.array([
... # aa x aa -> aa
... [[0, 0], [0, 0], [0, 0], [-1, -1], [-1, -1], [-1, -1]],
... [[1, 1], [1, 1], [1, 1], [-1, -1], [-1, -1], [-1, -1]],
... [[2, 2], [2, 2], [2, 2], [-1, -1], [-1, -1], [-1, -1]],
... # aa x ab -> aa or ab
... [[0, 0], [0, 1], [0, 0], [0, 1], [-1, -1], [-1, -1]],
... [[0, 0], [0, 2], [0, 0], [0, 2], [-1, -1], [-1, -1]],
... [[1, 1], [0, 1], [1, 1], [0, 1], [-1, -1], [-1, -1]],
... # aa x bb -> ab
... [[0, 0], [1, 1], [0, 1], [-1, -1], [-1, -1], [-1, -1]],
... [[0, 0], [2, 2], [0, 2], [-1, -1], [-1, -1], [-1, -1]],
... [[1, 1], [2, 2], [1, 2], [-1, -1], [-1, -1], [-1, -1]],
... # aa x bc -> ab or ac
... [[0, 0], [1, 2], [0, 1], [0, 2], [-1, -1], [-1, -1]],
... [[1, 1], [0, 2], [0, 1], [1, 2], [-1, -1], [-1, -1]],
... # ab x ab -> aa or ab or bb
... [[0, 1], [0, 1], [0, 0], [0, 1], [1, 1], [-1, -1]],
... [[1, 2], [1, 2], [1, 1], [1, 2], [2, 2], [-1, -1]],
... [[0, 2], [0, 2], [0, 0], [0, 2], [2, 2], [-1, -1]],
... # ab x bc -> ab or ac or bb or bc
... [[0, 1], [1, 2], [0, 1], [0, 2], [1, 1], [1, 2]],
... [[0, 1], [0, 2], [0, 0], [0, 1], [0, 1], [1, 2]],
... # ab x cd -> ac or ad or bc or bd
... [[0, 1], [2, 3], [0, 2], [0, 3], [1, 2], [1, 3]],
... ])
>>> me = allel.mendel_errors(genotypes[:, :2], genotypes[:, 2:])
>>> me
array([[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0]])
The following are cases of 'non-parental' inheritance where one or two
alleles are found in the progeny that are not present in either parent.
Note that the number of errors may be 1 or 2 depending on the number of
non-parental alleles::
>>> genotypes = np.array([
... # aa x aa -> ab or ac or bb or cc
... [[0, 0], [0, 0], [0, 1], [0, 2], [1, 1], [2, 2]],
... [[1, 1], [1, 1], [0, 1], [1, 2], [0, 0], [2, 2]],
... [[2, 2], [2, 2], [0, 2], [1, 2], [0, 0], [1, 1]],
... # aa x ab -> ac or bc or cc
... [[0, 0], [0, 1], [0, 2], [1, 2], [2, 2], [2, 2]],
... [[0, 0], [0, 2], [0, 1], [1, 2], [1, 1], [1, 1]],
... [[1, 1], [0, 1], [1, 2], [0, 2], [2, 2], [2, 2]],
... # aa x bb -> ac or bc or cc
... [[0, 0], [1, 1], [0, 2], [1, 2], [2, 2], [2, 2]],
... [[0, 0], [2, 2], [0, 1], [1, 2], [1, 1], [1, 1]],
... [[1, 1], [2, 2], [0, 1], [0, 2], [0, 0], [0, 0]],
... # ab x ab -> ac or bc or cc
... [[0, 1], [0, 1], [0, 2], [1, 2], [2, 2], [2, 2]],
... [[0, 2], [0, 2], [0, 1], [1, 2], [1, 1], [1, 1]],
... [[1, 2], [1, 2], [0, 1], [0, 2], [0, 0], [0, 0]],
... # ab x bc -> ad or bd or cd or dd
... [[0, 1], [1, 2], [0, 3], [1, 3], [2, 3], [3, 3]],
... [[0, 1], [0, 2], [0, 3], [1, 3], [2, 3], [3, 3]],
... [[0, 2], [1, 2], [0, 3], [1, 3], [2, 3], [3, 3]],
... # ab x cd -> ae or be or ce or de
... [[0, 1], [2, 3], [0, 4], [1, 4], [2, 4], [3, 4]],
... ])
>>> me = allel.mendel_errors(genotypes[:, :2], genotypes[:, 2:])
>>> me
array([[1, 1, 2, 2],
[1, 1, 2, 2],
[1, 1, 2, 2],
[1, 1, 2, 2],
[1, 1, 2, 2],
[1, 1, 2, 2],
[1, 1, 2, 2],
[1, 1, 2, 2],
[1, 1, 2, 2],
[1, 1, 2, 2],
[1, 1, 2, 2],
[1, 1, 2, 2],
[1, 1, 1, 2],
[1, 1, 1, 2],
[1, 1, 1, 2],
[1, 1, 1, 1]])
The following are cases of 'hemi-parental' inheritance, where progeny
appear to have inherited two copies of an allele found only once in one of
the parents::
>>> genotypes = np.array([
... # aa x ab -> bb
... [[0, 0], [0, 1], [1, 1], [-1, -1]],
... [[0, 0], [0, 2], [2, 2], [-1, -1]],
... [[1, 1], [0, 1], [0, 0], [-1, -1]],
... # ab x bc -> aa or cc
... [[0, 1], [1, 2], [0, 0], [2, 2]],
... [[0, 1], [0, 2], [1, 1], [2, 2]],
... [[0, 2], [1, 2], [0, 0], [1, 1]],
... # ab x cd -> aa or bb or cc or dd
... [[0, 1], [2, 3], [0, 0], [1, 1]],
... [[0, 1], [2, 3], [2, 2], [3, 3]],
... ])
>>> me = allel.mendel_errors(genotypes[:, :2], genotypes[:, 2:])
>>> me
array([[1, 0],
[1, 0],
[1, 0],
[1, 1],
[1, 1],
[1, 1],
[1, 1],
[1, 1]])
The following are cases of 'uni-parental' inheritance, where progeny
appear to have inherited both alleles from a single parent::
>>> genotypes = np.array([
... # aa x bb -> aa or bb
... [[0, 0], [1, 1], [0, 0], [1, 1]],
... [[0, 0], [2, 2], [0, 0], [2, 2]],
... [[1, 1], [2, 2], [1, 1], [2, 2]],
... # aa x bc -> aa or bc
... [[0, 0], [1, 2], [0, 0], [1, 2]],
... [[1, 1], [0, 2], [1, 1], [0, 2]],
... # ab x cd -> ab or cd
... [[0, 1], [2, 3], [0, 1], [2, 3]],
... ])
>>> me = allel.mendel_errors(genotypes[:, :2], genotypes[:, 2:])
>>> me
array([[1, 1],
[1, 1],
[1, 1],
[1, 1],
[1, 1],
[1, 1]])
"""
# setup
parent_genotypes = GenotypeArray(parent_genotypes)
progeny_genotypes = GenotypeArray(progeny_genotypes)
check_ploidy(parent_genotypes.ploidy, 2)
check_ploidy(progeny_genotypes.ploidy, 2)
# transform into per-call allele counts
max_allele = max(parent_genotypes.max(), progeny_genotypes.max())
parent_gc = parent_genotypes.to_allele_counts(max_allele=max_allele, dtype='i1')
progeny_gc = progeny_genotypes.to_allele_counts(max_allele=max_allele, dtype='i1')
# detect nonparental and hemiparental inheritance by comparing allele
# counts between parents and progeny
max_progeny_gc = parent_gc.clip(max=1).sum(axis=1)
max_progeny_gc = max_progeny_gc[:, np.newaxis, :]
me = (progeny_gc - max_progeny_gc).clip(min=0).sum(axis=2)
# detect uniparental inheritance by finding cases where no alleles are
# shared between parents, then comparing progeny allele counts to each
# parent
p1_gc = parent_gc[:, 0, np.newaxis, :]
p2_gc = parent_gc[:, 1, np.newaxis, :]
# find variants where parents don't share any alleles
is_shared_allele = (p1_gc > 0) & (p2_gc > 0)
no_shared_alleles = ~np.any(is_shared_allele, axis=2)
# find calls where progeny genotype is identical to one or the other parent
me[no_shared_alleles &
(np.all(progeny_gc == p1_gc, axis=2) |
np.all(progeny_gc == p2_gc, axis=2))] = 1
# retrofit where either or both parent has a missing call
me[np.any(parent_genotypes.is_missing(), axis=1)] = 0
return me | python | def mendel_errors(parent_genotypes, progeny_genotypes):
"""Locate genotype calls not consistent with Mendelian transmission of
alleles.
Parameters
----------
parent_genotypes : array_like, int, shape (n_variants, 2, 2)
Genotype calls for the two parents.
progeny_genotypes : array_like, int, shape (n_variants, n_progeny, 2)
Genotype calls for the progeny.
Returns
-------
me : ndarray, int, shape (n_variants, n_progeny)
Count of Mendel errors for each progeny genotype call.
Examples
--------
The following are all consistent with Mendelian transmission. Note that a
value of 0 is returned for missing calls::
>>> import allel
>>> import numpy as np
>>> genotypes = np.array([
... # aa x aa -> aa
... [[0, 0], [0, 0], [0, 0], [-1, -1], [-1, -1], [-1, -1]],
... [[1, 1], [1, 1], [1, 1], [-1, -1], [-1, -1], [-1, -1]],
... [[2, 2], [2, 2], [2, 2], [-1, -1], [-1, -1], [-1, -1]],
... # aa x ab -> aa or ab
... [[0, 0], [0, 1], [0, 0], [0, 1], [-1, -1], [-1, -1]],
... [[0, 0], [0, 2], [0, 0], [0, 2], [-1, -1], [-1, -1]],
... [[1, 1], [0, 1], [1, 1], [0, 1], [-1, -1], [-1, -1]],
... # aa x bb -> ab
... [[0, 0], [1, 1], [0, 1], [-1, -1], [-1, -1], [-1, -1]],
... [[0, 0], [2, 2], [0, 2], [-1, -1], [-1, -1], [-1, -1]],
... [[1, 1], [2, 2], [1, 2], [-1, -1], [-1, -1], [-1, -1]],
... # aa x bc -> ab or ac
... [[0, 0], [1, 2], [0, 1], [0, 2], [-1, -1], [-1, -1]],
... [[1, 1], [0, 2], [0, 1], [1, 2], [-1, -1], [-1, -1]],
... # ab x ab -> aa or ab or bb
... [[0, 1], [0, 1], [0, 0], [0, 1], [1, 1], [-1, -1]],
... [[1, 2], [1, 2], [1, 1], [1, 2], [2, 2], [-1, -1]],
... [[0, 2], [0, 2], [0, 0], [0, 2], [2, 2], [-1, -1]],
... # ab x bc -> ab or ac or bb or bc
... [[0, 1], [1, 2], [0, 1], [0, 2], [1, 1], [1, 2]],
... [[0, 1], [0, 2], [0, 0], [0, 1], [0, 1], [1, 2]],
... # ab x cd -> ac or ad or bc or bd
... [[0, 1], [2, 3], [0, 2], [0, 3], [1, 2], [1, 3]],
... ])
>>> me = allel.mendel_errors(genotypes[:, :2], genotypes[:, 2:])
>>> me
array([[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0]])
The following are cases of 'non-parental' inheritance where one or two
alleles are found in the progeny that are not present in either parent.
Note that the number of errors may be 1 or 2 depending on the number of
non-parental alleles::
>>> genotypes = np.array([
... # aa x aa -> ab or ac or bb or cc
... [[0, 0], [0, 0], [0, 1], [0, 2], [1, 1], [2, 2]],
... [[1, 1], [1, 1], [0, 1], [1, 2], [0, 0], [2, 2]],
... [[2, 2], [2, 2], [0, 2], [1, 2], [0, 0], [1, 1]],
... # aa x ab -> ac or bc or cc
... [[0, 0], [0, 1], [0, 2], [1, 2], [2, 2], [2, 2]],
... [[0, 0], [0, 2], [0, 1], [1, 2], [1, 1], [1, 1]],
... [[1, 1], [0, 1], [1, 2], [0, 2], [2, 2], [2, 2]],
... # aa x bb -> ac or bc or cc
... [[0, 0], [1, 1], [0, 2], [1, 2], [2, 2], [2, 2]],
... [[0, 0], [2, 2], [0, 1], [1, 2], [1, 1], [1, 1]],
... [[1, 1], [2, 2], [0, 1], [0, 2], [0, 0], [0, 0]],
... # ab x ab -> ac or bc or cc
... [[0, 1], [0, 1], [0, 2], [1, 2], [2, 2], [2, 2]],
... [[0, 2], [0, 2], [0, 1], [1, 2], [1, 1], [1, 1]],
... [[1, 2], [1, 2], [0, 1], [0, 2], [0, 0], [0, 0]],
... # ab x bc -> ad or bd or cd or dd
... [[0, 1], [1, 2], [0, 3], [1, 3], [2, 3], [3, 3]],
... [[0, 1], [0, 2], [0, 3], [1, 3], [2, 3], [3, 3]],
... [[0, 2], [1, 2], [0, 3], [1, 3], [2, 3], [3, 3]],
... # ab x cd -> ae or be or ce or de
... [[0, 1], [2, 3], [0, 4], [1, 4], [2, 4], [3, 4]],
... ])
>>> me = allel.mendel_errors(genotypes[:, :2], genotypes[:, 2:])
>>> me
array([[1, 1, 2, 2],
[1, 1, 2, 2],
[1, 1, 2, 2],
[1, 1, 2, 2],
[1, 1, 2, 2],
[1, 1, 2, 2],
[1, 1, 2, 2],
[1, 1, 2, 2],
[1, 1, 2, 2],
[1, 1, 2, 2],
[1, 1, 2, 2],
[1, 1, 2, 2],
[1, 1, 1, 2],
[1, 1, 1, 2],
[1, 1, 1, 2],
[1, 1, 1, 1]])
The following are cases of 'hemi-parental' inheritance, where progeny
appear to have inherited two copies of an allele found only once in one of
the parents::
>>> genotypes = np.array([
... # aa x ab -> bb
... [[0, 0], [0, 1], [1, 1], [-1, -1]],
... [[0, 0], [0, 2], [2, 2], [-1, -1]],
... [[1, 1], [0, 1], [0, 0], [-1, -1]],
... # ab x bc -> aa or cc
... [[0, 1], [1, 2], [0, 0], [2, 2]],
... [[0, 1], [0, 2], [1, 1], [2, 2]],
... [[0, 2], [1, 2], [0, 0], [1, 1]],
... # ab x cd -> aa or bb or cc or dd
... [[0, 1], [2, 3], [0, 0], [1, 1]],
... [[0, 1], [2, 3], [2, 2], [3, 3]],
... ])
>>> me = allel.mendel_errors(genotypes[:, :2], genotypes[:, 2:])
>>> me
array([[1, 0],
[1, 0],
[1, 0],
[1, 1],
[1, 1],
[1, 1],
[1, 1],
[1, 1]])
The following are cases of 'uni-parental' inheritance, where progeny
appear to have inherited both alleles from a single parent::
>>> genotypes = np.array([
... # aa x bb -> aa or bb
... [[0, 0], [1, 1], [0, 0], [1, 1]],
... [[0, 0], [2, 2], [0, 0], [2, 2]],
... [[1, 1], [2, 2], [1, 1], [2, 2]],
... # aa x bc -> aa or bc
... [[0, 0], [1, 2], [0, 0], [1, 2]],
... [[1, 1], [0, 2], [1, 1], [0, 2]],
... # ab x cd -> ab or cd
... [[0, 1], [2, 3], [0, 1], [2, 3]],
... ])
>>> me = allel.mendel_errors(genotypes[:, :2], genotypes[:, 2:])
>>> me
array([[1, 1],
[1, 1],
[1, 1],
[1, 1],
[1, 1],
[1, 1]])
"""
# setup
parent_genotypes = GenotypeArray(parent_genotypes)
progeny_genotypes = GenotypeArray(progeny_genotypes)
check_ploidy(parent_genotypes.ploidy, 2)
check_ploidy(progeny_genotypes.ploidy, 2)
# transform into per-call allele counts
max_allele = max(parent_genotypes.max(), progeny_genotypes.max())
parent_gc = parent_genotypes.to_allele_counts(max_allele=max_allele, dtype='i1')
progeny_gc = progeny_genotypes.to_allele_counts(max_allele=max_allele, dtype='i1')
# detect nonparental and hemiparental inheritance by comparing allele
# counts between parents and progeny
max_progeny_gc = parent_gc.clip(max=1).sum(axis=1)
max_progeny_gc = max_progeny_gc[:, np.newaxis, :]
me = (progeny_gc - max_progeny_gc).clip(min=0).sum(axis=2)
# detect uniparental inheritance by finding cases where no alleles are
# shared between parents, then comparing progeny allele counts to each
# parent
p1_gc = parent_gc[:, 0, np.newaxis, :]
p2_gc = parent_gc[:, 1, np.newaxis, :]
# find variants where parents don't share any alleles
is_shared_allele = (p1_gc > 0) & (p2_gc > 0)
no_shared_alleles = ~np.any(is_shared_allele, axis=2)
# find calls where progeny genotype is identical to one or the other parent
me[no_shared_alleles &
(np.all(progeny_gc == p1_gc, axis=2) |
np.all(progeny_gc == p2_gc, axis=2))] = 1
# retrofit where either or both parent has a missing call
me[np.any(parent_genotypes.is_missing(), axis=1)] = 0
return me | [
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"parent... | Locate genotype calls not consistent with Mendelian transmission of
alleles.
Parameters
----------
parent_genotypes : array_like, int, shape (n_variants, 2, 2)
Genotype calls for the two parents.
progeny_genotypes : array_like, int, shape (n_variants, n_progeny, 2)
Genotype calls for the progeny.
Returns
-------
me : ndarray, int, shape (n_variants, n_progeny)
Count of Mendel errors for each progeny genotype call.
Examples
--------
The following are all consistent with Mendelian transmission. Note that a
value of 0 is returned for missing calls::
>>> import allel
>>> import numpy as np
>>> genotypes = np.array([
... # aa x aa -> aa
... [[0, 0], [0, 0], [0, 0], [-1, -1], [-1, -1], [-1, -1]],
... [[1, 1], [1, 1], [1, 1], [-1, -1], [-1, -1], [-1, -1]],
... [[2, 2], [2, 2], [2, 2], [-1, -1], [-1, -1], [-1, -1]],
... # aa x ab -> aa or ab
... [[0, 0], [0, 1], [0, 0], [0, 1], [-1, -1], [-1, -1]],
... [[0, 0], [0, 2], [0, 0], [0, 2], [-1, -1], [-1, -1]],
... [[1, 1], [0, 1], [1, 1], [0, 1], [-1, -1], [-1, -1]],
... # aa x bb -> ab
... [[0, 0], [1, 1], [0, 1], [-1, -1], [-1, -1], [-1, -1]],
... [[0, 0], [2, 2], [0, 2], [-1, -1], [-1, -1], [-1, -1]],
... [[1, 1], [2, 2], [1, 2], [-1, -1], [-1, -1], [-1, -1]],
... # aa x bc -> ab or ac
... [[0, 0], [1, 2], [0, 1], [0, 2], [-1, -1], [-1, -1]],
... [[1, 1], [0, 2], [0, 1], [1, 2], [-1, -1], [-1, -1]],
... # ab x ab -> aa or ab or bb
... [[0, 1], [0, 1], [0, 0], [0, 1], [1, 1], [-1, -1]],
... [[1, 2], [1, 2], [1, 1], [1, 2], [2, 2], [-1, -1]],
... [[0, 2], [0, 2], [0, 0], [0, 2], [2, 2], [-1, -1]],
... # ab x bc -> ab or ac or bb or bc
... [[0, 1], [1, 2], [0, 1], [0, 2], [1, 1], [1, 2]],
... [[0, 1], [0, 2], [0, 0], [0, 1], [0, 1], [1, 2]],
... # ab x cd -> ac or ad or bc or bd
... [[0, 1], [2, 3], [0, 2], [0, 3], [1, 2], [1, 3]],
... ])
>>> me = allel.mendel_errors(genotypes[:, :2], genotypes[:, 2:])
>>> me
array([[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0]])
The following are cases of 'non-parental' inheritance where one or two
alleles are found in the progeny that are not present in either parent.
Note that the number of errors may be 1 or 2 depending on the number of
non-parental alleles::
>>> genotypes = np.array([
... # aa x aa -> ab or ac or bb or cc
... [[0, 0], [0, 0], [0, 1], [0, 2], [1, 1], [2, 2]],
... [[1, 1], [1, 1], [0, 1], [1, 2], [0, 0], [2, 2]],
... [[2, 2], [2, 2], [0, 2], [1, 2], [0, 0], [1, 1]],
... # aa x ab -> ac or bc or cc
... [[0, 0], [0, 1], [0, 2], [1, 2], [2, 2], [2, 2]],
... [[0, 0], [0, 2], [0, 1], [1, 2], [1, 1], [1, 1]],
... [[1, 1], [0, 1], [1, 2], [0, 2], [2, 2], [2, 2]],
... # aa x bb -> ac or bc or cc
... [[0, 0], [1, 1], [0, 2], [1, 2], [2, 2], [2, 2]],
... [[0, 0], [2, 2], [0, 1], [1, 2], [1, 1], [1, 1]],
... [[1, 1], [2, 2], [0, 1], [0, 2], [0, 0], [0, 0]],
... # ab x ab -> ac or bc or cc
... [[0, 1], [0, 1], [0, 2], [1, 2], [2, 2], [2, 2]],
... [[0, 2], [0, 2], [0, 1], [1, 2], [1, 1], [1, 1]],
... [[1, 2], [1, 2], [0, 1], [0, 2], [0, 0], [0, 0]],
... # ab x bc -> ad or bd or cd or dd
... [[0, 1], [1, 2], [0, 3], [1, 3], [2, 3], [3, 3]],
... [[0, 1], [0, 2], [0, 3], [1, 3], [2, 3], [3, 3]],
... [[0, 2], [1, 2], [0, 3], [1, 3], [2, 3], [3, 3]],
... # ab x cd -> ae or be or ce or de
... [[0, 1], [2, 3], [0, 4], [1, 4], [2, 4], [3, 4]],
... ])
>>> me = allel.mendel_errors(genotypes[:, :2], genotypes[:, 2:])
>>> me
array([[1, 1, 2, 2],
[1, 1, 2, 2],
[1, 1, 2, 2],
[1, 1, 2, 2],
[1, 1, 2, 2],
[1, 1, 2, 2],
[1, 1, 2, 2],
[1, 1, 2, 2],
[1, 1, 2, 2],
[1, 1, 2, 2],
[1, 1, 2, 2],
[1, 1, 2, 2],
[1, 1, 1, 2],
[1, 1, 1, 2],
[1, 1, 1, 2],
[1, 1, 1, 1]])
The following are cases of 'hemi-parental' inheritance, where progeny
appear to have inherited two copies of an allele found only once in one of
the parents::
>>> genotypes = np.array([
... # aa x ab -> bb
... [[0, 0], [0, 1], [1, 1], [-1, -1]],
... [[0, 0], [0, 2], [2, 2], [-1, -1]],
... [[1, 1], [0, 1], [0, 0], [-1, -1]],
... # ab x bc -> aa or cc
... [[0, 1], [1, 2], [0, 0], [2, 2]],
... [[0, 1], [0, 2], [1, 1], [2, 2]],
... [[0, 2], [1, 2], [0, 0], [1, 1]],
... # ab x cd -> aa or bb or cc or dd
... [[0, 1], [2, 3], [0, 0], [1, 1]],
... [[0, 1], [2, 3], [2, 2], [3, 3]],
... ])
>>> me = allel.mendel_errors(genotypes[:, :2], genotypes[:, 2:])
>>> me
array([[1, 0],
[1, 0],
[1, 0],
[1, 1],
[1, 1],
[1, 1],
[1, 1],
[1, 1]])
The following are cases of 'uni-parental' inheritance, where progeny
appear to have inherited both alleles from a single parent::
>>> genotypes = np.array([
... # aa x bb -> aa or bb
... [[0, 0], [1, 1], [0, 0], [1, 1]],
... [[0, 0], [2, 2], [0, 0], [2, 2]],
... [[1, 1], [2, 2], [1, 1], [2, 2]],
... # aa x bc -> aa or bc
... [[0, 0], [1, 2], [0, 0], [1, 2]],
... [[1, 1], [0, 2], [1, 1], [0, 2]],
... # ab x cd -> ab or cd
... [[0, 1], [2, 3], [0, 1], [2, 3]],
... ])
>>> me = allel.mendel_errors(genotypes[:, :2], genotypes[:, 2:])
>>> me
array([[1, 1],
[1, 1],
[1, 1],
[1, 1],
[1, 1],
[1, 1]]) | [
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"alleles",
"."
] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/stats/mendel.py#L15-L218 | train | Locate genotype calls not consistent with Mendelian transmission of the base genotypes. | 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(0b110010) + chr(0b0 + 0o62) + chr(478 - 425), ord("\x08")), nzTpIcepk0o8(chr(0b101000 + 0o10) + chr(0b1101111) + chr(53) + chr(1680 - 1628), 0o10), nzTpIcepk0o8('\x30' + '\157' + '\066' + '\x35', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(49), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b1010 + 0o55) + '\065', 0o10), nzTpIcepk0o8(chr(1280 - 1232) + '\x6f' + chr(52) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(49) + chr(797 - 749) + '\x35', 0b1000), nzTpIcepk0o8(chr(0b111 + 0o51) + chr(0b1101111) + chr(0b110001) + chr(0b101000 + 0o13) + chr(51), 32369 - 32361), nzTpIcepk0o8(chr(939 - 891) + chr(0b1101111) + chr(0b110010) + chr(0b110001) + chr(53), 2197 - 2189), nzTpIcepk0o8(chr(0b10000 + 0o40) + chr(0b1101111) + '\x31' + chr(2956 - 2901), 0b1000), nzTpIcepk0o8(chr(0b10 + 0o56) + '\157' + chr(967 - 912) + '\065', 8), nzTpIcepk0o8(chr(729 - 681) + chr(1828 - 1717) + '\062' + chr(50) + chr(0b100101 + 0o16), ord("\x08")), nzTpIcepk0o8(chr(263 - 215) + chr(0b1100001 + 0o16) + '\062' + chr(1663 - 1612), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(50) + chr(1886 - 1838) + chr(0b100011 + 0o20), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(11070 - 10959) + chr(0b10111 + 0o32) + chr(0b110011) + '\x31', 0b1000), nzTpIcepk0o8(chr(1371 - 1323) + chr(5370 - 5259) + chr(0b10 + 0o57) + chr(2531 - 2477) + chr(1051 - 1000), ord("\x08")), nzTpIcepk0o8(chr(0b1 + 0o57) + '\157' + '\x34' + chr(0b100101 + 0o16), 8), nzTpIcepk0o8(chr(209 - 161) + chr(0b1100000 + 0o17) + '\x31' + chr(48) + '\064', ord("\x08")), nzTpIcepk0o8(chr(0b11100 + 0o24) + '\x6f' + chr(49) + chr(0b1110 + 0o44) + chr(0b100000 + 0o24), 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(1145 - 1096) + chr(0b110010) + '\062', 0b1000), nzTpIcepk0o8('\060' + chr(0b111101 + 0o62) + chr(212 - 163) + '\x37' + '\x35', 0o10), nzTpIcepk0o8(chr(48) + '\157' + '\x32' + chr(2040 - 1991) + '\x32', 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(52) + chr(0b10000 + 0o47), 0o10), nzTpIcepk0o8(chr(1073 - 1025) + chr(111) + chr(0b110011) + chr(0b110010) + '\062', 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(1391 - 1341) + chr(49) + chr(0b1001 + 0o53), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + '\x32' + chr(53 - 2) + chr(51), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + '\063' + '\067' + chr(1552 - 1498), 30048 - 30040), nzTpIcepk0o8(chr(0b110000) + chr(4476 - 4365) + chr(51) + '\x33' + chr(0b110101), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + '\062' + chr(458 - 403) + '\067', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\063' + chr(0b110001) + '\x32', 65280 - 65272), nzTpIcepk0o8(chr(0b101101 + 0o3) + chr(0b1101111) + chr(2243 - 2194) + chr(1664 - 1613), ord("\x08")), nzTpIcepk0o8(chr(0b101110 + 0o2) + chr(111) + chr(275 - 225) + '\064' + chr(51), ord("\x08")), nzTpIcepk0o8(chr(0b1101 + 0o43) + chr(0b1101111) + '\063' + chr(0b10101 + 0o42) + chr(0b1000 + 0o51), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b101 + 0o55) + chr(55) + chr(1131 - 1080), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(50) + '\x31' + chr(0b11111 + 0o24), 61574 - 61566), nzTpIcepk0o8(chr(48) + '\x6f' + chr(2500 - 2449) + chr(54) + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(7136 - 7025) + chr(0b1111 + 0o44) + '\x31' + chr(1067 - 1013), 0b1000), nzTpIcepk0o8(chr(48) + chr(1739 - 1628) + chr(1150 - 1099) + chr(0b110111) + chr(53), 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + '\062' + '\x30' + chr(0b101010 + 0o12), 0b1000), nzTpIcepk0o8(chr(2237 - 2189) + chr(1596 - 1485) + '\x33' + '\x34' + chr(1398 - 1349), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b101101 + 0o3) + chr(111) + chr(1432 - 1379) + chr(0b100110 + 0o12), 26962 - 26954)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xbb'), '\144' + chr(9232 - 9131) + chr(99) + chr(5613 - 5502) + chr(0b1100100) + chr(0b10101 + 0o120))('\165' + chr(116) + chr(4325 - 4223) + chr(0b11001 + 0o24) + chr(363 - 307)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def enmxpSo12E5Z(IT67RmAJisaz, F4xSaBq1X6P3):
IT67RmAJisaz = kkrDeTnxPwnD(IT67RmAJisaz)
F4xSaBq1X6P3 = kkrDeTnxPwnD(F4xSaBq1X6P3)
S0Uypoo4zSP9(roI3spqORKae(IT67RmAJisaz, roI3spqORKae(ES5oEprVxulp(b'\xe5@ZhYZ'), chr(5345 - 5245) + chr(2720 - 2619) + '\x63' + chr(111) + chr(0b101001 + 0o73) + chr(0b1100101))('\x75' + chr(0b1001000 + 0o54) + '\x66' + '\055' + chr(0b111000 + 0o0))), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x32', 35794 - 35786))
S0Uypoo4zSP9(roI3spqORKae(F4xSaBq1X6P3, roI3spqORKae(ES5oEprVxulp(b'\xe5@ZhYZ'), chr(0b1100100) + chr(0b1100101) + chr(2061 - 1962) + chr(5582 - 5471) + '\144' + chr(3425 - 3324))(chr(0b1110101) + chr(0b1110100) + chr(0b1011101 + 0o11) + chr(45) + chr(56))), nzTpIcepk0o8(chr(0b110000) + chr(3891 - 3780) + chr(67 - 17), 8))
j75eupAGs_rK = KV9ckIhroIia(IT67RmAJisaz.KV9ckIhroIia(), F4xSaBq1X6P3.KV9ckIhroIia())
Unn3nPuaqSVf = IT67RmAJisaz.to_allele_counts(max_allele=j75eupAGs_rK, dtype=roI3spqORKae(ES5oEprVxulp(b'\xfc\x1d'), chr(9303 - 9203) + chr(0b1100101) + '\x63' + chr(3446 - 3335) + chr(0b1100010 + 0o2) + '\x65')('\x75' + chr(0b1011011 + 0o31) + chr(102) + chr(1220 - 1175) + '\070'))
fvOnHMtd4Ltd = F4xSaBq1X6P3.to_allele_counts(max_allele=j75eupAGs_rK, dtype=roI3spqORKae(ES5oEprVxulp(b'\xfc\x1d'), chr(0b100100 + 0o100) + '\x65' + '\x63' + chr(0b10001 + 0o136) + chr(100) + '\x65')(chr(0b111 + 0o156) + chr(0b10011 + 0o141) + chr(0b1100110) + chr(770 - 725) + '\070'))
jxHMUnB0e3KQ = Unn3nPuaqSVf.clip(max=nzTpIcepk0o8('\060' + chr(0b1100111 + 0o10) + '\061', 8)).oclC8DLjA_lV(axis=nzTpIcepk0o8('\x30' + '\x6f' + chr(49), 8))
jxHMUnB0e3KQ = jxHMUnB0e3KQ[:, nDF4gVNx0u9Q.newaxis, :]
il06faWJ3dK3 = (fvOnHMtd4Ltd - jxHMUnB0e3KQ).clip(min=nzTpIcepk0o8('\x30' + '\157' + '\060', 0b1000)).oclC8DLjA_lV(axis=nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110010), 8))
oHCxXwckt_Lw = Unn3nPuaqSVf[:, nzTpIcepk0o8(chr(0b1000 + 0o50) + chr(0b1101111) + '\060', 8), nDF4gVNx0u9Q.newaxis, :]
YJq8dHq5FVX5 = Unn3nPuaqSVf[:, nzTpIcepk0o8('\x30' + chr(0b1001110 + 0o41) + '\x31', 8), nDF4gVNx0u9Q.newaxis, :]
jiGrsqNeyYiR = (oHCxXwckt_Lw > nzTpIcepk0o8(chr(0b110000) + chr(2626 - 2515) + chr(48), 8)) & (YJq8dHq5FVX5 > nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110000), 8))
r6t8OOZr6Npv = ~nDF4gVNx0u9Q.VF4pKOObtlPc(jiGrsqNeyYiR, axis=nzTpIcepk0o8(chr(0b10 + 0o56) + chr(0b1101111) + chr(0b10000 + 0o42), 8))
il06faWJ3dK3[r6t8OOZr6Npv & (nDF4gVNx0u9Q.qX60lO1lgHA5(fvOnHMtd4Ltd == oHCxXwckt_Lw, axis=nzTpIcepk0o8('\x30' + '\157' + '\062', 8)) | nDF4gVNx0u9Q.qX60lO1lgHA5(fvOnHMtd4Ltd == YJq8dHq5FVX5, axis=nzTpIcepk0o8('\060' + chr(3383 - 3272) + chr(0b11101 + 0o25), 8)))] = nzTpIcepk0o8('\060' + chr(0b1101111) + chr(209 - 160), 8)
il06faWJ3dK3[nDF4gVNx0u9Q.VF4pKOObtlPc(IT67RmAJisaz.zYFtC4_vxWk9(), axis=nzTpIcepk0o8('\x30' + '\x6f' + '\061', 8))] = nzTpIcepk0o8(chr(0b101000 + 0o10) + chr(11459 - 11348) + chr(48), 8)
return il06faWJ3dK3 |
cggh/scikit-allel | allel/stats/mendel.py | paint_transmission | def paint_transmission(parent_haplotypes, progeny_haplotypes):
"""Paint haplotypes inherited from a single diploid parent according to
their allelic inheritance.
Parameters
----------
parent_haplotypes : array_like, int, shape (n_variants, 2)
Both haplotypes from a single diploid parent.
progeny_haplotypes : array_like, int, shape (n_variants, n_progeny)
Haplotypes found in progeny of the given parent, inherited from the
given parent. I.e., haplotypes from gametes of the given parent.
Returns
-------
painting : ndarray, uint8, shape (n_variants, n_progeny)
An array of integers coded as follows: 1 = allele inherited from
first parental haplotype; 2 = allele inherited from second parental
haplotype; 3 = reference allele, also carried by both parental
haplotypes; 4 = non-reference allele, also carried by both parental
haplotypes; 5 = non-parental allele; 6 = either or both parental
alleles missing; 7 = missing allele; 0 = undetermined.
Examples
--------
>>> import allel
>>> haplotypes = allel.HaplotypeArray([
... [0, 0, 0, 1, 2, -1],
... [0, 1, 0, 1, 2, -1],
... [1, 0, 0, 1, 2, -1],
... [1, 1, 0, 1, 2, -1],
... [0, 2, 0, 1, 2, -1],
... [0, -1, 0, 1, 2, -1],
... [-1, 1, 0, 1, 2, -1],
... [-1, -1, 0, 1, 2, -1],
... ], dtype='i1')
>>> painting = allel.paint_transmission(haplotypes[:, :2],
... haplotypes[:, 2:])
>>> painting
array([[3, 5, 5, 7],
[1, 2, 5, 7],
[2, 1, 5, 7],
[5, 4, 5, 7],
[1, 5, 2, 7],
[6, 6, 6, 7],
[6, 6, 6, 7],
[6, 6, 6, 7]], dtype=uint8)
"""
# check inputs
parent_haplotypes = HaplotypeArray(parent_haplotypes)
progeny_haplotypes = HaplotypeArray(progeny_haplotypes)
if parent_haplotypes.n_haplotypes != 2:
raise ValueError('exactly two parental haplotypes should be provided')
# convenience variables
parent1 = parent_haplotypes[:, 0, np.newaxis]
parent2 = parent_haplotypes[:, 1, np.newaxis]
progeny_is_missing = progeny_haplotypes < 0
parent_is_missing = np.any(parent_haplotypes < 0, axis=1)
# need this for broadcasting, but also need to retain original for later
parent_is_missing_bc = parent_is_missing[:, np.newaxis]
parent_diplotype = GenotypeArray(parent_haplotypes[:, np.newaxis, :])
parent_is_hom_ref = parent_diplotype.is_hom_ref()
parent_is_het = parent_diplotype.is_het()
parent_is_hom_alt = parent_diplotype.is_hom_alt()
# identify allele calls where inheritance can be determined
is_callable = ~progeny_is_missing & ~parent_is_missing_bc
is_callable_seg = is_callable & parent_is_het
# main inheritance states
inherit_parent1 = is_callable_seg & (progeny_haplotypes == parent1)
inherit_parent2 = is_callable_seg & (progeny_haplotypes == parent2)
nonseg_ref = (is_callable & parent_is_hom_ref & (progeny_haplotypes == parent1))
nonseg_alt = (is_callable & parent_is_hom_alt & (progeny_haplotypes == parent1))
nonparental = (
is_callable & (progeny_haplotypes != parent1) & (progeny_haplotypes != parent2)
)
# record inheritance states
# N.B., order in which these are set matters
painting = np.zeros(progeny_haplotypes.shape, dtype='u1')
painting[inherit_parent1] = INHERIT_PARENT1
painting[inherit_parent2] = INHERIT_PARENT2
painting[nonseg_ref] = INHERIT_NONSEG_REF
painting[nonseg_alt] = INHERIT_NONSEG_ALT
painting[nonparental] = INHERIT_NONPARENTAL
painting[parent_is_missing] = INHERIT_PARENT_MISSING
painting[progeny_is_missing] = INHERIT_MISSING
return painting | python | def paint_transmission(parent_haplotypes, progeny_haplotypes):
"""Paint haplotypes inherited from a single diploid parent according to
their allelic inheritance.
Parameters
----------
parent_haplotypes : array_like, int, shape (n_variants, 2)
Both haplotypes from a single diploid parent.
progeny_haplotypes : array_like, int, shape (n_variants, n_progeny)
Haplotypes found in progeny of the given parent, inherited from the
given parent. I.e., haplotypes from gametes of the given parent.
Returns
-------
painting : ndarray, uint8, shape (n_variants, n_progeny)
An array of integers coded as follows: 1 = allele inherited from
first parental haplotype; 2 = allele inherited from second parental
haplotype; 3 = reference allele, also carried by both parental
haplotypes; 4 = non-reference allele, also carried by both parental
haplotypes; 5 = non-parental allele; 6 = either or both parental
alleles missing; 7 = missing allele; 0 = undetermined.
Examples
--------
>>> import allel
>>> haplotypes = allel.HaplotypeArray([
... [0, 0, 0, 1, 2, -1],
... [0, 1, 0, 1, 2, -1],
... [1, 0, 0, 1, 2, -1],
... [1, 1, 0, 1, 2, -1],
... [0, 2, 0, 1, 2, -1],
... [0, -1, 0, 1, 2, -1],
... [-1, 1, 0, 1, 2, -1],
... [-1, -1, 0, 1, 2, -1],
... ], dtype='i1')
>>> painting = allel.paint_transmission(haplotypes[:, :2],
... haplotypes[:, 2:])
>>> painting
array([[3, 5, 5, 7],
[1, 2, 5, 7],
[2, 1, 5, 7],
[5, 4, 5, 7],
[1, 5, 2, 7],
[6, 6, 6, 7],
[6, 6, 6, 7],
[6, 6, 6, 7]], dtype=uint8)
"""
# check inputs
parent_haplotypes = HaplotypeArray(parent_haplotypes)
progeny_haplotypes = HaplotypeArray(progeny_haplotypes)
if parent_haplotypes.n_haplotypes != 2:
raise ValueError('exactly two parental haplotypes should be provided')
# convenience variables
parent1 = parent_haplotypes[:, 0, np.newaxis]
parent2 = parent_haplotypes[:, 1, np.newaxis]
progeny_is_missing = progeny_haplotypes < 0
parent_is_missing = np.any(parent_haplotypes < 0, axis=1)
# need this for broadcasting, but also need to retain original for later
parent_is_missing_bc = parent_is_missing[:, np.newaxis]
parent_diplotype = GenotypeArray(parent_haplotypes[:, np.newaxis, :])
parent_is_hom_ref = parent_diplotype.is_hom_ref()
parent_is_het = parent_diplotype.is_het()
parent_is_hom_alt = parent_diplotype.is_hom_alt()
# identify allele calls where inheritance can be determined
is_callable = ~progeny_is_missing & ~parent_is_missing_bc
is_callable_seg = is_callable & parent_is_het
# main inheritance states
inherit_parent1 = is_callable_seg & (progeny_haplotypes == parent1)
inherit_parent2 = is_callable_seg & (progeny_haplotypes == parent2)
nonseg_ref = (is_callable & parent_is_hom_ref & (progeny_haplotypes == parent1))
nonseg_alt = (is_callable & parent_is_hom_alt & (progeny_haplotypes == parent1))
nonparental = (
is_callable & (progeny_haplotypes != parent1) & (progeny_haplotypes != parent2)
)
# record inheritance states
# N.B., order in which these are set matters
painting = np.zeros(progeny_haplotypes.shape, dtype='u1')
painting[inherit_parent1] = INHERIT_PARENT1
painting[inherit_parent2] = INHERIT_PARENT2
painting[nonseg_ref] = INHERIT_NONSEG_REF
painting[nonseg_alt] = INHERIT_NONSEG_ALT
painting[nonparental] = INHERIT_NONPARENTAL
painting[parent_is_missing] = INHERIT_PARENT_MISSING
painting[progeny_is_missing] = INHERIT_MISSING
return painting | [
"def",
"paint_transmission",
"(",
"parent_haplotypes",
",",
"progeny_haplotypes",
")",
":",
"# check inputs",
"parent_haplotypes",
"=",
"HaplotypeArray",
"(",
"parent_haplotypes",
")",
"progeny_haplotypes",
"=",
"HaplotypeArray",
"(",
"progeny_haplotypes",
")",
"if",
"par... | Paint haplotypes inherited from a single diploid parent according to
their allelic inheritance.
Parameters
----------
parent_haplotypes : array_like, int, shape (n_variants, 2)
Both haplotypes from a single diploid parent.
progeny_haplotypes : array_like, int, shape (n_variants, n_progeny)
Haplotypes found in progeny of the given parent, inherited from the
given parent. I.e., haplotypes from gametes of the given parent.
Returns
-------
painting : ndarray, uint8, shape (n_variants, n_progeny)
An array of integers coded as follows: 1 = allele inherited from
first parental haplotype; 2 = allele inherited from second parental
haplotype; 3 = reference allele, also carried by both parental
haplotypes; 4 = non-reference allele, also carried by both parental
haplotypes; 5 = non-parental allele; 6 = either or both parental
alleles missing; 7 = missing allele; 0 = undetermined.
Examples
--------
>>> import allel
>>> haplotypes = allel.HaplotypeArray([
... [0, 0, 0, 1, 2, -1],
... [0, 1, 0, 1, 2, -1],
... [1, 0, 0, 1, 2, -1],
... [1, 1, 0, 1, 2, -1],
... [0, 2, 0, 1, 2, -1],
... [0, -1, 0, 1, 2, -1],
... [-1, 1, 0, 1, 2, -1],
... [-1, -1, 0, 1, 2, -1],
... ], dtype='i1')
>>> painting = allel.paint_transmission(haplotypes[:, :2],
... haplotypes[:, 2:])
>>> painting
array([[3, 5, 5, 7],
[1, 2, 5, 7],
[2, 1, 5, 7],
[5, 4, 5, 7],
[1, 5, 2, 7],
[6, 6, 6, 7],
[6, 6, 6, 7],
[6, 6, 6, 7]], dtype=uint8) | [
"Paint",
"haplotypes",
"inherited",
"from",
"a",
"single",
"diploid",
"parent",
"according",
"to",
"their",
"allelic",
"inheritance",
"."
] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/stats/mendel.py#L232-L323 | train | Paints the given parent s haplotypes inherited from the given parent s progeny s haplotypes. | 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(0b110001) + chr(2398 - 2348) + chr(52), 38672 - 38664), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b101100 + 0o6) + chr(0b110001) + chr(0b1000 + 0o52), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(50) + chr(280 - 232) + '\065', 24111 - 24103), nzTpIcepk0o8(chr(0b1100 + 0o44) + '\157' + '\x31' + chr(0b110111 + 0o0), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x31' + chr(777 - 724) + chr(0b110000), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x32' + '\x37' + '\x32', ord("\x08")), nzTpIcepk0o8(chr(924 - 876) + chr(111) + '\x34' + chr(53), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1010111 + 0o30) + chr(50) + chr(0b101011 + 0o7) + '\064', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(50) + chr(1881 - 1832) + chr(0b110001), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110010) + '\064', ord("\x08")), nzTpIcepk0o8(chr(2112 - 2064) + chr(0b1101111) + chr(49) + '\x32', 0b1000), nzTpIcepk0o8('\x30' + '\157' + '\x35' + chr(0b1 + 0o61), ord("\x08")), nzTpIcepk0o8(chr(0b100111 + 0o11) + '\157' + chr(190 - 138) + '\066', 57249 - 57241), nzTpIcepk0o8(chr(0b10110 + 0o32) + '\157' + chr(944 - 893) + chr(0b110010), 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x31' + chr(0b11111 + 0o24) + '\060', ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(898 - 849) + '\061', 13763 - 13755), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x32' + '\x34', 8), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110010) + '\061' + '\063', ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + '\x31' + chr(51), 30480 - 30472), nzTpIcepk0o8(chr(348 - 300) + chr(111) + chr(0b100110 + 0o14) + '\062' + chr(55), 17586 - 17578), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110010) + chr(527 - 473) + chr(50), 0o10), nzTpIcepk0o8(chr(183 - 135) + chr(6848 - 6737) + chr(1943 - 1888) + chr(0b11000 + 0o36), 0b1000), nzTpIcepk0o8('\060' + chr(11036 - 10925) + chr(748 - 696) + chr(0b10011 + 0o41), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(52) + chr(0b110101), 8), nzTpIcepk0o8('\060' + '\157' + '\x33' + chr(0b100000 + 0o26) + chr(1512 - 1464), 35279 - 35271), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\063' + '\x36' + chr(52), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(49) + '\x35' + chr(0b100001 + 0o17), 8), nzTpIcepk0o8('\060' + chr(0b111111 + 0o60) + '\x37' + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(0b101110 + 0o2) + chr(111) + '\061' + '\061' + '\065', ord("\x08")), nzTpIcepk0o8(chr(715 - 667) + chr(111) + '\061' + chr(48) + '\066', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b100100 + 0o17) + chr(827 - 774) + chr(0b101010 + 0o12), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + '\x32' + chr(0b100000 + 0o22) + '\x31', 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110001) + chr(0b101110 + 0o6) + chr(54), 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x33' + chr(1256 - 1203) + chr(0b110011), ord("\x08")), nzTpIcepk0o8(chr(1509 - 1461) + chr(0b1101111) + chr(0b1101 + 0o44) + chr(49) + '\060', 53802 - 53794), nzTpIcepk0o8(chr(1380 - 1332) + '\157' + chr(0b100100 + 0o15) + chr(2484 - 2429) + '\063', 0o10), nzTpIcepk0o8(chr(0b1010 + 0o46) + '\157' + chr(781 - 729) + chr(0b1100 + 0o50), 8), nzTpIcepk0o8(chr(0b110000) + chr(0b1001011 + 0o44) + chr(1935 - 1885) + chr(0b10000 + 0o43) + chr(0b110011), 45674 - 45666), nzTpIcepk0o8(chr(0b110000) + chr(0b1001000 + 0o47) + chr(0b11000 + 0o32) + chr(0b100011 + 0o16) + chr(55), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\062' + '\063' + chr(48), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b1011 + 0o45) + chr(111) + chr(53) + chr(0b110000), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'z'), chr(0b1100100) + chr(8844 - 8743) + chr(0b1100011) + chr(111) + chr(100) + chr(101))(chr(117) + chr(1252 - 1136) + chr(102) + '\x2d' + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def QQfFq6ckj9Az(socWCF523ChX, Inmmpc2PhF6K):
socWCF523ChX = qbEQNEu82teb(socWCF523ChX)
Inmmpc2PhF6K = qbEQNEu82teb(Inmmpc2PhF6K)
if roI3spqORKae(socWCF523ChX, roI3spqORKae(ES5oEprVxulp(b':\xd5\xedn\x18\xd6J\xe0\xf0doY'), chr(0b1001010 + 0o32) + '\x65' + chr(0b1100011) + chr(0b1101111) + chr(2907 - 2807) + '\x65')('\x75' + chr(10010 - 9894) + '\146' + '\055' + chr(2563 - 2507))) != nzTpIcepk0o8('\x30' + chr(142 - 31) + chr(1576 - 1526), 0b1000):
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b"1\xf2\xe4l\x1c\xd6\\\xb4\xfdce\nV{*lz\xffj\xfb\x92VEU\x9c\x9b\x1cF=#\x9f\xb1\x15\x83'\x0eH\xff\xaf\xfa1\xaa\xf5}\x07\xccL\xf0\xecp"), chr(0b1100100) + chr(0b1000001 + 0o44) + chr(99) + '\x6f' + chr(825 - 725) + chr(0b1100001 + 0o4))('\165' + chr(0b1110100) + chr(3693 - 3591) + chr(0b10001 + 0o34) + chr(56)))
FoArZNwF_kJW = socWCF523ChX[:, nzTpIcepk0o8('\060' + chr(0b1101111) + chr(48), 0o10), nDF4gVNx0u9Q.newaxis]
Ld4QJcCF_mkN = socWCF523ChX[:, nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b1111 + 0o42), ord("\x08")), nDF4gVNx0u9Q.newaxis]
ZiqvxZDBE5YB = Inmmpc2PhF6K < nzTpIcepk0o8(chr(1527 - 1479) + chr(9600 - 9489) + '\060', 8)
ekAz0XH5N1Hy = nDF4gVNx0u9Q.VF4pKOObtlPc(socWCF523ChX < nzTpIcepk0o8(chr(48) + chr(4943 - 4832) + chr(0b110000), 8), axis=nzTpIcepk0o8(chr(1164 - 1116) + '\x6f' + chr(1767 - 1718), 8))
djZe1fd7mcLP = ekAz0XH5N1Hy[:, nDF4gVNx0u9Q.newaxis]
A24msTvkoMgJ = kkrDeTnxPwnD(socWCF523ChX[:, nDF4gVNx0u9Q.newaxis, :])
zPhzNNaqOg3B = A24msTvkoMgJ.is_hom_ref()
mHhZ8Lx8jUlu = A24msTvkoMgJ.is_het()
ryt2m3nyff31 = A24msTvkoMgJ.is_hom_alt()
h5VQzvBtTJ9F = ~ZiqvxZDBE5YB & ~djZe1fd7mcLP
ce1JvrrYY26o = h5VQzvBtTJ9F & mHhZ8Lx8jUlu
kzdJVS76uq0G = ce1JvrrYY26o & (Inmmpc2PhF6K == FoArZNwF_kJW)
HtImVzRKbt20 = ce1JvrrYY26o & (Inmmpc2PhF6K == Ld4QJcCF_mkN)
z8tmgWGOa8xK = h5VQzvBtTJ9F & zPhzNNaqOg3B & (Inmmpc2PhF6K == FoArZNwF_kJW)
UiMo5Uea28ME = h5VQzvBtTJ9F & ryt2m3nyff31 & (Inmmpc2PhF6K == FoArZNwF_kJW)
fNmDHVMBdwws = h5VQzvBtTJ9F & (Inmmpc2PhF6K != FoArZNwF_kJW) & (Inmmpc2PhF6K != Ld4QJcCF_mkN)
f5netnFl5WiL = nDF4gVNx0u9Q.UmwwEp7MzR6q(Inmmpc2PhF6K.lhbM092AFW8f, dtype=roI3spqORKae(ES5oEprVxulp(b'!\xbb'), '\144' + chr(0b1100101) + chr(99) + chr(0b1101111) + chr(100) + chr(0b100 + 0o141))(chr(0b1110101) + chr(116) + chr(0b10010 + 0o124) + '\x2d' + chr(0b111000)))
f5netnFl5WiL[kzdJVS76uq0G] = DWu39ZhAVTHu
f5netnFl5WiL[HtImVzRKbt20] = NB5mAQh6WRZd
f5netnFl5WiL[z8tmgWGOa8xK] = A2hsgRjQfJtD
f5netnFl5WiL[UiMo5Uea28ME] = JWRTifsskPzE
f5netnFl5WiL[fNmDHVMBdwws] = vgjh889ISeyL
f5netnFl5WiL[ekAz0XH5N1Hy] = nkinNtPyo1f5
f5netnFl5WiL[ZiqvxZDBE5YB] = _pcX2MJlRB6h
return f5netnFl5WiL |
cggh/scikit-allel | allel/stats/mendel.py | phase_progeny_by_transmission | def phase_progeny_by_transmission(g):
"""Phase progeny genotypes from a trio or cross using Mendelian
transmission.
Parameters
----------
g : array_like, int, shape (n_variants, n_samples, 2)
Genotype array, with parents as first two columns and progeny as
remaining columns.
Returns
-------
g : ndarray, int8, shape (n_variants, n_samples, 2)
Genotype array with progeny phased where possible.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([
... [[0, 0], [0, 0], [0, 0]],
... [[1, 1], [1, 1], [1, 1]],
... [[0, 0], [1, 1], [0, 1]],
... [[1, 1], [0, 0], [0, 1]],
... [[0, 0], [0, 1], [0, 0]],
... [[0, 0], [0, 1], [0, 1]],
... [[0, 1], [0, 0], [0, 1]],
... [[0, 1], [0, 1], [0, 1]],
... [[0, 1], [1, 2], [0, 1]],
... [[1, 2], [0, 1], [1, 2]],
... [[0, 1], [2, 3], [0, 2]],
... [[2, 3], [0, 1], [1, 3]],
... [[0, 0], [0, 0], [-1, -1]],
... [[0, 0], [0, 0], [1, 1]],
... ], dtype='i1')
>>> g = allel.phase_progeny_by_transmission(g)
>>> print(g.to_str(row_threshold=None))
0/0 0/0 0|0
1/1 1/1 1|1
0/0 1/1 0|1
1/1 0/0 1|0
0/0 0/1 0|0
0/0 0/1 0|1
0/1 0/0 1|0
0/1 0/1 0/1
0/1 1/2 0|1
1/2 0/1 2|1
0/1 2/3 0|2
2/3 0/1 3|1
0/0 0/0 ./.
0/0 0/0 1/1
>>> g.is_phased
array([[False, False, True],
[False, False, True],
[False, False, True],
[False, False, True],
[False, False, True],
[False, False, True],
[False, False, True],
[False, False, False],
[False, False, True],
[False, False, True],
[False, False, True],
[False, False, True],
[False, False, False],
[False, False, False]])
"""
# setup
g = GenotypeArray(g, dtype='i1', copy=True)
check_ploidy(g.ploidy, 2)
check_min_samples(g.n_samples, 3)
# run the phasing
# N.B., a copy has already been made, so no need to make memoryview safe
is_phased = _opt_phase_progeny_by_transmission(g.values)
g.is_phased = np.asarray(is_phased).view(bool)
# outputs
return g | python | def phase_progeny_by_transmission(g):
"""Phase progeny genotypes from a trio or cross using Mendelian
transmission.
Parameters
----------
g : array_like, int, shape (n_variants, n_samples, 2)
Genotype array, with parents as first two columns and progeny as
remaining columns.
Returns
-------
g : ndarray, int8, shape (n_variants, n_samples, 2)
Genotype array with progeny phased where possible.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([
... [[0, 0], [0, 0], [0, 0]],
... [[1, 1], [1, 1], [1, 1]],
... [[0, 0], [1, 1], [0, 1]],
... [[1, 1], [0, 0], [0, 1]],
... [[0, 0], [0, 1], [0, 0]],
... [[0, 0], [0, 1], [0, 1]],
... [[0, 1], [0, 0], [0, 1]],
... [[0, 1], [0, 1], [0, 1]],
... [[0, 1], [1, 2], [0, 1]],
... [[1, 2], [0, 1], [1, 2]],
... [[0, 1], [2, 3], [0, 2]],
... [[2, 3], [0, 1], [1, 3]],
... [[0, 0], [0, 0], [-1, -1]],
... [[0, 0], [0, 0], [1, 1]],
... ], dtype='i1')
>>> g = allel.phase_progeny_by_transmission(g)
>>> print(g.to_str(row_threshold=None))
0/0 0/0 0|0
1/1 1/1 1|1
0/0 1/1 0|1
1/1 0/0 1|0
0/0 0/1 0|0
0/0 0/1 0|1
0/1 0/0 1|0
0/1 0/1 0/1
0/1 1/2 0|1
1/2 0/1 2|1
0/1 2/3 0|2
2/3 0/1 3|1
0/0 0/0 ./.
0/0 0/0 1/1
>>> g.is_phased
array([[False, False, True],
[False, False, True],
[False, False, True],
[False, False, True],
[False, False, True],
[False, False, True],
[False, False, True],
[False, False, False],
[False, False, True],
[False, False, True],
[False, False, True],
[False, False, True],
[False, False, False],
[False, False, False]])
"""
# setup
g = GenotypeArray(g, dtype='i1', copy=True)
check_ploidy(g.ploidy, 2)
check_min_samples(g.n_samples, 3)
# run the phasing
# N.B., a copy has already been made, so no need to make memoryview safe
is_phased = _opt_phase_progeny_by_transmission(g.values)
g.is_phased = np.asarray(is_phased).view(bool)
# outputs
return g | [
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... | Phase progeny genotypes from a trio or cross using Mendelian
transmission.
Parameters
----------
g : array_like, int, shape (n_variants, n_samples, 2)
Genotype array, with parents as first two columns and progeny as
remaining columns.
Returns
-------
g : ndarray, int8, shape (n_variants, n_samples, 2)
Genotype array with progeny phased where possible.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([
... [[0, 0], [0, 0], [0, 0]],
... [[1, 1], [1, 1], [1, 1]],
... [[0, 0], [1, 1], [0, 1]],
... [[1, 1], [0, 0], [0, 1]],
... [[0, 0], [0, 1], [0, 0]],
... [[0, 0], [0, 1], [0, 1]],
... [[0, 1], [0, 0], [0, 1]],
... [[0, 1], [0, 1], [0, 1]],
... [[0, 1], [1, 2], [0, 1]],
... [[1, 2], [0, 1], [1, 2]],
... [[0, 1], [2, 3], [0, 2]],
... [[2, 3], [0, 1], [1, 3]],
... [[0, 0], [0, 0], [-1, -1]],
... [[0, 0], [0, 0], [1, 1]],
... ], dtype='i1')
>>> g = allel.phase_progeny_by_transmission(g)
>>> print(g.to_str(row_threshold=None))
0/0 0/0 0|0
1/1 1/1 1|1
0/0 1/1 0|1
1/1 0/0 1|0
0/0 0/1 0|0
0/0 0/1 0|1
0/1 0/0 1|0
0/1 0/1 0/1
0/1 1/2 0|1
1/2 0/1 2|1
0/1 2/3 0|2
2/3 0/1 3|1
0/0 0/0 ./.
0/0 0/0 1/1
>>> g.is_phased
array([[False, False, True],
[False, False, True],
[False, False, True],
[False, False, True],
[False, False, True],
[False, False, True],
[False, False, True],
[False, False, False],
[False, False, True],
[False, False, True],
[False, False, True],
[False, False, True],
[False, False, False],
[False, False, False]]) | [
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transmission. | 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) + chr(0b110011) + '\x33', 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(0b110010) + chr(0b1101 + 0o46) + chr(0b100101 + 0o16), 8), nzTpIcepk0o8(chr(0b10111 + 0o31) + '\x6f' + '\x32' + '\063' + chr(887 - 838), 0b1000), nzTpIcepk0o8('\060' + chr(4404 - 4293) + chr(0b110011) + chr(0b100000 + 0o25) + chr(53), 0b1000), nzTpIcepk0o8('\060' + chr(111) + '\x31' + '\x37' + chr(0b1110 + 0o46), 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(0b10000 + 0o43) + '\x37', 0o10), nzTpIcepk0o8(chr(0b11111 + 0o21) + chr(0b1101111) + chr(1769 - 1718) + chr(589 - 537) + '\x37', 0o10), nzTpIcepk0o8(chr(48) + chr(0b100110 + 0o111) + '\063' + '\064', 17266 - 17258), nzTpIcepk0o8('\060' + chr(0b1010011 + 0o34) + chr(1501 - 1452) + chr(0b110011) + chr(0b101111 + 0o4), 0b1000), nzTpIcepk0o8('\060' + chr(0b1000001 + 0o56) + chr(992 - 941) + chr(0b110001) + chr(0b110010), 13751 - 13743), nzTpIcepk0o8(chr(0b10011 + 0o35) + '\157' + chr(0b110011) + chr(49) + chr(0b110001), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1011110 + 0o21) + chr(0b110001) + chr(0b110001), 42161 - 42153), nzTpIcepk0o8(chr(0b110000) + chr(12001 - 11890) + '\061' + chr(55) + chr(0b110100 + 0o1), 0o10), nzTpIcepk0o8(chr(48) + '\157' + '\x31' + '\x36' + '\x36', 60975 - 60967), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(51) + '\067' + '\x34', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x31' + '\x36' + chr(0b110000), 0o10), nzTpIcepk0o8(chr(98 - 50) + chr(0b1101111) + chr(0b10 + 0o61), ord("\x08")), nzTpIcepk0o8(chr(398 - 350) + chr(0b11010 + 0o125) + chr(0b100001 + 0o20) + '\x35' + chr(302 - 250), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(50) + '\x30' + chr(0b100000 + 0o21), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x31' + chr(381 - 326) + chr(0b100 + 0o56), 0b1000), nzTpIcepk0o8('\x30' + chr(111) + '\x33' + chr(53) + '\x36', ord("\x08")), nzTpIcepk0o8('\060' + chr(348 - 237) + chr(0b11110 + 0o30) + chr(0b11110 + 0o24), ord("\x08")), nzTpIcepk0o8(chr(0b1100 + 0o44) + '\157' + chr(0b10101 + 0o34) + chr(0b110111) + chr(0b110111), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1100011 + 0o14) + '\065' + '\063', 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(1938 - 1887), 8), nzTpIcepk0o8('\060' + chr(10641 - 10530) + chr(912 - 862) + chr(1137 - 1085) + '\x33', 0b1000), nzTpIcepk0o8(chr(1583 - 1535) + chr(0b1101111) + chr(0b110001) + chr(1687 - 1636) + chr(0b1010 + 0o47), 0b1000), nzTpIcepk0o8(chr(0b110 + 0o52) + chr(0b1101111) + chr(0b1101 + 0o45) + '\065' + chr(49), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x31' + chr(0b110011) + '\x33', 8), nzTpIcepk0o8(chr(0b11110 + 0o22) + '\157' + chr(0b10101 + 0o42) + '\x31', 18656 - 18648), nzTpIcepk0o8(chr(0b11110 + 0o22) + chr(6019 - 5908) + chr(0b110100) + chr(0b110010), 0b1000), nzTpIcepk0o8(chr(48) + chr(7104 - 6993) + '\x32' + chr(0b101101 + 0o5) + chr(54), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1100 + 0o143) + chr(49) + '\x33' + chr(53), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(49), 0b1000), nzTpIcepk0o8(chr(0b11 + 0o55) + chr(0b1000110 + 0o51) + '\067', 47738 - 47730), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x33' + '\060' + chr(0b11101 + 0o24), ord("\x08")), nzTpIcepk0o8(chr(0b0 + 0o60) + chr(111) + '\061' + chr(0b110011) + chr(0b101101 + 0o12), 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110000), 0o10), nzTpIcepk0o8(chr(159 - 111) + chr(111) + '\x32' + chr(0b1010 + 0o50) + '\065', 0o10), nzTpIcepk0o8(chr(48) + '\157' + '\061' + chr(0b101010 + 0o14) + '\x35', ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + chr(11955 - 11844) + '\065' + chr(0b11000 + 0o30), ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xb5'), '\x64' + '\x65' + chr(7299 - 7200) + chr(2382 - 2271) + chr(0b11011 + 0o111) + chr(8290 - 8189))(chr(0b1001011 + 0o52) + chr(0b1110100) + chr(0b1100110) + chr(45) + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def AzJ1UFkIObXQ(KQq7Z9J63zv1):
KQq7Z9J63zv1 = kkrDeTnxPwnD(KQq7Z9J63zv1, dtype=roI3spqORKae(ES5oEprVxulp(b'\xf2\xaa'), chr(8395 - 8295) + '\x65' + '\x63' + chr(0b1000011 + 0o54) + '\144' + '\x65')(chr(0b1110101) + chr(116) + chr(0b1100110) + chr(45) + chr(0b1010 + 0o56)), copy=nzTpIcepk0o8('\060' + '\157' + chr(49), 8))
S0Uypoo4zSP9(roI3spqORKae(KQq7Z9J63zv1, roI3spqORKae(ES5oEprVxulp(b'\xeb\xf7\xf6\x84\x18f'), chr(9214 - 9114) + '\x65' + chr(3253 - 3154) + chr(10835 - 10724) + chr(100) + '\x65')(chr(6704 - 6587) + chr(116) + chr(0b1100110) + chr(1825 - 1780) + chr(2205 - 2149))), nzTpIcepk0o8(chr(48) + '\x6f' + '\x32', ord("\x08")))
F81zpSjBcsoa(roI3spqORKae(KQq7Z9J63zv1, roI3spqORKae(ES5oEprVxulp(b'\xdc\xff\xab\xa0\x1dl\x80p\x1a\xaf\x8f8'), '\x64' + chr(0b110110 + 0o57) + chr(0b1100011) + chr(0b1100101 + 0o12) + chr(5075 - 4975) + chr(4192 - 4091))(chr(6788 - 6671) + chr(116) + '\146' + chr(1245 - 1200) + chr(0b111000))), nzTpIcepk0o8(chr(48) + chr(0b1111 + 0o140) + chr(219 - 168), 8))
fUab2YaX8axD = kximeyhDUB1b(KQq7Z9J63zv1.CsodZJH6x9Tx)
KQq7Z9J63zv1.fUab2YaX8axD = nDF4gVNx0u9Q.asarray(fUab2YaX8axD).mJI8h1w8YmYz(TVUhqOt5_BbS)
return KQq7Z9J63zv1 |
cggh/scikit-allel | allel/stats/mendel.py | phase_parents_by_transmission | def phase_parents_by_transmission(g, window_size):
"""Phase parent genotypes from a trio or cross, given progeny genotypes
already phased by Mendelian transmission.
Parameters
----------
g : GenotypeArray
Genotype array, with parents as first two columns and progeny as
remaining columns, where progeny genotypes are already phased.
window_size : int
Number of previous heterozygous sites to include when phasing each
parent. A number somewhere between 10 and 100 may be appropriate,
depending on levels of heterozygosity and quality of data.
Returns
-------
g : GenotypeArray
Genotype array with parents phased where possible.
"""
# setup
check_type(g, GenotypeArray)
check_dtype(g.values, 'i1')
check_ploidy(g.ploidy, 2)
if g.is_phased is None:
raise ValueError('genotype array must first have progeny phased by transmission')
check_min_samples(g.n_samples, 3)
# run the phasing
g._values = memoryview_safe(g.values)
g._is_phased = memoryview_safe(g.is_phased)
_opt_phase_parents_by_transmission(g.values, g.is_phased.view('u1'), window_size)
# outputs
return g | python | def phase_parents_by_transmission(g, window_size):
"""Phase parent genotypes from a trio or cross, given progeny genotypes
already phased by Mendelian transmission.
Parameters
----------
g : GenotypeArray
Genotype array, with parents as first two columns and progeny as
remaining columns, where progeny genotypes are already phased.
window_size : int
Number of previous heterozygous sites to include when phasing each
parent. A number somewhere between 10 and 100 may be appropriate,
depending on levels of heterozygosity and quality of data.
Returns
-------
g : GenotypeArray
Genotype array with parents phased where possible.
"""
# setup
check_type(g, GenotypeArray)
check_dtype(g.values, 'i1')
check_ploidy(g.ploidy, 2)
if g.is_phased is None:
raise ValueError('genotype array must first have progeny phased by transmission')
check_min_samples(g.n_samples, 3)
# run the phasing
g._values = memoryview_safe(g.values)
g._is_phased = memoryview_safe(g.is_phased)
_opt_phase_parents_by_transmission(g.values, g.is_phased.view('u1'), window_size)
# outputs
return g | [
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already phased by Mendelian transmission.
Parameters
----------
g : GenotypeArray
Genotype array, with parents as first two columns and progeny as
remaining columns, where progeny genotypes are already phased.
window_size : int
Number of previous heterozygous sites to include when phasing each
parent. A number somewhere between 10 and 100 may be appropriate,
depending on levels of heterozygosity and quality of data.
Returns
-------
g : GenotypeArray
Genotype array with parents phased where possible. | [
"Phase",
"parent",
"genotypes",
"from",
"a",
"trio",
"or",
"cross",
"given",
"progeny",
"genotypes",
"already",
"phased",
"by",
"Mendelian",
"transmission",
"."
] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/stats/mendel.py#L408-L443 | train | Phase parent genotypes from a trio or cross given progeny genotypes
already phased by Mendelian transmission. | 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(0b1000100 + 0o53) + chr(53) + chr(1155 - 1102), 58806 - 58798), nzTpIcepk0o8('\060' + chr(111) + '\x33' + '\x36' + '\x35', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b101011 + 0o104) + chr(0b110001) + '\063' + chr(0b110111), 59043 - 59035), nzTpIcepk0o8('\060' + chr(6297 - 6186) + chr(0b10010 + 0o37) + '\063' + chr(0b101010 + 0o10), 0b1000), nzTpIcepk0o8(chr(1185 - 1137) + '\157' + chr(0b1000 + 0o54) + chr(0b110000), 0o10), nzTpIcepk0o8(chr(2158 - 2110) + chr(0b1110 + 0o141) + '\x31' + chr(0b110001) + chr(50), 20067 - 20059), nzTpIcepk0o8('\060' + chr(0b1101111) + '\061' + chr(1600 - 1551) + '\x30', 0o10), nzTpIcepk0o8(chr(1364 - 1316) + '\157' + chr(49) + chr(51) + chr(49), 0o10), nzTpIcepk0o8(chr(1802 - 1754) + chr(0b1101111) + chr(647 - 598) + '\063' + chr(2600 - 2547), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(1087 - 1037) + '\066' + '\064', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(51) + '\x33' + chr(55), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(3300 - 3189) + chr(0b110010) + '\061' + '\x30', ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(1832 - 1781) + chr(0b100111 + 0o16), ord("\x08")), nzTpIcepk0o8(chr(1385 - 1337) + chr(0b1101111) + '\063' + '\065', 8), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110010) + chr(0b1000 + 0o52) + chr(50), 0o10), nzTpIcepk0o8(chr(1304 - 1256) + chr(111) + chr(0b110001 + 0o0) + chr(0b110001 + 0o1) + chr(0b100010 + 0o21), 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(101 - 51) + chr(0b111 + 0o56) + chr(0b11 + 0o60), 21681 - 21673), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x33' + '\x30' + chr(54), 1298 - 1290), nzTpIcepk0o8(chr(48) + '\157' + '\x31' + chr(0b110101) + chr(0b11010 + 0o31), 0o10), nzTpIcepk0o8(chr(1625 - 1577) + '\157' + chr(2235 - 2185) + chr(0b110011) + chr(50), 0o10), nzTpIcepk0o8(chr(1363 - 1315) + chr(0b1101101 + 0o2) + chr(2906 - 2852) + chr(0b10111 + 0o35), 0b1000), nzTpIcepk0o8(chr(300 - 252) + chr(157 - 46) + chr(50) + chr(55) + '\061', 0o10), nzTpIcepk0o8('\x30' + chr(8983 - 8872) + '\064', ord("\x08")), nzTpIcepk0o8(chr(1192 - 1144) + chr(0b1101111) + chr(214 - 163) + chr(0b110111) + chr(0b110001), 50161 - 50153), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\061' + chr(0b110101) + '\x33', 8), nzTpIcepk0o8('\x30' + chr(111) + chr(0b10101 + 0o34) + chr(873 - 818) + '\067', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(10992 - 10881) + '\062' + chr(52) + chr(53), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(0b101010 + 0o7) + chr(0b10 + 0o60) + chr(0b10001 + 0o46), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(51) + chr(55) + chr(0b110011), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(1851 - 1740) + chr(0b110001) + chr(0b110110) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1011010 + 0o25) + '\x32' + chr(52) + chr(1516 - 1463), 8), nzTpIcepk0o8(chr(0b100001 + 0o17) + '\157' + '\x33' + chr(2285 - 2235) + chr(0b11111 + 0o23), ord("\x08")), nzTpIcepk0o8(chr(300 - 252) + '\157' + chr(0b110011) + chr(0b1011 + 0o51) + '\067', 0o10), nzTpIcepk0o8(chr(1295 - 1247) + chr(0b101001 + 0o106) + chr(0b0 + 0o62) + '\x30' + '\x36', 0b1000), nzTpIcepk0o8('\060' + chr(0b10111 + 0o130) + chr(51) + chr(0b110010) + '\065', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(50) + chr(1020 - 968) + chr(490 - 437), 8), nzTpIcepk0o8(chr(48) + chr(540 - 429) + '\063' + chr(0b100000 + 0o22) + chr(52), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x32' + chr(0b110111) + '\067', 0b1000), nzTpIcepk0o8(chr(0b101101 + 0o3) + '\157' + chr(0b110010) + '\067' + chr(0b110001), 8), nzTpIcepk0o8(chr(0b110000) + chr(0b1000011 + 0o54) + chr(298 - 248) + chr(0b11011 + 0o34) + '\062', 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\065' + chr(0b110000), 27663 - 27655)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x03'), '\144' + chr(0b1001010 + 0o33) + '\143' + '\x6f' + chr(100) + chr(0b1100101))('\x75' + '\x74' + chr(0b1100110) + '\x2d' + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def PhaGyhfEmwHI(KQq7Z9J63zv1, sr1jcqYH2Bwu):
T75hoc3LeLcE(KQq7Z9J63zv1, kkrDeTnxPwnD)
u2kL2hIrgS6F(roI3spqORKae(KQq7Z9J63zv1, roI3spqORKae(ES5oEprVxulp(b'n\x860>z\x00\x00o%\x8d\x8b\xf0'), '\144' + chr(0b10101 + 0o120) + chr(99) + chr(0b1101111) + chr(100) + '\x65')(chr(0b1101100 + 0o11) + chr(9279 - 9163) + chr(0b1100110 + 0o0) + chr(0b1000 + 0o45) + '\x38')), roI3spqORKae(ES5oEprVxulp(b'D\xc4'), chr(6301 - 6201) + '\x65' + chr(0b1100011) + chr(924 - 813) + '\x64' + chr(101))(chr(0b1110101) + chr(10840 - 10724) + '\x66' + '\x2d' + chr(739 - 683)))
S0Uypoo4zSP9(roI3spqORKae(KQq7Z9J63zv1, roI3spqORKae(ES5oEprVxulp(b']\x9903D3'), chr(100) + chr(0b1011010 + 0o13) + chr(0b1100011) + chr(0b1011111 + 0o20) + chr(0b1100100) + chr(0b1100101))('\165' + '\164' + chr(1609 - 1507) + chr(298 - 253) + '\x38')), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110010), 0b1000))
if roI3spqORKae(KQq7Z9J63zv1, roI3spqORKae(ES5oEprVxulp(b'K\xa0>8\x12\x13)\x01e\xd5\xa7\xcc'), chr(0b1100100) + '\x65' + '\x63' + '\157' + chr(0b11011 + 0o111) + '\145')(chr(0b1110101) + chr(8936 - 8820) + chr(0b1100110) + '\055' + '\x38')) is None:
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'J\x9015T38<}\xd5\xad\xfa|d\xb2>\xde\xb5\x1f\xbaR\xd0v\x8a\x1f_\xcd6\x8d\x16\x85\xa2\x95\xe9\xb2\xc0\xba\xc6\x99\xcaE\x94,?Dj* }\xc0\xad\xe9sn\xff:\xd8\xb5\x02\xf5Z'), chr(100) + chr(5838 - 5737) + chr(99) + chr(111) + chr(100) + chr(0b1100101))(chr(117) + '\x74' + chr(102) + '\x2d' + chr(56)))
F81zpSjBcsoa(roI3spqORKae(KQq7Z9J63zv1, roI3spqORKae(ES5oEprVxulp(b'j\x91m\x17A9/5\x1c\xd1\x99\xb9'), chr(0b10001 + 0o123) + '\145' + chr(2421 - 2322) + chr(111) + chr(7244 - 7144) + '\x65')(chr(0b110011 + 0o102) + chr(4454 - 4338) + '\x66' + chr(0b100100 + 0o11) + chr(941 - 885))), nzTpIcepk0o8('\060' + chr(6479 - 6368) + '\063', ord("\x08")))
KQq7Z9J63zv1.NisoCHjtrfMU = ygMIbkSSXS59(KQq7Z9J63zv1.CsodZJH6x9Tx)
KQq7Z9J63zv1.FLCw3ubJoF82 = ygMIbkSSXS59(KQq7Z9J63zv1.fUab2YaX8axD)
ge3KU8zXMrAX(roI3spqORKae(KQq7Z9J63zv1, roI3spqORKae(ES5oEprVxulp(b'n\x860>z\x00\x00o%\x8d\x8b\xf0'), chr(100) + '\x65' + '\x63' + chr(0b10101 + 0o132) + chr(0b1100100) + chr(0b1000100 + 0o41))(chr(117) + chr(0b1101 + 0o147) + '\x66' + '\x2d' + chr(56))), roI3spqORKae(KQq7Z9J63zv1.is_phased, roI3spqORKae(ES5oEprVxulp(b'@\xbf\x16bH{?a\x04\xd9\x86\xf2'), chr(0b111001 + 0o53) + chr(101) + chr(3782 - 3683) + '\x6f' + '\144' + chr(3570 - 3469))(chr(0b11001 + 0o134) + '\x74' + '\146' + '\x2d' + chr(0b0 + 0o70)))(roI3spqORKae(ES5oEprVxulp(b'X\xc4'), '\x64' + chr(0b110010 + 0o63) + '\x63' + chr(0b1101111) + chr(100) + chr(0b1100101))(chr(2449 - 2332) + chr(0b1110100) + '\146' + '\055' + chr(0b110110 + 0o2))), sr1jcqYH2Bwu)
return KQq7Z9J63zv1 |
cggh/scikit-allel | allel/stats/mendel.py | phase_by_transmission | def phase_by_transmission(g, window_size, copy=True):
"""Phase genotypes in a trio or cross where possible using Mendelian
transmission.
Parameters
----------
g : array_like, int, shape (n_variants, n_samples, 2)
Genotype array, with parents as first two columns and progeny as
remaining columns.
window_size : int
Number of previous heterozygous sites to include when phasing each
parent. A number somewhere between 10 and 100 may be appropriate,
depending on levels of heterozygosity and quality of data.
copy : bool, optional
If False, attempt to phase genotypes in-place. Note that this is
only possible if the input array has int8 dtype, otherwise a copy is
always made regardless of this parameter.
Returns
-------
g : GenotypeArray
Genotype array with progeny phased where possible.
"""
# setup
g = np.asarray(g, dtype='i1')
g = GenotypeArray(g, copy=copy)
g._values = memoryview_safe(g.values)
check_ploidy(g.ploidy, 2)
check_min_samples(g.n_samples, 3)
# phase the progeny
is_phased = _opt_phase_progeny_by_transmission(g.values)
g.is_phased = np.asarray(is_phased).view(bool)
# phase the parents
_opt_phase_parents_by_transmission(g.values, is_phased, window_size)
return g | python | def phase_by_transmission(g, window_size, copy=True):
"""Phase genotypes in a trio or cross where possible using Mendelian
transmission.
Parameters
----------
g : array_like, int, shape (n_variants, n_samples, 2)
Genotype array, with parents as first two columns and progeny as
remaining columns.
window_size : int
Number of previous heterozygous sites to include when phasing each
parent. A number somewhere between 10 and 100 may be appropriate,
depending on levels of heterozygosity and quality of data.
copy : bool, optional
If False, attempt to phase genotypes in-place. Note that this is
only possible if the input array has int8 dtype, otherwise a copy is
always made regardless of this parameter.
Returns
-------
g : GenotypeArray
Genotype array with progeny phased where possible.
"""
# setup
g = np.asarray(g, dtype='i1')
g = GenotypeArray(g, copy=copy)
g._values = memoryview_safe(g.values)
check_ploidy(g.ploidy, 2)
check_min_samples(g.n_samples, 3)
# phase the progeny
is_phased = _opt_phase_progeny_by_transmission(g.values)
g.is_phased = np.asarray(is_phased).view(bool)
# phase the parents
_opt_phase_parents_by_transmission(g.values, is_phased, window_size)
return g | [
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")... | Phase genotypes in a trio or cross where possible using Mendelian
transmission.
Parameters
----------
g : array_like, int, shape (n_variants, n_samples, 2)
Genotype array, with parents as first two columns and progeny as
remaining columns.
window_size : int
Number of previous heterozygous sites to include when phasing each
parent. A number somewhere between 10 and 100 may be appropriate,
depending on levels of heterozygosity and quality of data.
copy : bool, optional
If False, attempt to phase genotypes in-place. Note that this is
only possible if the input array has int8 dtype, otherwise a copy is
always made regardless of this parameter.
Returns
-------
g : GenotypeArray
Genotype array with progeny phased where possible. | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/stats/mendel.py#L446-L485 | train | Phase genotypes in a trio or cross where possible using Mendelian
transmission. | 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(10385 - 10274) + '\062' + chr(1081 - 1033) + chr(0b10111 + 0o32), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(2182 - 2133) + chr(53) + chr(2232 - 2177), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b10101 + 0o132) + chr(0b110010) + '\x36' + chr(0b110001), 1168 - 1160), nzTpIcepk0o8(chr(48) + chr(5160 - 5049) + chr(0b110011) + '\060' + chr(0b11101 + 0o25), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x33' + chr(50) + chr(0b110000 + 0o6), 61757 - 61749), nzTpIcepk0o8(chr(1612 - 1564) + chr(0b111 + 0o150) + '\061' + '\065' + '\062', 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110100) + chr(0b111 + 0o57), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(49) + '\063' + '\065', 0b1000), nzTpIcepk0o8(chr(0b100101 + 0o13) + chr(111) + chr(1750 - 1696), 30761 - 30753), nzTpIcepk0o8('\x30' + chr(111) + '\061' + '\066' + '\x34', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x33' + '\x33' + chr(0b0 + 0o64), 25964 - 25956), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(1387 - 1336) + chr(0b110101), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(523 - 473) + chr(1629 - 1581) + '\064', 33080 - 33072), nzTpIcepk0o8(chr(2140 - 2092) + chr(0b1010100 + 0o33) + chr(2667 - 2613) + chr(52), 0b1000), nzTpIcepk0o8(chr(1305 - 1257) + chr(111) + chr(51) + '\062' + '\x32', 29274 - 29266), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x32' + '\x33' + chr(0b1101 + 0o43), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(5969 - 5858) + chr(0b10111 + 0o34) + '\062', ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(55) + chr(1323 - 1273), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(0b110100) + chr(0b1101 + 0o46), 0o10), nzTpIcepk0o8(chr(0b100 + 0o54) + chr(111) + '\x33' + '\x30' + '\067', 49071 - 49063), nzTpIcepk0o8(chr(222 - 174) + '\x6f' + chr(0b1001 + 0o50) + chr(1741 - 1688) + chr(770 - 716), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\061' + '\061' + '\x35', 0b1000), nzTpIcepk0o8(chr(0b110000 + 0o0) + chr(111) + chr(0b110010) + chr(50) + chr(0b101100 + 0o12), 0b1000), nzTpIcepk0o8(chr(1329 - 1281) + '\x6f' + '\x32' + chr(0b110111) + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(49) + '\062' + chr(0b1000 + 0o53), 48921 - 48913), nzTpIcepk0o8(chr(397 - 349) + '\157' + '\x31' + chr(2063 - 2010) + '\062', 8), nzTpIcepk0o8(chr(1844 - 1796) + chr(111) + '\063' + '\061' + chr(55), 0o10), nzTpIcepk0o8(chr(1321 - 1273) + chr(0b100000 + 0o117) + chr(50) + chr(0b110011) + '\062', 5576 - 5568), nzTpIcepk0o8('\x30' + chr(2009 - 1898) + chr(193 - 144) + chr(54) + '\x37', 0b1000), nzTpIcepk0o8(chr(1540 - 1492) + chr(0b1101111) + chr(0b110001) + '\062' + chr(962 - 908), 7054 - 7046), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\063' + chr(1814 - 1759) + chr(0b110001), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(55) + '\x30', 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(0b10111 + 0o34) + chr(52) + chr(51), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b11011 + 0o34) + chr(55), 0o10), nzTpIcepk0o8(chr(1178 - 1130) + '\157' + chr(0b110011) + '\062' + chr(55), 0o10), nzTpIcepk0o8(chr(0b1010 + 0o46) + '\157' + chr(2467 - 2416) + chr(1850 - 1800) + chr(0b11011 + 0o34), 8), nzTpIcepk0o8(chr(2203 - 2155) + chr(10489 - 10378) + chr(0b11101 + 0o25) + chr(50) + chr(0b110110), 8), nzTpIcepk0o8(chr(0b110000) + chr(5695 - 5584) + chr(158 - 108) + '\x30' + chr(1746 - 1698), 0b1000), nzTpIcepk0o8(chr(0b10001 + 0o37) + chr(7502 - 7391) + chr(0b110010) + '\060', 46698 - 46690), nzTpIcepk0o8(chr(497 - 449) + '\x6f' + chr(0b110001) + chr(876 - 825) + '\067', 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(1291 - 1243) + chr(0b1101000 + 0o7) + '\065' + '\x30', 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xaf'), chr(0b1100100) + chr(0b1100101) + '\x63' + chr(0b11111 + 0o120) + '\144' + chr(101))('\165' + chr(116) + chr(0b1011000 + 0o16) + '\x2d' + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def jAHBuTSR4zMr(KQq7Z9J63zv1, sr1jcqYH2Bwu, aZTCj4v5QdfO=nzTpIcepk0o8('\x30' + '\x6f' + '\x31', ord("\x08"))):
KQq7Z9J63zv1 = nDF4gVNx0u9Q.asarray(KQq7Z9J63zv1, dtype=roI3spqORKae(ES5oEprVxulp(b'\xe8^'), chr(0b1100100) + chr(101) + chr(99) + '\157' + chr(0b1100100) + chr(101))('\x75' + chr(116) + chr(4332 - 4230) + chr(45) + chr(56)))
KQq7Z9J63zv1 = kkrDeTnxPwnD(KQq7Z9J63zv1, copy=aZTCj4v5QdfO)
KQq7Z9J63zv1.NisoCHjtrfMU = ygMIbkSSXS59(KQq7Z9J63zv1.CsodZJH6x9Tx)
S0Uypoo4zSP9(roI3spqORKae(KQq7Z9J63zv1, roI3spqORKae(ES5oEprVxulp(b'\xf1\x03\xde\xab\xb2\x13'), chr(0b1100100) + '\x65' + chr(1238 - 1139) + chr(0b1101111) + '\144' + chr(101))(chr(0b0 + 0o165) + '\164' + chr(0b10011 + 0o123) + chr(0b101101) + chr(0b111000))), nzTpIcepk0o8(chr(2173 - 2125) + '\157' + chr(0b101000 + 0o12), 0o10))
F81zpSjBcsoa(roI3spqORKae(KQq7Z9J63zv1, roI3spqORKae(ES5oEprVxulp(b'\xc6\x0b\x83\x8f\xb7\x19A1G\x11\x9a,'), '\x64' + chr(0b1100101) + chr(7493 - 7394) + '\x6f' + '\x64' + '\x65')(chr(0b1101011 + 0o12) + chr(0b1000100 + 0o60) + chr(102) + '\055' + chr(1623 - 1567))), nzTpIcepk0o8('\060' + '\157' + '\x33', ord("\x08")))
fUab2YaX8axD = kximeyhDUB1b(KQq7Z9J63zv1.CsodZJH6x9Tx)
KQq7Z9J63zv1.fUab2YaX8axD = nDF4gVNx0u9Q.asarray(fUab2YaX8axD).mJI8h1w8YmYz(TVUhqOt5_BbS)
ge3KU8zXMrAX(roI3spqORKae(KQq7Z9J63zv1, roI3spqORKae(ES5oEprVxulp(b'\xc2\x1c\xde\xa6\x8c nk~M\x88e'), '\144' + chr(0b1100101) + chr(6382 - 6283) + chr(1774 - 1663) + chr(5217 - 5117) + chr(8909 - 8808))(chr(0b1110101) + '\x74' + chr(0b10010 + 0o124) + '\x2d' + chr(0b111000))), fUab2YaX8axD, sr1jcqYH2Bwu)
return KQq7Z9J63zv1 |
cggh/scikit-allel | allel/chunked/util.py | get_blen_array | def get_blen_array(data, blen=None):
"""Try to guess a reasonable block length to use for block-wise iteration
over `data`."""
if blen is None:
if hasattr(data, 'chunklen'):
# bcolz carray
return data.chunklen
elif hasattr(data, 'chunks') and \
hasattr(data, 'shape') and \
hasattr(data.chunks, '__len__') and \
hasattr(data.shape, '__len__') and \
len(data.chunks) == len(data.shape):
# something like h5py dataset
return data.chunks[0]
else:
# fall back to something simple, ~1Mb chunks
row = np.asarray(data[0])
return max(1, (2**20) // row.nbytes)
else:
return blen | python | def get_blen_array(data, blen=None):
"""Try to guess a reasonable block length to use for block-wise iteration
over `data`."""
if blen is None:
if hasattr(data, 'chunklen'):
# bcolz carray
return data.chunklen
elif hasattr(data, 'chunks') and \
hasattr(data, 'shape') and \
hasattr(data.chunks, '__len__') and \
hasattr(data.shape, '__len__') and \
len(data.chunks) == len(data.shape):
# something like h5py dataset
return data.chunks[0]
else:
# fall back to something simple, ~1Mb chunks
row = np.asarray(data[0])
return max(1, (2**20) // row.nbytes)
else:
return blen | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/chunked/util.py#L96-L120 | train | Try to guess a reasonable block length to use for block - wise iteration
over data. | 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(0b110011) + chr(0b110011) + '\063', 0o10), nzTpIcepk0o8('\x30' + chr(0b111100 + 0o63) + '\061' + '\x37' + '\x34', 65268 - 65260), nzTpIcepk0o8(chr(711 - 663) + chr(0b111000 + 0o67) + chr(1154 - 1105) + chr(0b1101 + 0o43) + '\x36', 0b1000), nzTpIcepk0o8('\x30' + '\157' + '\063' + chr(2401 - 2347) + chr(0b110000), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(0b110010) + chr(0b110110) + chr(50), ord("\x08")), nzTpIcepk0o8('\x30' + chr(329 - 218) + chr(49) + chr(0b101100 + 0o6) + chr(48), 0b1000), nzTpIcepk0o8('\060' + chr(0b1011 + 0o144) + '\x35' + chr(0b1000 + 0o57), 0o10), nzTpIcepk0o8(chr(0b100101 + 0o13) + chr(0b1000 + 0o147) + chr(0b1100 + 0o46) + chr(0b110000) + '\061', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110010) + chr(1517 - 1468) + '\x36', 3976 - 3968), nzTpIcepk0o8('\x30' + '\157' + chr(0b110001) + chr(0b110000) + chr(0b110001), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110001) + chr(49) + chr(1674 - 1626), 39403 - 39395), nzTpIcepk0o8(chr(191 - 143) + chr(111) + chr(52) + chr(0b0 + 0o60), 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110001) + '\067' + chr(0b1000 + 0o57), 51481 - 51473), nzTpIcepk0o8(chr(0b1111 + 0o41) + chr(3162 - 3051) + '\x37' + '\062', 17603 - 17595), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(50) + chr(0b1001 + 0o51) + chr(0b110001), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110111) + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b11010 + 0o27) + chr(0b110100 + 0o1) + '\x33', 27056 - 27048), nzTpIcepk0o8(chr(0b110000) + '\157' + '\061' + chr(0b110001), 43776 - 43768), nzTpIcepk0o8(chr(0b110000) + chr(0b1100011 + 0o14) + '\063' + chr(1499 - 1446) + chr(0b10 + 0o62), ord("\x08")), nzTpIcepk0o8(chr(0b1000 + 0o50) + '\x6f' + chr(52) + chr(51), 0b1000), nzTpIcepk0o8(chr(1039 - 991) + chr(0b110100 + 0o73) + chr(49) + chr(0b100010 + 0o20) + chr(0b110001), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(55) + '\062', 8), nzTpIcepk0o8(chr(1133 - 1085) + chr(0b11101 + 0o122) + chr(1949 - 1899) + '\x37' + chr(0b110111), 0o10), nzTpIcepk0o8('\060' + chr(0b1100110 + 0o11) + '\x33' + '\x36' + chr(0b110011), 0b1000), nzTpIcepk0o8('\060' + '\x6f' + '\x32' + '\060' + chr(54), ord("\x08")), nzTpIcepk0o8(chr(966 - 918) + chr(0b1001 + 0o146) + chr(2230 - 2181) + chr(48) + '\x35', 21856 - 21848), nzTpIcepk0o8(chr(0b11001 + 0o27) + '\157' + chr(1323 - 1272) + '\x31' + '\x31', 0b1000), nzTpIcepk0o8(chr(0b10111 + 0o31) + '\x6f' + '\062' + '\x36' + chr(1501 - 1450), 20672 - 20664), nzTpIcepk0o8('\060' + chr(6536 - 6425) + chr(0b110001) + chr(1908 - 1860) + '\x30', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b100001 + 0o116) + '\063' + '\x30' + chr(0b110001), 0o10), nzTpIcepk0o8('\x30' + chr(0b111001 + 0o66) + chr(0b110011) + '\067', 4316 - 4308), nzTpIcepk0o8('\x30' + chr(7043 - 6932) + chr(0b11101 + 0o24) + '\x32' + chr(51), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x31' + chr(0b101000 + 0o17) + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110001) + chr(893 - 841) + '\065', 0b1000), nzTpIcepk0o8(chr(0b101011 + 0o5) + chr(0b1101111) + '\x32' + '\x31', 0o10), nzTpIcepk0o8(chr(1472 - 1424) + chr(111) + '\062', 26410 - 26402), nzTpIcepk0o8(chr(0b10110 + 0o32) + chr(111) + '\066' + '\064', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x32' + chr(53) + chr(0b110100), 51229 - 51221), nzTpIcepk0o8(chr(48) + '\157' + '\x31' + chr(0b11000 + 0o34) + '\060', 0b1000), nzTpIcepk0o8(chr(439 - 391) + chr(0b1101111) + chr(1476 - 1427) + '\x34' + '\064', 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110101) + '\060', 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xf5'), '\x64' + '\145' + chr(0b1100011) + '\157' + chr(0b1100100) + chr(0b101101 + 0o70))(chr(0b1110101 + 0o0) + chr(0b1110100) + '\x66' + chr(0b101101) + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def nZgk6gh1b3dy(FfKOThdpoDTb, YRX9Ch4rysP9=None):
if YRX9Ch4rysP9 is None:
if dRKdVnHPFq7C(FfKOThdpoDTb, roI3spqORKae(ES5oEprVxulp(b'\xb8\x143\x9e\xd9<J\xef'), chr(0b1001011 + 0o31) + chr(0b1100101) + '\143' + chr(9971 - 9860) + chr(100) + '\x65')(chr(12420 - 12303) + chr(0b1110100) + chr(0b1011110 + 0o10) + '\055' + '\x38')):
return roI3spqORKae(FfKOThdpoDTb, roI3spqORKae(ES5oEprVxulp(b'\xb8\x143\x9e\xd9<J\xef'), chr(0b1100100) + chr(9526 - 9425) + chr(0b1100011) + chr(0b1101111) + '\x64' + chr(0b1000100 + 0o41))(chr(0b1001111 + 0o46) + chr(0b1010110 + 0o36) + chr(2816 - 2714) + chr(0b101101) + '\x38'))
elif dRKdVnHPFq7C(FfKOThdpoDTb, roI3spqORKae(ES5oEprVxulp(b'\xb8\x143\x9e\xd9#'), chr(0b1101 + 0o127) + chr(0b10000 + 0o125) + chr(0b1100011) + chr(0b1101111) + chr(100) + '\x65')(chr(0b1110101) + chr(0b1100000 + 0o24) + chr(0b110 + 0o140) + chr(45) + chr(0b111000))) and dRKdVnHPFq7C(FfKOThdpoDTb, roI3spqORKae(ES5oEprVxulp(b"\xa8\x14'\x80\xd7"), chr(3086 - 2986) + chr(210 - 109) + chr(0b1100011) + '\157' + '\x64' + chr(0b1011 + 0o132))(chr(7965 - 7848) + chr(116) + chr(3956 - 3854) + '\055' + chr(0b11111 + 0o31))) and dRKdVnHPFq7C(roI3spqORKae(FfKOThdpoDTb, roI3spqORKae(ES5oEprVxulp(b"\xb4&\x08\x83\xdc'A\xea\xd9\x1b\x1bH"), chr(8132 - 8032) + chr(0b1110 + 0o127) + chr(0b1100011) + chr(11447 - 11336) + chr(0b1100100) + chr(0b1001110 + 0o27))('\x75' + chr(9281 - 9165) + chr(102) + chr(0b101101) + '\x38')), roI3spqORKae(ES5oEprVxulp(b'\x84#*\x95\xdc\x0fp'), '\144' + chr(0b1100101) + chr(0b1001001 + 0o32) + chr(0b1010 + 0o145) + '\x64' + '\x65')('\x75' + chr(116) + '\x66' + chr(0b101101) + '\070')) and dRKdVnHPFq7C(roI3spqORKae(FfKOThdpoDTb, roI3spqORKae(ES5oEprVxulp(b'\xb7\x14$\xbd\x82i\x1d\xc0\xc8\x16pF'), '\x64' + chr(0b1000000 + 0o45) + chr(99) + '\157' + '\x64' + chr(0b10011 + 0o122))(chr(117) + '\x74' + chr(0b101 + 0o141) + '\x2d' + chr(0b10010 + 0o46))), roI3spqORKae(ES5oEprVxulp(b'\x84#*\x95\xdc\x0fp'), '\144' + chr(0b1100101) + chr(99) + '\157' + '\144' + '\x65')('\x75' + chr(116) + chr(0b100101 + 0o101) + chr(0b101011 + 0o2) + chr(0b111000))) and (ftfygxgFas5X(roI3spqORKae(FfKOThdpoDTb, roI3spqORKae(ES5oEprVxulp(b"\xb4&\x08\x83\xdc'A\xea\xd9\x1b\x1bH"), '\x64' + chr(0b1100101) + chr(7029 - 6930) + '\157' + chr(100) + chr(0b1100101))(chr(0b1001001 + 0o54) + chr(116) + chr(102) + chr(45) + chr(0b111000)))) == ftfygxgFas5X(roI3spqORKae(FfKOThdpoDTb, roI3spqORKae(ES5oEprVxulp(b'\xb7\x14$\xbd\x82i\x1d\xc0\xc8\x16pF'), '\x64' + chr(7674 - 7573) + chr(99) + chr(0b111110 + 0o61) + chr(0b1100100) + '\145')(chr(7753 - 7636) + chr(116) + '\x66' + chr(0b100110 + 0o7) + chr(0b1011 + 0o55))))):
return roI3spqORKae(FfKOThdpoDTb, roI3spqORKae(ES5oEprVxulp(b"\xb4&\x08\x83\xdc'A\xea\xd9\x1b\x1bH"), chr(100) + '\x65' + chr(0b1100011) + '\157' + chr(0b1010001 + 0o23) + '\145')('\x75' + chr(0b1001111 + 0o45) + chr(2264 - 2162) + chr(233 - 188) + chr(400 - 344)))[nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(109 - 61), 0b1000)]
else:
o6UWUO21mH25 = nDF4gVNx0u9Q.asarray(FfKOThdpoDTb[nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110000), 8)])
return KV9ckIhroIia(nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\061', 12817 - 12809), nzTpIcepk0o8('\060' + chr(8921 - 8810) + '\x32', 8) ** nzTpIcepk0o8('\x30' + chr(8395 - 8284) + '\062' + '\x34', 0b1000) // roI3spqORKae(o6UWUO21mH25, roI3spqORKae(ES5oEprVxulp(b'\xbf2)\x91\xe57j\xb5\xf8\r=B'), chr(0b1100100) + '\x65' + chr(99) + '\157' + '\144' + chr(101))(chr(117) + chr(116) + chr(0b1010 + 0o134) + '\055' + chr(0b111000))))
else:
return YRX9Ch4rysP9 |
cggh/scikit-allel | allel/chunked/storage_hdf5.py | h5fmem | def h5fmem(**kwargs):
"""Create an in-memory HDF5 file."""
# need a file name even tho nothing is ever written
fn = tempfile.mktemp()
# file creation args
kwargs['mode'] = 'w'
kwargs['driver'] = 'core'
kwargs['backing_store'] = False
# open HDF5 file
h5f = h5py.File(fn, **kwargs)
return h5f | python | def h5fmem(**kwargs):
"""Create an in-memory HDF5 file."""
# need a file name even tho nothing is ever written
fn = tempfile.mktemp()
# file creation args
kwargs['mode'] = 'w'
kwargs['driver'] = 'core'
kwargs['backing_store'] = False
# open HDF5 file
h5f = h5py.File(fn, **kwargs)
return h5f | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/chunked/storage_hdf5.py#L17-L31 | train | Create an in - memory HDF5 file. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(49) + '\063' + chr(2486 - 2431), 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(0b100100 + 0o15) + '\x35' + chr(0b110000), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1000010 + 0o55) + chr(0b110010) + chr(53) + '\065', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(10090 - 9979) + chr(1565 - 1516) + chr(0b110111) + '\x36', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(8482 - 8371) + '\063' + '\x32' + '\065', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b11110 + 0o121) + '\062', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b100001 + 0o21) + chr(55) + chr(53), ord("\x08")), nzTpIcepk0o8(chr(2256 - 2208) + chr(0b11001 + 0o126) + chr(0b1001 + 0o54) + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(538 - 490) + chr(4776 - 4665) + '\063' + '\x37' + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1011100 + 0o23) + chr(0b110001) + chr(0b110011), ord("\x08")), nzTpIcepk0o8('\060' + chr(4640 - 4529) + chr(0b110010) + chr(1804 - 1755) + chr(97 - 43), 32212 - 32204), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(49) + chr(286 - 233) + chr(48), 8), nzTpIcepk0o8(chr(0b100011 + 0o15) + chr(8782 - 8671) + chr(393 - 342) + '\x34' + chr(48), ord("\x08")), nzTpIcepk0o8(chr(1174 - 1126) + chr(8200 - 8089) + chr(0b1111 + 0o42) + chr(1191 - 1138) + chr(0b110100), 8016 - 8008), nzTpIcepk0o8(chr(1915 - 1867) + chr(2364 - 2253) + '\x34' + '\067', 0o10), nzTpIcepk0o8('\x30' + chr(8412 - 8301) + chr(51) + chr(0b110100 + 0o3) + chr(481 - 428), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(0b110010) + '\060' + chr(50), 55034 - 55026), nzTpIcepk0o8(chr(48) + '\157' + chr(1384 - 1335) + '\063' + chr(51), 0o10), nzTpIcepk0o8(chr(48) + chr(0b100011 + 0o114) + chr(50) + chr(542 - 490) + chr(0b110001), 31905 - 31897), nzTpIcepk0o8(chr(48) + '\157' + chr(0b100 + 0o55) + '\x30' + '\x32', 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(0b100100 + 0o15) + '\x33' + chr(0b10000 + 0o42), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(49) + chr(48), 27487 - 27479), nzTpIcepk0o8('\060' + '\157' + chr(0b110011) + '\067', 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(49) + chr(48) + '\x32', 8), nzTpIcepk0o8(chr(0b110000) + chr(291 - 180) + '\x32' + chr(0b101 + 0o60) + '\063', 2019 - 2011), nzTpIcepk0o8('\060' + '\157' + chr(51) + chr(1695 - 1642) + chr(0b100000 + 0o26), ord("\x08")), nzTpIcepk0o8(chr(0b11000 + 0o30) + chr(0b1101111) + chr(49) + chr(51) + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b111011 + 0o64) + chr(0b11111 + 0o24) + chr(0b101001 + 0o10) + chr(0b11111 + 0o27), 8381 - 8373), nzTpIcepk0o8(chr(48) + chr(0b11110 + 0o121) + '\x31' + '\061' + '\064', 33216 - 33208), nzTpIcepk0o8('\x30' + '\x6f' + chr(77 - 26) + chr(0b10100 + 0o40) + chr(0b110110), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(50) + chr(51) + chr(0b110000), 0b1000), nzTpIcepk0o8(chr(0b101001 + 0o7) + chr(9534 - 9423) + chr(51) + '\064' + chr(0b101000 + 0o13), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(4620 - 4509) + chr(49) + chr(54) + chr(0b111 + 0o57), 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(0b10001 + 0o41) + '\x30', 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110010) + chr(0b110000 + 0o7) + '\060', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b100100 + 0o113) + '\062' + '\x30' + chr(1269 - 1215), 23404 - 23396), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\061' + chr(50), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(50 - 0) + chr(392 - 339) + chr(1779 - 1730), 13806 - 13798), nzTpIcepk0o8('\060' + '\x6f' + chr(215 - 163), 34646 - 34638), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110010) + '\x34', 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + chr(0b1 + 0o156) + chr(0b100101 + 0o20) + chr(48), ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'q'), '\x64' + chr(101) + chr(99) + chr(111) + chr(0b1100100) + '\145')(chr(0b110010 + 0o103) + '\x74' + '\x66' + chr(0b10010 + 0o33) + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def GSz6hVRVY__z(**q5n0sHDDTy90):
oo8448oP2LJ8 = VfV2QW3Td2UZ.mktemp()
q5n0sHDDTy90[roI3spqORKae(ES5oEprVxulp(b'2\x07\xc9\x1b'), chr(3608 - 3508) + chr(101) + '\143' + chr(0b1101111) + '\x64' + '\145')(chr(117) + chr(8748 - 8632) + '\x66' + '\x2d' + chr(0b111000))] = roI3spqORKae(ES5oEprVxulp(b'('), '\144' + chr(0b1011101 + 0o10) + '\143' + chr(0b1101111) + chr(0b1100100) + '\145')('\x75' + chr(0b1110100) + '\x66' + '\x2d' + chr(1258 - 1202))
q5n0sHDDTy90[roI3spqORKae(ES5oEprVxulp(b';\x1a\xc4\x08\xb0p'), chr(100) + chr(0b1100101) + chr(99) + chr(11916 - 11805) + chr(0b1010110 + 0o16) + chr(101))('\x75' + chr(116) + chr(102) + chr(0b11000 + 0o25) + '\x38')] = roI3spqORKae(ES5oEprVxulp(b'<\x07\xdf\x1b'), chr(7768 - 7668) + '\145' + '\143' + chr(2058 - 1947) + chr(3480 - 3380) + chr(9638 - 9537))('\165' + chr(116) + '\146' + chr(0b101101) + chr(0b10110 + 0o42))
q5n0sHDDTy90[roI3spqORKae(ES5oEprVxulp(b'=\t\xce\x15\xbcl\xdap\x8b\x7f\xe1\x1a\x85'), chr(5714 - 5614) + chr(0b1010001 + 0o24) + chr(884 - 785) + chr(0b101111 + 0o100) + chr(0b1100100) + chr(669 - 568))(chr(0b1110101) + chr(0b1100001 + 0o23) + chr(102) + '\055' + chr(0b110111 + 0o1))] = nzTpIcepk0o8('\060' + chr(111) + chr(48), 37561 - 37553)
uqjdddtgqsHt = RqFza2bfJyrc.File(oo8448oP2LJ8, **q5n0sHDDTy90)
return uqjdddtgqsHt |
cggh/scikit-allel | allel/chunked/storage_hdf5.py | h5ftmp | def h5ftmp(**kwargs):
"""Create an HDF5 file backed by a temporary file."""
# create temporary file name
suffix = kwargs.pop('suffix', '.h5')
prefix = kwargs.pop('prefix', 'scikit_allel_')
tempdir = kwargs.pop('dir', None)
fn = tempfile.mktemp(suffix=suffix, prefix=prefix, dir=tempdir)
atexit.register(os.remove, fn)
# file creation args
kwargs['mode'] = 'w'
# open HDF5 file
h5f = h5py.File(fn, **kwargs)
return h5f | python | def h5ftmp(**kwargs):
"""Create an HDF5 file backed by a temporary file."""
# create temporary file name
suffix = kwargs.pop('suffix', '.h5')
prefix = kwargs.pop('prefix', 'scikit_allel_')
tempdir = kwargs.pop('dir', None)
fn = tempfile.mktemp(suffix=suffix, prefix=prefix, dir=tempdir)
atexit.register(os.remove, fn)
# file creation args
kwargs['mode'] = 'w'
# open HDF5 file
h5f = h5py.File(fn, **kwargs)
return h5f | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/chunked/storage_hdf5.py#L34-L50 | train | Create an HDF5 file backed by a temporary 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('\060' + chr(6517 - 6406) + '\061' + chr(0b110111), 42026 - 42018), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(51) + chr(0b110100) + chr(2220 - 2168), 0o10), nzTpIcepk0o8(chr(0b1001 + 0o47) + '\x6f' + chr(0b110010) + chr(0b110001) + chr(0b110110), 0o10), nzTpIcepk0o8('\x30' + chr(111) + '\061' + chr(51) + chr(52), 0o10), nzTpIcepk0o8('\060' + chr(4820 - 4709) + chr(1799 - 1745) + '\x37', 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110001 + 0o0) + chr(0b110110), 0b1000), nzTpIcepk0o8('\060' + chr(0b10111 + 0o130) + chr(0b110010) + '\065' + chr(0b110110), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + '\x33' + '\064', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b11000 + 0o32) + chr(50) + chr(0b1 + 0o61), 55505 - 55497), nzTpIcepk0o8(chr(48) + chr(0b1101001 + 0o6) + chr(54) + chr(1880 - 1826), 40337 - 40329), nzTpIcepk0o8(chr(1867 - 1819) + '\x6f' + chr(2076 - 2023) + chr(55), 9205 - 9197), nzTpIcepk0o8('\060' + chr(0b1011101 + 0o22) + '\x33' + chr(0b11111 + 0o22) + chr(0b110000), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(830 - 780) + '\x31' + '\x32', 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(0b1000 + 0o51) + '\064' + chr(0b110001), 23649 - 23641), nzTpIcepk0o8('\x30' + '\157' + chr(0b110011) + '\x37' + chr(0b110010), 50362 - 50354), nzTpIcepk0o8(chr(0b110000) + chr(1206 - 1095) + '\x33' + chr(0b110011) + '\x31', ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(0b101011 + 0o7) + chr(54) + chr(0b111 + 0o51), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110 + 0o54) + '\x33' + '\x36', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1000011 + 0o54) + chr(0b110010) + chr(951 - 898), 0o10), nzTpIcepk0o8(chr(1839 - 1791) + chr(0b1011000 + 0o27) + chr(2236 - 2187) + '\x36' + '\x34', 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x34', 0o10), nzTpIcepk0o8(chr(48) + chr(8032 - 7921) + '\063' + chr(0b10111 + 0o36) + '\061', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(6991 - 6880) + chr(50) + chr(0b1111 + 0o46), 8), nzTpIcepk0o8(chr(1392 - 1344) + '\157' + chr(1328 - 1277) + chr(0b11101 + 0o24), 4402 - 4394), nzTpIcepk0o8('\x30' + chr(0b111000 + 0o67) + chr(0b110111) + chr(0b11110 + 0o27), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b11101 + 0o30) + chr(0b110001), 35078 - 35070), nzTpIcepk0o8(chr(0b11001 + 0o27) + '\x6f' + chr(0b1 + 0o62) + '\x32' + chr(0b110010), ord("\x08")), nzTpIcepk0o8('\x30' + chr(5931 - 5820) + '\066' + '\061', 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110101) + chr(49), 8), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110011) + chr(0b110001) + chr(0b100010 + 0o16), 8), nzTpIcepk0o8(chr(611 - 563) + '\x6f' + '\067' + chr(0b110111), 0o10), nzTpIcepk0o8('\060' + chr(0b1010111 + 0o30) + '\061' + chr(51) + chr(0b101010 + 0o7), ord("\x08")), nzTpIcepk0o8(chr(1217 - 1169) + '\157' + chr(50) + chr(1871 - 1819) + '\x32', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x37' + chr(52), 23604 - 23596), nzTpIcepk0o8('\x30' + chr(0b1100100 + 0o13) + '\x33' + '\x37' + chr(0b110110), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + '\x33' + chr(1202 - 1150) + '\x32', ord("\x08")), nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(6946 - 6835) + '\061' + chr(0b11110 + 0o30) + chr(48), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(6992 - 6881) + chr(0b110101) + chr(0b110111), 8), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(53) + chr(0b11 + 0o56), 8), nzTpIcepk0o8('\060' + chr(10854 - 10743) + '\061' + chr(0b101000 + 0o14) + chr(54), 40050 - 40042)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(1041 - 993) + chr(111) + '\x35' + chr(0b10010 + 0o36), ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'!'), '\144' + chr(0b1100101) + '\x63' + '\157' + chr(0b1100100) + '\x65')(chr(7464 - 7347) + '\164' + '\146' + chr(0b1101 + 0o40) + chr(2830 - 2774)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def EVqHmOK7riBQ(**q5n0sHDDTy90):
biRCFepsLie5 = q5n0sHDDTy90.uC_Yoybx7J0I(roI3spqORKae(ES5oEprVxulp(b'|\x91\xe8:^v'), '\x64' + '\145' + chr(99) + chr(6331 - 6220) + '\x64' + chr(101))(chr(937 - 820) + chr(6812 - 6696) + chr(8963 - 8861) + '\x2d' + chr(1834 - 1778)), roI3spqORKae(ES5oEprVxulp(b'!\x8c\xbb'), '\x64' + chr(101) + chr(99) + chr(0b100101 + 0o112) + '\x64' + '\145')('\165' + '\164' + chr(0b111 + 0o137) + chr(1056 - 1011) + '\070'))
ZJwZgaHE72Po = q5n0sHDDTy90.uC_Yoybx7J0I(roI3spqORKae(ES5oEprVxulp(b'\x7f\x96\xeb:^v'), '\x64' + chr(0b1100101) + '\143' + chr(8707 - 8596) + chr(0b111110 + 0o46) + chr(0b1100101))('\x75' + '\x74' + chr(5717 - 5615) + chr(0b11011 + 0o22) + '\070'), roI3spqORKae(ES5oEprVxulp(b'|\x87\xe77^z\xf1}\xfeZJ\xa4\xd5'), chr(0b1000110 + 0o36) + chr(7326 - 7225) + '\x63' + chr(111) + chr(100) + chr(0b1100101))(chr(12248 - 12131) + chr(10196 - 10080) + '\146' + '\x2d' + '\x38'))
KBB7A0ocQUrE = q5n0sHDDTy90.uC_Yoybx7J0I(roI3spqORKae(ES5oEprVxulp(b'k\x8d\xfc'), chr(0b10110 + 0o116) + chr(0b111 + 0o136) + chr(0b1100011) + '\x6f' + '\144' + chr(101))('\x75' + chr(0b1110100) + chr(102) + chr(0b101101) + chr(0b100 + 0o64)), None)
oo8448oP2LJ8 = VfV2QW3Td2UZ.mktemp(suffix=biRCFepsLie5, prefix=ZJwZgaHE72Po, dir=KBB7A0ocQUrE)
roI3spqORKae(fHU0TT4mmrR6, roI3spqORKae(ES5oEprVxulp(b'v\x87\xc3\x08\x05b\xdeF\xa4t_\x99'), chr(4870 - 4770) + '\x65' + chr(99) + chr(111) + '\144' + chr(0b1100101))(chr(117) + chr(116) + chr(8731 - 8629) + '\055' + chr(0b101101 + 0o13)))(roI3spqORKae(aHUqKstZLeS6, roI3spqORKae(ES5oEprVxulp(b'\x7f\xa9\xe2\t_j\x9cV\xff}n\x8d'), '\x64' + '\145' + chr(99) + '\157' + '\144' + chr(8346 - 8245))(chr(0b1110101) + '\x74' + chr(0b1100110) + '\x2d' + chr(0b11011 + 0o35))), oo8448oP2LJ8)
q5n0sHDDTy90[roI3spqORKae(ES5oEprVxulp(b'b\x8b\xea9'), chr(0b101000 + 0o74) + chr(101) + chr(0b1100011) + '\157' + chr(0b1011110 + 0o6) + chr(0b1100101))(chr(0b110001 + 0o104) + chr(116) + chr(102) + chr(0b101101) + chr(56))] = roI3spqORKae(ES5oEprVxulp(b'x'), '\144' + chr(101) + '\143' + chr(8074 - 7963) + '\x64' + '\x65')('\x75' + chr(2698 - 2582) + chr(0b110101 + 0o61) + chr(0b101101) + chr(1515 - 1459))
uqjdddtgqsHt = RqFza2bfJyrc.File(oo8448oP2LJ8, **q5n0sHDDTy90)
return uqjdddtgqsHt |
cggh/scikit-allel | allel/chunked/core.py | store | def store(data, arr, start=0, stop=None, offset=0, blen=None):
"""Copy `data` block-wise into `arr`."""
# setup
blen = _util.get_blen_array(data, blen)
if stop is None:
stop = len(data)
else:
stop = min(stop, len(data))
length = stop - start
if length < 0:
raise ValueError('invalid stop/start')
# copy block-wise
for bi in range(start, stop, blen):
bj = min(bi+blen, stop)
bl = bj - bi
arr[offset:offset+bl] = data[bi:bj]
offset += bl | python | def store(data, arr, start=0, stop=None, offset=0, blen=None):
"""Copy `data` block-wise into `arr`."""
# setup
blen = _util.get_blen_array(data, blen)
if stop is None:
stop = len(data)
else:
stop = min(stop, len(data))
length = stop - start
if length < 0:
raise ValueError('invalid stop/start')
# copy block-wise
for bi in range(start, stop, blen):
bj = min(bi+blen, stop)
bl = bj - bi
arr[offset:offset+bl] = data[bi:bj]
offset += bl | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/chunked/core.py#L16-L34 | train | Copy data block - wise into arr. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110011) + chr(0b110110), 0b1000), nzTpIcepk0o8(chr(645 - 597) + chr(0b111000 + 0o67) + '\061' + chr(51) + chr(0b110111), 0b1000), nzTpIcepk0o8('\x30' + chr(111) + '\x36' + '\066', 46641 - 46633), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(50) + '\062' + chr(51), 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(49) + chr(49) + '\x32', 0o10), nzTpIcepk0o8(chr(2183 - 2135) + '\157' + chr(586 - 535) + chr(0b110000) + chr(48), 37307 - 37299), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x33' + chr(0b110000) + chr(53), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(7970 - 7859) + chr(1711 - 1662) + chr(50) + chr(49), 34710 - 34702), nzTpIcepk0o8(chr(0b1101 + 0o43) + chr(0b1101111) + chr(50) + chr(48) + '\065', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(1051 - 1002) + chr(0b110001) + chr(53), 21700 - 21692), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(51) + '\x33' + '\x30', 3249 - 3241), nzTpIcepk0o8('\x30' + chr(7290 - 7179) + chr(253 - 203) + '\064' + chr(0b110000), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x35' + '\x37', 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110100) + chr(0b110011), ord("\x08")), nzTpIcepk0o8(chr(0b10 + 0o56) + chr(5161 - 5050) + chr(55) + chr(1153 - 1105), 0b1000), nzTpIcepk0o8('\060' + chr(6758 - 6647) + '\x31' + chr(2412 - 2360) + chr(55), 0b1000), nzTpIcepk0o8(chr(0b101001 + 0o7) + chr(0b1010 + 0o145) + '\x32' + chr(0b110010) + '\x30', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b10001 + 0o40) + chr(0b10111 + 0o31) + '\064', 27318 - 27310), nzTpIcepk0o8(chr(1491 - 1443) + chr(0b100111 + 0o110) + chr(0b11101 + 0o25) + chr(0b110000 + 0o4) + chr(2648 - 2594), 37081 - 37073), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b11100 + 0o27) + chr(269 - 220) + chr(53), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b10101 + 0o132) + chr(49) + '\x30' + chr(0b110100), 8), nzTpIcepk0o8(chr(0b101000 + 0o10) + '\x6f' + chr(0b101 + 0o60) + chr(341 - 292), 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(0b100100 + 0o15) + chr(2168 - 2119) + '\063', 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(51) + chr(2693 - 2641) + '\065', 0b1000), nzTpIcepk0o8(chr(1838 - 1790) + '\157' + '\x33' + chr(0b11010 + 0o35) + '\061', 0o10), nzTpIcepk0o8(chr(1069 - 1021) + '\157' + chr(0b10111 + 0o34) + chr(0b110110) + '\x30', 0o10), nzTpIcepk0o8(chr(1982 - 1934) + chr(10816 - 10705) + '\x31' + chr(55) + chr(55), 27723 - 27715), nzTpIcepk0o8(chr(1389 - 1341) + chr(111) + chr(572 - 523) + chr(0b110001), ord("\x08")), nzTpIcepk0o8(chr(0b101000 + 0o10) + chr(10180 - 10069) + chr(1268 - 1219) + '\x35' + '\065', 22424 - 22416), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110010) + chr(2150 - 2098) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(0b101001 + 0o7) + chr(6536 - 6425) + chr(827 - 777) + chr(52), 36670 - 36662), nzTpIcepk0o8(chr(48) + chr(0b1001000 + 0o47) + chr(50) + chr(0b11011 + 0o31) + chr(49), ord("\x08")), nzTpIcepk0o8(chr(1244 - 1196) + chr(0b10011 + 0o134) + '\x35' + chr(0b1100 + 0o53), 8), nzTpIcepk0o8(chr(0b110000) + chr(0b11011 + 0o124) + chr(0b11110 + 0o24) + chr(0b110100) + '\066', 8), nzTpIcepk0o8(chr(0b11101 + 0o23) + chr(5684 - 5573) + chr(0b10100 + 0o37) + chr(1426 - 1378) + chr(48), 8), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(49) + '\x30' + chr(0b10001 + 0o42), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + '\061' + chr(51) + chr(0b110110), 0b1000), nzTpIcepk0o8('\060' + chr(2394 - 2283) + '\061' + '\060' + chr(0b110101), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(829 - 779) + chr(0b110100) + chr(1576 - 1527), 8), nzTpIcepk0o8(chr(221 - 173) + chr(0b1101011 + 0o4) + '\062' + '\061', 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + chr(0b110010 + 0o75) + chr(0b10000 + 0o45) + '\x30', 58600 - 58592)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'0'), '\144' + '\145' + chr(0b1100011) + chr(0b1101111) + '\144' + chr(101))(chr(117) + chr(9629 - 9513) + chr(0b1100110) + chr(0b11010 + 0o23) + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def Yws2kZcdmcdB(FfKOThdpoDTb, JaZEP80kXwoT, KQbHFTcl_LKy=nzTpIcepk0o8(chr(0b11111 + 0o21) + chr(3504 - 3393) + '\x30', 0b1000), dYJbBiYO_nGE=None, GuX46MBAOnaQ=nzTpIcepk0o8(chr(2063 - 2015) + chr(0b1000111 + 0o50) + chr(1437 - 1389), 8), YRX9Ch4rysP9=None):
YRX9Ch4rysP9 = jEKHUML0AUn7.get_blen_array(FfKOThdpoDTb, YRX9Ch4rysP9)
if dYJbBiYO_nGE is None:
dYJbBiYO_nGE = ftfygxgFas5X(FfKOThdpoDTb)
else:
dYJbBiYO_nGE = XURpmPuEWCNF(dYJbBiYO_nGE, ftfygxgFas5X(FfKOThdpoDTb))
a1RCQZREo3Kd = dYJbBiYO_nGE - KQbHFTcl_LKy
if a1RCQZREo3Kd < nzTpIcepk0o8(chr(48) + '\x6f' + '\060', 8):
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'w1@\xf2&\xa9\xa1q\xf69\xb7\xd0\x00PL\x06\xe20'), chr(0b1100100) + '\145' + '\x63' + '\x6f' + '\x64' + '\145')(chr(0b1110101) + chr(0b11000 + 0o134) + chr(3520 - 3418) + '\055' + chr(56)))
for Bm59fX0zXbot in bbT2xIe5pzk7(KQbHFTcl_LKy, dYJbBiYO_nGE, YRX9Ch4rysP9):
J0k7ptpS4utW = XURpmPuEWCNF(Bm59fX0zXbot + YRX9Ch4rysP9, dYJbBiYO_nGE)
UsIpVMDUDSVi = J0k7ptpS4utW - Bm59fX0zXbot
JaZEP80kXwoT[GuX46MBAOnaQ:GuX46MBAOnaQ + UsIpVMDUDSVi] = FfKOThdpoDTb[Bm59fX0zXbot:J0k7ptpS4utW]
GuX46MBAOnaQ += UsIpVMDUDSVi |
cggh/scikit-allel | allel/chunked/core.py | copy | def copy(data, start=0, stop=None, blen=None, storage=None, create='array',
**kwargs):
"""Copy `data` block-wise into a new array."""
# setup
storage = _util.get_storage(storage)
blen = _util.get_blen_array(data, blen)
if stop is None:
stop = len(data)
else:
stop = min(stop, len(data))
length = stop - start
if length < 0:
raise ValueError('invalid stop/start')
# copy block-wise
out = None
for i in range(start, stop, blen):
j = min(i+blen, stop)
block = data[i:j]
if out is None:
out = getattr(storage, create)(block, expectedlen=length, **kwargs)
else:
out.append(block)
return out | python | def copy(data, start=0, stop=None, blen=None, storage=None, create='array',
**kwargs):
"""Copy `data` block-wise into a new array."""
# setup
storage = _util.get_storage(storage)
blen = _util.get_blen_array(data, blen)
if stop is None:
stop = len(data)
else:
stop = min(stop, len(data))
length = stop - start
if length < 0:
raise ValueError('invalid stop/start')
# copy block-wise
out = None
for i in range(start, stop, blen):
j = min(i+blen, stop)
block = data[i:j]
if out is None:
out = getattr(storage, create)(block, expectedlen=length, **kwargs)
else:
out.append(block)
return out | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/chunked/core.py#L37-L62 | train | Copy data block - wise into a new array. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(1883 - 1835) + chr(803 - 692) + chr(0b110011) + chr(2440 - 2385) + chr(49), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1011100 + 0o23) + chr(1716 - 1667) + chr(580 - 529) + chr(0b10111 + 0o36), 0o10), nzTpIcepk0o8(chr(48) + '\157' + '\x32' + chr(54), 62464 - 62456), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(2807 - 2752) + '\x34', ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(50) + '\067' + chr(0b110101), 21339 - 21331), nzTpIcepk0o8(chr(1133 - 1085) + '\157' + chr(55) + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(4099 - 3988) + chr(0b110010) + chr(2049 - 1997) + '\064', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(8536 - 8425) + chr(0b110010) + chr(502 - 451) + '\x30', 0o10), nzTpIcepk0o8(chr(48) + chr(7783 - 7672) + chr(0b110111) + chr(1343 - 1290), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(0b110011) + '\x30', ord("\x08")), nzTpIcepk0o8(chr(586 - 538) + chr(0b1101111) + chr(0b111 + 0o54) + '\064' + chr(0b110101), 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(0b110011) + chr(0b110101), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + '\063' + chr(2421 - 2368) + '\060', 42369 - 42361), nzTpIcepk0o8('\x30' + chr(7846 - 7735) + chr(0b110010) + '\x36', 8), nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(0b1101111) + chr(0b10100 + 0o36) + chr(0b110100), 0o10), nzTpIcepk0o8('\060' + chr(0b11011 + 0o124) + '\063' + chr(0b101110 + 0o2) + chr(1748 - 1693), 42844 - 42836), nzTpIcepk0o8(chr(2213 - 2165) + '\x6f' + '\063' + '\064' + chr(56 - 1), 33358 - 33350), nzTpIcepk0o8(chr(48) + '\157' + '\063' + chr(0b110111) + '\067', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(2033 - 1922) + chr(760 - 709) + chr(734 - 680) + '\062', 4718 - 4710), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b1001 + 0o52) + chr(53) + chr(0b110011 + 0o0), 0b1000), nzTpIcepk0o8(chr(2204 - 2156) + chr(0b1101111) + chr(49) + chr(0b110100) + chr(1426 - 1371), 1363 - 1355), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\063' + chr(48) + chr(51), 31542 - 31534), nzTpIcepk0o8(chr(1407 - 1359) + '\x6f' + chr(0b110011) + chr(822 - 774) + chr(2068 - 2014), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(1193 - 1143) + chr(0b110100) + '\x31', 0o10), nzTpIcepk0o8('\060' + chr(0b101001 + 0o106) + '\x32' + chr(0b110000) + chr(1162 - 1108), 17418 - 17410), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(803 - 753) + '\x30' + chr(0b110111), 28570 - 28562), nzTpIcepk0o8(chr(552 - 504) + chr(0b10011 + 0o134) + chr(0b10101 + 0o35) + '\065' + '\065', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(1651 - 1600) + chr(0b110001) + chr(0b10001 + 0o40), 0o10), nzTpIcepk0o8('\060' + '\x6f' + '\x32' + '\063' + '\x31', 8603 - 8595), nzTpIcepk0o8(chr(983 - 935) + chr(0b1101111) + chr(0b10101 + 0o34) + '\x33' + '\x30', ord("\x08")), nzTpIcepk0o8(chr(1653 - 1605) + chr(0b1101001 + 0o6) + '\061' + '\x30' + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(1721 - 1673) + chr(111) + chr(0b11010 + 0o33) + chr(51), 53883 - 53875), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110110) + chr(52), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(1015 - 966) + chr(862 - 808) + chr(0b11000 + 0o32), 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(51) + '\060' + chr(1126 - 1074), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b101000 + 0o11) + chr(55) + '\x37', 0b1000), nzTpIcepk0o8(chr(0b101100 + 0o4) + '\x6f' + chr(0b110010) + '\x37' + '\x35', 8), nzTpIcepk0o8('\x30' + chr(0b10000 + 0o137) + chr(0b1011 + 0o47) + chr(2187 - 2139) + '\062', 59638 - 59630), nzTpIcepk0o8(chr(1699 - 1651) + chr(206 - 95) + chr(0b110001) + chr(0b110010 + 0o2), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + chr(0b10001 + 0o41) + '\061' + '\061', 55735 - 55727)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + '\157' + '\065' + '\060', 2605 - 2597)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xd7'), chr(0b1100100 + 0o0) + chr(4128 - 4027) + '\143' + chr(0b1101111) + chr(100) + chr(0b1100101))(chr(117) + chr(0b1101000 + 0o14) + '\146' + chr(0b11110 + 0o17) + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def aZTCj4v5QdfO(FfKOThdpoDTb, KQbHFTcl_LKy=nzTpIcepk0o8(chr(0b1100 + 0o44) + chr(4534 - 4423) + '\x30', 0o10), dYJbBiYO_nGE=None, YRX9Ch4rysP9=None, A2YPCXgFSG1t=None, uTw5CPPMOlxD=roI3spqORKae(ES5oEprVxulp(b'\x98/d]\xc4'), chr(100) + chr(0b100011 + 0o102) + '\x63' + '\x6f' + chr(100) + chr(101))(chr(117) + chr(116) + chr(102) + '\055' + chr(0b110100 + 0o4)), **q5n0sHDDTy90):
A2YPCXgFSG1t = jEKHUML0AUn7.get_storage(A2YPCXgFSG1t)
YRX9Ch4rysP9 = jEKHUML0AUn7.get_blen_array(FfKOThdpoDTb, YRX9Ch4rysP9)
if dYJbBiYO_nGE is None:
dYJbBiYO_nGE = ftfygxgFas5X(FfKOThdpoDTb)
else:
dYJbBiYO_nGE = XURpmPuEWCNF(dYJbBiYO_nGE, ftfygxgFas5X(FfKOThdpoDTb))
a1RCQZREo3Kd = dYJbBiYO_nGE - KQbHFTcl_LKy
if a1RCQZREo3Kd < nzTpIcepk0o8(chr(48) + chr(0b101111 + 0o100) + chr(0b110000), 8):
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'\x903`]\xd1V\xc0\xb8Nl\x8am\xc7e`\xa6\x95\x8b'), '\x64' + '\145' + chr(0b1100011) + '\157' + chr(0b1100100) + '\145')(chr(0b1110101) + chr(0b1110100) + chr(0b1100110) + '\055' + '\070'))
VwOu8WkJ9cpc = None
for ZlbFMSG8gCoF in bbT2xIe5pzk7(KQbHFTcl_LKy, dYJbBiYO_nGE, YRX9Ch4rysP9):
sChW4gUsXrIC = XURpmPuEWCNF(ZlbFMSG8gCoF + YRX9Ch4rysP9, dYJbBiYO_nGE)
TvT0D2rIGW5A = FfKOThdpoDTb[ZlbFMSG8gCoF:sChW4gUsXrIC]
if VwOu8WkJ9cpc is None:
VwOu8WkJ9cpc = roI3spqORKae(A2YPCXgFSG1t, uTw5CPPMOlxD)(TvT0D2rIGW5A, expectedlen=a1RCQZREo3Kd, **q5n0sHDDTy90)
else:
roI3spqORKae(VwOu8WkJ9cpc, roI3spqORKae(ES5oEprVxulp(b'\xb1\tE\x08\xc5X\xe3\xf7Ww\xb0('), chr(3716 - 3616) + chr(0b1011011 + 0o12) + chr(0b1100011) + chr(5196 - 5085) + '\x64' + chr(0b1100101))('\165' + chr(12312 - 12196) + chr(0b1100110) + chr(45) + chr(1989 - 1933)))(TvT0D2rIGW5A)
return VwOu8WkJ9cpc |
cggh/scikit-allel | allel/chunked/core.py | copy_table | def copy_table(tbl, start=0, stop=None, blen=None, storage=None,
create='table', **kwargs):
"""Copy `tbl` block-wise into a new table."""
# setup
names, columns = _util.check_table_like(tbl)
storage = _util.get_storage(storage)
blen = _util.get_blen_table(tbl, blen)
if stop is None:
stop = len(columns[0])
else:
stop = min(stop, len(columns[0]))
length = stop - start
if length < 0:
raise ValueError('invalid stop/start')
# copy block-wise
out = None
for i in range(start, stop, blen):
j = min(i+blen, stop)
res = [c[i:j] for c in columns]
if out is None:
out = getattr(storage, create)(res, names=names,
expectedlen=length, **kwargs)
else:
out.append(res)
return out | python | def copy_table(tbl, start=0, stop=None, blen=None, storage=None,
create='table', **kwargs):
"""Copy `tbl` block-wise into a new table."""
# setup
names, columns = _util.check_table_like(tbl)
storage = _util.get_storage(storage)
blen = _util.get_blen_table(tbl, blen)
if stop is None:
stop = len(columns[0])
else:
stop = min(stop, len(columns[0]))
length = stop - start
if length < 0:
raise ValueError('invalid stop/start')
# copy block-wise
out = None
for i in range(start, stop, blen):
j = min(i+blen, stop)
res = [c[i:j] for c in columns]
if out is None:
out = getattr(storage, create)(res, names=names,
expectedlen=length, **kwargs)
else:
out.append(res)
return out | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/chunked/core.py#L65-L92 | train | Copy a table block - wise into a new 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('\060' + chr(1894 - 1783) + chr(0b11111 + 0o24) + chr(52) + chr(1010 - 956), 0b1000), nzTpIcepk0o8(chr(2122 - 2074) + chr(0b1101111) + chr(0b100 + 0o55) + '\x37' + chr(0b110001), 61698 - 61690), nzTpIcepk0o8('\060' + '\157' + chr(1331 - 1280) + chr(54) + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110010 + 0o5) + chr(55), 0o10), nzTpIcepk0o8(chr(0b101000 + 0o10) + chr(0b1101111) + chr(2375 - 2326) + '\061' + chr(0b110100 + 0o2), 52206 - 52198), nzTpIcepk0o8(chr(0b10010 + 0o36) + chr(3363 - 3252) + chr(49) + chr(1689 - 1641) + chr(2317 - 2267), 23005 - 22997), nzTpIcepk0o8('\x30' + chr(111) + '\x31' + '\x33' + chr(51), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(50) + '\x36' + chr(0b110100), 0o10), nzTpIcepk0o8(chr(0b100110 + 0o12) + chr(111) + '\062' + '\x35' + '\066', ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(51) + chr(1845 - 1793) + chr(54), 8), nzTpIcepk0o8('\060' + '\x6f' + chr(0b100110 + 0o13) + '\x37' + chr(50), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + '\x31' + chr(0b110100) + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(49) + chr(2206 - 2156) + chr(2098 - 2048), 25446 - 25438), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b11010 + 0o30) + '\060' + chr(49), 0o10), nzTpIcepk0o8(chr(0b110 + 0o52) + chr(0b1101111) + chr(49) + chr(0b110100) + chr(905 - 853), 29505 - 29497), nzTpIcepk0o8('\x30' + chr(0b111 + 0o150) + '\x31' + chr(0b110010) + chr(2137 - 2088), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b111010 + 0o65) + '\063' + chr(0b110110), 24685 - 24677), nzTpIcepk0o8(chr(48) + chr(10902 - 10791) + '\x32' + chr(51) + chr(1170 - 1116), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b11010 + 0o125) + chr(49) + chr(55) + '\060', 0o10), nzTpIcepk0o8(chr(574 - 526) + chr(111) + chr(0b110010) + chr(0b110000) + chr(53), 44062 - 44054), nzTpIcepk0o8(chr(0b10010 + 0o36) + chr(0b1101111) + chr(0b100011 + 0o20) + chr(0b110000) + chr(0b101111 + 0o5), 0b1000), nzTpIcepk0o8(chr(1102 - 1054) + chr(0b1101111) + '\063' + chr(52) + '\062', ord("\x08")), nzTpIcepk0o8(chr(0b0 + 0o60) + chr(0b1101111) + chr(1062 - 1011) + chr(0b100101 + 0o22) + '\061', 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(55) + chr(55), 8), nzTpIcepk0o8(chr(241 - 193) + chr(0b1101111) + chr(216 - 166) + '\062', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(50) + chr(0b101001 + 0o15) + '\x37', 0o10), nzTpIcepk0o8(chr(0b100000 + 0o20) + chr(0b11110 + 0o121) + '\062' + chr(0b110010) + chr(0b110000), 5425 - 5417), nzTpIcepk0o8('\060' + chr(5767 - 5656) + chr(0b110110) + chr(1725 - 1670), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1110 + 0o141) + '\x31' + chr(53) + '\062', ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(0b110001) + chr(0b110111) + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(1572 - 1524) + chr(0b1101111) + '\x32' + '\066' + chr(0b110100), 8), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x32' + chr(317 - 268) + '\067', 0o10), nzTpIcepk0o8(chr(786 - 738) + chr(0b1000000 + 0o57) + '\x32' + '\x32' + chr(49), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + '\x32' + chr(998 - 945) + chr(0b110010 + 0o2), 0b1000), nzTpIcepk0o8(chr(891 - 843) + chr(111) + chr(51) + chr(48) + chr(0b110110), 38182 - 38174), nzTpIcepk0o8('\x30' + chr(10626 - 10515) + '\x32' + chr(2046 - 1991) + chr(53), 46097 - 46089), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x32' + chr(48) + chr(2301 - 2250), 0b1000), nzTpIcepk0o8(chr(0b100010 + 0o16) + chr(6094 - 5983) + chr(0b110001) + chr(0b110000), 27678 - 27670), nzTpIcepk0o8(chr(0b10110 + 0o32) + '\x6f' + chr(0b0 + 0o61) + chr(0b0 + 0o61) + chr(1077 - 1028), ord("\x08")), nzTpIcepk0o8(chr(1968 - 1920) + chr(1713 - 1602) + chr(49) + chr(0b110000 + 0o1) + chr(0b110011), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + '\157' + '\x35' + '\060', 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xc8'), chr(0b10010 + 0o122) + chr(7857 - 7756) + chr(99) + chr(0b1101111) + '\x64' + '\x65')(chr(0b1110101) + chr(0b1110100) + '\146' + '\055' + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def erR5mqzfTZvD(nJ2Kaz8maxAX, KQbHFTcl_LKy=nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110000), 0o10), dYJbBiYO_nGE=None, YRX9Ch4rysP9=None, A2YPCXgFSG1t=None, uTw5CPPMOlxD=roI3spqORKae(ES5oEprVxulp(b'\x92\x18\x92S+'), chr(0b1100100) + chr(4704 - 4603) + chr(0b110010 + 0o61) + chr(0b1101111) + chr(386 - 286) + chr(101))('\x75' + '\164' + chr(102) + chr(0b101101) + '\x38'), **q5n0sHDDTy90):
(TMMrjsiU6eED, U39jSiI54Mlp) = jEKHUML0AUn7.check_table_like(nJ2Kaz8maxAX)
A2YPCXgFSG1t = jEKHUML0AUn7.get_storage(A2YPCXgFSG1t)
YRX9Ch4rysP9 = jEKHUML0AUn7.get_blen_table(nJ2Kaz8maxAX, YRX9Ch4rysP9)
if dYJbBiYO_nGE is None:
dYJbBiYO_nGE = ftfygxgFas5X(U39jSiI54Mlp[nzTpIcepk0o8(chr(0b11110 + 0o22) + '\157' + chr(48), 8)])
else:
dYJbBiYO_nGE = XURpmPuEWCNF(dYJbBiYO_nGE, ftfygxgFas5X(U39jSiI54Mlp[nzTpIcepk0o8('\x30' + chr(0b11110 + 0o121) + '\060', 8)]))
a1RCQZREo3Kd = dYJbBiYO_nGE - KQbHFTcl_LKy
if a1RCQZREo3Kd < nzTpIcepk0o8(chr(48) + chr(111) + '\060', 8):
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'\x8f\x17\x86^"+?\x94\xdd\x92\x15\x12}\xf2\x100l\xea'), chr(8214 - 8114) + '\145' + chr(99) + chr(0b1101111) + '\144' + chr(0b1100101))(chr(0b1110101) + chr(12915 - 12799) + '\x66' + chr(45) + '\x38'))
VwOu8WkJ9cpc = None
for ZlbFMSG8gCoF in bbT2xIe5pzk7(KQbHFTcl_LKy, dYJbBiYO_nGE, YRX9Ch4rysP9):
sChW4gUsXrIC = XURpmPuEWCNF(ZlbFMSG8gCoF + YRX9Ch4rysP9, dYJbBiYO_nGE)
_XdQFJpnzJor = [teUmM7cKWZUa[ZlbFMSG8gCoF:sChW4gUsXrIC] for teUmM7cKWZUa in U39jSiI54Mlp]
if VwOu8WkJ9cpc is None:
VwOu8WkJ9cpc = roI3spqORKae(A2YPCXgFSG1t, uTw5CPPMOlxD)(_XdQFJpnzJor, names=TMMrjsiU6eED, expectedlen=a1RCQZREo3Kd, **q5n0sHDDTy90)
else:
roI3spqORKae(VwOu8WkJ9cpc, roI3spqORKae(ES5oEprVxulp(b'\xae-\xa3\x0b6%\x1c\xdb\xc4\x89/W'), '\x64' + chr(0b1011110 + 0o7) + chr(0b1000 + 0o133) + chr(111) + '\144' + '\x65')('\165' + chr(0b1110100) + chr(0b111001 + 0o55) + chr(1668 - 1623) + chr(56)))(_XdQFJpnzJor)
return VwOu8WkJ9cpc |
cggh/scikit-allel | allel/chunked/core.py | map_blocks | def map_blocks(data, f, blen=None, storage=None, create='array', **kwargs):
"""Apply function `f` block-wise over `data`."""
# setup
storage = _util.get_storage(storage)
if isinstance(data, tuple):
blen = max(_util.get_blen_array(d, blen) for d in data)
else:
blen = _util.get_blen_array(data, blen)
if isinstance(data, tuple):
_util.check_equal_length(*data)
length = len(data[0])
else:
length = len(data)
# block-wise iteration
out = None
for i in range(0, length, blen):
j = min(i+blen, length)
# obtain blocks
if isinstance(data, tuple):
blocks = [d[i:j] for d in data]
else:
blocks = [data[i:j]]
# map
res = f(*blocks)
# store
if out is None:
out = getattr(storage, create)(res, expectedlen=length, **kwargs)
else:
out.append(res)
return out | python | def map_blocks(data, f, blen=None, storage=None, create='array', **kwargs):
"""Apply function `f` block-wise over `data`."""
# setup
storage = _util.get_storage(storage)
if isinstance(data, tuple):
blen = max(_util.get_blen_array(d, blen) for d in data)
else:
blen = _util.get_blen_array(data, blen)
if isinstance(data, tuple):
_util.check_equal_length(*data)
length = len(data[0])
else:
length = len(data)
# block-wise iteration
out = None
for i in range(0, length, blen):
j = min(i+blen, length)
# obtain blocks
if isinstance(data, tuple):
blocks = [d[i:j] for d in data]
else:
blocks = [data[i:j]]
# map
res = f(*blocks)
# store
if out is None:
out = getattr(storage, create)(res, expectedlen=length, **kwargs)
else:
out.append(res)
return out | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/chunked/core.py#L95-L130 | train | Apply function f block - wise over data. | 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(0b110001) + chr(0b110110 + 0o0) + '\067', ord("\x08")), nzTpIcepk0o8(chr(949 - 901) + '\157' + chr(1689 - 1638) + chr(737 - 686) + chr(0b110100), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(0b111 + 0o52) + chr(0b101111 + 0o5) + chr(48), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(51) + '\x34' + chr(1488 - 1435), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b10001 + 0o136) + chr(0b110011) + chr(0b110010) + chr(0b10 + 0o57), 37394 - 37386), nzTpIcepk0o8(chr(48) + chr(5472 - 5361) + chr(0b101 + 0o54) + chr(48) + chr(49), 23759 - 23751), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110011) + chr(52) + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(0b1001 + 0o47) + chr(111) + '\063' + chr(1036 - 986) + chr(563 - 509), 0o10), nzTpIcepk0o8(chr(0b100111 + 0o11) + chr(2045 - 1934) + chr(0b110011) + chr(53) + '\065', 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(515 - 465) + chr(52) + '\063', 20465 - 20457), nzTpIcepk0o8('\060' + '\157' + '\x31' + chr(2286 - 2232) + '\060', ord("\x08")), nzTpIcepk0o8('\x30' + chr(12263 - 12152) + chr(0b110011) + '\065' + chr(0b1011 + 0o45), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + '\061' + chr(52) + chr(0b11011 + 0o31), 0b1000), nzTpIcepk0o8(chr(0b100010 + 0o16) + chr(0b1101111) + chr(0b110010) + '\064' + chr(1592 - 1539), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(9600 - 9489) + chr(401 - 351) + chr(1689 - 1637) + chr(0b110111), 47873 - 47865), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\061' + chr(910 - 862) + chr(48), 0o10), nzTpIcepk0o8(chr(869 - 821) + '\157' + '\061' + chr(0b110000) + '\062', 0o10), nzTpIcepk0o8(chr(2105 - 2057) + '\157' + chr(0b110010) + '\x32' + '\060', 11367 - 11359), nzTpIcepk0o8(chr(1833 - 1785) + chr(111) + chr(50) + chr(1059 - 1005) + chr(55), 0b1000), nzTpIcepk0o8(chr(0b1010 + 0o46) + chr(675 - 564) + chr(0b101100 + 0o5) + chr(53) + chr(0b110011), 0o10), nzTpIcepk0o8('\060' + chr(0b11000 + 0o127) + chr(0b110011) + chr(55), 261 - 253), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(50) + chr(0b10000 + 0o42) + chr(55), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1001110 + 0o41) + '\x31' + chr(48) + chr(0b101000 + 0o11), 8), nzTpIcepk0o8('\x30' + chr(0b110 + 0o151) + chr(489 - 439) + chr(1309 - 1258) + chr(52), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110010) + '\067' + chr(58 - 3), 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(0b110100) + chr(0b110110), ord("\x08")), nzTpIcepk0o8(chr(1419 - 1371) + chr(111) + '\063' + chr(50) + chr(747 - 699), 0o10), nzTpIcepk0o8(chr(0b101101 + 0o3) + chr(0b1101111) + chr(51) + '\061' + chr(0b1001 + 0o53), 0b1000), nzTpIcepk0o8('\x30' + chr(0b10010 + 0o135) + '\x32' + chr(51) + chr(51), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1010101 + 0o32) + chr(49) + chr(0b110100) + chr(0b110001), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110001) + '\x36', ord("\x08")), nzTpIcepk0o8(chr(0b1 + 0o57) + chr(0b1000010 + 0o55) + '\x33' + chr(0b10 + 0o56) + chr(0b100101 + 0o22), 0b1000), nzTpIcepk0o8('\060' + chr(7016 - 6905) + '\x32' + chr(621 - 570) + chr(1629 - 1575), 0o10), nzTpIcepk0o8(chr(1058 - 1010) + chr(10190 - 10079) + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(49) + chr(0b1 + 0o63) + chr(550 - 496), 0b1000), nzTpIcepk0o8('\x30' + chr(111) + '\063' + '\063' + '\062', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(6757 - 6646) + '\x36' + '\x34', 0b1000), nzTpIcepk0o8('\x30' + chr(111) + '\062' + '\066' + chr(0b110101), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(657 - 608) + '\067' + chr(1828 - 1774), 64938 - 64930), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(52) + chr(0b110110), 8)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(10682 - 10571) + chr(0b100111 + 0o16) + chr(48), ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'Y'), chr(0b1100100) + chr(0b1100101) + chr(3884 - 3785) + chr(111) + chr(0b1100100) + chr(101))('\x75' + chr(0b111101 + 0o67) + chr(0b11 + 0o143) + chr(0b1110 + 0o37) + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def P9Hpx4hhzMbT(FfKOThdpoDTb, _R8IKF5IwAfX, YRX9Ch4rysP9=None, A2YPCXgFSG1t=None, uTw5CPPMOlxD=roI3spqORKae(ES5oEprVxulp(b'\x16\xae\x12\x84\xa8'), chr(100) + chr(0b1011111 + 0o6) + '\x63' + chr(878 - 767) + '\x64' + chr(101))('\x75' + chr(0b10001 + 0o143) + '\146' + chr(0b101101) + chr(0b111000)), **q5n0sHDDTy90):
A2YPCXgFSG1t = jEKHUML0AUn7.get_storage(A2YPCXgFSG1t)
if suIjIS24Zkqw(FfKOThdpoDTb, nfNqtJL5aRaY):
YRX9Ch4rysP9 = KV9ckIhroIia((jEKHUML0AUn7.get_blen_array(vPPlOXQgR3SM, YRX9Ch4rysP9) for vPPlOXQgR3SM in FfKOThdpoDTb))
else:
YRX9Ch4rysP9 = jEKHUML0AUn7.get_blen_array(FfKOThdpoDTb, YRX9Ch4rysP9)
if suIjIS24Zkqw(FfKOThdpoDTb, nfNqtJL5aRaY):
roI3spqORKae(jEKHUML0AUn7, roI3spqORKae(ES5oEprVxulp(b"\x14\xb4\x05\x86\xba\x1e\x87\xa7\x98\xc2\x1c\xb7\x08\xc0\xc9'6\xf8"), chr(0b10101 + 0o117) + chr(0b11 + 0o142) + '\x63' + chr(0b1101111) + chr(100) + chr(4317 - 4216))(chr(117) + '\164' + '\146' + '\055' + chr(0b101001 + 0o17)))(*FfKOThdpoDTb)
a1RCQZREo3Kd = ftfygxgFas5X(FfKOThdpoDTb[nzTpIcepk0o8(chr(48) + '\157' + '\060', 37334 - 37326)])
else:
a1RCQZREo3Kd = ftfygxgFas5X(FfKOThdpoDTb)
VwOu8WkJ9cpc = None
for ZlbFMSG8gCoF in bbT2xIe5pzk7(nzTpIcepk0o8(chr(0b10000 + 0o40) + chr(111) + chr(831 - 783), 8), a1RCQZREo3Kd, YRX9Ch4rysP9):
sChW4gUsXrIC = XURpmPuEWCNF(ZlbFMSG8gCoF + YRX9Ch4rysP9, a1RCQZREo3Kd)
if suIjIS24Zkqw(FfKOThdpoDTb, nfNqtJL5aRaY):
vW1vZPNUOvkW = [vPPlOXQgR3SM[ZlbFMSG8gCoF:sChW4gUsXrIC] for vPPlOXQgR3SM in FfKOThdpoDTb]
else:
vW1vZPNUOvkW = [FfKOThdpoDTb[ZlbFMSG8gCoF:sChW4gUsXrIC]]
_XdQFJpnzJor = _R8IKF5IwAfX(*vW1vZPNUOvkW)
if VwOu8WkJ9cpc is None:
VwOu8WkJ9cpc = roI3spqORKae(A2YPCXgFSG1t, uTw5CPPMOlxD)(_XdQFJpnzJor, expectedlen=a1RCQZREo3Kd, **q5n0sHDDTy90)
else:
roI3spqORKae(VwOu8WkJ9cpc, roI3spqORKae(ES5oEprVxulp(b'?\x883\xd1\xa9&\xa5\xb9\x87\xcc%\xdd'), chr(9718 - 9618) + chr(0b100011 + 0o102) + chr(0b1100011) + chr(111) + '\144' + '\145')('\165' + '\x74' + chr(102) + chr(45) + '\070'))(_XdQFJpnzJor)
return VwOu8WkJ9cpc |
cggh/scikit-allel | allel/chunked/core.py | reduce_axis | def reduce_axis(data, reducer, block_reducer, mapper=None, axis=None,
blen=None, storage=None, create='array', **kwargs):
"""Apply an operation to `data` that reduces over one or more axes."""
# setup
storage = _util.get_storage(storage)
blen = _util.get_blen_array(data, blen)
length = len(data)
# normalise axis arg
if isinstance(axis, int):
axis = (axis,)
# deal with 'out' kwarg if supplied, can arise if a chunked array is
# passed as an argument to numpy.sum(), see also
# https://github.com/cggh/scikit-allel/issues/66
kwarg_out = kwargs.pop('out', None)
if kwarg_out is not None:
raise ValueError('keyword argument "out" is not supported')
if axis is None or 0 in axis:
# two-step reduction
out = None
for i in range(0, length, blen):
j = min(i+blen, length)
block = data[i:j]
if mapper:
block = mapper(block)
res = reducer(block, axis=axis)
if out is None:
out = res
else:
out = block_reducer(out, res)
if np.isscalar(out):
return out
elif len(out.shape) == 0:
return out[()]
else:
return getattr(storage, create)(out, **kwargs)
else:
# first dimension is preserved, no need to reduce blocks
out = None
for i in range(0, length, blen):
j = min(i+blen, length)
block = data[i:j]
if mapper:
block = mapper(block)
r = reducer(block, axis=axis)
if out is None:
out = getattr(storage, create)(r, expectedlen=length, **kwargs)
else:
out.append(r)
return out | python | def reduce_axis(data, reducer, block_reducer, mapper=None, axis=None,
blen=None, storage=None, create='array', **kwargs):
"""Apply an operation to `data` that reduces over one or more axes."""
# setup
storage = _util.get_storage(storage)
blen = _util.get_blen_array(data, blen)
length = len(data)
# normalise axis arg
if isinstance(axis, int):
axis = (axis,)
# deal with 'out' kwarg if supplied, can arise if a chunked array is
# passed as an argument to numpy.sum(), see also
# https://github.com/cggh/scikit-allel/issues/66
kwarg_out = kwargs.pop('out', None)
if kwarg_out is not None:
raise ValueError('keyword argument "out" is not supported')
if axis is None or 0 in axis:
# two-step reduction
out = None
for i in range(0, length, blen):
j = min(i+blen, length)
block = data[i:j]
if mapper:
block = mapper(block)
res = reducer(block, axis=axis)
if out is None:
out = res
else:
out = block_reducer(out, res)
if np.isscalar(out):
return out
elif len(out.shape) == 0:
return out[()]
else:
return getattr(storage, create)(out, **kwargs)
else:
# first dimension is preserved, no need to reduce blocks
out = None
for i in range(0, length, blen):
j = min(i+blen, length)
block = data[i:j]
if mapper:
block = mapper(block)
r = reducer(block, axis=axis)
if out is None:
out = getattr(storage, create)(r, expectedlen=length, **kwargs)
else:
out.append(r)
return out | [
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"."
] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/chunked/core.py#L133-L185 | train | Apply an operation to data that reduces over one or more axes. | 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(1936 - 1888) + chr(0b1101111) + '\063' + chr(1525 - 1473) + '\060', 51590 - 51582), nzTpIcepk0o8(chr(0b110000) + '\157' + '\063' + '\x31' + chr(53), 0o10), nzTpIcepk0o8('\x30' + chr(4564 - 4453) + chr(245 - 190) + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(2301 - 2253) + chr(1723 - 1612) + '\066' + chr(187 - 135), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110011) + chr(54), 0b1000), nzTpIcepk0o8(chr(818 - 770) + chr(0b1101111) + chr(1716 - 1666) + chr(0b110110) + chr(0b110101), 3944 - 3936), nzTpIcepk0o8(chr(48) + chr(0b111000 + 0o67) + chr(49) + '\064' + '\x32', 52737 - 52729), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(1659 - 1608) + chr(0b100 + 0o63) + chr(54), 59325 - 59317), nzTpIcepk0o8(chr(0b1001 + 0o47) + chr(111) + chr(51) + chr(0b11100 + 0o24) + chr(48), 56204 - 56196), nzTpIcepk0o8('\x30' + chr(0b111 + 0o150) + chr(0b101 + 0o55) + chr(0b100010 + 0o22), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(7164 - 7053) + chr(50) + chr(0b110111) + chr(0b101 + 0o57), 0o10), nzTpIcepk0o8(chr(0b100001 + 0o17) + '\157' + '\064' + chr(50), 0o10), nzTpIcepk0o8(chr(0b10011 + 0o35) + chr(0b1101 + 0o142) + chr(52), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110001) + '\064' + '\064', 0o10), nzTpIcepk0o8(chr(0b110000 + 0o0) + chr(0b1101111) + '\x31', 1544 - 1536), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b101010 + 0o7) + chr(0b110000) + '\x34', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b100110 + 0o111) + chr(119 - 68) + '\x31' + chr(54), 28229 - 28221), nzTpIcepk0o8(chr(48) + chr(9452 - 9341) + chr(0b110011) + '\064' + chr(412 - 363), 0o10), nzTpIcepk0o8(chr(1264 - 1216) + chr(111) + chr(49) + chr(1286 - 1236) + '\063', 50118 - 50110), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b10010 + 0o41) + chr(659 - 609) + chr(0b111 + 0o57), 27748 - 27740), nzTpIcepk0o8(chr(0b110000) + chr(856 - 745) + '\062' + chr(0b110101) + chr(0b100110 + 0o17), 21503 - 21495), nzTpIcepk0o8(chr(48) + chr(6577 - 6466) + chr(1877 - 1826) + chr(0b110010) + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110001) + '\x31' + chr(1997 - 1943), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(2274 - 2224) + chr(459 - 408) + '\x36', ord("\x08")), nzTpIcepk0o8('\x30' + chr(1928 - 1817) + '\061' + '\063' + '\063', 15095 - 15087), nzTpIcepk0o8('\060' + chr(0b110011 + 0o74) + '\x31' + chr(0b110001 + 0o1) + chr(48), 33316 - 33308), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(657 - 607) + chr(0b110000), 4120 - 4112), nzTpIcepk0o8('\x30' + chr(111) + '\062' + '\067' + chr(0b110110), 60034 - 60026), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b11 + 0o63) + chr(0b10111 + 0o32), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(0b110001) + '\x31' + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + '\063' + '\x30' + chr(52), 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(0b1010 + 0o50) + '\x33' + '\064', 311 - 303), nzTpIcepk0o8(chr(0b1101 + 0o43) + '\157' + chr(1223 - 1172) + chr(667 - 618) + chr(55), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + '\061' + '\x35' + chr(0b100111 + 0o16), ord("\x08")), nzTpIcepk0o8(chr(0b0 + 0o60) + '\157' + '\062' + '\x35' + chr(1096 - 1041), 0o10), nzTpIcepk0o8(chr(1924 - 1876) + '\x6f' + chr(0b100111 + 0o14) + '\062' + chr(0b1101 + 0o45), ord("\x08")), nzTpIcepk0o8(chr(0b101 + 0o53) + chr(4902 - 4791) + '\062' + chr(49), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + chr(0b101001 + 0o10) + '\066' + chr(0b110001), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1001100 + 0o43) + '\x32' + chr(51) + '\x36', 8), nzTpIcepk0o8('\x30' + chr(111) + '\061' + chr(1762 - 1712) + chr(0b100 + 0o54), 8)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(1851 - 1803) + chr(0b1010011 + 0o34) + chr(2774 - 2721) + chr(0b110000), ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xce'), chr(0b101111 + 0o65) + chr(101) + chr(99) + '\157' + chr(0b1011100 + 0o10) + chr(0b111 + 0o136))('\x75' + chr(7357 - 7241) + chr(0b1000111 + 0o37) + '\x2d' + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def aUi0Z6_vSwAH(FfKOThdpoDTb, X61vDGqpC4f7, ynbRcdT3abBs, UgDcoW0t6xdm=None, JD902pvyCLH1=None, YRX9Ch4rysP9=None, A2YPCXgFSG1t=None, uTw5CPPMOlxD=roI3spqORKae(ES5oEprVxulp(b'\x81\xbfOUg'), chr(8464 - 8364) + '\145' + '\x63' + '\x6f' + chr(6258 - 6158) + chr(732 - 631))('\x75' + chr(0b1101110 + 0o6) + chr(6775 - 6673) + '\055' + chr(0b110110 + 0o2)), **q5n0sHDDTy90):
A2YPCXgFSG1t = jEKHUML0AUn7.get_storage(A2YPCXgFSG1t)
YRX9Ch4rysP9 = jEKHUML0AUn7.get_blen_array(FfKOThdpoDTb, YRX9Ch4rysP9)
a1RCQZREo3Kd = ftfygxgFas5X(FfKOThdpoDTb)
if suIjIS24Zkqw(JD902pvyCLH1, nzTpIcepk0o8):
JD902pvyCLH1 = (JD902pvyCLH1,)
XeYYHNbCogPt = q5n0sHDDTy90.uC_Yoybx7J0I(roI3spqORKae(ES5oEprVxulp(b'\x8f\xb8I'), chr(100) + chr(0b1100101) + '\x63' + chr(0b100011 + 0o114) + chr(1221 - 1121) + '\x65')('\x75' + '\164' + chr(0b110000 + 0o66) + chr(1977 - 1932) + '\070'), None)
if XeYYHNbCogPt is not None:
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'\x8b\xa8DCq\xc7\x06\xde\xa1f\xdbWi\x01o0\xee\xc3<\xa3\xd9\xf5n\xf7(p~\xd1El\xb7\xe9\xbf\x1d\xc0\xa0e\x14\xfa'), chr(0b1100100) + chr(0b1100101) + '\x63' + chr(0b1101111) + chr(1751 - 1651) + chr(0b1100101))('\x75' + '\164' + chr(0b11001 + 0o115) + chr(45) + chr(0b1001 + 0o57)))
if JD902pvyCLH1 is None or nzTpIcepk0o8('\x30' + chr(8404 - 8293) + '\060', 27822 - 27814) in JD902pvyCLH1:
VwOu8WkJ9cpc = None
for ZlbFMSG8gCoF in bbT2xIe5pzk7(nzTpIcepk0o8('\x30' + chr(7612 - 7501) + chr(0b110 + 0o52), 8), a1RCQZREo3Kd, YRX9Ch4rysP9):
sChW4gUsXrIC = XURpmPuEWCNF(ZlbFMSG8gCoF + YRX9Ch4rysP9, a1RCQZREo3Kd)
TvT0D2rIGW5A = FfKOThdpoDTb[ZlbFMSG8gCoF:sChW4gUsXrIC]
if UgDcoW0t6xdm:
TvT0D2rIGW5A = UgDcoW0t6xdm(TvT0D2rIGW5A)
_XdQFJpnzJor = X61vDGqpC4f7(TvT0D2rIGW5A, axis=JD902pvyCLH1)
if VwOu8WkJ9cpc is None:
VwOu8WkJ9cpc = _XdQFJpnzJor
else:
VwOu8WkJ9cpc = ynbRcdT3abBs(VwOu8WkJ9cpc, _XdQFJpnzJor)
if roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'\x89\xbeNW\x7f\xd9\x03\x8c'), chr(296 - 196) + chr(0b101010 + 0o73) + chr(0b1100011) + '\x6f' + '\x64' + '\145')(chr(117) + '\164' + chr(0b1100110) + chr(0b10011 + 0o32) + chr(2509 - 2453)))(VwOu8WkJ9cpc):
return VwOu8WkJ9cpc
elif ftfygxgFas5X(roI3spqORKae(VwOu8WkJ9cpc, roI3spqORKae(ES5oEprVxulp(b'\x8c\xa5_y.\x8cP\xbf\x86C\x84D'), '\x64' + chr(842 - 741) + chr(0b110 + 0o135) + chr(0b1101111) + chr(0b1100100) + '\x65')(chr(1183 - 1066) + chr(0b11010 + 0o132) + '\x66' + '\055' + chr(0b111000 + 0o0)))) == nzTpIcepk0o8('\x30' + '\157' + '\x30', 8):
return VwOu8WkJ9cpc[()]
else:
return roI3spqORKae(A2YPCXgFSG1t, uTw5CPPMOlxD)(VwOu8WkJ9cpc, **q5n0sHDDTy90)
else:
VwOu8WkJ9cpc = None
for ZlbFMSG8gCoF in bbT2xIe5pzk7(nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(48), 8), a1RCQZREo3Kd, YRX9Ch4rysP9):
sChW4gUsXrIC = XURpmPuEWCNF(ZlbFMSG8gCoF + YRX9Ch4rysP9, a1RCQZREo3Kd)
TvT0D2rIGW5A = FfKOThdpoDTb[ZlbFMSG8gCoF:sChW4gUsXrIC]
if UgDcoW0t6xdm:
TvT0D2rIGW5A = UgDcoW0t6xdm(TvT0D2rIGW5A)
LCrwg7lcbmU9 = X61vDGqpC4f7(TvT0D2rIGW5A, axis=JD902pvyCLH1)
if VwOu8WkJ9cpc is None:
VwOu8WkJ9cpc = roI3spqORKae(A2YPCXgFSG1t, uTw5CPPMOlxD)(LCrwg7lcbmU9, expectedlen=a1RCQZREo3Kd, **q5n0sHDDTy90)
else:
roI3spqORKae(VwOu8WkJ9cpc, roI3spqORKae(ES5oEprVxulp(b'\xa8\x99n\x00f\xd2%\x91\xaa{\xe9\x17'), '\144' + '\x65' + '\143' + chr(111) + chr(100) + chr(0b1100101))(chr(117) + chr(9758 - 9642) + chr(0b1100110) + chr(45) + chr(0b10100 + 0o44)))(LCrwg7lcbmU9)
return VwOu8WkJ9cpc |
cggh/scikit-allel | allel/chunked/core.py | amax | def amax(data, axis=None, mapper=None, blen=None, storage=None,
create='array', **kwargs):
"""Compute the maximum value."""
return reduce_axis(data, axis=axis, reducer=np.amax,
block_reducer=np.maximum, mapper=mapper,
blen=blen, storage=storage, create=create, **kwargs) | python | def amax(data, axis=None, mapper=None, blen=None, storage=None,
create='array', **kwargs):
"""Compute the maximum value."""
return reduce_axis(data, axis=axis, reducer=np.amax,
block_reducer=np.maximum, mapper=mapper,
blen=blen, storage=storage, create=create, **kwargs) | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/chunked/core.py#L188-L193 | train | Compute the maximum 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(48) + chr(0b1101111) + chr(0b110000 + 0o4) + '\x34', 0o10), nzTpIcepk0o8(chr(1469 - 1421) + '\x6f' + chr(69 - 18) + chr(55) + chr(0b110101 + 0o2), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x33' + chr(0b10001 + 0o40), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110011) + chr(55) + chr(54), 48140 - 48132), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b1101 + 0o45) + chr(0b100000 + 0o25) + '\061', 25624 - 25616), nzTpIcepk0o8('\x30' + chr(2718 - 2607) + chr(0b110011) + chr(0b100000 + 0o21) + chr(880 - 830), 0o10), nzTpIcepk0o8(chr(1865 - 1817) + '\157' + chr(1495 - 1445) + '\x35' + chr(0b101100 + 0o10), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(0b110010) + '\063' + chr(1513 - 1463), 46444 - 46436), nzTpIcepk0o8(chr(602 - 554) + chr(111) + '\062' + chr(0b101001 + 0o13) + chr(1549 - 1499), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(54) + '\067', 0o10), nzTpIcepk0o8('\x30' + chr(7608 - 7497) + '\063' + chr(0b110011) + '\x30', ord("\x08")), nzTpIcepk0o8(chr(0b100010 + 0o16) + chr(0b1000 + 0o147) + '\x32' + '\067' + chr(979 - 924), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + '\062' + chr(0b110101) + chr(1452 - 1402), 0o10), nzTpIcepk0o8(chr(48) + chr(3889 - 3778) + chr(567 - 517) + chr(2293 - 2241) + chr(0b110001), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b10000 + 0o41) + chr(0b110111) + chr(50), 8671 - 8663), nzTpIcepk0o8(chr(1335 - 1287) + chr(0b1101111) + '\063' + '\064' + chr(0b110010 + 0o1), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(4957 - 4846) + chr(0b110010 + 0o1), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(51) + chr(0b110110) + '\060', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(88 - 38) + '\062' + chr(0b101110 + 0o7), ord("\x08")), nzTpIcepk0o8(chr(1648 - 1600) + chr(0b1101111) + chr(0b10011 + 0o36) + '\062' + '\x36', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101001 + 0o6) + chr(49) + chr(0b10110 + 0o32) + '\063', 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(1319 - 1269) + chr(0b10 + 0o64) + chr(0b110000), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1001101 + 0o42) + '\062' + '\x30' + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(50) + '\x36' + '\x33', 0b1000), nzTpIcepk0o8(chr(48) + chr(10703 - 10592) + '\x33' + '\061' + chr(1707 - 1658), 338 - 330), nzTpIcepk0o8('\x30' + chr(0b1110 + 0o141) + chr(2009 - 1958) + '\061' + chr(365 - 311), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110010) + '\x35', 4366 - 4358), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x32' + chr(152 - 100) + '\067', 0o10), nzTpIcepk0o8(chr(592 - 544) + '\x6f' + '\x32' + chr(0b110101) + chr(310 - 259), ord("\x08")), nzTpIcepk0o8(chr(0b10110 + 0o32) + chr(1927 - 1816) + chr(1581 - 1531) + '\061' + chr(0b110111), 0o10), nzTpIcepk0o8(chr(0b100110 + 0o12) + '\x6f' + chr(406 - 355) + '\x32' + chr(53), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(5416 - 5305) + '\x31' + chr(2466 - 2414) + '\x30', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b1000 + 0o53) + chr(173 - 122) + chr(0b11111 + 0o23), 56420 - 56412), nzTpIcepk0o8('\x30' + chr(10967 - 10856) + chr(360 - 305) + chr(0b110010), 23476 - 23468), nzTpIcepk0o8(chr(530 - 482) + '\x6f' + '\x31' + chr(741 - 689) + '\x30', 8), nzTpIcepk0o8(chr(1599 - 1551) + chr(0b1101111) + '\x33' + chr(0b110011) + '\066', 0o10), nzTpIcepk0o8(chr(0b11101 + 0o23) + '\157' + '\x32' + chr(2010 - 1960), 0o10), nzTpIcepk0o8(chr(1185 - 1137) + chr(111) + chr(0b110011) + '\x32' + chr(50), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(6168 - 6057) + chr(0b11 + 0o60) + chr(0b110101) + chr(67 - 14), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\065' + chr(0b110111), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + '\157' + chr(0b110101) + chr(48), ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\n'), '\x64' + chr(0b1100101) + chr(99) + chr(5433 - 5322) + '\144' + chr(0b1100101))(chr(0b1100000 + 0o25) + chr(116) + '\146' + chr(1645 - 1600) + chr(931 - 875)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def o3SuW33uOWrs(FfKOThdpoDTb, JD902pvyCLH1=None, UgDcoW0t6xdm=None, YRX9Ch4rysP9=None, A2YPCXgFSG1t=None, uTw5CPPMOlxD=roI3spqORKae(ES5oEprVxulp(b'E\x8dk\x9f\xd0'), '\144' + chr(101) + chr(6066 - 5967) + '\157' + chr(7902 - 7802) + '\x65')(chr(0b1110101) + chr(0b1001101 + 0o47) + '\x66' + chr(1884 - 1839) + '\070'), **q5n0sHDDTy90):
return aUi0Z6_vSwAH(FfKOThdpoDTb, axis=JD902pvyCLH1, reducer=roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'E\x92x\x86'), '\x64' + '\x65' + chr(0b100000 + 0o103) + '\157' + chr(100) + chr(101))('\x75' + '\x74' + '\x66' + chr(0b101101) + chr(551 - 495))), block_reducer=roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'b\xa0O\xaa\xf8\xf2\xef\xdf\xeeX\x89\xdb'), chr(9559 - 9459) + chr(0b101110 + 0o67) + chr(99) + chr(0b1101111) + chr(0b1100100) + chr(0b10101 + 0o120))(chr(0b1010111 + 0o36) + chr(0b100 + 0o160) + chr(0b1000 + 0o136) + chr(0b10101 + 0o30) + '\x38')), mapper=UgDcoW0t6xdm, blen=YRX9Ch4rysP9, storage=A2YPCXgFSG1t, create=uTw5CPPMOlxD, **q5n0sHDDTy90) |
cggh/scikit-allel | allel/chunked/core.py | amin | def amin(data, axis=None, mapper=None, blen=None, storage=None,
create='array', **kwargs):
"""Compute the minimum value."""
return reduce_axis(data, axis=axis, reducer=np.amin,
block_reducer=np.minimum, mapper=mapper,
blen=blen, storage=storage, create=create, **kwargs) | python | def amin(data, axis=None, mapper=None, blen=None, storage=None,
create='array', **kwargs):
"""Compute the minimum value."""
return reduce_axis(data, axis=axis, reducer=np.amin,
block_reducer=np.minimum, mapper=mapper,
blen=blen, storage=storage, create=create, **kwargs) | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/chunked/core.py#L196-L201 | train | Compute the minimum 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(1799 - 1751) + '\157' + '\x31' + chr(51) + chr(0b100100 + 0o22), 2143 - 2135), nzTpIcepk0o8(chr(48) + chr(5923 - 5812) + chr(50) + chr(51) + '\x32', 44756 - 44748), nzTpIcepk0o8('\x30' + '\157' + chr(0b110011) + '\x32' + chr(431 - 376), 42707 - 42699), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x33' + '\063' + chr(1614 - 1564), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110010) + '\064' + chr(0b110011), 0o10), nzTpIcepk0o8(chr(1966 - 1918) + chr(111) + chr(0b1010 + 0o47) + '\061' + chr(0b110100), 3631 - 3623), nzTpIcepk0o8(chr(0b100100 + 0o14) + '\157' + chr(0b10010 + 0o44) + chr(0b110100), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(49) + '\062' + chr(1767 - 1712), 0o10), nzTpIcepk0o8(chr(0b101111 + 0o1) + chr(111) + chr(0b1101 + 0o46) + '\060' + '\067', 10223 - 10215), nzTpIcepk0o8(chr(0b110000 + 0o0) + '\x6f' + chr(1908 - 1859) + chr(0b110100) + chr(2064 - 2014), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + '\x31' + chr(0b1011 + 0o50) + '\063', 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(50) + chr(0b1111 + 0o45) + chr(51), 8), nzTpIcepk0o8(chr(48 - 0) + chr(0b1101111) + chr(0b110010) + chr(55) + '\x36', ord("\x08")), nzTpIcepk0o8(chr(556 - 508) + '\157' + chr(0b110001) + chr(944 - 892) + chr(1023 - 972), 11563 - 11555), nzTpIcepk0o8(chr(1855 - 1807) + '\x6f' + '\062' + chr(49) + '\066', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b111110 + 0o61) + chr(0b110000 + 0o3) + '\x30' + chr(0b100010 + 0o25), 8), nzTpIcepk0o8(chr(0b10110 + 0o32) + chr(8438 - 8327) + '\062' + chr(0b100001 + 0o22) + '\x30', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(8194 - 8083) + chr(49) + chr(0b110110) + '\x32', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(50) + chr(0b110001), ord("\x08")), nzTpIcepk0o8(chr(0b10010 + 0o36) + '\157' + chr(2232 - 2182) + chr(52) + '\x31', 31612 - 31604), nzTpIcepk0o8(chr(48) + '\x6f' + chr(562 - 513) + chr(590 - 542) + chr(50), 26627 - 26619), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b100011 + 0o20) + chr(0b1 + 0o64) + chr(822 - 773), 39461 - 39453), nzTpIcepk0o8(chr(48) + chr(0b111011 + 0o64) + chr(913 - 862) + chr(0b110000) + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(198 - 148) + chr(1350 - 1298) + '\067', ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + '\x31' + '\060' + '\060', ord("\x08")), nzTpIcepk0o8(chr(1668 - 1620) + chr(111) + chr(51) + chr(0b110100) + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(0b101011 + 0o5) + chr(111) + '\063' + chr(0b110010) + chr(49), 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(1120 - 1070) + '\x33' + chr(0b110100), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110001) + chr(2750 - 2697) + chr(0b11 + 0o57), 0o10), nzTpIcepk0o8(chr(1515 - 1467) + chr(111) + chr(0b10000 + 0o41) + '\065', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b10101 + 0o132) + '\062' + chr(0b110010), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110011) + chr(1416 - 1363) + chr(0b110001), 8), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(52), 34668 - 34660), nzTpIcepk0o8(chr(2016 - 1968) + '\157' + '\x33' + '\062' + chr(0b1001 + 0o50), 8), nzTpIcepk0o8(chr(0b110000) + chr(0b10 + 0o155) + chr(0b1111 + 0o46) + chr(1901 - 1848), 0b1000), nzTpIcepk0o8(chr(0b10111 + 0o31) + chr(0b1101111) + chr(667 - 616) + '\060' + chr(0b10011 + 0o40), 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(0b10011 + 0o40) + chr(637 - 584) + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(0b10110 + 0o32) + chr(8220 - 8109) + chr(0b100110 + 0o14) + '\065' + chr(0b110011), 0o10), nzTpIcepk0o8(chr(1603 - 1555) + chr(0b1101111) + chr(0b11100 + 0o27) + '\065' + '\063', 0o10), nzTpIcepk0o8(chr(1631 - 1583) + chr(111) + chr(50) + chr(1778 - 1729) + '\x36', 8)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(0b1101100 + 0o3) + chr(53) + chr(204 - 156), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'p'), '\x64' + chr(5676 - 5575) + chr(0b11000 + 0o113) + chr(0b1101111) + '\144' + '\145')(chr(117) + chr(0b1101 + 0o147) + chr(0b1100110) + '\055' + chr(0b11110 + 0o32)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def RYdkBUje3R81(FfKOThdpoDTb, JD902pvyCLH1=None, UgDcoW0t6xdm=None, YRX9Ch4rysP9=None, A2YPCXgFSG1t=None, uTw5CPPMOlxD=roI3spqORKae(ES5oEprVxulp(b'?\xe8\xa5\xbb\xda'), chr(100) + chr(714 - 613) + '\x63' + chr(6446 - 6335) + chr(0b1100100) + chr(0b1100101))(chr(0b1000110 + 0o57) + '\x74' + chr(102) + '\055' + chr(0b111000)), **q5n0sHDDTy90):
return aUi0Z6_vSwAH(FfKOThdpoDTb, axis=JD902pvyCLH1, reducer=roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'?\xf7\xbe\xb4'), chr(100) + chr(0b1100101) + chr(99) + chr(111) + chr(9132 - 9032) + chr(7183 - 7082))('\165' + '\164' + chr(0b10 + 0o144) + chr(0b101 + 0o50) + '\x38')), block_reducer=roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'(\xce\xbd\xbb\x92&\x06d\x8f\x17n\xc7'), chr(0b1100100) + chr(0b1100101) + chr(0b1100011) + chr(2836 - 2725) + '\x64' + '\145')(chr(117) + chr(9038 - 8922) + chr(0b11101 + 0o111) + chr(45) + chr(0b1011 + 0o55))), mapper=UgDcoW0t6xdm, blen=YRX9Ch4rysP9, storage=A2YPCXgFSG1t, create=uTw5CPPMOlxD, **q5n0sHDDTy90) |
cggh/scikit-allel | allel/chunked/core.py | asum | def asum(data, axis=None, mapper=None, blen=None, storage=None,
create='array', **kwargs):
"""Compute the sum."""
return reduce_axis(data, axis=axis, reducer=np.sum,
block_reducer=np.add, mapper=mapper,
blen=blen, storage=storage, create=create, **kwargs) | python | def asum(data, axis=None, mapper=None, blen=None, storage=None,
create='array', **kwargs):
"""Compute the sum."""
return reduce_axis(data, axis=axis, reducer=np.sum,
block_reducer=np.add, mapper=mapper,
blen=blen, storage=storage, create=create, **kwargs) | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/chunked/core.py#L205-L210 | train | Compute the sum. | 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(11488 - 11377) + chr(1044 - 994) + '\063', 0b1000), nzTpIcepk0o8('\x30' + chr(9328 - 9217) + chr(0b101011 + 0o10) + chr(353 - 302) + chr(0b1010 + 0o52), 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(0b100001 + 0o25) + chr(0b100110 + 0o17), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(9551 - 9440) + chr(51) + chr(0b110111) + '\063', ord("\x08")), nzTpIcepk0o8(chr(0b101100 + 0o4) + '\157' + '\x32' + chr(0b110101 + 0o0) + '\062', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1100011 + 0o14) + '\062' + chr(0b10101 + 0o34) + '\x33', 0o10), nzTpIcepk0o8(chr(48) + chr(0b101010 + 0o105) + '\061' + '\065' + chr(0b110011), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b10000 + 0o137) + chr(0b10100 + 0o36) + chr(0b110010) + chr(0b110001 + 0o1), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110011) + chr(0b110100) + '\x32', ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + chr(402 - 353) + '\x30' + chr(52), 0o10), nzTpIcepk0o8(chr(0b100110 + 0o12) + chr(111) + chr(50) + chr(1612 - 1561) + '\x31', 35934 - 35926), nzTpIcepk0o8('\x30' + chr(3332 - 3221) + '\x31' + '\062', 56479 - 56471), nzTpIcepk0o8(chr(0b110000) + chr(0b10010 + 0o135) + '\063', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b11010 + 0o30) + '\x30', 0o10), nzTpIcepk0o8('\x30' + chr(12017 - 11906) + chr(0b11 + 0o56) + '\065' + chr(2503 - 2450), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\061' + chr(0b100 + 0o61) + '\061', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(9146 - 9035) + chr(0b110011) + chr(55) + chr(0b110001), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101101 + 0o2) + '\x37' + '\x30', 42789 - 42781), nzTpIcepk0o8('\x30' + '\157' + chr(2195 - 2145) + chr(0b110111) + '\061', 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\061' + chr(0b11010 + 0o30) + chr(0b110101), 0o10), nzTpIcepk0o8('\060' + '\x6f' + '\061' + '\x34' + chr(635 - 580), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b100110 + 0o111) + '\x32' + chr(51) + chr(48), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(2488 - 2437) + chr(0b110011) + chr(251 - 196), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(53), 0b1000), nzTpIcepk0o8(chr(60 - 12) + chr(0b110011 + 0o74) + chr(0b11101 + 0o26) + '\x36' + chr(1413 - 1363), 39392 - 39384), nzTpIcepk0o8(chr(0b110000) + chr(0b1001110 + 0o41) + chr(0b1 + 0o60) + chr(0b10011 + 0o44) + chr(55), 62700 - 62692), nzTpIcepk0o8(chr(1336 - 1288) + chr(5190 - 5079) + '\062' + '\x37' + chr(2187 - 2134), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(467 - 356) + chr(0b110001) + chr(0b1000 + 0o51) + '\x35', ord("\x08")), nzTpIcepk0o8(chr(0b101 + 0o53) + chr(3784 - 3673) + chr(0b1010 + 0o50) + chr(51) + '\062', 0b1000), nzTpIcepk0o8(chr(1624 - 1576) + '\x6f' + '\x32' + chr(0b1111 + 0o42) + chr(1348 - 1298), 22571 - 22563), nzTpIcepk0o8('\x30' + chr(111) + chr(51) + chr(0b110101) + chr(0b1011 + 0o52), 0o10), nzTpIcepk0o8(chr(0b1001 + 0o47) + '\x6f' + chr(725 - 675) + chr(2356 - 2304) + chr(55), ord("\x08")), nzTpIcepk0o8(chr(1900 - 1852) + chr(111) + chr(0b110011) + chr(0b100 + 0o54) + chr(0b110000), 0b1000), nzTpIcepk0o8(chr(669 - 621) + chr(0b100001 + 0o116) + chr(53) + '\064', 0o10), nzTpIcepk0o8('\060' + chr(0b100000 + 0o117) + chr(1434 - 1381) + chr(2061 - 2007), ord("\x08")), nzTpIcepk0o8('\060' + chr(9667 - 9556) + chr(0b100011 + 0o22) + chr(0b100010 + 0o23), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b101110 + 0o5) + chr(0b110001) + chr(51), 0o10), nzTpIcepk0o8(chr(0b101111 + 0o1) + chr(0b1101111) + chr(0b100100 + 0o16) + chr(52), ord("\x08")), nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(111) + chr(0b10 + 0o57) + chr(50) + chr(755 - 704), 24453 - 24445), nzTpIcepk0o8(chr(163 - 115) + '\157' + chr(2157 - 2108) + '\061' + '\061', ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + chr(111) + '\065' + chr(690 - 642), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'='), chr(0b111010 + 0o52) + '\145' + chr(0b1100011) + '\157' + chr(8454 - 8354) + '\145')('\165' + chr(0b1110000 + 0o4) + '\x66' + '\055' + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def g6XoaL3jCShd(FfKOThdpoDTb, JD902pvyCLH1=None, UgDcoW0t6xdm=None, YRX9Ch4rysP9=None, A2YPCXgFSG1t=None, uTw5CPPMOlxD=roI3spqORKae(ES5oEprVxulp(b'r\xaeG\x9a\xd3'), '\144' + chr(8684 - 8583) + '\143' + '\157' + '\144' + '\145')('\x75' + chr(8915 - 8799) + chr(0b1001011 + 0o33) + '\055' + chr(3004 - 2948)), **q5n0sHDDTy90):
return aUi0Z6_vSwAH(FfKOThdpoDTb, axis=JD902pvyCLH1, reducer=roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b"|\xbfY\xb8\x92\xcf'\xf8\xa3\x1b\xf5\\"), chr(0b1010110 + 0o16) + chr(101) + chr(0b1100011) + chr(0b1001100 + 0o43) + '\x64' + chr(0b1100101))(chr(0b11111 + 0o126) + chr(0b1110100) + chr(0b1100110) + '\x2d' + chr(0b111000))), block_reducer=roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'f\xefd\x9f\xc3\xf8"\xe3\xa6"\xdan'), '\144' + chr(0b1100101) + '\x63' + chr(0b1100110 + 0o11) + '\x64' + '\x65')(chr(0b1110101) + '\164' + chr(5775 - 5673) + chr(45) + chr(56))), mapper=UgDcoW0t6xdm, blen=YRX9Ch4rysP9, storage=A2YPCXgFSG1t, create=uTw5CPPMOlxD, **q5n0sHDDTy90) |
cggh/scikit-allel | allel/chunked/core.py | count_nonzero | def count_nonzero(data, mapper=None, blen=None, storage=None,
create='array', **kwargs):
"""Count the number of non-zero elements."""
return reduce_axis(data, reducer=np.count_nonzero,
block_reducer=np.add, mapper=mapper,
blen=blen, storage=storage, create=create, **kwargs) | python | def count_nonzero(data, mapper=None, blen=None, storage=None,
create='array', **kwargs):
"""Count the number of non-zero elements."""
return reduce_axis(data, reducer=np.count_nonzero,
block_reducer=np.add, mapper=mapper,
blen=blen, storage=storage, create=create, **kwargs) | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/chunked/core.py#L213-L218 | train | Count the number of non - zero 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(chr(0b11 + 0o55) + chr(8216 - 8105) + '\x33' + chr(55) + chr(82 - 33), 64134 - 64126), nzTpIcepk0o8(chr(996 - 948) + chr(0b110111 + 0o70) + '\062' + chr(0b110111) + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(2215 - 2167) + chr(6901 - 6790) + chr(51) + '\060' + chr(49), 25248 - 25240), nzTpIcepk0o8(chr(0b110000) + chr(11815 - 11704) + chr(49) + chr(2864 - 2809) + chr(1822 - 1771), 0b1000), nzTpIcepk0o8(chr(1800 - 1752) + chr(0b1101111) + '\x32' + chr(0b100000 + 0o21) + chr(0b110011), 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(0b111 + 0o54) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(1475 - 1427) + chr(111) + chr(49) + chr(49) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(1188 - 1140) + chr(0b1101111) + chr(49) + chr(2666 - 2614) + chr(0b110111), 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(1511 - 1462) + '\064' + chr(161 - 108), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b100101 + 0o14) + chr(51) + chr(0b1001 + 0o52), 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(1011 - 961) + chr(0b10110 + 0o34) + chr(0b11010 + 0o26), 3063 - 3055), nzTpIcepk0o8('\x30' + '\x6f' + '\063' + chr(2455 - 2404), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(497 - 446) + '\067' + chr(524 - 476), ord("\x08")), nzTpIcepk0o8(chr(0b100110 + 0o12) + chr(0b1001 + 0o146) + chr(2148 - 2099) + chr(53) + chr(629 - 577), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + '\063' + chr(51) + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110000 + 0o2) + chr(49) + '\x34', ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(1209 - 1157) + '\061', ord("\x08")), nzTpIcepk0o8(chr(922 - 874) + '\x6f' + chr(50) + '\061' + '\x35', 24411 - 24403), nzTpIcepk0o8('\x30' + chr(111) + '\x32' + chr(0b11100 + 0o30) + '\x33', 12890 - 12882), nzTpIcepk0o8(chr(48) + chr(0b110000 + 0o77) + chr(0b101010 + 0o12), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(1887 - 1837) + '\x32' + chr(1984 - 1936), 8), nzTpIcepk0o8('\060' + chr(111) + chr(1814 - 1764) + '\066', 61953 - 61945), nzTpIcepk0o8('\060' + chr(2034 - 1923) + '\065' + chr(445 - 395), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(51) + chr(0b110001) + '\x30', ord("\x08")), nzTpIcepk0o8(chr(729 - 681) + chr(0b1100000 + 0o17) + chr(1883 - 1832) + chr(0b110011) + chr(645 - 593), ord("\x08")), nzTpIcepk0o8(chr(0b110000 + 0o0) + '\157' + chr(0b110010) + '\x30' + chr(0b110100), 0b1000), nzTpIcepk0o8('\060' + chr(0b1010010 + 0o35) + chr(0b101011 + 0o6) + chr(0b110000) + chr(1863 - 1810), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(4134 - 4023) + '\x31' + chr(0b10 + 0o64) + chr(54), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(843 - 793) + chr(52) + '\064', 887 - 879), nzTpIcepk0o8('\x30' + chr(8453 - 8342) + chr(591 - 536) + chr(0b110000), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(52) + chr(0b111 + 0o51), 63363 - 63355), nzTpIcepk0o8(chr(0b100010 + 0o16) + chr(8176 - 8065) + '\x33' + chr(1562 - 1507) + chr(0b11100 + 0o33), 56395 - 56387), nzTpIcepk0o8(chr(1513 - 1465) + '\x6f' + chr(51) + '\064' + chr(0b110100), 0o10), nzTpIcepk0o8(chr(0b10101 + 0o33) + '\157' + chr(54) + chr(0b110001), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(417 - 306) + chr(0b100010 + 0o20) + chr(0b110011), 34036 - 34028), nzTpIcepk0o8(chr(1395 - 1347) + chr(9654 - 9543) + chr(1523 - 1470) + chr(0b101111 + 0o3), 8), nzTpIcepk0o8('\060' + chr(7565 - 7454) + chr(2468 - 2417) + chr(671 - 623) + '\065', 59650 - 59642), nzTpIcepk0o8(chr(0b1010 + 0o46) + chr(0b1011001 + 0o26) + '\x32' + '\065' + chr(0b110111), 0o10), nzTpIcepk0o8('\x30' + chr(0b100110 + 0o111) + '\061' + chr(49) + chr(53), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(11223 - 11112) + '\x33' + chr(0b11101 + 0o24) + chr(50), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + chr(0b1011010 + 0o25) + chr(53) + '\060', ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xd7'), chr(0b1100100) + chr(101) + chr(0b1100011) + chr(0b100000 + 0o117) + '\144' + chr(101))(chr(117) + chr(6602 - 6486) + chr(5991 - 5889) + chr(0b101101) + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def p21t5fNwtRJY(FfKOThdpoDTb, UgDcoW0t6xdm=None, YRX9Ch4rysP9=None, A2YPCXgFSG1t=None, uTw5CPPMOlxD=roI3spqORKae(ES5oEprVxulp(b'\x98\xca\xb3\x1a\xf2'), chr(0b1100100) + chr(1760 - 1659) + '\x63' + '\157' + chr(0b110110 + 0o56) + chr(9782 - 9681))('\x75' + '\x74' + '\146' + chr(0b0 + 0o55) + chr(0b111000)), **q5n0sHDDTy90):
return aUi0Z6_vSwAH(FfKOThdpoDTb, reducer=roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'\x9a\xd7\xb4\x15\xffC"\x08\x0b!\xf5i\x97'), '\144' + chr(0b1100100 + 0o1) + chr(0b1100011) + chr(1115 - 1004) + chr(1539 - 1439) + chr(0b111 + 0o136))(chr(6040 - 5923) + chr(0b1101010 + 0o12) + chr(0b100100 + 0o102) + '\055' + chr(0b101100 + 0o14))), block_reducer=roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'\x8c\x8b\x90\x1f\xe2o\x05\x16!=\xd3\x7f'), chr(100) + chr(0b1100101) + chr(0b100111 + 0o74) + '\x6f' + '\x64' + chr(1128 - 1027))('\165' + chr(116) + '\x66' + chr(0b1011 + 0o42) + chr(0b111000))), mapper=UgDcoW0t6xdm, blen=YRX9Ch4rysP9, storage=A2YPCXgFSG1t, create=uTw5CPPMOlxD, **q5n0sHDDTy90) |
cggh/scikit-allel | allel/chunked/core.py | compress | def compress(condition, data, axis=0, out=None, blen=None, storage=None, create='array',
**kwargs):
"""Return selected slices of an array along given axis."""
# setup
if out is not None:
# argument is only there for numpy API compatibility
raise NotImplementedError('out argument is not supported')
storage = _util.get_storage(storage)
blen = _util.get_blen_array(data, blen)
length = len(data)
nnz = count_nonzero(condition)
if axis == 0:
_util.check_equal_length(data, condition)
# block iteration
out = None
for i in range(0, length, blen):
j = min(i+blen, length)
bcond = np.asarray(condition[i:j])
# don't access any data unless we have to
if np.any(bcond):
block = np.asarray(data[i:j])
res = np.compress(bcond, block, axis=0)
if out is None:
out = getattr(storage, create)(res, expectedlen=nnz, **kwargs)
else:
out.append(res)
return out
elif axis == 1:
# block iteration
out = None
condition = np.asanyarray(condition)
for i in range(0, length, blen):
j = min(i+blen, length)
block = np.asarray(data[i:j])
res = np.compress(condition, block, axis=1)
if out is None:
out = getattr(storage, create)(res, expectedlen=length,
**kwargs)
else:
out.append(res)
return out
else:
raise NotImplementedError('axis not supported: %s' % axis) | python | def compress(condition, data, axis=0, out=None, blen=None, storage=None, create='array',
**kwargs):
"""Return selected slices of an array along given axis."""
# setup
if out is not None:
# argument is only there for numpy API compatibility
raise NotImplementedError('out argument is not supported')
storage = _util.get_storage(storage)
blen = _util.get_blen_array(data, blen)
length = len(data)
nnz = count_nonzero(condition)
if axis == 0:
_util.check_equal_length(data, condition)
# block iteration
out = None
for i in range(0, length, blen):
j = min(i+blen, length)
bcond = np.asarray(condition[i:j])
# don't access any data unless we have to
if np.any(bcond):
block = np.asarray(data[i:j])
res = np.compress(bcond, block, axis=0)
if out is None:
out = getattr(storage, create)(res, expectedlen=nnz, **kwargs)
else:
out.append(res)
return out
elif axis == 1:
# block iteration
out = None
condition = np.asanyarray(condition)
for i in range(0, length, blen):
j = min(i+blen, length)
block = np.asarray(data[i:j])
res = np.compress(condition, block, axis=1)
if out is None:
out = getattr(storage, create)(res, expectedlen=length,
**kwargs)
else:
out.append(res)
return out
else:
raise NotImplementedError('axis not supported: %s' % axis) | [
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"axis",
"."
] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/chunked/core.py#L221-L270 | train | Return selected slices of an array along given axis. | 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(0b1101100 + 0o3) + '\061' + '\x35' + chr(54), ord("\x08")), nzTpIcepk0o8(chr(0b100000 + 0o20) + chr(0b101 + 0o152) + chr(0b110001 + 0o0) + '\x34' + '\063', 59100 - 59092), nzTpIcepk0o8(chr(0b11110 + 0o22) + chr(111) + chr(0b10111 + 0o34) + chr(0b101101 + 0o12) + chr(0b110100 + 0o2), ord("\x08")), nzTpIcepk0o8(chr(0b11000 + 0o30) + chr(111) + chr(1002 - 952) + chr(0b1111 + 0o41) + '\x35', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b101110 + 0o101) + '\061' + chr(0b110010) + chr(0b1011 + 0o45), 64892 - 64884), nzTpIcepk0o8(chr(0b110000 + 0o0) + chr(111) + chr(1226 - 1175) + chr(0b1110 + 0o44) + chr(48), 40322 - 40314), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\061' + chr(51) + chr(48), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + '\063' + chr(578 - 528) + chr(54), 48214 - 48206), nzTpIcepk0o8(chr(0b100100 + 0o14) + chr(111) + '\x32' + '\x32' + chr(2270 - 2215), 28958 - 28950), nzTpIcepk0o8(chr(2288 - 2240) + chr(6200 - 6089) + '\062', 53084 - 53076), nzTpIcepk0o8(chr(0b1001 + 0o47) + chr(111) + '\062' + '\x31' + chr(0b101010 + 0o10), 0b1000), nzTpIcepk0o8(chr(1687 - 1639) + '\157' + chr(54) + '\x30', 15227 - 15219), nzTpIcepk0o8(chr(48) + chr(0b1001101 + 0o42) + chr(55), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(8992 - 8881) + chr(50) + '\065' + '\064', ord("\x08")), nzTpIcepk0o8(chr(86 - 38) + chr(0b1101111) + '\061' + chr(2555 - 2500) + chr(0b100010 + 0o23), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(5968 - 5857) + chr(0b110001) + '\x37', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110011) + chr(0b11101 + 0o27) + chr(0b110000), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + chr(0b10001 + 0o42) + chr(0b11111 + 0o23) + '\x35', 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(2434 - 2381) + chr(0b10100 + 0o42), 0b1000), nzTpIcepk0o8(chr(0b100001 + 0o17) + chr(111) + '\062' + chr(2675 - 2622) + '\x32', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1010110 + 0o31) + chr(49) + chr(0b100101 + 0o14) + '\x30', 0o10), nzTpIcepk0o8(chr(0b101000 + 0o10) + chr(111) + chr(538 - 487) + chr(0b10000 + 0o47) + '\067', 42201 - 42193), nzTpIcepk0o8(chr(169 - 121) + chr(0b1101111) + chr(0b110001) + '\061' + '\063', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110010) + chr(859 - 811) + chr(0b100100 + 0o16), 0o10), nzTpIcepk0o8(chr(0b11101 + 0o23) + chr(3019 - 2908) + chr(0b101111 + 0o3) + chr(0b10010 + 0o37) + chr(1256 - 1208), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1000110 + 0o51) + chr(477 - 427) + '\060' + chr(0b1111 + 0o44), 0o10), nzTpIcepk0o8(chr(0b11100 + 0o24) + '\x6f' + chr(0b110 + 0o55) + chr(50) + chr(48), 8), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(1215 - 1166) + chr(102 - 52) + '\063', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x31' + '\x36' + chr(1110 - 1060), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110001) + chr(0b110000) + chr(0b110011), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b110010 + 0o75) + chr(0b1000 + 0o56) + chr(0b101010 + 0o13), 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110001) + chr(54) + chr(0b11000 + 0o30), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + '\x36' + chr(2185 - 2135), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(2493 - 2382) + chr(0b110001) + chr(0b110000 + 0o0) + '\065', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b111110 + 0o61) + chr(0b110010) + '\x30' + chr(190 - 142), 0b1000), nzTpIcepk0o8(chr(2080 - 2032) + chr(0b1001 + 0o146) + '\x33' + '\x35' + chr(0b110100 + 0o1), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(49) + '\061' + chr(0b10111 + 0o31), 8), nzTpIcepk0o8(chr(48) + chr(0b1010 + 0o145) + chr(52) + chr(109 - 56), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(4329 - 4218) + chr(2193 - 2142) + '\x35' + '\x37', 53054 - 53046), nzTpIcepk0o8(chr(171 - 123) + chr(0b1101010 + 0o5) + '\x33' + '\x37' + '\065', 7892 - 7884)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(0b0 + 0o157) + chr(0b110101) + chr(48), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'@'), chr(0b11001 + 0o113) + chr(101) + chr(0b1011011 + 0o10) + '\x6f' + chr(100) + chr(101))(chr(0b111110 + 0o67) + chr(0b10111 + 0o135) + '\x66' + '\x2d' + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def jx3TPOy_L63w(ihXi_REa_8XA, FfKOThdpoDTb, JD902pvyCLH1=nzTpIcepk0o8('\x30' + chr(9914 - 9803) + '\060', 0b1000), VwOu8WkJ9cpc=None, YRX9Ch4rysP9=None, A2YPCXgFSG1t=None, uTw5CPPMOlxD=roI3spqORKae(ES5oEprVxulp(b'\x0f\x11\x8c\xe4)'), chr(2342 - 2242) + chr(0b101100 + 0o71) + '\x63' + '\157' + chr(0b1100100) + chr(101))(chr(0b1110101) + '\164' + chr(102) + chr(1845 - 1800) + chr(893 - 837)), **q5n0sHDDTy90):
if VwOu8WkJ9cpc is not None:
raise Y1otPTwLRJvi(roI3spqORKae(ES5oEprVxulp(b"\x01\x16\x8a\xa51\xa2?\xa3\xfag\xe4D'\xc5\x0e/\x8e\xbaZ\x8a;\x8a;\xf2\xe7\xf1\xa46\x16"), chr(0b11101 + 0o107) + chr(101) + '\143' + chr(111) + chr(0b1100100) + '\145')('\x75' + chr(0b1110100) + '\x66' + chr(0b101 + 0o50) + chr(56)))
A2YPCXgFSG1t = jEKHUML0AUn7.get_storage(A2YPCXgFSG1t)
YRX9Ch4rysP9 = jEKHUML0AUn7.get_blen_array(FfKOThdpoDTb, YRX9Ch4rysP9)
a1RCQZREo3Kd = ftfygxgFas5X(FfKOThdpoDTb)
YnB3_Prfmdpu = p21t5fNwtRJY(ihXi_REa_8XA)
if JD902pvyCLH1 == nzTpIcepk0o8('\060' + '\x6f' + '\060', 8):
roI3spqORKae(jEKHUML0AUn7, roI3spqORKae(ES5oEprVxulp(b'\r\x0b\x9b\xe6;\x8f=\xa7\xe2c\xe6ok\xc9\x13h\x94\xbd'), chr(100) + chr(0b1100001 + 0o4) + chr(99) + chr(906 - 795) + chr(0b1100100) + chr(0b1100101))(chr(117) + chr(10176 - 10060) + '\x66' + chr(0b101101 + 0o0) + '\070'))(FfKOThdpoDTb, ihXi_REa_8XA)
VwOu8WkJ9cpc = None
for ZlbFMSG8gCoF in bbT2xIe5pzk7(nzTpIcepk0o8(chr(1564 - 1516) + chr(0b1101111) + chr(858 - 810), 8), a1RCQZREo3Kd, YRX9Ch4rysP9):
sChW4gUsXrIC = XURpmPuEWCNF(ZlbFMSG8gCoF + YRX9Ch4rysP9, a1RCQZREo3Kd)
ppJOhPBvxLBM = nDF4gVNx0u9Q.asarray(ihXi_REa_8XA[ZlbFMSG8gCoF:sChW4gUsXrIC])
if roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'8%\xca\xf5\x1b\x9f\x17\xb4\xe3n\xdaS'), '\144' + chr(0b11001 + 0o114) + chr(0b1100011) + chr(111) + '\144' + chr(0b1000010 + 0o43))(chr(0b1110101) + '\164' + '\x66' + '\055' + chr(1521 - 1465)))(ppJOhPBvxLBM):
TvT0D2rIGW5A = nDF4gVNx0u9Q.asarray(FfKOThdpoDTb[ZlbFMSG8gCoF:sChW4gUsXrIC])
_XdQFJpnzJor = nDF4gVNx0u9Q.compress(ppJOhPBvxLBM, TvT0D2rIGW5A, axis=nzTpIcepk0o8('\x30' + chr(0b1101111) + '\060', 8))
if VwOu8WkJ9cpc is None:
VwOu8WkJ9cpc = roI3spqORKae(A2YPCXgFSG1t, uTw5CPPMOlxD)(_XdQFJpnzJor, expectedlen=YnB3_Prfmdpu, **q5n0sHDDTy90)
else:
roI3spqORKae(VwOu8WkJ9cpc, roI3spqORKae(ES5oEprVxulp(b'&7\xad\xb1(\xb7\x1f\xb9\xfdm\xdf\x05'), chr(0b10011 + 0o121) + chr(5478 - 5377) + chr(0b1011110 + 0o5) + '\x6f' + chr(100) + '\145')(chr(0b1000101 + 0o60) + '\164' + chr(8802 - 8700) + '\x2d' + chr(56)))(_XdQFJpnzJor)
return VwOu8WkJ9cpc
elif JD902pvyCLH1 == nzTpIcepk0o8(chr(48) + '\x6f' + '\061', 0b1000):
VwOu8WkJ9cpc = None
ihXi_REa_8XA = nDF4gVNx0u9Q.asanyarray(ihXi_REa_8XA)
for ZlbFMSG8gCoF in bbT2xIe5pzk7(nzTpIcepk0o8(chr(0b110000) + chr(111) + '\060', 8), a1RCQZREo3Kd, YRX9Ch4rysP9):
sChW4gUsXrIC = XURpmPuEWCNF(ZlbFMSG8gCoF + YRX9Ch4rysP9, a1RCQZREo3Kd)
TvT0D2rIGW5A = nDF4gVNx0u9Q.asarray(FfKOThdpoDTb[ZlbFMSG8gCoF:sChW4gUsXrIC])
_XdQFJpnzJor = nDF4gVNx0u9Q.compress(ihXi_REa_8XA, TvT0D2rIGW5A, axis=nzTpIcepk0o8('\x30' + '\x6f' + chr(49), 8))
if VwOu8WkJ9cpc is None:
VwOu8WkJ9cpc = roI3spqORKae(A2YPCXgFSG1t, uTw5CPPMOlxD)(_XdQFJpnzJor, expectedlen=a1RCQZREo3Kd, **q5n0sHDDTy90)
else:
roI3spqORKae(VwOu8WkJ9cpc, roI3spqORKae(ES5oEprVxulp(b'&7\xad\xb1(\xb7\x1f\xb9\xfdm\xdf\x05'), '\144' + chr(101) + '\143' + '\157' + chr(8234 - 8134) + chr(101))(chr(0b1011101 + 0o30) + chr(116) + chr(0b1100000 + 0o6) + chr(0b101101) + chr(56)))(_XdQFJpnzJor)
return VwOu8WkJ9cpc
else:
raise Y1otPTwLRJvi(roI3spqORKae(ES5oEprVxulp(b'\x0f\x1b\x97\xf6p\xbe7\xa2\xb7q\xff@w\xc3\x0f{\x85\xb1\x14\x8am\x8c'), '\144' + '\145' + chr(5305 - 5206) + chr(0b111110 + 0o61) + chr(1900 - 1800) + chr(101))(chr(0b1110101) + chr(0b1110100) + '\146' + chr(0b101101) + chr(0b1100 + 0o54)) % JD902pvyCLH1) |
cggh/scikit-allel | allel/chunked/core.py | take | def take(data, indices, axis=0, out=None, mode='raise', blen=None, storage=None,
create='array', **kwargs):
"""Take elements from an array along an axis."""
# setup
if out is not None:
# argument is only there for numpy API compatibility
raise NotImplementedError('out argument is not supported')
length = len(data)
if axis == 0:
# check that indices are strictly increasing
indices = np.asanyarray(indices)
if np.any(indices[1:] <= indices[:-1]):
raise NotImplementedError(
'indices must be strictly increasing'
)
# implement via compress()
condition = np.zeros((length,), dtype=bool)
condition[indices] = True
return compress(condition, data, axis=0, blen=blen, storage=storage,
create=create, **kwargs)
elif axis == 1:
# setup
storage = _util.get_storage(storage)
blen = _util.get_blen_array(data, blen)
# block iteration
out = None
for i in range(0, length, blen):
j = min(i+blen, length)
block = data[i:j]
res = np.take(block, indices, axis=1, mode=mode)
if out is None:
out = getattr(storage, create)(res, expectedlen=length,
**kwargs)
else:
out.append(res)
return out
else:
raise NotImplementedError('axis not supported: %s' % axis) | python | def take(data, indices, axis=0, out=None, mode='raise', blen=None, storage=None,
create='array', **kwargs):
"""Take elements from an array along an axis."""
# setup
if out is not None:
# argument is only there for numpy API compatibility
raise NotImplementedError('out argument is not supported')
length = len(data)
if axis == 0:
# check that indices are strictly increasing
indices = np.asanyarray(indices)
if np.any(indices[1:] <= indices[:-1]):
raise NotImplementedError(
'indices must be strictly increasing'
)
# implement via compress()
condition = np.zeros((length,), dtype=bool)
condition[indices] = True
return compress(condition, data, axis=0, blen=blen, storage=storage,
create=create, **kwargs)
elif axis == 1:
# setup
storage = _util.get_storage(storage)
blen = _util.get_blen_array(data, blen)
# block iteration
out = None
for i in range(0, length, blen):
j = min(i+blen, length)
block = data[i:j]
res = np.take(block, indices, axis=1, mode=mode)
if out is None:
out = getattr(storage, create)(res, expectedlen=length,
**kwargs)
else:
out.append(res)
return out
else:
raise NotImplementedError('axis not supported: %s' % axis) | [
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"axis",
"."
] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/chunked/core.py#L273-L318 | train | Take elements from an array along an axis. | 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(50) + chr(0b101 + 0o60) + chr(1668 - 1613), 0o10), nzTpIcepk0o8(chr(0b100110 + 0o12) + chr(0b1101111) + chr(50) + chr(1687 - 1638) + chr(0b110001), 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(50) + '\067' + chr(54), 40247 - 40239), nzTpIcepk0o8(chr(0b10100 + 0o34) + chr(0b1101111) + chr(0b110011) + chr(2228 - 2180) + '\066', 0b1000), nzTpIcepk0o8(chr(48) + '\157' + '\062' + '\063' + chr(51), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1001001 + 0o46) + '\x33' + '\x33' + '\060', 49766 - 49758), nzTpIcepk0o8('\060' + chr(111) + '\x36' + '\x35', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\061' + chr(48) + chr(766 - 717), 11759 - 11751), nzTpIcepk0o8(chr(48) + '\x6f' + '\x33' + '\060' + chr(2134 - 2083), 0o10), nzTpIcepk0o8(chr(966 - 918) + '\157' + '\063' + chr(0b110111) + chr(0b11110 + 0o26), 0b1000), nzTpIcepk0o8(chr(785 - 737) + chr(0b1101111) + '\x32' + chr(49) + '\x31', 8), nzTpIcepk0o8(chr(0b101011 + 0o5) + chr(0b1010101 + 0o32) + chr(1696 - 1647) + '\x32' + chr(0b11000 + 0o33), 0b1000), nzTpIcepk0o8(chr(1130 - 1082) + chr(111) + chr(0b10011 + 0o36) + chr(51) + chr(0b110001 + 0o1), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(8867 - 8756) + chr(0b110001) + chr(0b110111) + chr(0b110011), 0o10), nzTpIcepk0o8(chr(0b10000 + 0o40) + '\x6f' + chr(50) + '\x35', 0b1000), nzTpIcepk0o8('\060' + chr(0b1011000 + 0o27) + chr(0b1101 + 0o46) + chr(50) + '\067', 0o10), nzTpIcepk0o8(chr(48) + chr(12232 - 12121) + chr(0b110010) + '\x31' + chr(0b1 + 0o63), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(4324 - 4213) + '\063' + chr(0b110011) + chr(0b101011 + 0o7), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(2306 - 2257) + chr(0b100101 + 0o21) + chr(0b10100 + 0o36), ord("\x08")), nzTpIcepk0o8(chr(1357 - 1309) + chr(0b1001010 + 0o45) + chr(731 - 682) + chr(1739 - 1688) + '\066', 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110010) + '\066' + '\x30', 0b1000), nzTpIcepk0o8(chr(729 - 681) + chr(0b1101111) + chr(0b1001 + 0o52) + chr(1031 - 982) + chr(0b110011 + 0o4), ord("\x08")), nzTpIcepk0o8(chr(249 - 201) + '\x6f' + '\x33' + chr(0b10000 + 0o42) + '\x31', 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + '\062' + chr(0b110100 + 0o3) + '\066', 8), nzTpIcepk0o8(chr(1924 - 1876) + chr(0b1101111) + '\063' + '\064' + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b111010 + 0o65) + chr(0b11010 + 0o31) + '\065' + '\065', 37729 - 37721), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(55), 0o10), nzTpIcepk0o8(chr(852 - 804) + '\157' + chr(49) + '\065' + chr(2485 - 2434), 55545 - 55537), nzTpIcepk0o8(chr(811 - 763) + '\x6f' + chr(867 - 816) + chr(0b110000) + '\x37', 0o10), nzTpIcepk0o8('\060' + '\157' + chr(0b110010 + 0o5) + chr(55), 0b1000), nzTpIcepk0o8('\060' + '\x6f' + '\x33' + chr(0b101101 + 0o7) + chr(49), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(51) + chr(1613 - 1565) + chr(585 - 533), 0b1000), nzTpIcepk0o8(chr(1669 - 1621) + chr(0b10111 + 0o130) + chr(49) + chr(0b110111) + chr(322 - 271), 8), nzTpIcepk0o8('\060' + '\157' + chr(51) + chr(0b110010) + chr(51), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110011) + chr(0b110011) + chr(0b11001 + 0o36), 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(0b110010) + chr(0b110111) + chr(0b111 + 0o55), 30580 - 30572), nzTpIcepk0o8('\x30' + chr(111) + chr(0b101100 + 0o6) + chr(0b11 + 0o60) + chr(49), 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(0b110011) + chr(0b101100 + 0o5) + chr(48), 35323 - 35315), nzTpIcepk0o8(chr(0b110000) + chr(0b1001010 + 0o45) + chr(338 - 287) + '\x33' + chr(0b110111), 8), nzTpIcepk0o8('\x30' + chr(10936 - 10825) + '\x31' + chr(48) + '\060', ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b1010 + 0o46) + chr(0b1000000 + 0o57) + '\065' + chr(0b100 + 0o54), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x81'), '\x64' + chr(0b1100101) + chr(0b1100010 + 0o1) + chr(111) + chr(0b1100100) + chr(0b1100101))('\165' + chr(0b1000011 + 0o61) + chr(102) + chr(45) + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def rsCvcerQ1_8f(FfKOThdpoDTb, eQBPfEuGz7C1, JD902pvyCLH1=nzTpIcepk0o8(chr(0b110000) + chr(0b1001010 + 0o45) + '\060', 0o10), VwOu8WkJ9cpc=None, bmJ7SvuZE3jD=roI3spqORKae(ES5oEprVxulp(b'\xdd\xe8\xd7\xb5\xfe'), '\x64' + chr(0b1011010 + 0o13) + '\x63' + chr(0b1101111) + chr(0b111001 + 0o53) + chr(101))(chr(0b1110101) + chr(116) + chr(793 - 691) + chr(1987 - 1942) + chr(0b111000)), YRX9Ch4rysP9=None, A2YPCXgFSG1t=None, uTw5CPPMOlxD=roI3spqORKae(ES5oEprVxulp(b'\xce\xfb\xcc\xa7\xe2'), chr(8845 - 8745) + chr(838 - 737) + chr(0b1100011) + '\157' + chr(0b111100 + 0o50) + '\x65')(chr(117) + '\164' + chr(0b1100110) + chr(0b100110 + 0o7) + chr(0b111000)), **q5n0sHDDTy90):
if VwOu8WkJ9cpc is not None:
raise Y1otPTwLRJvi(roI3spqORKae(ES5oEprVxulp(b"\xc0\xfc\xca\xe6\xfa\xaaR4\xae\x99\xe7'z\x12f\xf7\xe2\xb5\x06~\xc3\xba\xa1\xce\x8a\x9fs\x0e\xa3"), chr(0b1100100) + '\x65' + chr(0b1100011) + chr(0b1000110 + 0o51) + '\144' + '\145')(chr(117) + chr(12580 - 12464) + chr(102) + chr(0b11100 + 0o21) + chr(1137 - 1081)))
a1RCQZREo3Kd = ftfygxgFas5X(FfKOThdpoDTb)
if JD902pvyCLH1 == nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(48), 8):
eQBPfEuGz7C1 = nDF4gVNx0u9Q.asanyarray(eQBPfEuGz7C1)
if roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'\xf9\xcf\x8a\xb6\xd0\x97z#\xb7\x90\xd90'), chr(100) + chr(1969 - 1868) + chr(0b100111 + 0o74) + chr(0b1011111 + 0o20) + chr(0b1100100) + chr(0b1100101))(chr(117) + '\164' + '\x66' + '\x2d' + chr(0b110011 + 0o5)))(eQBPfEuGz7C1[nzTpIcepk0o8(chr(2096 - 2048) + chr(0b100001 + 0o116) + chr(0b100011 + 0o16), ord("\x08")):] <= eQBPfEuGz7C1[:-nzTpIcepk0o8(chr(910 - 862) + chr(111) + chr(122 - 73), 8)]):
raise Y1otPTwLRJvi(roI3spqORKae(ES5oEprVxulp(b"\xc6\xe7\xda\xaf\xf8\xbdFa\xae\x89\xfa'z\x19p\xf7\xff\xae\x007\xd3\xbb\xbd\xc7\xc5\x84i\x08\xb5Z\x80\xb7\x12\xbd\xb8"), chr(0b1100100) + chr(0b111010 + 0o53) + chr(0b100110 + 0o75) + chr(0b1010010 + 0o35) + '\144' + '\x65')(chr(0b1110101) + '\x74' + chr(0b1100110) + '\055' + chr(0b101100 + 0o14)))
ihXi_REa_8XA = nDF4gVNx0u9Q.UmwwEp7MzR6q((a1RCQZREo3Kd,), dtype=TVUhqOt5_BbS)
ihXi_REa_8XA[eQBPfEuGz7C1] = nzTpIcepk0o8(chr(0b110000) + chr(0b100 + 0o153) + chr(49), 8)
return jx3TPOy_L63w(ihXi_REa_8XA, FfKOThdpoDTb, axis=nzTpIcepk0o8(chr(1310 - 1262) + chr(0b1101111) + '\x30', 8), blen=YRX9Ch4rysP9, storage=A2YPCXgFSG1t, create=uTw5CPPMOlxD, **q5n0sHDDTy90)
elif JD902pvyCLH1 == nzTpIcepk0o8(chr(48) + chr(6356 - 6245) + chr(49), 8):
A2YPCXgFSG1t = jEKHUML0AUn7.get_storage(A2YPCXgFSG1t)
YRX9Ch4rysP9 = jEKHUML0AUn7.get_blen_array(FfKOThdpoDTb, YRX9Ch4rysP9)
VwOu8WkJ9cpc = None
for ZlbFMSG8gCoF in bbT2xIe5pzk7(nzTpIcepk0o8(chr(0b10110 + 0o32) + '\157' + '\060', 8), a1RCQZREo3Kd, YRX9Ch4rysP9):
sChW4gUsXrIC = XURpmPuEWCNF(ZlbFMSG8gCoF + YRX9Ch4rysP9, a1RCQZREo3Kd)
TvT0D2rIGW5A = FfKOThdpoDTb[ZlbFMSG8gCoF:sChW4gUsXrIC]
_XdQFJpnzJor = nDF4gVNx0u9Q.take(TvT0D2rIGW5A, eQBPfEuGz7C1, axis=nzTpIcepk0o8(chr(829 - 781) + chr(0b10110 + 0o131) + chr(533 - 484), 8), mode=bmJ7SvuZE3jD)
if VwOu8WkJ9cpc is None:
VwOu8WkJ9cpc = roI3spqORKae(A2YPCXgFSG1t, uTw5CPPMOlxD)(_XdQFJpnzJor, expectedlen=a1RCQZREo3Kd, **q5n0sHDDTy90)
else:
roI3spqORKae(VwOu8WkJ9cpc, roI3spqORKae(ES5oEprVxulp(b'\xe7\xdd\xed\xf2\xe3\xbfr.\xa9\x93\xdcf'), chr(100) + '\x65' + chr(0b100100 + 0o77) + chr(5709 - 5598) + '\x64' + '\145')(chr(117) + chr(0b1110100) + '\x66' + chr(457 - 412) + '\070'))(_XdQFJpnzJor)
return VwOu8WkJ9cpc
else:
raise Y1otPTwLRJvi(roI3spqORKae(ES5oEprVxulp(b'\xce\xf1\xd7\xb5\xbb\xb6Z5\xe3\x8f\xfc#*\x14g\xa3\xe9\xbeH~\x95\xbc'), chr(0b1100100) + chr(0b1011110 + 0o7) + '\143' + chr(6260 - 6149) + chr(0b1100100) + chr(9549 - 9448))('\x75' + chr(116) + '\146' + chr(0b0 + 0o55) + chr(2241 - 2185)) % JD902pvyCLH1) |
cggh/scikit-allel | allel/chunked/core.py | compress_table | def compress_table(condition, tbl, axis=None, out=None, blen=None, storage=None,
create='table', **kwargs):
"""Return selected rows of a table."""
# setup
if axis is not None and axis != 0:
raise NotImplementedError('only axis 0 is supported')
if out is not None:
# argument is only there for numpy API compatibility
raise NotImplementedError('out argument is not supported')
storage = _util.get_storage(storage)
names, columns = _util.check_table_like(tbl)
blen = _util.get_blen_table(tbl, blen)
_util.check_equal_length(columns[0], condition)
length = len(columns[0])
nnz = count_nonzero(condition)
# block iteration
out = None
for i in range(0, length, blen):
j = min(i+blen, length)
bcond = condition[i:j]
# don't access any data unless we have to
if np.any(bcond):
bcolumns = [c[i:j] for c in columns]
res = [np.compress(bcond, c, axis=0) for c in bcolumns]
if out is None:
out = getattr(storage, create)(res, names=names,
expectedlen=nnz, **kwargs)
else:
out.append(res)
return out | python | def compress_table(condition, tbl, axis=None, out=None, blen=None, storage=None,
create='table', **kwargs):
"""Return selected rows of a table."""
# setup
if axis is not None and axis != 0:
raise NotImplementedError('only axis 0 is supported')
if out is not None:
# argument is only there for numpy API compatibility
raise NotImplementedError('out argument is not supported')
storage = _util.get_storage(storage)
names, columns = _util.check_table_like(tbl)
blen = _util.get_blen_table(tbl, blen)
_util.check_equal_length(columns[0], condition)
length = len(columns[0])
nnz = count_nonzero(condition)
# block iteration
out = None
for i in range(0, length, blen):
j = min(i+blen, length)
bcond = condition[i:j]
# don't access any data unless we have to
if np.any(bcond):
bcolumns = [c[i:j] for c in columns]
res = [np.compress(bcond, c, axis=0) for c in bcolumns]
if out is None:
out = getattr(storage, create)(res, names=names,
expectedlen=nnz, **kwargs)
else:
out.append(res)
return out | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/chunked/core.py#L321-L352 | train | Compress a 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('\x30' + chr(111) + '\x31' + '\065' + chr(0b110001), 0b1000), nzTpIcepk0o8('\060' + '\x6f' + '\062' + chr(1112 - 1058) + '\x35', 0b1000), nzTpIcepk0o8(chr(1421 - 1373) + '\x6f' + chr(1598 - 1548) + '\x33' + chr(0b111 + 0o51), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + '\x37' + chr(2634 - 2582), 38560 - 38552), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b10101 + 0o34) + '\067' + chr(1515 - 1462), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110101) + '\x37', ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(1234 - 1183) + '\x36' + chr(0b110000 + 0o7), 0o10), nzTpIcepk0o8(chr(1161 - 1113) + '\157' + chr(0b100010 + 0o17) + chr(0b110000) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b11111 + 0o120) + chr(50) + chr(254 - 206) + chr(52), 0o10), nzTpIcepk0o8(chr(0b11111 + 0o21) + chr(0b1010101 + 0o32) + '\062' + chr(0b101001 + 0o10) + '\x36', ord("\x08")), nzTpIcepk0o8(chr(0b110 + 0o52) + chr(0b1101111) + chr(0b11110 + 0o25) + chr(0b110011) + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b100100 + 0o16) + chr(0b110010 + 0o5) + '\x34', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110001) + chr(193 - 140) + chr(51), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x31' + '\061' + '\x31', 46153 - 46145), nzTpIcepk0o8(chr(1094 - 1046) + chr(111) + chr(1334 - 1281) + chr(0b100001 + 0o24), 0b1000), nzTpIcepk0o8('\060' + chr(0b1010101 + 0o32) + chr(49) + chr(0b110101) + chr(0b10100 + 0o35), 8), nzTpIcepk0o8(chr(0b110000) + chr(8334 - 8223) + chr(0b110011) + chr(52) + chr(0b101000 + 0o16), 0o10), nzTpIcepk0o8(chr(0b1100 + 0o44) + '\157' + '\x33' + '\060' + '\067', 38497 - 38489), nzTpIcepk0o8(chr(298 - 250) + chr(7592 - 7481) + chr(52) + chr(220 - 170), 0o10), nzTpIcepk0o8('\x30' + chr(0b10001 + 0o136) + '\x32' + chr(0b110111) + chr(0b101000 + 0o13), 0b1000), nzTpIcepk0o8(chr(48) + chr(3069 - 2958) + chr(50) + '\x30' + chr(1223 - 1171), 8), nzTpIcepk0o8(chr(0b1110 + 0o42) + chr(0b1101111) + '\x36' + chr(1987 - 1932), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(50) + chr(0b110011 + 0o3) + '\x33', 53131 - 53123), nzTpIcepk0o8(chr(48) + chr(2632 - 2521) + '\063', 35737 - 35729), nzTpIcepk0o8('\060' + '\x6f' + chr(51) + chr(0b110011 + 0o1) + chr(1510 - 1455), 59454 - 59446), nzTpIcepk0o8('\x30' + chr(7831 - 7720) + chr(52) + chr(0b110011), 54328 - 54320), nzTpIcepk0o8(chr(1334 - 1286) + chr(0b1101111) + chr(267 - 216) + chr(2026 - 1977), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\061' + '\060', 40156 - 40148), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(51) + chr(50) + chr(1239 - 1189), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + '\x33' + '\064' + chr(0b110001), 0o10), nzTpIcepk0o8('\x30' + chr(0b111011 + 0o64) + '\x36' + chr(0b0 + 0o64), 0b1000), nzTpIcepk0o8(chr(791 - 743) + chr(0b1101111) + '\x32' + chr(1201 - 1152) + chr(0b110100), 44358 - 44350), nzTpIcepk0o8(chr(0b10000 + 0o40) + chr(1509 - 1398) + '\061' + chr(1899 - 1847) + chr(0b110011), 0o10), nzTpIcepk0o8(chr(0b101000 + 0o10) + chr(0b1000111 + 0o50) + chr(0b110111) + '\x31', 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x33' + '\x30' + chr(0b110001), 0b1000), nzTpIcepk0o8(chr(51 - 3) + '\x6f' + chr(0b1000 + 0o55) + chr(0b110110), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + '\x32' + chr(0b110001) + chr(1756 - 1707), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1100000 + 0o17) + chr(0b11000 + 0o32) + chr(0b100001 + 0o17) + chr(0b110101), 23666 - 23658), nzTpIcepk0o8(chr(0b10100 + 0o34) + chr(0b1110 + 0o141) + chr(0b101 + 0o54) + '\060' + chr(0b10001 + 0o43), 8), nzTpIcepk0o8(chr(1950 - 1902) + '\x6f' + chr(0b11011 + 0o27) + chr(50) + chr(579 - 524), 38132 - 38124)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + '\157' + chr(0b10 + 0o63) + '\x30', 58282 - 58274)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'G'), '\144' + '\145' + chr(0b1001 + 0o132) + chr(0b1101111) + chr(0b1010000 + 0o24) + chr(0b1100101))('\x75' + chr(116) + '\146' + '\055' + chr(0b110100 + 0o4)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def N50Ep08xJAbJ(ihXi_REa_8XA, nJ2Kaz8maxAX, JD902pvyCLH1=None, VwOu8WkJ9cpc=None, YRX9Ch4rysP9=None, A2YPCXgFSG1t=None, uTw5CPPMOlxD=roI3spqORKae(ES5oEprVxulp(b'\x1d\xd4\xfaP\x18'), '\144' + chr(7931 - 7830) + chr(0b1001000 + 0o33) + chr(0b1101111) + chr(0b1110 + 0o126) + chr(0b1100101))(chr(1693 - 1576) + chr(0b1110100) + chr(0b1011110 + 0o10) + chr(0b1011 + 0o42) + '\x38'), **q5n0sHDDTy90):
if JD902pvyCLH1 is not None and JD902pvyCLH1 != nzTpIcepk0o8('\x30' + chr(11201 - 11090) + '\060', 59878 - 59870):
raise Y1otPTwLRJvi(roI3spqORKae(ES5oEprVxulp(b'\x06\xdb\xf4E]N\x8f-\xf7\xae\xea\x9c\x02:\r\x1a\x93\xb7R\xd4\xf6C\xd6g'), chr(0b1100100) + chr(773 - 672) + '\143' + chr(111) + chr(100) + chr(0b101101 + 0o70))(chr(117) + chr(0b1110100) + chr(0b1100110) + chr(966 - 921) + chr(0b11100 + 0o34)))
if VwOu8WkJ9cpc is not None:
raise Y1otPTwLRJvi(roI3spqORKae(ES5oEprVxulp(b'\x06\xc0\xec\x1c\x1c]\x901\xe9\xeb\xb4\xc8K ^I\x88\xa8V\x9b\xf7B\xc3s\x88Qmm\xb6'), '\144' + chr(0b1100101) + '\x63' + '\157' + '\144' + '\145')('\x75' + chr(0b1110100) + chr(671 - 569) + chr(1010 - 965) + chr(56)))
A2YPCXgFSG1t = jEKHUML0AUn7.get_storage(A2YPCXgFSG1t)
(TMMrjsiU6eED, U39jSiI54Mlp) = jEKHUML0AUn7.check_table_like(nJ2Kaz8maxAX)
YRX9Ch4rysP9 = jEKHUML0AUn7.get_blen_table(nJ2Kaz8maxAX, YRX9Ch4rysP9)
roI3spqORKae(jEKHUML0AUn7, roI3spqORKae(ES5oEprVxulp(b'\n\xdd\xfd_\x16p\x925\xf1\xef\xb6\xe3\x07,C\x0e\x92\xaf'), chr(0b1100100) + chr(101) + chr(2757 - 2658) + chr(8428 - 8317) + chr(0b1100100) + chr(0b1100101))(chr(0b1110101) + '\164' + chr(102) + chr(0b101101) + '\x38'))(U39jSiI54Mlp[nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110000), 8)], ihXi_REa_8XA)
a1RCQZREo3Kd = ftfygxgFas5X(U39jSiI54Mlp[nzTpIcepk0o8(chr(48) + '\157' + chr(0b1000 + 0o50), 8)])
YnB3_Prfmdpu = p21t5fNwtRJY(ihXi_REa_8XA)
VwOu8WkJ9cpc = None
for ZlbFMSG8gCoF in bbT2xIe5pzk7(nzTpIcepk0o8(chr(0b11001 + 0o27) + chr(111) + chr(48), 8), a1RCQZREo3Kd, YRX9Ch4rysP9):
sChW4gUsXrIC = XURpmPuEWCNF(ZlbFMSG8gCoF + YRX9Ch4rysP9, a1RCQZREo3Kd)
ppJOhPBvxLBM = ihXi_REa_8XA[ZlbFMSG8gCoF:sChW4gUsXrIC]
if roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'?\xf3\xacL6`\xb8&\xf0\xe2\x8a\xdf'), chr(0b1000111 + 0o35) + '\x65' + chr(0b1 + 0o142) + chr(0b111111 + 0o60) + chr(5722 - 5622) + '\145')(chr(0b1110101) + '\x74' + chr(0b1100110) + chr(914 - 869) + chr(0b111000)))(ppJOhPBvxLBM):
BfAGfn0di5IX = [teUmM7cKWZUa[ZlbFMSG8gCoF:sChW4gUsXrIC] for teUmM7cKWZUa in U39jSiI54Mlp]
_XdQFJpnzJor = [nDF4gVNx0u9Q.compress(ppJOhPBvxLBM, teUmM7cKWZUa, axis=nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110000), 8)) for teUmM7cKWZUa in BfAGfn0di5IX]
if VwOu8WkJ9cpc is None:
VwOu8WkJ9cpc = roI3spqORKae(A2YPCXgFSG1t, uTw5CPPMOlxD)(_XdQFJpnzJor, names=TMMrjsiU6eED, expectedlen=YnB3_Prfmdpu, **q5n0sHDDTy90)
else:
roI3spqORKae(VwOu8WkJ9cpc, roI3spqORKae(ES5oEprVxulp(b'!\xe1\xcb\x08\x05H\xb0+\xee\xe1\x8f\x89'), chr(0b1100100) + chr(0b1000101 + 0o40) + chr(0b1000001 + 0o42) + chr(0b1001011 + 0o44) + chr(100) + chr(101))(chr(0b1000101 + 0o60) + chr(0b1110100) + chr(7844 - 7742) + chr(0b11 + 0o52) + chr(56)))(_XdQFJpnzJor)
return VwOu8WkJ9cpc |
cggh/scikit-allel | allel/chunked/core.py | take_table | def take_table(tbl, indices, axis=None, out=None, mode='raise', blen=None, storage=None,
create='table', **kwargs):
"""Return selected rows of a table."""
# setup
if axis is not None and axis != 0:
raise NotImplementedError('only axis 0 is supported')
if out is not None:
# argument is only there for numpy API compatibility
raise NotImplementedError('out argument is not supported')
if mode is not None and mode != 'raise':
raise NotImplementedError('only mode=raise is supported')
names, columns = _util.check_table_like(tbl)
length = len(columns[0])
# check that indices are strictly increasing
indices = np.asanyarray(indices)
if np.any(indices[1:] <= indices[:-1]):
raise NotImplementedError(
'indices must be strictly increasing'
)
# implement via compress()
condition = np.zeros((length,), dtype=bool)
condition[indices] = True
return compress_table(condition, tbl, blen=blen, storage=storage,
create=create, **kwargs) | python | def take_table(tbl, indices, axis=None, out=None, mode='raise', blen=None, storage=None,
create='table', **kwargs):
"""Return selected rows of a table."""
# setup
if axis is not None and axis != 0:
raise NotImplementedError('only axis 0 is supported')
if out is not None:
# argument is only there for numpy API compatibility
raise NotImplementedError('out argument is not supported')
if mode is not None and mode != 'raise':
raise NotImplementedError('only mode=raise is supported')
names, columns = _util.check_table_like(tbl)
length = len(columns[0])
# check that indices are strictly increasing
indices = np.asanyarray(indices)
if np.any(indices[1:] <= indices[:-1]):
raise NotImplementedError(
'indices must be strictly increasing'
)
# implement via compress()
condition = np.zeros((length,), dtype=bool)
condition[indices] = True
return compress_table(condition, tbl, blen=blen, storage=storage,
create=create, **kwargs) | [
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"table",
"."
] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/chunked/core.py#L355-L381 | train | Take a table and return a new 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(687 - 639) + chr(111) + '\x35' + chr(0b1101 + 0o50), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + '\061', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(50) + chr(1307 - 1255) + chr(437 - 382), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + '\062' + '\064' + '\061', 0o10), nzTpIcepk0o8(chr(375 - 327) + chr(0b100000 + 0o117) + chr(0b110010) + '\x34', 55570 - 55562), nzTpIcepk0o8('\060' + '\x6f' + '\062' + '\x37' + chr(167 - 117), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1001101 + 0o42) + chr(2570 - 2519) + chr(0b101001 + 0o12) + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(1966 - 1918) + chr(0b1101111) + '\062' + chr(0b11001 + 0o33) + chr(0b110001), 8), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(49) + '\061' + chr(0b110000), 0b1000), nzTpIcepk0o8(chr(0b11110 + 0o22) + '\x6f' + chr(0b110010) + chr(51) + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(0b1111 + 0o41) + chr(0b101111 + 0o100) + '\061' + chr(0b110100) + '\x30', 18869 - 18861), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(52) + chr(659 - 606), 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(0b110010) + chr(52) + '\x32', 0b1000), nzTpIcepk0o8(chr(0b101001 + 0o7) + chr(111) + chr(498 - 448) + '\062' + '\060', ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(329 - 274) + '\x37', 30271 - 30263), nzTpIcepk0o8(chr(48) + chr(12279 - 12168) + chr(0b11110 + 0o25) + '\x36' + chr(0b100011 + 0o17), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + '\062' + '\062' + '\x35', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\067' + '\x32', ord("\x08")), nzTpIcepk0o8('\x30' + chr(3351 - 3240) + '\x33' + '\x30' + chr(52), ord("\x08")), nzTpIcepk0o8(chr(120 - 72) + chr(7563 - 7452) + chr(54) + chr(0b1100 + 0o52), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + '\062' + '\067' + '\061', ord("\x08")), nzTpIcepk0o8(chr(0b11000 + 0o30) + chr(0b1101111) + '\x32' + chr(2606 - 2551) + chr(0b110111), 0o10), nzTpIcepk0o8('\060' + chr(1133 - 1022) + chr(0b110001) + chr(51) + chr(51), ord("\x08")), nzTpIcepk0o8('\x30' + chr(10607 - 10496) + '\x32' + '\060' + chr(246 - 192), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x32' + '\066' + '\x31', ord("\x08")), nzTpIcepk0o8(chr(949 - 901) + chr(0b10010 + 0o135) + '\062' + chr(0b100000 + 0o26) + chr(0b100100 + 0o20), 0b1000), nzTpIcepk0o8(chr(70 - 22) + chr(0b1100101 + 0o12) + chr(51) + chr(54) + chr(48), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + '\067', 0o10), nzTpIcepk0o8(chr(48) + chr(6601 - 6490) + chr(0b110101) + chr(0b11010 + 0o26), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1100111 + 0o10) + '\063' + chr(49) + chr(55), 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110010) + chr(0b1 + 0o57), ord("\x08")), nzTpIcepk0o8(chr(1844 - 1796) + chr(0b1101111) + chr(1677 - 1624) + chr(0b100011 + 0o15), 8), nzTpIcepk0o8('\060' + chr(0b1011101 + 0o22) + '\063' + '\062', 0b1000), nzTpIcepk0o8(chr(1173 - 1125) + chr(4194 - 4083) + '\062' + chr(0b111 + 0o51) + chr(0b11001 + 0o36), 64299 - 64291), nzTpIcepk0o8(chr(0b110000) + chr(0b11000 + 0o127) + chr(0b11110 + 0o24) + '\x31' + chr(558 - 505), 0b1000), nzTpIcepk0o8('\x30' + chr(9647 - 9536) + chr(51) + chr(459 - 407) + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(0b100010 + 0o16) + chr(0b1101111) + chr(0b0 + 0o62) + chr(0b110010) + chr(0b100010 + 0o21), 29003 - 28995), nzTpIcepk0o8('\060' + '\x6f' + chr(50) + '\062' + '\066', 25670 - 25662), nzTpIcepk0o8('\x30' + chr(9495 - 9384) + chr(1669 - 1615) + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(2028 - 1980) + '\157' + chr(0b0 + 0o63) + chr(48) + '\060', 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b101001 + 0o7) + '\x6f' + chr(53) + chr(1305 - 1257), 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x03'), chr(0b1100100) + chr(0b1001110 + 0o27) + chr(0b1100011) + '\157' + chr(0b100101 + 0o77) + chr(0b1100101))(chr(117) + chr(0b1110100) + chr(0b1011100 + 0o12) + '\055' + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def pLv0haYOwtQ4(nJ2Kaz8maxAX, eQBPfEuGz7C1, JD902pvyCLH1=None, VwOu8WkJ9cpc=None, bmJ7SvuZE3jD=roI3spqORKae(ES5oEprVxulp(b'_`\xce\xd2q'), chr(4273 - 4173) + chr(8211 - 8110) + chr(0b110001 + 0o62) + chr(0b1101111) + '\144' + '\145')('\165' + chr(0b1110100) + '\x66' + chr(0b11110 + 0o17) + chr(1577 - 1521)), YRX9Ch4rysP9=None, A2YPCXgFSG1t=None, uTw5CPPMOlxD=roI3spqORKae(ES5oEprVxulp(b'Y`\xc5\xcdq'), chr(100) + chr(2062 - 1961) + chr(0b1100011) + '\x6f' + chr(0b1100100) + chr(0b1100101))(chr(0b1110101) + chr(116) + chr(6404 - 6302) + chr(0b101101) + chr(56)), **q5n0sHDDTy90):
if JD902pvyCLH1 is not None and JD902pvyCLH1 != nzTpIcepk0o8('\x30' + chr(0b1001100 + 0o43) + '\x30', ord("\x08")):
raise Y1otPTwLRJvi(roI3spqORKae(ES5oEprVxulp(b'Bo\xcb\xd84\xdb\xa5\xc8;\xb8P\x05\xcb\xe3\x1f\x81\xe0J\xb4Y\xcb\xcb>\xe2'), chr(0b1000110 + 0o36) + chr(0b0 + 0o145) + '\143' + chr(0b1101111) + chr(7292 - 7192) + chr(0b1001001 + 0o34))(chr(117) + '\x74' + '\x66' + chr(443 - 398) + chr(56)))
if VwOu8WkJ9cpc is not None:
raise Y1otPTwLRJvi(roI3spqORKae(ES5oEprVxulp(b'Bt\xd3\x81u\xc8\xba\xd4%\xfd\x0eQ\x82\xf9L\xd2\xfbU\xb0\x16\xca\xca+\xf6\xde\xc6\x84bL'), chr(100) + '\x65' + chr(1820 - 1721) + chr(111) + chr(0b1100100) + chr(0b1001100 + 0o31))(chr(0b1110101) + chr(5292 - 5176) + chr(0b1100110) + chr(0b101101) + '\x38'))
if bmJ7SvuZE3jD is not None and bmJ7SvuZE3jD != roI3spqORKae(ES5oEprVxulp(b'_`\xce\xd2q'), chr(100) + '\x65' + chr(99) + chr(111) + chr(8730 - 8630) + chr(0b1100101))(chr(0b10010 + 0o143) + chr(0b11111 + 0o125) + '\146' + chr(621 - 576) + chr(0b111000)):
raise Y1otPTwLRJvi(roI3spqORKae(ES5oEprVxulp(b'Bo\xcb\xd84\xd7\xb2\xc5-\xa5\x12D\xcb\xe3Z\xd2\xfcI\xe4E\xcc\xcf+\xe9\xc3\xc0\x95c'), '\x64' + '\x65' + '\x63' + chr(111) + chr(6851 - 6751) + chr(6364 - 6263))('\x75' + '\x74' + '\146' + chr(0b101101) + chr(0b11100 + 0o34)))
(TMMrjsiU6eED, U39jSiI54Mlp) = jEKHUML0AUn7.check_table_like(nJ2Kaz8maxAX)
a1RCQZREo3Kd = ftfygxgFas5X(U39jSiI54Mlp[nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110000), 8)])
eQBPfEuGz7C1 = nDF4gVNx0u9Q.asanyarray(eQBPfEuGz7C1)
if roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'{G\x93\xd1_\xf5\x92\xc3<\xf40F'), '\144' + '\x65' + '\x63' + chr(0b1101111) + chr(0b10 + 0o142) + '\x65')('\165' + chr(3135 - 3019) + chr(102) + chr(0b11111 + 0o16) + chr(0b111000)))(eQBPfEuGz7C1[nzTpIcepk0o8(chr(200 - 152) + chr(111) + '\061', 8):] <= eQBPfEuGz7C1[:-nzTpIcepk0o8(chr(1772 - 1724) + chr(0b1101111) + chr(49), 8)]):
raise Y1otPTwLRJvi(roI3spqORKae(ES5oEprVxulp(b'Do\xc3\xc8w\xdf\xae\x81%\xed\x13Q\x82\xf2Z\xd2\xe6N\xb6_\xda\xcb7\xff\x91\xdd\x9edZ\xaaq[s\xe9\xea'), chr(100) + chr(0b1100101) + chr(0b1100011) + '\x6f' + chr(0b1100100) + chr(0b10100 + 0o121))(chr(0b1110101) + chr(0b10101 + 0o137) + chr(0b1100110 + 0o0) + chr(0b1000 + 0o45) + chr(0b111000)))
ihXi_REa_8XA = nDF4gVNx0u9Q.UmwwEp7MzR6q((a1RCQZREo3Kd,), dtype=TVUhqOt5_BbS)
ihXi_REa_8XA[eQBPfEuGz7C1] = nzTpIcepk0o8('\060' + chr(0b1101000 + 0o7) + chr(49), 8)
return N50Ep08xJAbJ(ihXi_REa_8XA, nJ2Kaz8maxAX, blen=YRX9Ch4rysP9, storage=A2YPCXgFSG1t, create=uTw5CPPMOlxD, **q5n0sHDDTy90) |
cggh/scikit-allel | allel/chunked/core.py | subset | def subset(data, sel0=None, sel1=None, blen=None, storage=None, create='array',
**kwargs):
"""Return selected rows and columns of an array."""
# TODO refactor sel0 and sel1 normalization with ndarray.subset
# setup
storage = _util.get_storage(storage)
blen = _util.get_blen_array(data, blen)
length = len(data)
if sel0 is not None:
sel0 = np.asanyarray(sel0)
if sel1 is not None:
sel1 = np.asanyarray(sel1)
# ensure boolean array for dim 0
if sel0 is not None and sel0.dtype.kind != 'b':
# assume indices, convert to boolean condition
tmp = np.zeros(length, dtype=bool)
tmp[sel0] = True
sel0 = tmp
# ensure indices for dim 1
if sel1 is not None and sel1.dtype.kind == 'b':
# assume boolean condition, convert to indices
sel1, = np.nonzero(sel1)
# shortcuts
if sel0 is None and sel1 is None:
return copy(data, blen=blen, storage=storage, create=create, **kwargs)
elif sel1 is None:
return compress(sel0, data, axis=0, blen=blen, storage=storage,
create=create, **kwargs)
elif sel0 is None:
return take(data, sel1, axis=1, blen=blen, storage=storage,
create=create, **kwargs)
# build output
sel0_nnz = count_nonzero(sel0)
out = None
for i in range(0, length, blen):
j = min(i+blen, length)
bsel0 = sel0[i:j]
# don't access data unless we have to
if np.any(bsel0):
block = data[i:j]
res = _numpy_subset(block, bsel0, sel1)
if out is None:
out = getattr(storage, create)(res, expectedlen=sel0_nnz,
**kwargs)
else:
out.append(res)
return out | python | def subset(data, sel0=None, sel1=None, blen=None, storage=None, create='array',
**kwargs):
"""Return selected rows and columns of an array."""
# TODO refactor sel0 and sel1 normalization with ndarray.subset
# setup
storage = _util.get_storage(storage)
blen = _util.get_blen_array(data, blen)
length = len(data)
if sel0 is not None:
sel0 = np.asanyarray(sel0)
if sel1 is not None:
sel1 = np.asanyarray(sel1)
# ensure boolean array for dim 0
if sel0 is not None and sel0.dtype.kind != 'b':
# assume indices, convert to boolean condition
tmp = np.zeros(length, dtype=bool)
tmp[sel0] = True
sel0 = tmp
# ensure indices for dim 1
if sel1 is not None and sel1.dtype.kind == 'b':
# assume boolean condition, convert to indices
sel1, = np.nonzero(sel1)
# shortcuts
if sel0 is None and sel1 is None:
return copy(data, blen=blen, storage=storage, create=create, **kwargs)
elif sel1 is None:
return compress(sel0, data, axis=0, blen=blen, storage=storage,
create=create, **kwargs)
elif sel0 is None:
return take(data, sel1, axis=1, blen=blen, storage=storage,
create=create, **kwargs)
# build output
sel0_nnz = count_nonzero(sel0)
out = None
for i in range(0, length, blen):
j = min(i+blen, length)
bsel0 = sel0[i:j]
# don't access data unless we have to
if np.any(bsel0):
block = data[i:j]
res = _numpy_subset(block, bsel0, sel1)
if out is None:
out = getattr(storage, create)(res, expectedlen=sel0_nnz,
**kwargs)
else:
out.append(res)
return out | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/chunked/core.py#L384-L437 | train | Return selected rows and columns of an array. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8('\x30' + '\x6f' + chr(0b1000 + 0o57) + '\x35', 0b1000), nzTpIcepk0o8(chr(1578 - 1530) + chr(0b111010 + 0o65) + chr(0b1001 + 0o50) + chr(0b11001 + 0o36) + chr(774 - 723), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\061' + '\x37' + chr(0b100011 + 0o20), 8), nzTpIcepk0o8(chr(1784 - 1736) + chr(0b1101111) + chr(50) + chr(0b1111 + 0o47), 0o10), nzTpIcepk0o8('\x30' + chr(0b101101 + 0o102) + chr(49) + chr(0b1101 + 0o47) + chr(0b100011 + 0o23), ord("\x08")), nzTpIcepk0o8(chr(0b1010 + 0o46) + '\157' + '\062' + chr(0b100011 + 0o20) + chr(1878 - 1825), ord("\x08")), nzTpIcepk0o8(chr(0b10101 + 0o33) + '\x6f' + '\063' + chr(0b110001) + '\x31', 0o10), nzTpIcepk0o8(chr(0b101000 + 0o10) + chr(4647 - 4536) + '\x32' + chr(0b10101 + 0o36) + chr(0b110110), 21294 - 21286), nzTpIcepk0o8(chr(722 - 674) + chr(111) + chr(0b100111 + 0o12) + '\062' + chr(0b110110), ord("\x08")), nzTpIcepk0o8(chr(0b100011 + 0o15) + '\157' + '\066' + chr(54), 0o10), nzTpIcepk0o8(chr(0b110 + 0o52) + chr(0b101101 + 0o102) + chr(0b110001) + '\x31' + '\060', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(51) + chr(50) + chr(53), 4386 - 4378), nzTpIcepk0o8(chr(0b10101 + 0o33) + '\157' + '\x33' + '\x35' + chr(0b110100), 24418 - 24410), nzTpIcepk0o8('\060' + chr(5154 - 5043) + chr(0b11001 + 0o33) + '\x37', 0o10), nzTpIcepk0o8(chr(1467 - 1419) + chr(0b1011 + 0o144) + '\x33' + '\x36' + '\064', 0o10), nzTpIcepk0o8(chr(0b11100 + 0o24) + '\x6f' + chr(50) + chr(0b10010 + 0o44) + chr(0b100010 + 0o16), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110001) + chr(53) + chr(2485 - 2431), 56736 - 56728), nzTpIcepk0o8(chr(1721 - 1673) + chr(111) + '\061' + chr(2156 - 2101) + chr(0b100100 + 0o23), 0o10), nzTpIcepk0o8(chr(0b100100 + 0o14) + chr(111) + chr(1638 - 1587) + chr(48) + '\x32', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b10111 + 0o34) + chr(0b110000) + chr(49), 0b1000), nzTpIcepk0o8('\060' + '\157' + '\061' + chr(0b110110) + chr(51), 1398 - 1390), nzTpIcepk0o8('\x30' + chr(5581 - 5470) + chr(1335 - 1285) + chr(1907 - 1853) + chr(1391 - 1341), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b11100 + 0o26) + '\061' + '\x30', ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(0b110001) + '\061' + chr(745 - 696), 29954 - 29946), nzTpIcepk0o8(chr(0b110000) + chr(0b1000001 + 0o56) + chr(0b101001 + 0o11) + chr(0b10001 + 0o43) + chr(0b110001), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(55) + chr(0b110110), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(1275 - 1225) + chr(0b110100) + chr(52), ord("\x08")), nzTpIcepk0o8(chr(1628 - 1580) + '\x6f' + chr(0b11111 + 0o26) + chr(53), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + '\x33' + '\063', 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + '\065', 0o10), nzTpIcepk0o8(chr(0b110 + 0o52) + chr(5517 - 5406) + '\x33' + chr(51) + '\x32', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b100110 + 0o13) + chr(653 - 600) + '\064', ord("\x08")), nzTpIcepk0o8(chr(0b10111 + 0o31) + chr(0b1101111) + chr(50) + '\064' + chr(0b11010 + 0o30), 63166 - 63158), nzTpIcepk0o8(chr(2005 - 1957) + '\x6f' + '\x31' + chr(0b110010) + chr(2241 - 2192), ord("\x08")), nzTpIcepk0o8(chr(184 - 136) + '\157' + chr(0b10110 + 0o37) + chr(0b110000), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(52), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(51) + chr(0b100001 + 0o24) + chr(0b110101), 52324 - 52316), nzTpIcepk0o8(chr(238 - 190) + chr(111) + chr(0b110001) + chr(0b110101) + chr(54), 8), nzTpIcepk0o8(chr(812 - 764) + chr(7073 - 6962) + chr(50), 0b1000), nzTpIcepk0o8(chr(507 - 459) + chr(0b1010101 + 0o32) + chr(0b110011) + chr(0b100100 + 0o14), 19304 - 19296)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + '\157' + chr(124 - 71) + chr(48), 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x13'), chr(0b1100100) + chr(101) + chr(0b1100011) + '\157' + chr(5935 - 5835) + chr(0b100000 + 0o105))(chr(0b100100 + 0o121) + chr(116) + chr(6690 - 6588) + '\x2d' + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def kw37P8hgNdNY(FfKOThdpoDTb, xIIxKLhLgM7X=None, OjBOFYa5buna=None, YRX9Ch4rysP9=None, A2YPCXgFSG1t=None, uTw5CPPMOlxD=roI3spqORKae(ES5oEprVxulp(b'\\\t\tw\x1f'), '\x64' + '\x65' + '\143' + chr(0b1111 + 0o140) + '\x64' + '\x65')(chr(117) + chr(0b1110100) + chr(102) + chr(140 - 95) + chr(352 - 296)), **q5n0sHDDTy90):
A2YPCXgFSG1t = jEKHUML0AUn7.get_storage(A2YPCXgFSG1t)
YRX9Ch4rysP9 = jEKHUML0AUn7.get_blen_array(FfKOThdpoDTb, YRX9Ch4rysP9)
a1RCQZREo3Kd = ftfygxgFas5X(FfKOThdpoDTb)
if xIIxKLhLgM7X is not None:
xIIxKLhLgM7X = nDF4gVNx0u9Q.asanyarray(xIIxKLhLgM7X)
if OjBOFYa5buna is not None:
OjBOFYa5buna = nDF4gVNx0u9Q.asanyarray(OjBOFYa5buna)
if xIIxKLhLgM7X is not None and roI3spqORKae(xIIxKLhLgM7X.dtype, roI3spqORKae(ES5oEprVxulp(b'h\x1a\x01PR\xaf\xff\xfc#t-\x86'), chr(6846 - 6746) + '\145' + chr(0b1100010 + 0o1) + chr(0b1101111) + chr(0b1100100) + chr(5933 - 5832))(chr(117) + '\x74' + chr(0b1010011 + 0o23) + chr(0b101101) + '\x38')) != roI3spqORKae(ES5oEprVxulp(b'_'), chr(0b1100100) + chr(0b111101 + 0o50) + chr(0b1000110 + 0o35) + chr(0b1101111) + '\144' + '\145')('\165' + '\x74' + chr(0b11 + 0o143) + '\055' + '\x38'):
PT32xG247TS3 = nDF4gVNx0u9Q.UmwwEp7MzR6q(a1RCQZREo3Kd, dtype=TVUhqOt5_BbS)
PT32xG247TS3[xIIxKLhLgM7X] = nzTpIcepk0o8(chr(0b110000) + chr(5569 - 5458) + '\x31', 0b1000)
xIIxKLhLgM7X = PT32xG247TS3
if OjBOFYa5buna is not None and roI3spqORKae(OjBOFYa5buna.dtype, roI3spqORKae(ES5oEprVxulp(b'h\x1a\x01PR\xaf\xff\xfc#t-\x86'), chr(0b1001111 + 0o25) + chr(6443 - 6342) + chr(2418 - 2319) + '\x6f' + chr(100) + chr(8547 - 8446))(chr(13665 - 13548) + '\164' + '\146' + '\x2d' + chr(0b111000))) == roI3spqORKae(ES5oEprVxulp(b'_'), '\x64' + chr(0b100010 + 0o103) + chr(99) + chr(0b110100 + 0o73) + chr(100) + '\x65')('\x75' + chr(8639 - 8523) + chr(4452 - 4350) + '\x2d' + '\070'):
(OjBOFYa5buna,) = nDF4gVNx0u9Q.B3vb9auQy6eX(OjBOFYa5buna)
if xIIxKLhLgM7X is None and OjBOFYa5buna is None:
return aZTCj4v5QdfO(FfKOThdpoDTb, blen=YRX9Ch4rysP9, storage=A2YPCXgFSG1t, create=uTw5CPPMOlxD, **q5n0sHDDTy90)
elif OjBOFYa5buna is None:
return jx3TPOy_L63w(xIIxKLhLgM7X, FfKOThdpoDTb, axis=nzTpIcepk0o8('\060' + '\x6f' + chr(0b11111 + 0o21), 0b1000), blen=YRX9Ch4rysP9, storage=A2YPCXgFSG1t, create=uTw5CPPMOlxD, **q5n0sHDDTy90)
elif xIIxKLhLgM7X is None:
return rsCvcerQ1_8f(FfKOThdpoDTb, OjBOFYa5buna, axis=nzTpIcepk0o8(chr(1443 - 1395) + chr(111) + '\x31', 8), blen=YRX9Ch4rysP9, storage=A2YPCXgFSG1t, create=uTw5CPPMOlxD, **q5n0sHDDTy90)
K7p6AvJhsVe4 = p21t5fNwtRJY(xIIxKLhLgM7X)
VwOu8WkJ9cpc = None
for ZlbFMSG8gCoF in bbT2xIe5pzk7(nzTpIcepk0o8(chr(0b11 + 0o55) + '\157' + chr(0b110000), 8), a1RCQZREo3Kd, YRX9Ch4rysP9):
sChW4gUsXrIC = XURpmPuEWCNF(ZlbFMSG8gCoF + YRX9Ch4rysP9, a1RCQZREo3Kd)
MFOv9zqrYrkI = xIIxKLhLgM7X[ZlbFMSG8gCoF:sChW4gUsXrIC]
if roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'k=Of-\xd2\x86\xfc"Z\x18\xb6'), '\x64' + '\x65' + '\x63' + '\x6f' + '\x64' + chr(101))(chr(0b1110101) + chr(11652 - 11536) + chr(0b1100110) + '\055' + chr(0b101001 + 0o17)))(MFOv9zqrYrkI):
TvT0D2rIGW5A = FfKOThdpoDTb[ZlbFMSG8gCoF:sChW4gUsXrIC]
_XdQFJpnzJor = VWreZjh9b38Q(TvT0D2rIGW5A, MFOv9zqrYrkI, OjBOFYa5buna)
if VwOu8WkJ9cpc is None:
VwOu8WkJ9cpc = roI3spqORKae(A2YPCXgFSG1t, uTw5CPPMOlxD)(_XdQFJpnzJor, expectedlen=K7p6AvJhsVe4, **q5n0sHDDTy90)
else:
roI3spqORKae(VwOu8WkJ9cpc, roI3spqORKae(ES5oEprVxulp(b'u/("\x1e\xfa\x8e\xf1<Y\x1d\xe0'), chr(0b1100100) + chr(0b101111 + 0o66) + '\x63' + chr(0b1101111) + chr(100) + chr(101))('\x75' + chr(5667 - 5551) + chr(0b1100110) + chr(0b11110 + 0o17) + chr(0b1001 + 0o57)))(_XdQFJpnzJor)
return VwOu8WkJ9cpc |
cggh/scikit-allel | allel/chunked/core.py | concatenate_table | def concatenate_table(tup, blen=None, storage=None, create='table', **kwargs):
"""Stack tables in sequence vertically (row-wise)."""
# setup
storage = _util.get_storage(storage)
if not isinstance(tup, (tuple, list)):
raise ValueError('expected tuple or list, found %r' % tup)
if len(tup) < 2:
raise ValueError('expected two or more tables to stack')
# build output
expectedlen = sum(len(t) for t in tup)
out = None
tnames = None
for tdata in tup:
tblen = _util.get_blen_table(tdata, blen)
tnames, tcolumns = _util.check_table_like(tdata, names=tnames)
tlen = len(tcolumns[0])
for i in range(0, tlen, tblen):
j = min(i+tblen, tlen)
bcolumns = [c[i:j] for c in tcolumns]
if out is None:
out = getattr(storage, create)(bcolumns, names=tnames,
expectedlen=expectedlen,
**kwargs)
else:
out.append(bcolumns)
return out | python | def concatenate_table(tup, blen=None, storage=None, create='table', **kwargs):
"""Stack tables in sequence vertically (row-wise)."""
# setup
storage = _util.get_storage(storage)
if not isinstance(tup, (tuple, list)):
raise ValueError('expected tuple or list, found %r' % tup)
if len(tup) < 2:
raise ValueError('expected two or more tables to stack')
# build output
expectedlen = sum(len(t) for t in tup)
out = None
tnames = None
for tdata in tup:
tblen = _util.get_blen_table(tdata, blen)
tnames, tcolumns = _util.check_table_like(tdata, names=tnames)
tlen = len(tcolumns[0])
for i in range(0, tlen, tblen):
j = min(i+tblen, tlen)
bcolumns = [c[i:j] for c in tcolumns]
if out is None:
out = getattr(storage, create)(bcolumns, names=tnames,
expectedlen=expectedlen,
**kwargs)
else:
out.append(bcolumns)
return out | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/chunked/core.py#L440-L467 | train | Stack tables in sequence vertically ( row - wise ). | 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(0b110001) + chr(53) + chr(0b10001 + 0o44), 0o10), nzTpIcepk0o8(chr(1465 - 1417) + '\157' + '\063' + chr(210 - 157) + chr(49), 25331 - 25323), nzTpIcepk0o8('\060' + chr(9405 - 9294) + '\x31' + chr(0b100001 + 0o26) + '\065', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1010100 + 0o33) + '\061' + '\x34' + chr(48), 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(2421 - 2371) + chr(53) + chr(53), 0o10), nzTpIcepk0o8(chr(48) + chr(9639 - 9528) + '\062' + '\x31' + chr(1803 - 1751), 0o10), nzTpIcepk0o8('\060' + chr(111) + '\x31' + chr(0b110101), 41045 - 41037), nzTpIcepk0o8('\x30' + chr(111) + '\061' + '\x34' + '\066', ord("\x08")), nzTpIcepk0o8(chr(2051 - 2003) + chr(11873 - 11762) + chr(0b110001) + '\063' + '\062', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\063' + chr(0b101100 + 0o10) + '\x36', 0o10), nzTpIcepk0o8(chr(1235 - 1187) + chr(111) + '\063' + '\x37' + '\x35', 0b1000), nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(0b1101111) + chr(1597 - 1547) + chr(0b110101) + chr(0b11 + 0o55), 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(0b110101) + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b11000 + 0o33) + '\062', 0o10), nzTpIcepk0o8(chr(437 - 389) + chr(2136 - 2025) + chr(0b100110 + 0o13) + chr(1173 - 1120) + chr(0b110110), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b10111 + 0o33) + chr(0b11110 + 0o30) + chr(54), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x32' + chr(0b101001 + 0o12) + '\066', 27372 - 27364), nzTpIcepk0o8(chr(48) + chr(6227 - 6116) + chr(1181 - 1132) + chr(2794 - 2741) + chr(2342 - 2287), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b110101 + 0o72) + chr(50) + chr(0b110010), 47652 - 47644), nzTpIcepk0o8(chr(48) + '\157' + '\x33' + chr(0b110000) + chr(53), ord("\x08")), nzTpIcepk0o8(chr(1517 - 1469) + chr(0b10101 + 0o132) + chr(0b110 + 0o53) + chr(0b100011 + 0o15) + chr(0b110 + 0o61), 0b1000), nzTpIcepk0o8('\060' + chr(111) + '\x35' + '\x35', 8), nzTpIcepk0o8('\x30' + chr(0b1001011 + 0o44) + chr(0b1 + 0o62) + chr(204 - 149) + chr(48), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1000111 + 0o50) + chr(50) + '\x34' + '\061', 0o10), nzTpIcepk0o8(chr(1707 - 1659) + chr(7907 - 7796) + chr(1592 - 1541) + chr(0b110001), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(55) + chr(51), 62787 - 62779), nzTpIcepk0o8(chr(495 - 447) + '\x6f' + chr(0b11011 + 0o26) + chr(0b110010) + chr(48), 18660 - 18652), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(285 - 236) + chr(0b110101) + chr(0b110101), 8), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110100 + 0o0) + '\060', 31544 - 31536), nzTpIcepk0o8('\060' + chr(0b1000010 + 0o55) + '\063' + '\x33' + chr(0b110110), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b100010 + 0o17) + chr(783 - 733) + chr(51), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + chr(0b101010 + 0o14) + chr(0b110001), 54446 - 54438), nzTpIcepk0o8(chr(1257 - 1209) + chr(0b1101111) + '\061' + chr(314 - 262) + chr(0b110001), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b11011 + 0o31) + chr(0b1100 + 0o50), ord("\x08")), nzTpIcepk0o8(chr(959 - 911) + '\x6f' + chr(0b110010) + '\061' + '\062', 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(1706 - 1656) + chr(50) + '\061', 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(50) + chr(0b110010) + chr(53), 62998 - 62990), nzTpIcepk0o8(chr(1100 - 1052) + '\157' + chr(225 - 174) + chr(381 - 329) + chr(1240 - 1189), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(0b10110 + 0o35) + chr(0b1010 + 0o50) + chr(2607 - 2552), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(2303 - 2254) + '\x30' + chr(0b10011 + 0o44), 8)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b101010 + 0o6) + chr(0b1101111) + chr(0b0 + 0o65) + chr(0b110000), ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'C'), chr(0b1100100) + chr(0b1010001 + 0o24) + chr(99) + chr(111) + chr(0b110010 + 0o62) + chr(0b1100101))(chr(0b1110101) + chr(2554 - 2438) + chr(0b1010101 + 0o21) + chr(0b101101) + chr(0b110010 + 0o6)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def zxkz0cushH6E(WRQDInte8Ztr, YRX9Ch4rysP9=None, A2YPCXgFSG1t=None, uTw5CPPMOlxD=roI3spqORKae(ES5oEprVxulp(b'\x19\x88\x1f\x0c\xc8'), chr(0b1100100) + '\x65' + '\143' + chr(0b1101111) + chr(0b1100100) + chr(0b111000 + 0o55))(chr(1498 - 1381) + '\164' + chr(102) + '\055' + chr(0b111000)), **q5n0sHDDTy90):
A2YPCXgFSG1t = jEKHUML0AUn7.get_storage(A2YPCXgFSG1t)
if not suIjIS24Zkqw(WRQDInte8Ztr, (nfNqtJL5aRaY, H4NoA26ON7iG)):
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'\x08\x91\r\x05\xce\xf8h\x02z\x92\x88\xd8A\x7fN\xd9\xecO~\xac4Y\xd4\x81\x7fT%\x03D\xfevC'), '\144' + chr(8045 - 7944) + chr(0b1011011 + 0o10) + chr(10590 - 10479) + chr(100) + chr(6576 - 6475))(chr(117) + chr(1671 - 1555) + chr(6146 - 6044) + chr(0b10110 + 0o27) + chr(0b111000)) % WRQDInte8Ztr)
if ftfygxgFas5X(WRQDInte8Ztr) < nzTpIcepk0o8(chr(1743 - 1695) + chr(1869 - 1758) + '\062', ord("\x08")):
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'\x08\x91\r\x05\xce\xf8h\x02z\x92\x8a\xc7\ru\x1c\x96\xf3\x00`\xa0gY\x99\xc3u^#MT\xb1sB\x15E\xe9\xfa'), chr(413 - 313) + chr(0b1100101) + chr(0b10110 + 0o115) + '\x6f' + chr(0b1001111 + 0o25) + chr(0b1100101))(chr(8135 - 8018) + chr(0b1110100) + chr(0b1100110) + chr(0b110 + 0o47) + chr(56)))
UlZ2RQCsPjCu = oclC8DLjA_lV((ftfygxgFas5X(h3Vc_4wxEbgd) for h3Vc_4wxEbgd in WRQDInte8Ztr))
VwOu8WkJ9cpc = None
BfaK5ThXq6i6 = None
for i3xSaxAygKqP in WRQDInte8Ztr:
oS45agOyjBXe = jEKHUML0AUn7.get_blen_table(i3xSaxAygKqP, YRX9Ch4rysP9)
(BfaK5ThXq6i6, YnpBcGbzNTGY) = jEKHUML0AUn7.check_table_like(i3xSaxAygKqP, names=BfaK5ThXq6i6)
_xhU3QOHYy5O = ftfygxgFas5X(YnpBcGbzNTGY[nzTpIcepk0o8('\x30' + '\157' + chr(53 - 5), 0b1000)])
for ZlbFMSG8gCoF in bbT2xIe5pzk7(nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\060', 8), _xhU3QOHYy5O, oS45agOyjBXe):
sChW4gUsXrIC = XURpmPuEWCNF(ZlbFMSG8gCoF + oS45agOyjBXe, _xhU3QOHYy5O)
BfAGfn0di5IX = [teUmM7cKWZUa[ZlbFMSG8gCoF:sChW4gUsXrIC] for teUmM7cKWZUa in YnpBcGbzNTGY]
if VwOu8WkJ9cpc is None:
VwOu8WkJ9cpc = roI3spqORKae(A2YPCXgFSG1t, uTw5CPPMOlxD)(BfAGfn0di5IX, names=BfaK5ThXq6i6, expectedlen=UlZ2RQCsPjCu, **q5n0sHDDTy90)
else:
roI3spqORKae(VwOu8WkJ9cpc, roI3spqORKae(ES5oEprVxulp(b'%\xbd.T\xd5\xebJ\t0\x89\xa8\x9d'), chr(0b1011111 + 0o5) + '\145' + chr(0b1100011) + '\157' + chr(100) + chr(7917 - 7816))(chr(4808 - 4691) + chr(0b10101 + 0o137) + chr(102) + chr(0b101101) + chr(2960 - 2904)))(BfAGfn0di5IX)
return VwOu8WkJ9cpc |
cggh/scikit-allel | allel/chunked/core.py | concatenate | def concatenate(tup, axis=0, blen=None, storage=None, create='array', **kwargs):
"""Concatenate arrays."""
# setup
storage = _util.get_storage(storage)
if not isinstance(tup, (tuple, list)):
raise ValueError('expected tuple or list, found %r' % tup)
if len(tup) < 2:
raise ValueError('expected two or more arrays')
if axis == 0:
# build output
expectedlen = sum(len(a) for a in tup)
out = None
for a in tup:
ablen = _util.get_blen_array(a, blen)
for i in range(0, len(a), ablen):
j = min(i+ablen, len(a))
block = a[i:j]
if out is None:
out = getattr(storage, create)(block, expectedlen=expectedlen, **kwargs)
else:
out.append(block)
else:
def f(*blocks):
return np.concatenate(blocks, axis=axis)
out = map_blocks(tup, f, blen=blen, storage=storage, create=create, **kwargs)
return out | python | def concatenate(tup, axis=0, blen=None, storage=None, create='array', **kwargs):
"""Concatenate arrays."""
# setup
storage = _util.get_storage(storage)
if not isinstance(tup, (tuple, list)):
raise ValueError('expected tuple or list, found %r' % tup)
if len(tup) < 2:
raise ValueError('expected two or more arrays')
if axis == 0:
# build output
expectedlen = sum(len(a) for a in tup)
out = None
for a in tup:
ablen = _util.get_blen_array(a, blen)
for i in range(0, len(a), ablen):
j = min(i+ablen, len(a))
block = a[i:j]
if out is None:
out = getattr(storage, create)(block, expectedlen=expectedlen, **kwargs)
else:
out.append(block)
else:
def f(*blocks):
return np.concatenate(blocks, axis=axis)
out = map_blocks(tup, f, blen=blen, storage=storage, create=create, **kwargs)
return out | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/chunked/core.py#L470-L502 | train | Concatenate arrays. | 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(0b1011000 + 0o27) + chr(0b101000 + 0o11) + chr(0b1011 + 0o53) + '\x33', 0b1000), nzTpIcepk0o8(chr(1220 - 1172) + chr(111) + '\x33' + chr(54) + '\x36', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b0 + 0o157) + chr(1621 - 1572) + chr(0b110100) + chr(51), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + '\x33' + chr(54) + chr(0b110111), 0o10), nzTpIcepk0o8(chr(0b101001 + 0o7) + chr(0b111100 + 0o63) + chr(0b1000 + 0o53) + chr(0b1000 + 0o57) + chr(0b110110), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b101101 + 0o102) + chr(50) + chr(0b101110 + 0o5) + chr(0b1101 + 0o46), 0b1000), nzTpIcepk0o8(chr(1384 - 1336) + chr(0b1101000 + 0o7) + chr(50) + chr(0b11010 + 0o26) + chr(48), 0b1000), nzTpIcepk0o8(chr(0b100000 + 0o20) + chr(111) + '\x31' + '\065' + chr(0b100010 + 0o21), ord("\x08")), nzTpIcepk0o8(chr(1729 - 1681) + chr(0b110000 + 0o77) + chr(0b10 + 0o65) + chr(0b1010 + 0o51), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b11 + 0o154) + '\x33' + chr(0b100110 + 0o21) + chr(55), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1011100 + 0o23) + chr(2094 - 2040) + '\x32', 0o10), nzTpIcepk0o8('\x30' + '\157' + '\x31' + chr(0b110101) + chr(0b110110), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(49) + chr(1932 - 1877) + '\x34', 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + '\062' + '\x32' + chr(54), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b101011 + 0o104) + chr(1396 - 1345) + chr(50) + chr(52), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + '\061' + chr(49) + '\061', ord("\x08")), nzTpIcepk0o8(chr(0b1110 + 0o42) + chr(111) + chr(0b10 + 0o60) + chr(0b110111) + '\063', 0o10), nzTpIcepk0o8(chr(0b11 + 0o55) + chr(0b1101111) + chr(50) + '\x34' + chr(0b101011 + 0o7), 0o10), nzTpIcepk0o8(chr(0b11010 + 0o26) + chr(0b10010 + 0o135) + '\062' + chr(267 - 215) + chr(49), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(247 - 197) + chr(50) + chr(53), 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(50) + '\x30' + '\060', 8), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(1911 - 1862) + chr(0b110110) + '\066', 0b1000), nzTpIcepk0o8(chr(0b10101 + 0o33) + chr(111) + chr(0b10011 + 0o42) + chr(0b110010 + 0o1), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(401 - 350) + chr(0b110011) + chr(0b110010), 60735 - 60727), nzTpIcepk0o8(chr(0b1001 + 0o47) + '\x6f' + '\062' + '\064', ord("\x08")), nzTpIcepk0o8(chr(0b10101 + 0o33) + '\x6f' + '\061' + chr(0b10011 + 0o44) + chr(50), 24308 - 24300), nzTpIcepk0o8('\060' + chr(0b1101111) + '\061' + chr(0b110011) + chr(52), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(49) + chr(0b110100) + '\x31', 1564 - 1556), nzTpIcepk0o8(chr(0b11011 + 0o25) + '\157' + chr(51) + chr(0b110010) + chr(340 - 285), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b1011 + 0o50) + chr(48), 0b1000), nzTpIcepk0o8(chr(0b110000 + 0o0) + chr(0b110110 + 0o71) + chr(0b10000 + 0o42) + '\x31' + chr(53), 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(0b1 + 0o62) + chr(0b110111) + chr(0b110100), 23624 - 23616), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b1011 + 0o46) + chr(53) + '\x30', 0o10), nzTpIcepk0o8(chr(48) + chr(111) + '\x31' + chr(1888 - 1839), ord("\x08")), nzTpIcepk0o8(chr(0b1 + 0o57) + '\x6f' + '\062' + '\064' + '\x30', 15450 - 15442), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(50) + '\x36' + '\x34', 51376 - 51368), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110001) + '\066' + '\x35', 34679 - 34671), nzTpIcepk0o8('\060' + chr(111) + '\x31' + chr(0b110111) + chr(54), ord("\x08")), nzTpIcepk0o8(chr(0b1011 + 0o45) + chr(0b10001 + 0o136) + chr(49) + '\062' + chr(51), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110011) + chr(49), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(2082 - 2034) + '\157' + '\x35' + chr(118 - 70), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b']'), '\x64' + '\x65' + chr(4042 - 3943) + chr(0b10001 + 0o136) + chr(0b10111 + 0o115) + '\145')(chr(117) + '\164' + '\146' + '\x2d' + chr(1719 - 1663)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def cNUMWjTSOBqD(WRQDInte8Ztr, JD902pvyCLH1=nzTpIcepk0o8(chr(0b110000) + chr(8972 - 8861) + chr(48), 0b1000), YRX9Ch4rysP9=None, A2YPCXgFSG1t=None, uTw5CPPMOlxD=roI3spqORKae(ES5oEprVxulp(b'\x12\x84\x11\x96\x87'), '\x64' + chr(101) + chr(99) + '\x6f' + '\x64' + '\x65')('\x75' + chr(0b1101101 + 0o7) + chr(0b111010 + 0o54) + chr(0b101101) + '\x38'), **q5n0sHDDTy90):
A2YPCXgFSG1t = jEKHUML0AUn7.get_storage(A2YPCXgFSG1t)
if not suIjIS24Zkqw(WRQDInte8Ztr, (nfNqtJL5aRaY, H4NoA26ON7iG)):
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'\x16\x8e\x13\x92\x9d\xef\xe5\x0f\x1b\x8bG\x1e\x10\xf3\xf4&\xc9\x82\xcd\xfc\xf3\x02\x07\xfar\x15)\x0f\xb38\xa8\x8e'), chr(0b1100100) + chr(6881 - 6780) + chr(4671 - 4572) + chr(111) + chr(4277 - 4177) + chr(4400 - 4299))('\165' + '\x74' + chr(4703 - 4601) + chr(1818 - 1773) + '\x38') % WRQDInte8Ztr)
if ftfygxgFas5X(WRQDInte8Ztr) < nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110010), ord("\x08")):
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'\x16\x8e\x13\x92\x9d\xef\xe5\x0f\x1b\x8bE\x01\\\xf9\xa6i\xd6\xcd\xd3\xf0\xa0\x17Y\xa8u\x03/'), '\144' + '\x65' + '\x63' + chr(111) + '\144' + '\145')(chr(0b1110101) + '\x74' + '\x66' + chr(0b101101) + chr(0b111000)))
if JD902pvyCLH1 == nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(1059 - 1011), 8):
UlZ2RQCsPjCu = oclC8DLjA_lV((ftfygxgFas5X(AQ9ceR9AaoT1) for AQ9ceR9AaoT1 in WRQDInte8Ztr))
VwOu8WkJ9cpc = None
for AQ9ceR9AaoT1 in WRQDInte8Ztr:
pgZMlSwQG6b0 = jEKHUML0AUn7.get_blen_array(AQ9ceR9AaoT1, YRX9Ch4rysP9)
for ZlbFMSG8gCoF in bbT2xIe5pzk7(nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(547 - 499), 8), ftfygxgFas5X(AQ9ceR9AaoT1), pgZMlSwQG6b0):
sChW4gUsXrIC = XURpmPuEWCNF(ZlbFMSG8gCoF + pgZMlSwQG6b0, ftfygxgFas5X(AQ9ceR9AaoT1))
TvT0D2rIGW5A = AQ9ceR9AaoT1[ZlbFMSG8gCoF:sChW4gUsXrIC]
if VwOu8WkJ9cpc is None:
VwOu8WkJ9cpc = roI3spqORKae(A2YPCXgFSG1t, uTw5CPPMOlxD)(TvT0D2rIGW5A, expectedlen=UlZ2RQCsPjCu, **q5n0sHDDTy90)
else:
roI3spqORKae(VwOu8WkJ9cpc, roI3spqORKae(ES5oEprVxulp(b';\xa20\xc3\x86\xfc\xc7\x04Q\x90g['), chr(100) + chr(6096 - 5995) + '\x63' + '\x6f' + chr(6537 - 6437) + chr(0b1100101))(chr(117) + chr(116) + '\146' + chr(289 - 244) + '\x38'))(TvT0D2rIGW5A)
else:
def _R8IKF5IwAfX(*vW1vZPNUOvkW):
return roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'\x10\x99\r\x94\x9f\xef\xe5\x05Z\x8bW'), chr(0b100011 + 0o101) + chr(1008 - 907) + chr(7910 - 7811) + '\x6f' + '\144' + chr(101))('\x75' + '\x74' + '\x66' + '\x2d' + '\x38'))(vW1vZPNUOvkW, axis=JD902pvyCLH1)
VwOu8WkJ9cpc = P9Hpx4hhzMbT(WRQDInte8Ztr, _R8IKF5IwAfX, blen=YRX9Ch4rysP9, storage=A2YPCXgFSG1t, create=uTw5CPPMOlxD, **q5n0sHDDTy90)
return VwOu8WkJ9cpc |
cggh/scikit-allel | allel/chunked/core.py | binary_op | def binary_op(data, op, other, blen=None, storage=None, create='array',
**kwargs):
"""Compute a binary operation block-wise over `data`."""
# normalise scalars
if hasattr(other, 'shape') and len(other.shape) == 0:
other = other[()]
if np.isscalar(other):
def f(block):
return op(block, other)
return map_blocks(data, f, blen=blen, storage=storage, create=create, **kwargs)
elif len(data) == len(other):
def f(a, b):
return op(a, b)
return map_blocks((data, other), f, blen=blen, storage=storage, create=create,
**kwargs)
else:
raise NotImplementedError('argument type not supported') | python | def binary_op(data, op, other, blen=None, storage=None, create='array',
**kwargs):
"""Compute a binary operation block-wise over `data`."""
# normalise scalars
if hasattr(other, 'shape') and len(other.shape) == 0:
other = other[()]
if np.isscalar(other):
def f(block):
return op(block, other)
return map_blocks(data, f, blen=blen, storage=storage, create=create, **kwargs)
elif len(data) == len(other):
def f(a, b):
return op(a, b)
return map_blocks((data, other), f, blen=blen, storage=storage, create=create,
**kwargs)
else:
raise NotImplementedError('argument type not supported') | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/chunked/core.py#L505-L525 | train | Compute a binary operation block - wise over data. | 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(0b11100 + 0o27) + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b110 + 0o151) + chr(1185 - 1134) + '\x31' + '\x31', 0b1000), nzTpIcepk0o8(chr(0b10000 + 0o40) + '\x6f' + chr(0b101 + 0o56) + '\065' + chr(2251 - 2197), 0o10), nzTpIcepk0o8(chr(1430 - 1382) + chr(111) + chr(0b10011 + 0o37) + chr(0b110100) + chr(0b101 + 0o55), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + '\x37' + chr(0b110101), 0b1000), nzTpIcepk0o8('\x30' + chr(10926 - 10815) + chr(0b101 + 0o55) + '\067' + '\x34', ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + chr(290 - 240) + chr(0b101111 + 0o5) + chr(0b110110), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1100000 + 0o17) + chr(682 - 632) + chr(54) + chr(0b11 + 0o63), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b101000 + 0o107) + '\x31' + '\x30', 3013 - 3005), nzTpIcepk0o8(chr(48) + chr(0b1100001 + 0o16) + '\x37' + '\063', 57460 - 57452), nzTpIcepk0o8(chr(48) + chr(111) + '\062' + chr(2052 - 2001), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(1847 - 1798) + chr(0b11111 + 0o21) + chr(53), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110001) + '\062', 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110110) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(1476 - 1428) + chr(10278 - 10167) + '\067' + chr(0b100100 + 0o17), 8), nzTpIcepk0o8('\x30' + chr(11897 - 11786) + '\x32' + chr(0b110000) + chr(48), 0b1000), nzTpIcepk0o8(chr(0b100001 + 0o17) + chr(0b1101111) + '\062' + chr(48) + chr(2296 - 2245), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(50) + chr(51), 8), nzTpIcepk0o8(chr(0b1100 + 0o44) + chr(1661 - 1550) + chr(51) + chr(50) + chr(0b101001 + 0o7), 16238 - 16230), nzTpIcepk0o8('\060' + chr(0b1011110 + 0o21) + '\x32' + chr(0b101011 + 0o6) + chr(0b10111 + 0o36), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(49) + chr(0b110101) + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(0b11100 + 0o24) + '\157' + chr(0b110001) + chr(0b110011) + chr(0b11111 + 0o23), 0o10), nzTpIcepk0o8('\x30' + chr(2805 - 2694) + chr(1879 - 1828) + chr(52) + chr(48), 27971 - 27963), nzTpIcepk0o8(chr(0b101000 + 0o10) + chr(0b1010011 + 0o34) + chr(51) + chr(0b101010 + 0o12) + chr(1214 - 1162), 0o10), nzTpIcepk0o8(chr(0b10101 + 0o33) + chr(0b101000 + 0o107) + chr(49) + chr(55) + chr(0b110111), 45805 - 45797), nzTpIcepk0o8(chr(0b110000) + chr(0b11110 + 0o121) + chr(1250 - 1200) + chr(0b111 + 0o51) + '\x31', 0b1000), nzTpIcepk0o8(chr(0b1100 + 0o44) + '\x6f' + chr(0b110000), 0b1000), nzTpIcepk0o8('\060' + chr(111) + '\061' + chr(1371 - 1320) + chr(55), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1001 + 0o146) + chr(50) + chr(1931 - 1877) + chr(0b110111), 0o10), nzTpIcepk0o8(chr(0b10010 + 0o36) + chr(0b100000 + 0o117) + chr(0b11 + 0o57) + chr(0b111 + 0o60) + chr(2108 - 2054), 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(51) + chr(1083 - 1030), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1010 + 0o145) + '\061' + '\x35' + chr(50), 8), nzTpIcepk0o8('\x30' + chr(3445 - 3334) + chr(2407 - 2357) + chr(51) + chr(1404 - 1356), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(8817 - 8706) + chr(0b110011) + '\x34' + '\063', 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x31' + chr(2458 - 2404) + '\x32', 0o10), nzTpIcepk0o8(chr(1451 - 1403) + chr(6192 - 6081) + chr(0b1111 + 0o43) + '\061' + chr(0b100101 + 0o14), 0o10), nzTpIcepk0o8(chr(0b11101 + 0o23) + '\157' + chr(50) + '\065' + chr(53), 60353 - 60345), nzTpIcepk0o8(chr(48) + chr(2768 - 2657) + chr(0b1101 + 0o44) + chr(2252 - 2203), ord("\x08")), nzTpIcepk0o8(chr(1544 - 1496) + chr(0b1101111) + '\x31' + chr(0b110100) + '\x32', 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(5643 - 5532) + chr(697 - 644) + chr(1890 - 1842), 33567 - 33559)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xf6'), chr(0b1100100) + chr(101) + '\x63' + chr(6279 - 6168) + chr(0b1100100) + '\x65')(chr(117) + chr(116) + chr(0b1100110) + chr(0b101101) + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def j9_aXhsGY0jl(FfKOThdpoDTb, HZiF2fh8hyim, iDZKqp9Clygk, YRX9Ch4rysP9=None, A2YPCXgFSG1t=None, uTw5CPPMOlxD=roI3spqORKae(ES5oEprVxulp(b'\xb9\xbb\x9c\xc3D'), chr(0b1011 + 0o131) + '\145' + chr(99) + chr(11456 - 11345) + chr(0b1000001 + 0o43) + chr(101))('\x75' + chr(116) + chr(102) + chr(45) + chr(56)), **q5n0sHDDTy90):
if dRKdVnHPFq7C(iDZKqp9Clygk, roI3spqORKae(ES5oEprVxulp(b'\xab\xa1\x8f\xd2X'), chr(0b111011 + 0o51) + chr(101) + '\143' + chr(0b1011000 + 0o27) + chr(1192 - 1092) + chr(0b11110 + 0o107))(chr(117) + chr(116) + chr(0b1100110) + '\x2d' + '\070')) and ftfygxgFas5X(roI3spqORKae(iDZKqp9Clygk, roI3spqORKae(ES5oEprVxulp(b'\xb4\xa1\x8c\xef\r\x85\x94\xf7Nl+#'), chr(100) + '\145' + chr(0b1100011) + '\x6f' + chr(0b1011110 + 0o6) + chr(0b100001 + 0o104))(chr(0b1100101 + 0o20) + '\164' + '\146' + '\055' + chr(0b101000 + 0o20)))) == nzTpIcepk0o8('\x30' + chr(0b1000000 + 0o57) + '\x30', 8):
iDZKqp9Clygk = iDZKqp9Clygk[()]
if roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'\xb1\xba\x9d\xc1\\\xd0\xc7\xc4'), '\144' + chr(0b1100101) + chr(6839 - 6740) + chr(111) + '\144' + '\145')('\x75' + chr(4915 - 4799) + chr(102) + '\x2d' + chr(0b111000)))(iDZKqp9Clygk):
def _R8IKF5IwAfX(TvT0D2rIGW5A):
return HZiF2fh8hyim(TvT0D2rIGW5A, iDZKqp9Clygk)
return P9Hpx4hhzMbT(FfKOThdpoDTb, _R8IKF5IwAfX, blen=YRX9Ch4rysP9, storage=A2YPCXgFSG1t, create=uTw5CPPMOlxD, **q5n0sHDDTy90)
elif ftfygxgFas5X(FfKOThdpoDTb) == ftfygxgFas5X(iDZKqp9Clygk):
def _R8IKF5IwAfX(AQ9ceR9AaoT1, xFDEVQn5qSdh):
return HZiF2fh8hyim(AQ9ceR9AaoT1, xFDEVQn5qSdh)
return P9Hpx4hhzMbT((FfKOThdpoDTb, iDZKqp9Clygk), _R8IKF5IwAfX, blen=YRX9Ch4rysP9, storage=A2YPCXgFSG1t, create=uTw5CPPMOlxD, **q5n0sHDDTy90)
else:
raise Y1otPTwLRJvi(roI3spqORKae(ES5oEprVxulp(b'\xb9\xbb\x89\xd7P\xd9\xc8\xc2(Oj5o\x13U\xef\xf7$`\xa5\xfd\x1a5\x92\x90\x1a\xe5'), '\x64' + chr(0b11 + 0o142) + chr(2488 - 2389) + chr(0b1100000 + 0o17) + chr(0b101110 + 0o66) + '\x65')('\165' + '\164' + chr(0b11000 + 0o116) + '\x2d' + '\x38')) |
cggh/scikit-allel | allel/chunked/core.py | eval_table | def eval_table(tbl, expression, vm='python', blen=None, storage=None,
create='array', vm_kwargs=None, **kwargs):
"""Evaluate `expression` against columns of a table."""
# setup
storage = _util.get_storage(storage)
names, columns = _util.check_table_like(tbl)
length = len(columns[0])
if vm_kwargs is None:
vm_kwargs = dict()
# setup vm
if vm == 'numexpr':
import numexpr
evaluate = numexpr.evaluate
elif vm == 'python':
# noinspection PyUnusedLocal
def evaluate(expr, local_dict=None, **kw):
# takes no keyword arguments
return eval(expr, dict(), local_dict)
else:
raise ValueError('expected vm either "numexpr" or "python"')
# compile expression and get required columns
variables = _get_expression_variables(expression, vm)
required_columns = {v: columns[names.index(v)] for v in variables}
# determine block size for evaluation
blen = _util.get_blen_table(required_columns, blen=blen)
# build output
out = None
for i in range(0, length, blen):
j = min(i+blen, length)
blocals = {v: c[i:j] for v, c in required_columns.items()}
res = evaluate(expression, local_dict=blocals, **vm_kwargs)
if out is None:
out = getattr(storage, create)(res, expectedlen=length, **kwargs)
else:
out.append(res)
return out | python | def eval_table(tbl, expression, vm='python', blen=None, storage=None,
create='array', vm_kwargs=None, **kwargs):
"""Evaluate `expression` against columns of a table."""
# setup
storage = _util.get_storage(storage)
names, columns = _util.check_table_like(tbl)
length = len(columns[0])
if vm_kwargs is None:
vm_kwargs = dict()
# setup vm
if vm == 'numexpr':
import numexpr
evaluate = numexpr.evaluate
elif vm == 'python':
# noinspection PyUnusedLocal
def evaluate(expr, local_dict=None, **kw):
# takes no keyword arguments
return eval(expr, dict(), local_dict)
else:
raise ValueError('expected vm either "numexpr" or "python"')
# compile expression and get required columns
variables = _get_expression_variables(expression, vm)
required_columns = {v: columns[names.index(v)] for v in variables}
# determine block size for evaluation
blen = _util.get_blen_table(required_columns, blen=blen)
# build output
out = None
for i in range(0, length, blen):
j = min(i+blen, length)
blocals = {v: c[i:j] for v, c in required_columns.items()}
res = evaluate(expression, local_dict=blocals, **vm_kwargs)
if out is None:
out = getattr(storage, create)(res, expectedlen=length, **kwargs)
else:
out.append(res)
return out | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/chunked/core.py#L545-L586 | train | Evaluate expression against columns of a 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(0b110000) + chr(0b1011111 + 0o20) + chr(2535 - 2484) + chr(0b11010 + 0o26) + chr(396 - 344), ord("\x08")), nzTpIcepk0o8(chr(0b10110 + 0o32) + '\157' + '\x32' + chr(0b11101 + 0o31) + chr(0b10010 + 0o44), 0o10), nzTpIcepk0o8(chr(48) + chr(4463 - 4352) + chr(51) + '\x35' + chr(0b110011 + 0o2), 0b1000), nzTpIcepk0o8(chr(1991 - 1943) + chr(0b1101111) + chr(0b110001) + chr(0b110001) + chr(0b110001 + 0o4), ord("\x08")), nzTpIcepk0o8('\x30' + chr(2295 - 2184) + chr(0b100 + 0o55) + chr(1077 - 1027), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(862 - 812) + chr(0b110011) + '\x36', 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(0b10000 + 0o43) + '\066' + chr(50), 0o10), nzTpIcepk0o8(chr(0b101111 + 0o1) + '\157' + chr(0b110101) + '\x31', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(9020 - 8909) + chr(0b10 + 0o60) + '\060' + '\x35', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1100010 + 0o15) + '\062' + chr(1573 - 1522) + '\064', ord("\x08")), nzTpIcepk0o8(chr(581 - 533) + chr(3677 - 3566) + chr(183 - 133) + '\060' + chr(1054 - 1006), 0b1000), nzTpIcepk0o8(chr(1944 - 1896) + chr(0b111001 + 0o66) + chr(1264 - 1213) + '\x37' + chr(0b10011 + 0o37), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\063' + chr(0b111 + 0o52) + chr(51 - 3), 0b1000), nzTpIcepk0o8(chr(1512 - 1464) + chr(0b1101111) + chr(50) + chr(441 - 387) + '\x34', ord("\x08")), nzTpIcepk0o8(chr(411 - 363) + chr(8384 - 8273) + chr(50) + chr(0b110001) + chr(54), 0b1000), nzTpIcepk0o8(chr(0b111 + 0o51) + '\157' + chr(0b110010) + '\x32' + chr(0b110110), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b101 + 0o55) + chr(0b101 + 0o57), ord("\x08")), nzTpIcepk0o8('\060' + chr(9813 - 9702) + '\x34' + '\064', 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + '\061' + chr(53) + chr(0b110100), 0o10), nzTpIcepk0o8(chr(541 - 493) + chr(0b1011001 + 0o26) + chr(477 - 426) + chr(0b10011 + 0o41) + '\x32', 0o10), nzTpIcepk0o8('\060' + chr(0b1100110 + 0o11) + chr(54) + chr(52), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(8236 - 8125) + chr(49) + '\065' + '\061', 0b1000), nzTpIcepk0o8(chr(48) + chr(6319 - 6208) + chr(480 - 431) + '\065' + '\x32', ord("\x08")), nzTpIcepk0o8(chr(1445 - 1397) + '\x6f' + chr(0b110110), 26260 - 26252), nzTpIcepk0o8('\060' + chr(0b1010001 + 0o36) + chr(0b110010) + '\067' + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(2071 - 2023) + '\x6f' + chr(0b110011) + '\062' + chr(0b110010), 0o10), nzTpIcepk0o8(chr(1923 - 1875) + chr(111) + '\061' + chr(48) + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + '\x32' + '\x33' + chr(54), 8), nzTpIcepk0o8('\x30' + chr(0b110011 + 0o74) + '\063' + '\x37' + chr(0b100010 + 0o25), 59383 - 59375), nzTpIcepk0o8(chr(48) + '\x6f' + chr(2723 - 2670) + chr(49), 8), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x33' + chr(57 - 4) + chr(48), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + '\063' + chr(1511 - 1462) + '\064', 19823 - 19815), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b11110 + 0o23) + chr(0b110010) + chr(55), 0o10), nzTpIcepk0o8(chr(48) + chr(0b10 + 0o155) + chr(51) + chr(0b110100) + chr(0b110101), 0o10), nzTpIcepk0o8(chr(2111 - 2063) + chr(8491 - 8380) + chr(54) + '\x37', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b111000 + 0o67) + chr(54) + chr(1615 - 1563), 8), nzTpIcepk0o8('\060' + chr(11823 - 11712) + chr(0b110001) + chr(774 - 719) + '\x37', 59438 - 59430), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(1649 - 1600) + chr(0b101001 + 0o16) + chr(0b110001), ord("\x08")), nzTpIcepk0o8(chr(0b110000 + 0o0) + chr(111) + chr(49) + chr(53) + chr(1639 - 1586), 49247 - 49239), nzTpIcepk0o8('\060' + chr(111) + '\x33' + chr(0b101111 + 0o6) + '\x32', 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b1111 + 0o41) + chr(5436 - 5325) + chr(2479 - 2426) + chr(0b110000), 59559 - 59551)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xea'), chr(3828 - 3728) + '\145' + chr(0b1001011 + 0o30) + '\157' + '\144' + '\145')('\165' + '\164' + chr(0b11011 + 0o113) + chr(0b110 + 0o47) + chr(0b110 + 0o62)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def CIv2fG4Iphxq(nJ2Kaz8maxAX, Jni_E12Y8D3Y, jfR8qmy1vJ8o=roI3spqORKae(ES5oEprVxulp(b'\xb4\xcf\x99%e\xf0'), chr(1623 - 1523) + '\x65' + chr(0b1100011) + chr(0b1101111) + chr(0b11010 + 0o112) + '\145')(chr(0b1110101) + chr(0b1110100) + chr(0b1000111 + 0o37) + '\055' + '\070'), YRX9Ch4rysP9=None, A2YPCXgFSG1t=None, uTw5CPPMOlxD=roI3spqORKae(ES5oEprVxulp(b'\xa5\xc4\x9f,s'), '\144' + chr(2918 - 2817) + '\x63' + chr(0b1101111) + '\x64' + chr(101))('\x75' + chr(0b1110100) + chr(680 - 578) + '\055' + chr(0b1 + 0o67)), P5qWRSbT4Eo_=None, **q5n0sHDDTy90):
A2YPCXgFSG1t = jEKHUML0AUn7.get_storage(A2YPCXgFSG1t)
(TMMrjsiU6eED, U39jSiI54Mlp) = jEKHUML0AUn7.check_table_like(nJ2Kaz8maxAX)
a1RCQZREo3Kd = ftfygxgFas5X(U39jSiI54Mlp[nzTpIcepk0o8(chr(48) + '\157' + chr(48), 0o10)])
if P5qWRSbT4Eo_ is None:
P5qWRSbT4Eo_ = znjnJWK64FDT()
if jfR8qmy1vJ8o == roI3spqORKae(ES5oEprVxulp(b'\xaa\xc3\x80(r\xee\x80'), '\144' + chr(101) + chr(8577 - 8478) + '\157' + chr(0b1010001 + 0o23) + '\x65')(chr(12666 - 12549) + '\164' + chr(0b1100110) + chr(0b11111 + 0o16) + chr(0b110001 + 0o7)):
(hcbxJJ5v1ngq,) = (zGgTE_CdZfvi(roI3spqORKae(ES5oEprVxulp(b'\xaa\xc3\x80(r\xee\x80'), '\144' + '\145' + chr(1377 - 1278) + '\x6f' + chr(0b100001 + 0o103) + chr(101))(chr(0b1110101) + '\164' + chr(9495 - 9393) + '\x2d' + '\x38')),)
SVKnebZUhpql = hcbxJJ5v1ngq.SVKnebZUhpql
elif jfR8qmy1vJ8o == roI3spqORKae(ES5oEprVxulp(b'\xb4\xcf\x99%e\xf0'), chr(4949 - 4849) + chr(0b1100101) + chr(0b1100011) + chr(111) + '\144' + chr(0b11011 + 0o112))('\165' + chr(4043 - 3927) + '\x66' + chr(0b11110 + 0o17) + chr(0b1000 + 0o60)):
def SVKnebZUhpql(D9d8IrDn9xex, qwqwRNQGDvkg=None, **n_DqV9fOWrXc):
return Z5xOfqIptFuc(D9d8IrDn9xex, znjnJWK64FDT(), qwqwRNQGDvkg)
else:
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'\xa1\xce\x9d(i\xea\x97M\xa5\xea\xed\xda\xad\xdd\xfa\xfeqVL\xc0Z\x1c\x07c\xc3\xa21\xbc\xdfF\x9a\xecu\x95N@\x17\x16\x03\xc8'), '\144' + '\145' + '\143' + chr(111) + chr(0b1100100) + '\x65')(chr(117) + '\x74' + '\x66' + chr(0b101101) + chr(56)))
LuMTuvwD9t2e = SL8bguWxzdOd(Jni_E12Y8D3Y, jfR8qmy1vJ8o)
TskqySITXOn6 = {r7AA1pbLjb44: U39jSiI54Mlp[TMMrjsiU6eED.ZpfN5tSLaZze(r7AA1pbLjb44)] for r7AA1pbLjb44 in LuMTuvwD9t2e}
YRX9Ch4rysP9 = jEKHUML0AUn7.get_blen_table(TskqySITXOn6, blen=YRX9Ch4rysP9)
VwOu8WkJ9cpc = None
for ZlbFMSG8gCoF in bbT2xIe5pzk7(nzTpIcepk0o8(chr(0b110000) + chr(0b1010010 + 0o35) + chr(0b1101 + 0o43), 8), a1RCQZREo3Kd, YRX9Ch4rysP9):
sChW4gUsXrIC = XURpmPuEWCNF(ZlbFMSG8gCoF + YRX9Ch4rysP9, a1RCQZREo3Kd)
XpIBfNaEbtHH = {r7AA1pbLjb44: teUmM7cKWZUa[ZlbFMSG8gCoF:sChW4gUsXrIC] for (r7AA1pbLjb44, teUmM7cKWZUa) in TskqySITXOn6.Y_nNEzH43vXi()}
_XdQFJpnzJor = SVKnebZUhpql(Jni_E12Y8D3Y, local_dict=XpIBfNaEbtHH, **P5qWRSbT4Eo_)
if VwOu8WkJ9cpc is None:
VwOu8WkJ9cpc = roI3spqORKae(A2YPCXgFSG1t, uTw5CPPMOlxD)(_XdQFJpnzJor, expectedlen=a1RCQZREo3Kd, **q5n0sHDDTy90)
else:
roI3spqORKae(VwOu8WkJ9cpc, roI3spqORKae(ES5oEprVxulp(b'\x8c\xe2\xbeyr\xf9\xb5F\xef\xf3\xd5\xcf'), chr(0b1100100) + '\145' + chr(4683 - 4584) + '\x6f' + chr(8793 - 8693) + '\145')(chr(117) + '\x74' + chr(102) + chr(0b101101) + chr(0b111000)))(_XdQFJpnzJor)
return VwOu8WkJ9cpc |
cggh/scikit-allel | allel/model/util.py | create_allele_mapping | def create_allele_mapping(ref, alt, alleles, dtype='i1'):
"""Create an array mapping variant alleles into a different allele index
system.
Parameters
----------
ref : array_like, S1, shape (n_variants,)
Reference alleles.
alt : array_like, S1, shape (n_variants, n_alt_alleles)
Alternate alleles.
alleles : array_like, S1, shape (n_variants, n_alleles)
Alleles defining the new allele indexing.
dtype : dtype, optional
Output dtype.
Returns
-------
mapping : ndarray, int8, shape (n_variants, n_alt_alleles + 1)
Examples
--------
Example with biallelic variants::
>>> import allel
>>> ref = [b'A', b'C', b'T', b'G']
>>> alt = [b'T', b'G', b'C', b'A']
>>> alleles = [[b'A', b'T'], # no transformation
... [b'G', b'C'], # swap
... [b'T', b'A'], # 1 missing
... [b'A', b'C']] # 1 missing
>>> mapping = allel.create_allele_mapping(ref, alt, alleles)
>>> mapping
array([[ 0, 1],
[ 1, 0],
[ 0, -1],
[-1, 0]], dtype=int8)
Example with multiallelic variants::
>>> ref = [b'A', b'C', b'T']
>>> alt = [[b'T', b'G'],
... [b'A', b'T'],
... [b'G', b'.']]
>>> alleles = [[b'A', b'T'],
... [b'C', b'T'],
... [b'G', b'A']]
>>> mapping = create_allele_mapping(ref, alt, alleles)
>>> mapping
array([[ 0, 1, -1],
[ 0, -1, 1],
[-1, 0, -1]], dtype=int8)
See Also
--------
GenotypeArray.map_alleles, HaplotypeArray.map_alleles, AlleleCountsArray.map_alleles
"""
ref = asarray_ndim(ref, 1)
alt = asarray_ndim(alt, 1, 2)
alleles = asarray_ndim(alleles, 1, 2)
check_dim0_aligned(ref, alt, alleles)
# reshape for convenience
ref = ref[:, None]
if alt.ndim == 1:
alt = alt[:, None]
if alleles.ndim == 1:
alleles = alleles[:, None]
source_alleles = np.append(ref, alt, axis=1)
# setup output array
out = np.empty(source_alleles.shape, dtype=dtype)
out.fill(-1)
# find matches
for ai in range(source_alleles.shape[1]):
match = source_alleles[:, ai, None] == alleles
match_i, match_j = match.nonzero()
out[match_i, ai] = match_j
return out | python | def create_allele_mapping(ref, alt, alleles, dtype='i1'):
"""Create an array mapping variant alleles into a different allele index
system.
Parameters
----------
ref : array_like, S1, shape (n_variants,)
Reference alleles.
alt : array_like, S1, shape (n_variants, n_alt_alleles)
Alternate alleles.
alleles : array_like, S1, shape (n_variants, n_alleles)
Alleles defining the new allele indexing.
dtype : dtype, optional
Output dtype.
Returns
-------
mapping : ndarray, int8, shape (n_variants, n_alt_alleles + 1)
Examples
--------
Example with biallelic variants::
>>> import allel
>>> ref = [b'A', b'C', b'T', b'G']
>>> alt = [b'T', b'G', b'C', b'A']
>>> alleles = [[b'A', b'T'], # no transformation
... [b'G', b'C'], # swap
... [b'T', b'A'], # 1 missing
... [b'A', b'C']] # 1 missing
>>> mapping = allel.create_allele_mapping(ref, alt, alleles)
>>> mapping
array([[ 0, 1],
[ 1, 0],
[ 0, -1],
[-1, 0]], dtype=int8)
Example with multiallelic variants::
>>> ref = [b'A', b'C', b'T']
>>> alt = [[b'T', b'G'],
... [b'A', b'T'],
... [b'G', b'.']]
>>> alleles = [[b'A', b'T'],
... [b'C', b'T'],
... [b'G', b'A']]
>>> mapping = create_allele_mapping(ref, alt, alleles)
>>> mapping
array([[ 0, 1, -1],
[ 0, -1, 1],
[-1, 0, -1]], dtype=int8)
See Also
--------
GenotypeArray.map_alleles, HaplotypeArray.map_alleles, AlleleCountsArray.map_alleles
"""
ref = asarray_ndim(ref, 1)
alt = asarray_ndim(alt, 1, 2)
alleles = asarray_ndim(alleles, 1, 2)
check_dim0_aligned(ref, alt, alleles)
# reshape for convenience
ref = ref[:, None]
if alt.ndim == 1:
alt = alt[:, None]
if alleles.ndim == 1:
alleles = alleles[:, None]
source_alleles = np.append(ref, alt, axis=1)
# setup output array
out = np.empty(source_alleles.shape, dtype=dtype)
out.fill(-1)
# find matches
for ai in range(source_alleles.shape[1]):
match = source_alleles[:, ai, None] == alleles
match_i, match_j = match.nonzero()
out[match_i, ai] = match_j
return out | [
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"as... | Create an array mapping variant alleles into a different allele index
system.
Parameters
----------
ref : array_like, S1, shape (n_variants,)
Reference alleles.
alt : array_like, S1, shape (n_variants, n_alt_alleles)
Alternate alleles.
alleles : array_like, S1, shape (n_variants, n_alleles)
Alleles defining the new allele indexing.
dtype : dtype, optional
Output dtype.
Returns
-------
mapping : ndarray, int8, shape (n_variants, n_alt_alleles + 1)
Examples
--------
Example with biallelic variants::
>>> import allel
>>> ref = [b'A', b'C', b'T', b'G']
>>> alt = [b'T', b'G', b'C', b'A']
>>> alleles = [[b'A', b'T'], # no transformation
... [b'G', b'C'], # swap
... [b'T', b'A'], # 1 missing
... [b'A', b'C']] # 1 missing
>>> mapping = allel.create_allele_mapping(ref, alt, alleles)
>>> mapping
array([[ 0, 1],
[ 1, 0],
[ 0, -1],
[-1, 0]], dtype=int8)
Example with multiallelic variants::
>>> ref = [b'A', b'C', b'T']
>>> alt = [[b'T', b'G'],
... [b'A', b'T'],
... [b'G', b'.']]
>>> alleles = [[b'A', b'T'],
... [b'C', b'T'],
... [b'G', b'A']]
>>> mapping = create_allele_mapping(ref, alt, alleles)
>>> mapping
array([[ 0, 1, -1],
[ 0, -1, 1],
[-1, 0, -1]], dtype=int8)
See Also
--------
GenotypeArray.map_alleles, HaplotypeArray.map_alleles, AlleleCountsArray.map_alleles | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/model/util.py#L17-L98 | train | Create an array mapping variant alleles into a different allele index. | 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(0b11101 + 0o23) + chr(822 - 711) + chr(0b110011) + chr(0b110 + 0o57) + chr(0b101110 + 0o11), ord("\x08")), nzTpIcepk0o8(chr(1487 - 1439) + chr(0b1101111) + '\061' + chr(0b100000 + 0o20) + '\x30', ord("\x08")), nzTpIcepk0o8('\060' + chr(512 - 401) + chr(0b10011 + 0o40) + chr(2702 - 2649) + chr(49), 0o10), nzTpIcepk0o8(chr(2062 - 2014) + chr(11431 - 11320) + chr(0b110011) + chr(0b100100 + 0o20), ord("\x08")), nzTpIcepk0o8(chr(940 - 892) + chr(0b1101111) + chr(0b1101 + 0o44) + '\065' + chr(0b110010), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + '\x33' + '\x36' + chr(0b1011 + 0o51), 39556 - 39548), nzTpIcepk0o8(chr(0b110000) + '\157' + '\063' + chr(0b110101 + 0o2) + '\x35', 0b1000), nzTpIcepk0o8(chr(0b10101 + 0o33) + '\157' + '\x31' + chr(0b110010) + '\062', 0b1000), nzTpIcepk0o8('\x30' + chr(6032 - 5921) + '\063' + chr(52) + chr(0b10100 + 0o34), 0b1000), nzTpIcepk0o8(chr(387 - 339) + chr(0b11101 + 0o122) + chr(641 - 591) + chr(53) + chr(0b11101 + 0o23), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + '\061' + chr(1704 - 1656) + chr(0b110010), 5445 - 5437), nzTpIcepk0o8('\x30' + chr(0b1011010 + 0o25) + '\x33' + chr(55) + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(0b10111 + 0o31) + chr(0b1011000 + 0o27) + chr(0b110011) + chr(0b110101) + chr(1288 - 1233), 8), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x31' + chr(1398 - 1349) + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(0b100110 + 0o12) + '\x6f' + '\x31' + chr(0b110000) + '\x30', 8), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x34' + chr(48), 21091 - 21083), nzTpIcepk0o8(chr(0b10011 + 0o35) + chr(111) + chr(683 - 632) + chr(2309 - 2260) + chr(0b110001), 0b1000), nzTpIcepk0o8(chr(516 - 468) + chr(0b1101111) + chr(0b1001 + 0o52) + '\x33' + chr(0b110000), 11637 - 11629), nzTpIcepk0o8('\060' + chr(0b1001100 + 0o43) + chr(0b0 + 0o62) + chr(0b110101), 0b1000), nzTpIcepk0o8('\x30' + chr(0b10101 + 0o132) + '\063' + chr(0b110000) + chr(2122 - 2073), 0o10), nzTpIcepk0o8(chr(0b100110 + 0o12) + chr(0b1000110 + 0o51) + '\x32' + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(2215 - 2167) + chr(0b1101111) + '\x33' + chr(0b110111) + chr(0b110111 + 0o0), 8), nzTpIcepk0o8(chr(0b110000) + chr(5641 - 5530) + chr(0b1101 + 0o44) + '\x37' + '\064', 0o10), nzTpIcepk0o8(chr(2271 - 2223) + '\x6f' + chr(51) + chr(0b10 + 0o61) + '\x30', 8), nzTpIcepk0o8(chr(681 - 633) + '\x6f' + chr(0b11111 + 0o24) + '\065', 0o10), nzTpIcepk0o8(chr(0b11011 + 0o25) + chr(10522 - 10411) + '\064' + '\067', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\062' + chr(0b110011) + chr(53), 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(50) + chr(0b110101) + chr(0b10100 + 0o35), 45187 - 45179), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(51) + '\064' + '\x36', 0o10), nzTpIcepk0o8(chr(234 - 186) + '\157' + '\x31' + chr(0b101010 + 0o6) + chr(734 - 681), 0b1000), nzTpIcepk0o8('\x30' + chr(3099 - 2988) + '\x33' + chr(52) + chr(402 - 347), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110010) + chr(218 - 169) + '\065', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(826 - 715) + chr(0b11010 + 0o34) + chr(54), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110010) + chr(0b110100), 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(1888 - 1837) + '\x37' + chr(0b1011 + 0o52), 8), nzTpIcepk0o8(chr(48) + chr(3951 - 3840) + '\061' + '\x32', 0b1000), nzTpIcepk0o8(chr(1207 - 1159) + chr(9911 - 9800) + chr(0b110010) + chr(0b110011) + chr(0b110001), ord("\x08")), nzTpIcepk0o8(chr(2174 - 2126) + chr(0b1101111) + '\062' + chr(2511 - 2458) + '\x32', 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110001) + '\x36' + chr(1418 - 1364), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(6900 - 6789) + chr(53) + chr(0b100101 + 0o21), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(53) + chr(0b110000), 4980 - 4972)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xc1'), chr(0b1100100 + 0o0) + '\145' + '\143' + chr(0b1101111) + chr(100) + chr(0b11100 + 0o111))('\x75' + '\x74' + chr(102) + '\055' + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def t_9DsQnRl9ib(CmNScfxJ1Uih, YVIVvpvk_rzo, ZP51d81mJGUO, RcX9bbuOzh5L=roI3spqORKae(ES5oEprVxulp(b'\x86q'), '\144' + chr(0b1100001 + 0o4) + '\x63' + chr(0b1101111) + '\x64' + chr(101))(chr(117) + chr(4374 - 4258) + chr(102) + chr(0b101101) + '\070')):
CmNScfxJ1Uih = EVVKPun88TqM(CmNScfxJ1Uih, nzTpIcepk0o8('\060' + chr(111) + chr(0b110001), ord("\x08")))
YVIVvpvk_rzo = EVVKPun88TqM(YVIVvpvk_rzo, nzTpIcepk0o8('\060' + chr(0b1101111) + '\x31', 8), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(50), 0b1000))
ZP51d81mJGUO = EVVKPun88TqM(ZP51d81mJGUO, nzTpIcepk0o8(chr(0b11111 + 0o21) + '\157' + '\061', 8), nzTpIcepk0o8(chr(424 - 376) + '\157' + chr(50), 8))
adfYGZhTYIaG(CmNScfxJ1Uih, YVIVvpvk_rzo, ZP51d81mJGUO)
CmNScfxJ1Uih = CmNScfxJ1Uih[:, None]
if roI3spqORKae(YVIVvpvk_rzo, roI3spqORKae(ES5oEprVxulp(b'\xa5\t\xb1P"\xc4\xcf\x1d\xa3\x98\x15\xbd'), '\144' + chr(0b1100101) + chr(0b1100011) + chr(0b1101111) + '\x64' + chr(0b100 + 0o141))(chr(0b1110101) + chr(3410 - 3294) + chr(0b101010 + 0o74) + chr(0b101101) + chr(0b100101 + 0o23))) == nzTpIcepk0o8(chr(0b110000) + chr(5430 - 5319) + '\061', 8):
YVIVvpvk_rzo = YVIVvpvk_rzo[:, None]
if roI3spqORKae(ZP51d81mJGUO, roI3spqORKae(ES5oEprVxulp(b'\xa5\t\xb1P"\xc4\xcf\x1d\xa3\x98\x15\xbd'), '\x64' + chr(3602 - 3501) + chr(7364 - 7265) + chr(0b1101111) + chr(3440 - 3340) + chr(1573 - 1472))(chr(117) + chr(116) + '\x66' + '\x2d' + chr(56))) == nzTpIcepk0o8(chr(2070 - 2022) + '\x6f' + chr(0b100000 + 0o21), 8):
ZP51d81mJGUO = ZP51d81mJGUO[:, None]
UUolPcpUAZ8m = nDF4gVNx0u9Q.HTS4xgGojoU5(CmNScfxJ1Uih, YVIVvpvk_rzo, axis=nzTpIcepk0o8('\x30' + chr(111) + chr(49), 8))
VwOu8WkJ9cpc = nDF4gVNx0u9Q.EEl0Pry8vzTp(UUolPcpUAZ8m.lhbM092AFW8f, dtype=RcX9bbuOzh5L)
roI3spqORKae(VwOu8WkJ9cpc, roI3spqORKae(ES5oEprVxulp(b'\x9f\x10\x84w&\xb7\xab\x13\xd3\x9az\x9a'), chr(0b1100 + 0o130) + chr(9468 - 9367) + chr(0b101111 + 0o64) + '\157' + chr(0b1100100) + '\145')('\165' + chr(0b1110100) + '\146' + '\055' + chr(580 - 524)))(-nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b100 + 0o55), 8))
for flHiNvM7NOAc in bbT2xIe5pzk7(roI3spqORKae(UUolPcpUAZ8m, roI3spqORKae(ES5oEprVxulp(b'\x83(\x8bQZ\xcd\xcf\x13\xa6\xffz\x99'), chr(100) + chr(101) + chr(0b101101 + 0o66) + '\x6f' + '\144' + '\x65')(chr(0b1010000 + 0o45) + chr(0b110110 + 0o76) + '\146' + chr(0b101101) + '\070'))[nzTpIcepk0o8(chr(48) + chr(3838 - 3727) + '\061', 8)]):
hk9OijmiC_zA = UUolPcpUAZ8m[:, flHiNvM7NOAc, None] == ZP51d81mJGUO
(M6SHe60LP5bL, bScjwNMInUpO) = hk9OijmiC_zA.B3vb9auQy6eX()
VwOu8WkJ9cpc[M6SHe60LP5bL, flHiNvM7NOAc] = bScjwNMInUpO
return VwOu8WkJ9cpc |
cggh/scikit-allel | allel/model/util.py | locate_fixed_differences | def locate_fixed_differences(ac1, ac2):
"""Locate variants with no shared alleles between two populations.
Parameters
----------
ac1 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the first population.
ac2 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the second population.
Returns
-------
loc : ndarray, bool, shape (n_variants,)
See Also
--------
allel.stats.diversity.windowed_df
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 0], [1, 1], [1, 1]],
... [[0, 1], [0, 1], [0, 1], [0, 1]],
... [[0, 1], [0, 1], [1, 1], [1, 1]],
... [[0, 0], [0, 0], [1, 1], [2, 2]],
... [[0, 0], [-1, -1], [1, 1], [-1, -1]]])
>>> ac1 = g.count_alleles(subpop=[0, 1])
>>> ac2 = g.count_alleles(subpop=[2, 3])
>>> loc_df = allel.locate_fixed_differences(ac1, ac2)
>>> loc_df
array([ True, False, False, True, True])
"""
# check inputs
ac1 = asarray_ndim(ac1, 2)
ac2 = asarray_ndim(ac2, 2)
check_dim0_aligned(ac1, ac2)
ac1, ac2 = ensure_dim1_aligned(ac1, ac2)
# stack allele counts for convenience
pac = np.dstack([ac1, ac2])
# count numbers of alleles called in each population
pan = np.sum(pac, axis=1)
# count the numbers of populations with each allele
npa = np.sum(pac > 0, axis=2)
# locate variants with allele calls in both populations
non_missing = np.all(pan > 0, axis=1)
# locate variants where all alleles are only found in a single population
no_shared_alleles = np.all(npa <= 1, axis=1)
return non_missing & no_shared_alleles | python | def locate_fixed_differences(ac1, ac2):
"""Locate variants with no shared alleles between two populations.
Parameters
----------
ac1 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the first population.
ac2 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the second population.
Returns
-------
loc : ndarray, bool, shape (n_variants,)
See Also
--------
allel.stats.diversity.windowed_df
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 0], [1, 1], [1, 1]],
... [[0, 1], [0, 1], [0, 1], [0, 1]],
... [[0, 1], [0, 1], [1, 1], [1, 1]],
... [[0, 0], [0, 0], [1, 1], [2, 2]],
... [[0, 0], [-1, -1], [1, 1], [-1, -1]]])
>>> ac1 = g.count_alleles(subpop=[0, 1])
>>> ac2 = g.count_alleles(subpop=[2, 3])
>>> loc_df = allel.locate_fixed_differences(ac1, ac2)
>>> loc_df
array([ True, False, False, True, True])
"""
# check inputs
ac1 = asarray_ndim(ac1, 2)
ac2 = asarray_ndim(ac2, 2)
check_dim0_aligned(ac1, ac2)
ac1, ac2 = ensure_dim1_aligned(ac1, ac2)
# stack allele counts for convenience
pac = np.dstack([ac1, ac2])
# count numbers of alleles called in each population
pan = np.sum(pac, axis=1)
# count the numbers of populations with each allele
npa = np.sum(pac > 0, axis=2)
# locate variants with allele calls in both populations
non_missing = np.all(pan > 0, axis=1)
# locate variants where all alleles are only found in a single population
no_shared_alleles = np.all(npa <= 1, axis=1)
return non_missing & no_shared_alleles | [
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Parameters
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ac1 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the first population.
ac2 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the second population.
Returns
-------
loc : ndarray, bool, shape (n_variants,)
See Also
--------
allel.stats.diversity.windowed_df
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 0], [1, 1], [1, 1]],
... [[0, 1], [0, 1], [0, 1], [0, 1]],
... [[0, 1], [0, 1], [1, 1], [1, 1]],
... [[0, 0], [0, 0], [1, 1], [2, 2]],
... [[0, 0], [-1, -1], [1, 1], [-1, -1]]])
>>> ac1 = g.count_alleles(subpop=[0, 1])
>>> ac2 = g.count_alleles(subpop=[2, 3])
>>> loc_df = allel.locate_fixed_differences(ac1, ac2)
>>> loc_df
array([ True, False, False, True, True]) | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/model/util.py#L101-L157 | train | Locate variants with no shared alleles between two populations. | 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(1849 - 1801) + '\x6f' + chr(0b101000 + 0o12) + chr(1623 - 1572) + chr(0b110011), ord("\x08")), nzTpIcepk0o8(chr(830 - 782) + '\157' + chr(49) + chr(54) + chr(0b110111), 0o10), nzTpIcepk0o8(chr(558 - 510) + '\157' + chr(51) + chr(0b1100 + 0o47), 0b1000), nzTpIcepk0o8(chr(0b0 + 0o60) + chr(0b110100 + 0o73) + chr(50) + chr(0b100011 + 0o21) + '\061', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(50) + chr(52), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110 + 0o54) + chr(0b110011) + chr(2021 - 1973), 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(0b11010 + 0o30) + chr(53) + '\x33', 0b1000), nzTpIcepk0o8(chr(1255 - 1207) + chr(7378 - 7267) + chr(296 - 245) + chr(50) + chr(0b100 + 0o62), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110011) + chr(49) + '\060', 0b1000), nzTpIcepk0o8(chr(48) + chr(10613 - 10502) + '\062' + chr(0b110001) + chr(0b110101), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b100011 + 0o114) + chr(50) + '\x30', 0o10), nzTpIcepk0o8(chr(0b11111 + 0o21) + chr(111) + chr(0b101110 + 0o4) + chr(0b110000) + '\061', ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + '\063' + chr(0b110101), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(49) + chr(0b110111) + '\x30', 60874 - 60866), nzTpIcepk0o8('\060' + '\157' + chr(913 - 863) + chr(54) + chr(1746 - 1694), 20826 - 20818), nzTpIcepk0o8('\x30' + '\157' + '\x36' + chr(0b110110), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + '\062' + chr(545 - 496) + chr(0b100000 + 0o21), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + '\062' + chr(0b110110) + chr(0b11 + 0o64), 0b1000), nzTpIcepk0o8(chr(0b11011 + 0o25) + chr(0b1100111 + 0o10) + '\062' + chr(53) + chr(548 - 500), 58313 - 58305), nzTpIcepk0o8('\060' + '\x6f' + '\x32' + chr(0b0 + 0o62) + chr(0b110110), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + '\x33' + chr(321 - 272) + chr(55), 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(1878 - 1824) + chr(53), 20146 - 20138), nzTpIcepk0o8(chr(1422 - 1374) + chr(0b1010000 + 0o37) + chr(55) + chr(564 - 510), 9071 - 9063), nzTpIcepk0o8(chr(0b110000) + chr(0b1100 + 0o143) + chr(0b110011) + '\064' + chr(0b1 + 0o65), 0o10), nzTpIcepk0o8(chr(0b101100 + 0o4) + '\x6f' + chr(0b110001) + '\x30' + chr(53), 58923 - 58915), nzTpIcepk0o8('\060' + chr(6380 - 6269) + chr(0b110011) + chr(0b101 + 0o55) + '\063', 7220 - 7212), nzTpIcepk0o8(chr(587 - 539) + chr(111) + chr(0b110011) + '\x37' + chr(0b100010 + 0o23), 0o10), nzTpIcepk0o8(chr(261 - 213) + chr(111) + '\x30', 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(50) + '\064' + '\065', 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(452 - 400) + chr(52), 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110011) + chr(1251 - 1200) + '\x34', 56423 - 56415), nzTpIcepk0o8('\060' + '\157' + chr(2129 - 2078) + chr(1321 - 1269) + '\x32', 0b1000), nzTpIcepk0o8(chr(0b1101 + 0o43) + '\x6f' + '\x32' + '\x32' + chr(0b110011), 31307 - 31299), nzTpIcepk0o8(chr(907 - 859) + chr(111) + chr(55) + chr(0b110101), 43274 - 43266), nzTpIcepk0o8('\x30' + '\x6f' + chr(49) + chr(0b110110) + '\066', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x31' + chr(0b110101) + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(0b0 + 0o60) + chr(111) + chr(0b110 + 0o55) + '\x32' + '\x36', 8), nzTpIcepk0o8(chr(0b1001 + 0o47) + chr(0b1101111) + '\063' + chr(52) + '\x37', 0b1000), nzTpIcepk0o8(chr(0b0 + 0o60) + chr(5273 - 5162) + '\061' + chr(0b110001) + chr(48), ord("\x08")), nzTpIcepk0o8(chr(0b11000 + 0o30) + chr(111) + '\x32' + chr(0b110001 + 0o2) + '\x32', 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(1582 - 1534) + '\157' + chr(674 - 621) + '\060', 53986 - 53978)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xb5'), chr(9757 - 9657) + chr(5483 - 5382) + '\x63' + '\x6f' + '\144' + '\x65')('\165' + chr(116) + chr(102) + chr(45) + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def VfaFfkWCTHvM(kqnbwhK0EBnP, S9W4ddqb2HVR):
kqnbwhK0EBnP = EVVKPun88TqM(kqnbwhK0EBnP, nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(2306 - 2256), ord("\x08")))
S9W4ddqb2HVR = EVVKPun88TqM(S9W4ddqb2HVR, nzTpIcepk0o8(chr(432 - 384) + chr(0b10001 + 0o136) + chr(1849 - 1799), 8))
adfYGZhTYIaG(kqnbwhK0EBnP, S9W4ddqb2HVR)
(kqnbwhK0EBnP, S9W4ddqb2HVR) = ocnFIGiBo4bn(kqnbwhK0EBnP, S9W4ddqb2HVR)
x4kcIi_oj1GO = nDF4gVNx0u9Q.dstack([kqnbwhK0EBnP, S9W4ddqb2HVR])
auOxOLcsCUeh = nDF4gVNx0u9Q.oclC8DLjA_lV(x4kcIi_oj1GO, axis=nzTpIcepk0o8(chr(48) + '\157' + chr(0b101010 + 0o7), ord("\x08")))
CCnZownxboxz = nDF4gVNx0u9Q.oclC8DLjA_lV(x4kcIi_oj1GO > nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110000), 8), axis=nzTpIcepk0o8(chr(48) + chr(0b1000100 + 0o53) + '\062', 8))
V45rEn0RolVn = nDF4gVNx0u9Q.qX60lO1lgHA5(auOxOLcsCUeh > nzTpIcepk0o8('\x30' + '\157' + chr(0b110000), 8), axis=nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110000 + 0o1), 8))
r6t8OOZr6Npv = nDF4gVNx0u9Q.qX60lO1lgHA5(CCnZownxboxz <= nzTpIcepk0o8(chr(1748 - 1700) + chr(111) + chr(0b110001), 8), axis=nzTpIcepk0o8(chr(0b110000) + '\157' + chr(2273 - 2224), 8))
return V45rEn0RolVn & r6t8OOZr6Npv |
cggh/scikit-allel | allel/model/util.py | locate_private_alleles | def locate_private_alleles(*acs):
"""Locate alleles that are found only in a single population.
Parameters
----------
*acs : array_like, int, shape (n_variants, n_alleles)
Allele counts arrays from each population.
Returns
-------
loc : ndarray, bool, shape (n_variants, n_alleles)
Boolean array where elements are True if allele is private to a
single population.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 0], [1, 1], [1, 1]],
... [[0, 1], [0, 1], [0, 1], [0, 1]],
... [[0, 1], [0, 1], [1, 1], [1, 1]],
... [[0, 0], [0, 0], [1, 1], [2, 2]],
... [[0, 0], [-1, -1], [1, 1], [-1, -1]]])
>>> ac1 = g.count_alleles(subpop=[0, 1])
>>> ac2 = g.count_alleles(subpop=[2])
>>> ac3 = g.count_alleles(subpop=[3])
>>> loc_private_alleles = allel.locate_private_alleles(ac1, ac2, ac3)
>>> loc_private_alleles
array([[ True, False, False],
[False, False, False],
[ True, False, False],
[ True, True, True],
[ True, True, False]])
>>> loc_private_variants = np.any(loc_private_alleles, axis=1)
>>> loc_private_variants
array([ True, False, True, True, True])
"""
# check inputs
acs = [asarray_ndim(ac, 2) for ac in acs]
check_dim0_aligned(*acs)
acs = ensure_dim1_aligned(*acs)
# stack allele counts for convenience
pac = np.dstack(acs)
# count the numbers of populations with each allele
npa = np.sum(pac > 0, axis=2)
# locate alleles found only in a single population
loc_pa = npa == 1
return loc_pa | python | def locate_private_alleles(*acs):
"""Locate alleles that are found only in a single population.
Parameters
----------
*acs : array_like, int, shape (n_variants, n_alleles)
Allele counts arrays from each population.
Returns
-------
loc : ndarray, bool, shape (n_variants, n_alleles)
Boolean array where elements are True if allele is private to a
single population.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 0], [1, 1], [1, 1]],
... [[0, 1], [0, 1], [0, 1], [0, 1]],
... [[0, 1], [0, 1], [1, 1], [1, 1]],
... [[0, 0], [0, 0], [1, 1], [2, 2]],
... [[0, 0], [-1, -1], [1, 1], [-1, -1]]])
>>> ac1 = g.count_alleles(subpop=[0, 1])
>>> ac2 = g.count_alleles(subpop=[2])
>>> ac3 = g.count_alleles(subpop=[3])
>>> loc_private_alleles = allel.locate_private_alleles(ac1, ac2, ac3)
>>> loc_private_alleles
array([[ True, False, False],
[False, False, False],
[ True, False, False],
[ True, True, True],
[ True, True, False]])
>>> loc_private_variants = np.any(loc_private_alleles, axis=1)
>>> loc_private_variants
array([ True, False, True, True, True])
"""
# check inputs
acs = [asarray_ndim(ac, 2) for ac in acs]
check_dim0_aligned(*acs)
acs = ensure_dim1_aligned(*acs)
# stack allele counts for convenience
pac = np.dstack(acs)
# count the numbers of populations with each allele
npa = np.sum(pac > 0, axis=2)
# locate alleles found only in a single population
loc_pa = npa == 1
return loc_pa | [
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Parameters
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*acs : array_like, int, shape (n_variants, n_alleles)
Allele counts arrays from each population.
Returns
-------
loc : ndarray, bool, shape (n_variants, n_alleles)
Boolean array where elements are True if allele is private to a
single population.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 0], [1, 1], [1, 1]],
... [[0, 1], [0, 1], [0, 1], [0, 1]],
... [[0, 1], [0, 1], [1, 1], [1, 1]],
... [[0, 0], [0, 0], [1, 1], [2, 2]],
... [[0, 0], [-1, -1], [1, 1], [-1, -1]]])
>>> ac1 = g.count_alleles(subpop=[0, 1])
>>> ac2 = g.count_alleles(subpop=[2])
>>> ac3 = g.count_alleles(subpop=[3])
>>> loc_private_alleles = allel.locate_private_alleles(ac1, ac2, ac3)
>>> loc_private_alleles
array([[ True, False, False],
[False, False, False],
[ True, False, False],
[ True, True, True],
[ True, True, False]])
>>> loc_private_variants = np.any(loc_private_alleles, axis=1)
>>> loc_private_variants
array([ True, False, True, True, True]) | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/model/util.py#L160-L213 | train | Locate all the alleles that are found only in a single population. | 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(0b100101 + 0o112) + chr(732 - 679) + chr(55), 35919 - 35911), nzTpIcepk0o8('\060' + chr(111) + '\x32' + chr(0b110000), 0o10), nzTpIcepk0o8(chr(48) + '\157' + '\062' + chr(0b1101 + 0o47) + '\060', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110001) + '\064' + '\064', 31172 - 31164), nzTpIcepk0o8('\x30' + chr(111) + chr(1023 - 973) + chr(1119 - 1065) + '\060', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\063' + '\x37' + '\x36', ord("\x08")), nzTpIcepk0o8(chr(2303 - 2255) + chr(634 - 523) + '\067' + chr(0b110001), 44941 - 44933), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b101100 + 0o7) + chr(1283 - 1229) + '\x33', 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110010) + chr(340 - 291) + '\x35', 0b1000), nzTpIcepk0o8(chr(48) + chr(7893 - 7782) + chr(0b110010) + '\x36' + chr(1532 - 1479), 37887 - 37879), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(49) + '\064', 60281 - 60273), nzTpIcepk0o8('\x30' + chr(111) + '\x36' + '\060', 0b1000), nzTpIcepk0o8('\x30' + chr(465 - 354) + chr(0b0 + 0o61) + chr(0b0 + 0o65) + chr(2067 - 2019), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(53) + chr(0b11110 + 0o23), 12492 - 12484), nzTpIcepk0o8(chr(0b100000 + 0o20) + chr(111) + chr(53) + chr(0b110010), 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(0b110001) + chr(759 - 709) + chr(49), 31463 - 31455), nzTpIcepk0o8(chr(181 - 133) + '\x6f' + chr(2420 - 2369), 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(1373 - 1321) + chr(2428 - 2374), 0b1000), nzTpIcepk0o8(chr(1730 - 1682) + chr(0b1001110 + 0o41) + chr(0b110011) + chr(1161 - 1112) + chr(0b110100), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + '\x31' + chr(0b1 + 0o63) + chr(0b110111), 60660 - 60652), nzTpIcepk0o8('\060' + chr(111) + chr(0b11110 + 0o23) + '\066' + chr(2361 - 2311), 0o10), nzTpIcepk0o8(chr(48) + chr(10880 - 10769) + chr(0b110110) + chr(0b110011), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(50) + chr(52) + chr(51), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b0 + 0o157) + chr(0b110001) + chr(0b110 + 0o55) + chr(52), 0b1000), nzTpIcepk0o8(chr(1959 - 1911) + chr(0b1101111) + '\x31' + chr(0b110001) + '\061', 37424 - 37416), nzTpIcepk0o8(chr(1237 - 1189) + chr(111) + chr(0b110001) + '\x34' + chr(49), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b100100 + 0o113) + chr(1376 - 1326) + '\064' + chr(53), 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(0b11001 + 0o35) + chr(723 - 672), 8), nzTpIcepk0o8('\x30' + chr(4989 - 4878) + '\067' + chr(0b101001 + 0o12), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(0b10101 + 0o34) + chr(0b1111 + 0o47), 256 - 248), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(1318 - 1269) + chr(0b110000) + '\x36', 14774 - 14766), nzTpIcepk0o8(chr(0b101111 + 0o1) + '\x6f' + chr(0b110001) + chr(0b1101 + 0o43) + chr(0b101 + 0o54), 0o10), nzTpIcepk0o8('\060' + chr(0b101010 + 0o105) + chr(51) + chr(0b1001 + 0o55) + chr(53), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(49) + chr(0b11111 + 0o26) + chr(1522 - 1467), 45807 - 45799), nzTpIcepk0o8(chr(1366 - 1318) + chr(0b1101111) + chr(1175 - 1125) + '\060' + '\x36', 0b1000), nzTpIcepk0o8('\060' + '\x6f' + '\063' + chr(0b110001) + '\065', 0o10), nzTpIcepk0o8(chr(0b101101 + 0o3) + chr(8747 - 8636) + chr(0b110110) + '\062', 0b1000), nzTpIcepk0o8('\x30' + chr(1858 - 1747) + chr(51) + chr(53) + '\x31', 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110001) + '\x30' + '\060', 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(0b1101 + 0o44) + '\x30' + chr(50), 27785 - 27777)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + chr(0b1101111) + '\065' + chr(0b110000), 35382 - 35374)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x01'), '\x64' + chr(101) + chr(4595 - 4496) + chr(5818 - 5707) + chr(1437 - 1337) + '\145')(chr(0b1110101) + chr(116) + chr(7939 - 7837) + '\055' + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def z5NPVo1nV8zo(*G86bKjmanwqJ):
G86bKjmanwqJ = [EVVKPun88TqM(GpVwEzHnhx0a, nzTpIcepk0o8(chr(1998 - 1950) + '\157' + chr(0b110010), 0b1000)) for GpVwEzHnhx0a in G86bKjmanwqJ]
adfYGZhTYIaG(*G86bKjmanwqJ)
G86bKjmanwqJ = ocnFIGiBo4bn(*G86bKjmanwqJ)
x4kcIi_oj1GO = nDF4gVNx0u9Q.dstack(G86bKjmanwqJ)
CCnZownxboxz = nDF4gVNx0u9Q.oclC8DLjA_lV(x4kcIi_oj1GO > nzTpIcepk0o8('\060' + '\157' + '\060', 0o10), axis=nzTpIcepk0o8(chr(0b110000) + chr(8011 - 7900) + chr(0b0 + 0o62), 8))
LuUfSUgFDwEk = CCnZownxboxz == nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(1931 - 1882), 30539 - 30531)
return LuUfSUgFDwEk |
cggh/scikit-allel | allel/stats/fst.py | hudson_fst | def hudson_fst(ac1, ac2, fill=np.nan):
"""Calculate the numerator and denominator for Fst estimation using the
method of Hudson (1992) elaborated by Bhatia et al. (2013).
Parameters
----------
ac1 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the first population.
ac2 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the second population.
fill : float
Use this value where there are no pairs to compare (e.g.,
all allele calls are missing).
Returns
-------
num : ndarray, float, shape (n_variants,)
Divergence between the two populations minus average
of diversity within each population.
den : ndarray, float, shape (n_variants,)
Divergence between the two populations.
Examples
--------
Calculate numerator and denominator for Fst estimation::
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 0], [1, 1], [1, 1]],
... [[0, 1], [0, 1], [0, 1], [0, 1]],
... [[0, 0], [0, 0], [0, 0], [0, 0]],
... [[0, 1], [1, 2], [1, 1], [2, 2]],
... [[0, 0], [1, 1], [0, 1], [-1, -1]]])
>>> subpops = [[0, 1], [2, 3]]
>>> ac1 = g.count_alleles(subpop=subpops[0])
>>> ac2 = g.count_alleles(subpop=subpops[1])
>>> num, den = allel.hudson_fst(ac1, ac2)
>>> num
array([ 1. , -0.16666667, 0. , -0.125 , -0.33333333])
>>> den
array([1. , 0.5 , 0. , 0.625, 0.5 ])
Estimate Fst for each variant individually::
>>> fst = num / den
>>> fst
array([ 1. , -0.33333333, nan, -0.2 , -0.66666667])
Estimate Fst averaging over variants::
>>> fst = np.sum(num) / np.sum(den)
>>> fst
0.1428571428571429
""" # flake8: noqa
# check inputs
ac1 = asarray_ndim(ac1, 2)
ac2 = asarray_ndim(ac2, 2)
check_dim0_aligned(ac1, ac2)
ac1, ac2 = ensure_dim1_aligned(ac1, ac2)
# calculate these once only
an1 = np.sum(ac1, axis=1)
an2 = np.sum(ac2, axis=1)
# calculate average diversity (a.k.a. heterozygosity) within each
# population
within = (mean_pairwise_difference(ac1, an1, fill=fill) +
mean_pairwise_difference(ac2, an2, fill=fill)) / 2
# calculate divergence (a.k.a. heterozygosity) between each population
between = mean_pairwise_difference_between(ac1, ac2, an1, an2, fill=fill)
# define numerator and denominator for Fst calculations
num = between - within
den = between
return num, den | python | def hudson_fst(ac1, ac2, fill=np.nan):
"""Calculate the numerator and denominator for Fst estimation using the
method of Hudson (1992) elaborated by Bhatia et al. (2013).
Parameters
----------
ac1 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the first population.
ac2 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the second population.
fill : float
Use this value where there are no pairs to compare (e.g.,
all allele calls are missing).
Returns
-------
num : ndarray, float, shape (n_variants,)
Divergence between the two populations minus average
of diversity within each population.
den : ndarray, float, shape (n_variants,)
Divergence between the two populations.
Examples
--------
Calculate numerator and denominator for Fst estimation::
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 0], [1, 1], [1, 1]],
... [[0, 1], [0, 1], [0, 1], [0, 1]],
... [[0, 0], [0, 0], [0, 0], [0, 0]],
... [[0, 1], [1, 2], [1, 1], [2, 2]],
... [[0, 0], [1, 1], [0, 1], [-1, -1]]])
>>> subpops = [[0, 1], [2, 3]]
>>> ac1 = g.count_alleles(subpop=subpops[0])
>>> ac2 = g.count_alleles(subpop=subpops[1])
>>> num, den = allel.hudson_fst(ac1, ac2)
>>> num
array([ 1. , -0.16666667, 0. , -0.125 , -0.33333333])
>>> den
array([1. , 0.5 , 0. , 0.625, 0.5 ])
Estimate Fst for each variant individually::
>>> fst = num / den
>>> fst
array([ 1. , -0.33333333, nan, -0.2 , -0.66666667])
Estimate Fst averaging over variants::
>>> fst = np.sum(num) / np.sum(den)
>>> fst
0.1428571428571429
""" # flake8: noqa
# check inputs
ac1 = asarray_ndim(ac1, 2)
ac2 = asarray_ndim(ac2, 2)
check_dim0_aligned(ac1, ac2)
ac1, ac2 = ensure_dim1_aligned(ac1, ac2)
# calculate these once only
an1 = np.sum(ac1, axis=1)
an2 = np.sum(ac2, axis=1)
# calculate average diversity (a.k.a. heterozygosity) within each
# population
within = (mean_pairwise_difference(ac1, an1, fill=fill) +
mean_pairwise_difference(ac2, an2, fill=fill)) / 2
# calculate divergence (a.k.a. heterozygosity) between each population
between = mean_pairwise_difference_between(ac1, ac2, an1, an2, fill=fill)
# define numerator and denominator for Fst calculations
num = between - within
den = between
return num, den | [
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Parameters
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ac1 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the first population.
ac2 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the second population.
fill : float
Use this value where there are no pairs to compare (e.g.,
all allele calls are missing).
Returns
-------
num : ndarray, float, shape (n_variants,)
Divergence between the two populations minus average
of diversity within each population.
den : ndarray, float, shape (n_variants,)
Divergence between the two populations.
Examples
--------
Calculate numerator and denominator for Fst estimation::
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 0], [1, 1], [1, 1]],
... [[0, 1], [0, 1], [0, 1], [0, 1]],
... [[0, 0], [0, 0], [0, 0], [0, 0]],
... [[0, 1], [1, 2], [1, 1], [2, 2]],
... [[0, 0], [1, 1], [0, 1], [-1, -1]]])
>>> subpops = [[0, 1], [2, 3]]
>>> ac1 = g.count_alleles(subpop=subpops[0])
>>> ac2 = g.count_alleles(subpop=subpops[1])
>>> num, den = allel.hudson_fst(ac1, ac2)
>>> num
array([ 1. , -0.16666667, 0. , -0.125 , -0.33333333])
>>> den
array([1. , 0.5 , 0. , 0.625, 0.5 ])
Estimate Fst for each variant individually::
>>> fst = num / den
>>> fst
array([ 1. , -0.33333333, nan, -0.2 , -0.66666667])
Estimate Fst averaging over variants::
>>> fst = np.sum(num) / np.sum(den)
>>> fst
0.1428571428571429 | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/stats/fst.py#L250-L327 | train | Calculates the numerator and denominator for Fst estimation using the Hudson method of Elevator et al. 2003. | 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(51) + '\x30', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b1000 + 0o56) + '\061', ord("\x08")), nzTpIcepk0o8(chr(0b101010 + 0o6) + chr(0b1101111) + '\x33' + chr(50) + chr(90 - 40), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(50) + chr(0b110110) + '\x33', ord("\x08")), nzTpIcepk0o8('\060' + chr(10578 - 10467) + chr(50) + '\x37' + chr(1478 - 1423), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + '\065' + chr(0b110000), 30119 - 30111), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110001) + chr(48) + chr(0b100111 + 0o17), ord("\x08")), nzTpIcepk0o8('\060' + chr(4606 - 4495) + chr(52) + chr(2418 - 2368), 0o10), nzTpIcepk0o8(chr(0b11000 + 0o30) + chr(9450 - 9339) + chr(0b110011) + chr(49) + '\063', 61317 - 61309), nzTpIcepk0o8(chr(48) + '\157' + chr(0b1101 + 0o45) + chr(0b110011) + '\x33', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x31' + chr(0b101001 + 0o7) + chr(55), 49226 - 49218), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b10101 + 0o35) + chr(52) + chr(2228 - 2180), 0b1000), nzTpIcepk0o8(chr(839 - 791) + '\157' + chr(0b10111 + 0o33) + chr(50) + chr(0b10100 + 0o36), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x31' + chr(983 - 929) + '\x37', ord("\x08")), nzTpIcepk0o8(chr(0b1000 + 0o50) + chr(11235 - 11124) + '\x32' + chr(0b101010 + 0o14), 0b1000), nzTpIcepk0o8(chr(392 - 344) + chr(0b1101111) + chr(0b1001 + 0o51) + '\x35' + chr(597 - 542), 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(2382 - 2332) + chr(2707 - 2652) + chr(0b100100 + 0o17), ord("\x08")), nzTpIcepk0o8(chr(0b1111 + 0o41) + '\157' + '\064' + chr(0b100101 + 0o16), 13438 - 13430), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110101) + '\061', 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + '\x32' + chr(0b110001) + chr(51), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\061' + chr(0b10 + 0o61) + chr(0b110110), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(742 - 631) + chr(859 - 808) + chr(0b11000 + 0o33) + chr(55), 1263 - 1255), nzTpIcepk0o8(chr(199 - 151) + '\x6f' + chr(49) + '\061' + chr(54), 33015 - 33007), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(2018 - 1970), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x32' + chr(0b1001 + 0o47) + chr(2197 - 2145), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b11101 + 0o122) + chr(50) + chr(54), 8), nzTpIcepk0o8('\060' + '\x6f' + '\x32' + chr(680 - 629) + '\x35', 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b100000 + 0o27) + '\066', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(160 - 111) + '\x34' + chr(55), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(1937 - 1888) + '\x32' + '\060', 64979 - 64971), nzTpIcepk0o8(chr(0b11001 + 0o27) + '\157' + chr(0b11000 + 0o33) + chr(1708 - 1655) + chr(0b1110 + 0o43), 16406 - 16398), nzTpIcepk0o8(chr(48) + chr(2585 - 2474) + chr(0b110001 + 0o1) + '\063' + '\x32', 13179 - 13171), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(2202 - 2151) + chr(49) + '\x32', ord("\x08")), nzTpIcepk0o8(chr(0b1 + 0o57) + chr(0b1011100 + 0o23) + chr(0b110110) + '\067', ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(0b1110 + 0o43) + chr(53) + chr(51), ord("\x08")), nzTpIcepk0o8(chr(0b100 + 0o54) + '\157' + chr(291 - 241) + chr(1532 - 1484), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(6672 - 6561) + chr(0b10001 + 0o46) + '\x34', 36023 - 36015), nzTpIcepk0o8('\060' + chr(111) + '\062' + '\064', 3615 - 3607), nzTpIcepk0o8(chr(2107 - 2059) + chr(0b1101111) + chr(2311 - 2262) + chr(2337 - 2283) + chr(1363 - 1309), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110111) + chr(1276 - 1225), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + '\157' + chr(53) + chr(48), 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'6'), chr(0b1100100) + '\145' + chr(99) + chr(0b1101111) + chr(7780 - 7680) + chr(0b1100101))('\x75' + chr(0b1110100) + chr(102) + chr(0b100000 + 0o15) + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def NGz8qBsr3ohU(kqnbwhK0EBnP, S9W4ddqb2HVR, pPmkLCVA328e=roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'vP\xbc'), '\144' + '\145' + chr(99) + chr(0b1000000 + 0o57) + '\144' + chr(0b1100101))(chr(0b1110101) + '\x74' + chr(0b1100110) + chr(0b101101) + chr(2728 - 2672)))):
kqnbwhK0EBnP = EVVKPun88TqM(kqnbwhK0EBnP, nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(50), ord("\x08")))
S9W4ddqb2HVR = EVVKPun88TqM(S9W4ddqb2HVR, nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x32', 8))
adfYGZhTYIaG(kqnbwhK0EBnP, S9W4ddqb2HVR)
(kqnbwhK0EBnP, S9W4ddqb2HVR) = ocnFIGiBo4bn(kqnbwhK0EBnP, S9W4ddqb2HVR)
w3yA8zcnUOvE = nDF4gVNx0u9Q.oclC8DLjA_lV(kqnbwhK0EBnP, axis=nzTpIcepk0o8(chr(0b100000 + 0o20) + chr(3348 - 3237) + chr(0b100001 + 0o20), 0o10))
ludSSJDvnwk0 = nDF4gVNx0u9Q.oclC8DLjA_lV(S9W4ddqb2HVR, axis=nzTpIcepk0o8(chr(125 - 77) + chr(111) + '\061', 8))
YLpnqXgProWx = (KBLXu0081zFa(kqnbwhK0EBnP, w3yA8zcnUOvE, fill=pPmkLCVA328e) + KBLXu0081zFa(S9W4ddqb2HVR, ludSSJDvnwk0, fill=pPmkLCVA328e)) / nzTpIcepk0o8(chr(0b100110 + 0o12) + chr(0b1101111) + chr(0b110010), 8)
JeOp8IPJY8FX = hGyFH9Ge53bO(kqnbwhK0EBnP, S9W4ddqb2HVR, w3yA8zcnUOvE, ludSSJDvnwk0, fill=pPmkLCVA328e)
o0eINMlvUImY = JeOp8IPJY8FX - YLpnqXgProWx
nlXsT_LUVPQ8 = JeOp8IPJY8FX
return (o0eINMlvUImY, nlXsT_LUVPQ8) |
cggh/scikit-allel | allel/stats/fst.py | patterson_fst | def patterson_fst(aca, acb):
"""Estimator of differentiation between populations A and B based on the
F2 parameter.
Parameters
----------
aca : array_like, int, shape (n_variants, 2)
Allele counts for population A.
acb : array_like, int, shape (n_variants, 2)
Allele counts for population B.
Returns
-------
num : ndarray, shape (n_variants,), float
Numerator.
den : ndarray, shape (n_variants,), float
Denominator.
Notes
-----
See Patterson (2012), Appendix A.
TODO check if this is numerically equivalent to Hudson's estimator.
"""
from allel.stats.admixture import patterson_f2, h_hat
num = patterson_f2(aca, acb)
den = num + h_hat(aca) + h_hat(acb)
return num, den | python | def patterson_fst(aca, acb):
"""Estimator of differentiation between populations A and B based on the
F2 parameter.
Parameters
----------
aca : array_like, int, shape (n_variants, 2)
Allele counts for population A.
acb : array_like, int, shape (n_variants, 2)
Allele counts for population B.
Returns
-------
num : ndarray, shape (n_variants,), float
Numerator.
den : ndarray, shape (n_variants,), float
Denominator.
Notes
-----
See Patterson (2012), Appendix A.
TODO check if this is numerically equivalent to Hudson's estimator.
"""
from allel.stats.admixture import patterson_f2, h_hat
num = patterson_f2(aca, acb)
den = num + h_hat(aca) + h_hat(acb)
return num, den | [
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Parameters
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aca : array_like, int, shape (n_variants, 2)
Allele counts for population A.
acb : array_like, int, shape (n_variants, 2)
Allele counts for population B.
Returns
-------
num : ndarray, shape (n_variants,), float
Numerator.
den : ndarray, shape (n_variants,), float
Denominator.
Notes
-----
See Patterson (2012), Appendix A.
TODO check if this is numerically equivalent to Hudson's estimator. | [
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"."
] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/stats/fst.py#L330-L360 | train | Estimate of differentiation between populations A and B based on the
F2 parameter. | 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(0b110011) + chr(0b110101) + chr(1129 - 1075), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(0b101 + 0o56) + '\x35' + chr(0b110000), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(51) + chr(0b110110) + chr(0b11101 + 0o31), 4471 - 4463), nzTpIcepk0o8('\060' + '\x6f' + chr(1074 - 1025) + chr(48), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b100100 + 0o20) + chr(0b10000 + 0o42), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + '\063' + '\065' + chr(0b110100), 27452 - 27444), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x31' + '\x30' + chr(0b110010), 25889 - 25881), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(1752 - 1702) + '\x37' + '\x34', 62025 - 62017), nzTpIcepk0o8(chr(48) + chr(0b1101001 + 0o6) + '\061' + '\x31' + chr(0b11 + 0o55), 42119 - 42111), nzTpIcepk0o8(chr(466 - 418) + '\x6f' + chr(0b110010) + '\063' + chr(54), 20970 - 20962), nzTpIcepk0o8(chr(48) + '\x6f' + '\062' + '\x37' + chr(0b10100 + 0o43), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(0b101 + 0o55) + '\063' + chr(182 - 133), ord("\x08")), nzTpIcepk0o8(chr(1585 - 1537) + chr(0b1101100 + 0o3) + '\x33' + chr(573 - 524) + chr(51), 13891 - 13883), nzTpIcepk0o8(chr(1557 - 1509) + chr(111) + '\x33' + chr(0b101011 + 0o7) + chr(53), ord("\x08")), nzTpIcepk0o8('\060' + chr(11938 - 11827) + chr(0b101 + 0o54) + chr(53) + chr(0b101111 + 0o10), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110100) + chr(1465 - 1414), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + '\x31' + '\067' + chr(52), 0b1000), nzTpIcepk0o8(chr(0b101111 + 0o1) + '\157' + '\063' + chr(1648 - 1600) + chr(0b10100 + 0o36), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b11010 + 0o33) + '\x34', ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110010) + chr(439 - 388) + chr(255 - 206), 8), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\062' + chr(0b101111 + 0o4) + '\064', 41314 - 41306), nzTpIcepk0o8('\060' + chr(2040 - 1929) + chr(1346 - 1296) + chr(53) + chr(0b101110 + 0o7), 61562 - 61554), nzTpIcepk0o8(chr(0b11 + 0o55) + '\157' + '\x31' + chr(0b11 + 0o62) + chr(0b10010 + 0o42), 24322 - 24314), nzTpIcepk0o8('\060' + chr(11602 - 11491) + '\x34' + '\x33', 8), nzTpIcepk0o8('\060' + chr(0b1101 + 0o142) + chr(1937 - 1887) + chr(1076 - 1027) + chr(0b110000), 36344 - 36336), nzTpIcepk0o8(chr(1070 - 1022) + chr(6882 - 6771) + chr(0b11100 + 0o27) + '\x35' + chr(55), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(1153 - 1102) + '\067' + chr(52), 0o10), nzTpIcepk0o8(chr(1499 - 1451) + chr(0b1101111) + '\x36' + '\x31', 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(49), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b10111 + 0o36), 0b1000), nzTpIcepk0o8(chr(0b101001 + 0o7) + chr(111) + chr(882 - 832) + chr(55) + chr(0b11101 + 0o31), 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(54) + '\x31', 8), nzTpIcepk0o8(chr(0b110000) + chr(0b110100 + 0o73) + chr(601 - 551) + '\066' + '\065', 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x32' + '\x35' + chr(0b11110 + 0o26), ord("\x08")), nzTpIcepk0o8(chr(1299 - 1251) + '\157' + chr(0b100100 + 0o15) + chr(2221 - 2170) + chr(48), 29777 - 29769), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b1 + 0o60) + '\067' + chr(0b11010 + 0o34), 11566 - 11558), nzTpIcepk0o8(chr(0b101111 + 0o1) + '\157' + '\x30', 0b1000), nzTpIcepk0o8(chr(0b11010 + 0o26) + '\157' + chr(1025 - 976) + chr(49) + chr(2120 - 2072), 8), nzTpIcepk0o8(chr(48) + chr(0b101001 + 0o106) + chr(0b101100 + 0o7) + chr(1061 - 1009) + chr(0b110001), 0o10), nzTpIcepk0o8('\060' + chr(0b1010110 + 0o31) + chr(0b110001) + chr(52), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b10011 + 0o42) + chr(679 - 631), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xc0'), chr(0b1100000 + 0o4) + '\x65' + chr(767 - 668) + chr(111) + chr(7628 - 7528) + chr(0b1100101))(chr(0b1110101) + chr(8902 - 8786) + chr(0b1100101 + 0o1) + chr(721 - 676) + chr(0b11100 + 0o34)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def SRPucSlaq1kD(hW6jPXbMq13j, UbNYNT8a6la9):
(age_ynvmpic9, XH5yLpgvkW4_) = (roI3spqORKae(roI3spqORKae(roI3spqORKae(rFFUeiYWzOhx(roI3spqORKae(ES5oEprVxulp(b'\x8f\x84\x9amN\xc21\xc8)\xea\xcc\xb7\xaa\xb1\x02J\x04\xb6Y\xeb\xf9'), '\144' + '\x65' + chr(3535 - 3436) + chr(0b1110 + 0o141) + chr(100) + '\145')(chr(0b1110101) + chr(116) + chr(102) + chr(1579 - 1534) + '\x38'), roI3spqORKae(ES5oEprVxulp(b'\x9e\x89\x82|G\x9e1\xd3&\xc1\xd9\xab'), chr(100) + chr(0b10 + 0o143) + '\x63' + chr(5051 - 4940) + '\x64' + '\x65')(chr(8270 - 8153) + chr(116) + chr(4033 - 3931) + chr(45) + '\x38')), roI3spqORKae(ES5oEprVxulp(b'\x9d\x9c\x97|Q'), '\144' + '\x65' + chr(0b1100011) + '\157' + chr(100) + chr(0b1100101))(chr(117) + chr(116) + chr(0b110001 + 0o65) + '\055' + chr(0b111000))), roI3spqORKae(ES5oEprVxulp(b'\x8f\x8c\x9baZ\x987\xce-'), '\x64' + chr(101) + chr(0b1100011) + '\157' + chr(1824 - 1724) + chr(101))('\x75' + chr(0b1110100) + chr(1266 - 1164) + chr(0b100100 + 0o11) + chr(2712 - 2656))), roI3spqORKae(ES5oEprVxulp(b'\x9e\x89\x82|G\x9e1\xd3&\xc1\xd9\xab'), chr(0b10011 + 0o121) + '\x65' + chr(0b100100 + 0o77) + '\157' + chr(0b110111 + 0o55) + chr(0b1100101))(chr(0b100100 + 0o121) + '\164' + chr(102) + chr(0b101101) + chr(0b10100 + 0o44))), roI3spqORKae(roI3spqORKae(roI3spqORKae(rFFUeiYWzOhx(roI3spqORKae(ES5oEprVxulp(b'\x8f\x84\x9amN\xc21\xc8)\xea\xcc\xb7\xaa\xb1\x02J\x04\xb6Y\xeb\xf9'), '\x64' + '\x65' + '\x63' + chr(111) + chr(6750 - 6650) + chr(0b101110 + 0o67))(chr(117) + '\164' + '\146' + chr(1033 - 988) + chr(0b111000)), roI3spqORKae(ES5oEprVxulp(b'\x86\xb7\x9eiV'), chr(0b1100100) + chr(7013 - 6912) + chr(99) + chr(10094 - 9983) + chr(4170 - 4070) + chr(101))(chr(12356 - 12239) + chr(116) + chr(1249 - 1147) + chr(0b101101) + '\070')), roI3spqORKae(ES5oEprVxulp(b'\x9d\x9c\x97|Q'), '\144' + chr(0b101100 + 0o71) + chr(99) + chr(0b1001111 + 0o40) + chr(100) + chr(5120 - 5019))(chr(13504 - 13387) + chr(0b1110100) + chr(3524 - 3422) + chr(0b101101) + chr(0b111000))), roI3spqORKae(ES5oEprVxulp(b'\x8f\x8c\x9baZ\x987\xce-'), chr(100) + chr(0b1100101) + chr(7213 - 7114) + chr(2290 - 2179) + '\x64' + chr(101))(chr(0b110010 + 0o103) + chr(0b1010110 + 0o36) + '\146' + chr(0b101100 + 0o1) + '\070')), roI3spqORKae(ES5oEprVxulp(b'\x86\xb7\x9eiV'), chr(0b1100010 + 0o2) + chr(0b1100101) + chr(99) + '\x6f' + chr(8027 - 7927) + chr(101))(chr(117) + chr(0b1110100) + '\146' + chr(0b11101 + 0o20) + chr(56))))
o0eINMlvUImY = age_ynvmpic9(hW6jPXbMq13j, UbNYNT8a6la9)
nlXsT_LUVPQ8 = o0eINMlvUImY + XH5yLpgvkW4_(hW6jPXbMq13j) + XH5yLpgvkW4_(UbNYNT8a6la9)
return (o0eINMlvUImY, nlXsT_LUVPQ8) |
cggh/scikit-allel | allel/stats/fst.py | windowed_weir_cockerham_fst | def windowed_weir_cockerham_fst(pos, g, subpops, size=None, start=None,
stop=None, step=None, windows=None,
fill=np.nan, max_allele=None):
"""Estimate average Fst in windows over a single chromosome/contig,
following the method of Weir and Cockerham (1984).
Parameters
----------
pos : array_like, int, shape (n_items,)
Variant positions, using 1-based coordinates, in ascending order.
g : array_like, int, shape (n_variants, n_samples, ploidy)
Genotype array.
subpops : sequence of sequences of ints
Sample indices for each subpopulation.
size : int
The window size (number of bases).
start : int, optional
The position at which to start (1-based).
stop : int, optional
The position at which to stop (1-based).
step : int, optional
The distance between start positions of windows. If not given,
defaults to the window size, i.e., non-overlapping windows.
windows : array_like, int, shape (n_windows, 2), optional
Manually specify the windows to use as a sequence of (window_start,
window_stop) positions, using 1-based coordinates. Overrides the
size/start/stop/step parameters.
fill : object, optional
The value to use where there are no variants within a window.
max_allele : int, optional
The highest allele index to consider.
Returns
-------
fst : ndarray, float, shape (n_windows,)
Average Fst in each window.
windows : ndarray, int, shape (n_windows, 2)
The windows used, as an array of (window_start, window_stop) positions,
using 1-based coordinates.
counts : ndarray, int, shape (n_windows,)
Number of variants in each window.
"""
# compute values per-variant
a, b, c = weir_cockerham_fst(g, subpops, max_allele=max_allele)
# define the statistic to compute within each window
def average_fst(wa, wb, wc):
return np.nansum(wa) / (np.nansum(wa) + np.nansum(wb) + np.nansum(wc))
# calculate average Fst in windows
fst, windows, counts = windowed_statistic(pos, values=(a, b, c),
statistic=average_fst,
size=size, start=start,
stop=stop, step=step,
windows=windows, fill=fill)
return fst, windows, counts | python | def windowed_weir_cockerham_fst(pos, g, subpops, size=None, start=None,
stop=None, step=None, windows=None,
fill=np.nan, max_allele=None):
"""Estimate average Fst in windows over a single chromosome/contig,
following the method of Weir and Cockerham (1984).
Parameters
----------
pos : array_like, int, shape (n_items,)
Variant positions, using 1-based coordinates, in ascending order.
g : array_like, int, shape (n_variants, n_samples, ploidy)
Genotype array.
subpops : sequence of sequences of ints
Sample indices for each subpopulation.
size : int
The window size (number of bases).
start : int, optional
The position at which to start (1-based).
stop : int, optional
The position at which to stop (1-based).
step : int, optional
The distance between start positions of windows. If not given,
defaults to the window size, i.e., non-overlapping windows.
windows : array_like, int, shape (n_windows, 2), optional
Manually specify the windows to use as a sequence of (window_start,
window_stop) positions, using 1-based coordinates. Overrides the
size/start/stop/step parameters.
fill : object, optional
The value to use where there are no variants within a window.
max_allele : int, optional
The highest allele index to consider.
Returns
-------
fst : ndarray, float, shape (n_windows,)
Average Fst in each window.
windows : ndarray, int, shape (n_windows, 2)
The windows used, as an array of (window_start, window_stop) positions,
using 1-based coordinates.
counts : ndarray, int, shape (n_windows,)
Number of variants in each window.
"""
# compute values per-variant
a, b, c = weir_cockerham_fst(g, subpops, max_allele=max_allele)
# define the statistic to compute within each window
def average_fst(wa, wb, wc):
return np.nansum(wa) / (np.nansum(wa) + np.nansum(wb) + np.nansum(wc))
# calculate average Fst in windows
fst, windows, counts = windowed_statistic(pos, values=(a, b, c),
statistic=average_fst,
size=size, start=start,
stop=stop, step=step,
windows=windows, fill=fill)
return fst, windows, counts | [
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following the method of Weir and Cockerham (1984).
Parameters
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pos : array_like, int, shape (n_items,)
Variant positions, using 1-based coordinates, in ascending order.
g : array_like, int, shape (n_variants, n_samples, ploidy)
Genotype array.
subpops : sequence of sequences of ints
Sample indices for each subpopulation.
size : int
The window size (number of bases).
start : int, optional
The position at which to start (1-based).
stop : int, optional
The position at which to stop (1-based).
step : int, optional
The distance between start positions of windows. If not given,
defaults to the window size, i.e., non-overlapping windows.
windows : array_like, int, shape (n_windows, 2), optional
Manually specify the windows to use as a sequence of (window_start,
window_stop) positions, using 1-based coordinates. Overrides the
size/start/stop/step parameters.
fill : object, optional
The value to use where there are no variants within a window.
max_allele : int, optional
The highest allele index to consider.
Returns
-------
fst : ndarray, float, shape (n_windows,)
Average Fst in each window.
windows : ndarray, int, shape (n_windows, 2)
The windows used, as an array of (window_start, window_stop) positions,
using 1-based coordinates.
counts : ndarray, int, shape (n_windows,)
Number of variants in each window. | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/stats/fst.py#L363-L421 | train | Estimate average Fst in windows over a single chromosome or contig. | 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(0b10001 + 0o41) + chr(54) + chr(49), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + '\062' + chr(2289 - 2237) + '\066', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110001) + '\x36' + chr(0b110010), 21433 - 21425), nzTpIcepk0o8(chr(0b101010 + 0o6) + chr(11141 - 11030) + chr(0b1001 + 0o50) + chr(0b101110 + 0o4) + '\x31', 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(51) + chr(53) + '\063', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110001) + '\063' + chr(982 - 928), ord("\x08")), nzTpIcepk0o8('\060' + chr(6770 - 6659) + chr(0b110010) + chr(418 - 367), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(1930 - 1880) + '\x31' + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(498 - 450) + chr(111) + chr(54) + chr(2337 - 2288), 0b1000), nzTpIcepk0o8('\x30' + '\157' + '\067' + '\060', 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(786 - 735) + chr(0b110110) + '\x32', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x33' + '\064' + '\x36', 0o10), nzTpIcepk0o8('\060' + chr(0b1100001 + 0o16) + chr(53) + '\x31', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110010) + chr(0b110100) + chr(49), 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(2493 - 2442) + chr(0b1110 + 0o46) + '\060', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b1111 + 0o43) + '\062' + chr(0b101100 + 0o11), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(49) + chr(52) + chr(0b110100), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\061' + chr(48) + chr(48), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + '\x32' + chr(0b110100) + '\064', 11130 - 11122), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b101101 + 0o5) + chr(0b110000) + chr(0b11 + 0o57), 0o10), nzTpIcepk0o8(chr(1984 - 1936) + chr(10140 - 10029) + '\064' + chr(1718 - 1664), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1010000 + 0o37) + chr(54) + '\x34', 0b1000), nzTpIcepk0o8(chr(1743 - 1695) + '\x6f' + '\x32' + chr(2188 - 2139) + '\x30', 0b1000), nzTpIcepk0o8(chr(2088 - 2040) + chr(0b1101001 + 0o6) + chr(460 - 410) + chr(54) + '\064', 0o10), nzTpIcepk0o8(chr(913 - 865) + chr(0b1101111) + chr(1507 - 1457), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b100101 + 0o20) + '\x31', 8), nzTpIcepk0o8(chr(0b10001 + 0o37) + '\157' + chr(0b110001) + chr(50) + '\061', 8), nzTpIcepk0o8(chr(1841 - 1793) + '\157' + '\061' + chr(0b100001 + 0o20) + '\066', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b0 + 0o63) + chr(2527 - 2476) + chr(0b110110), 0o10), nzTpIcepk0o8(chr(0b1111 + 0o41) + chr(0b100101 + 0o112) + chr(2015 - 1965) + chr(0b1000 + 0o54) + chr(0b10101 + 0o36), ord("\x08")), nzTpIcepk0o8(chr(1917 - 1869) + '\x6f' + chr(0b10001 + 0o40) + '\067' + chr(0b11010 + 0o32), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(6753 - 6642) + chr(0b10101 + 0o35) + chr(53), 30758 - 30750), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b101110 + 0o5) + chr(51) + chr(0b101100 + 0o12), 8), nzTpIcepk0o8(chr(1321 - 1273) + chr(0b110001 + 0o76) + chr(49) + '\064' + chr(0b10100 + 0o36), 0o10), nzTpIcepk0o8(chr(762 - 714) + '\157' + chr(50) + '\063' + chr(0b100010 + 0o21), 6726 - 6718), nzTpIcepk0o8('\060' + '\157' + chr(0b110010) + chr(1356 - 1303) + chr(198 - 147), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1010110 + 0o31) + chr(0b110110), 58311 - 58303), nzTpIcepk0o8('\x30' + chr(6138 - 6027) + '\063' + chr(48) + '\061', 0o10), nzTpIcepk0o8(chr(0b10100 + 0o34) + chr(0b1101111) + '\x32' + chr(50) + chr(0b100110 + 0o21), 42417 - 42409), nzTpIcepk0o8('\x30' + chr(5187 - 5076) + chr(49) + '\062' + '\x30', 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(1351 - 1303) + chr(0b1101111) + chr(2752 - 2699) + chr(48), 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x9f'), chr(0b1100100) + chr(0b1100101) + chr(0b11011 + 0o110) + '\157' + chr(0b1100100) + chr(0b1010101 + 0o20))('\x75' + chr(4452 - 4336) + chr(0b1100110) + chr(45) + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def v9FH6u23qROZ(IGIA_fu6MbaO, KQq7Z9J63zv1, FsHH2qbtSh8t, e1HrJaQHACnl=None, KQbHFTcl_LKy=None, dYJbBiYO_nGE=None, ZiKB99Xs91Lo=None, hVZaXHr1SthH=None, pPmkLCVA328e=roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'\xdf\xc7\x1c'), chr(3091 - 2991) + chr(3445 - 3344) + chr(0b11101 + 0o106) + chr(0b1101111) + chr(0b1100100) + '\145')('\x75' + chr(0b1000 + 0o154) + chr(558 - 456) + '\055' + chr(0b111 + 0o61))), j75eupAGs_rK=None):
(AQ9ceR9AaoT1, xFDEVQn5qSdh, teUmM7cKWZUa) = HFXVdu3zdbXL(KQq7Z9J63zv1, FsHH2qbtSh8t, max_allele=j75eupAGs_rK)
def epK8bCqGWRjd(DMJDVpNjmrZm, wlHb9hja4SFe, lG9IY90bKBAC):
return roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'\xdf\xc7\x1c"\x9e3'), '\x64' + '\x65' + '\143' + chr(9281 - 9170) + chr(100) + chr(0b1100101))(chr(0b100111 + 0o116) + '\x74' + '\x66' + chr(45) + '\x38'))(DMJDVpNjmrZm) / (roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'\xdf\xc7\x1c"\x9e3'), chr(0b111101 + 0o47) + chr(101) + chr(9238 - 9139) + chr(111) + chr(4869 - 4769) + '\x65')(chr(117) + chr(116) + '\146' + chr(0b101010 + 0o3) + '\x38'))(DMJDVpNjmrZm) + roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'\xdf\xc7\x1c"\x9e3'), '\144' + chr(0b1100101) + chr(99) + chr(0b1010100 + 0o33) + chr(0b10100 + 0o120) + chr(767 - 666))(chr(117) + chr(0b1110100) + chr(0b1100110) + chr(0b101101) + chr(0b111000)))(wlHb9hja4SFe) + roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'\xdf\xc7\x1c"\x9e3'), '\x64' + '\x65' + chr(0b1100011) + '\157' + chr(0b1100100) + chr(101))('\165' + chr(0b100110 + 0o116) + chr(0b1001001 + 0o35) + '\055' + chr(1102 - 1046)))(lG9IY90bKBAC))
(LXRrGYiwSV8C, hVZaXHr1SthH, gm2kNaWYNE_r) = JOnlY4qTZIKz(IGIA_fu6MbaO, values=(AQ9ceR9AaoT1, xFDEVQn5qSdh, teUmM7cKWZUa), statistic=epK8bCqGWRjd, size=e1HrJaQHACnl, start=KQbHFTcl_LKy, stop=dYJbBiYO_nGE, step=ZiKB99Xs91Lo, windows=hVZaXHr1SthH, fill=pPmkLCVA328e)
return (LXRrGYiwSV8C, hVZaXHr1SthH, gm2kNaWYNE_r) |
cggh/scikit-allel | allel/stats/fst.py | windowed_hudson_fst | def windowed_hudson_fst(pos, ac1, ac2, size=None, start=None, stop=None,
step=None, windows=None, fill=np.nan):
"""Estimate average Fst in windows over a single chromosome/contig,
following the method of Hudson (1992) elaborated by Bhatia et al. (2013).
Parameters
----------
pos : array_like, int, shape (n_items,)
Variant positions, using 1-based coordinates, in ascending order.
ac1 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the first population.
ac2 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the second population.
size : int, optional
The window size (number of bases).
start : int, optional
The position at which to start (1-based).
stop : int, optional
The position at which to stop (1-based).
step : int, optional
The distance between start positions of windows. If not given,
defaults to the window size, i.e., non-overlapping windows.
windows : array_like, int, shape (n_windows, 2), optional
Manually specify the windows to use as a sequence of (window_start,
window_stop) positions, using 1-based coordinates. Overrides the
size/start/stop/step parameters.
fill : object, optional
The value to use where there are no variants within a window.
Returns
-------
fst : ndarray, float, shape (n_windows,)
Average Fst in each window.
windows : ndarray, int, shape (n_windows, 2)
The windows used, as an array of (window_start, window_stop) positions,
using 1-based coordinates.
counts : ndarray, int, shape (n_windows,)
Number of variants in each window.
"""
# compute values per-variants
num, den = hudson_fst(ac1, ac2)
# define the statistic to compute within each window
def average_fst(wn, wd):
return np.nansum(wn) / np.nansum(wd)
# calculate average Fst in windows
fst, windows, counts = windowed_statistic(pos, values=(num, den),
statistic=average_fst,
size=size, start=start,
stop=stop, step=step,
windows=windows, fill=fill)
return fst, windows, counts | python | def windowed_hudson_fst(pos, ac1, ac2, size=None, start=None, stop=None,
step=None, windows=None, fill=np.nan):
"""Estimate average Fst in windows over a single chromosome/contig,
following the method of Hudson (1992) elaborated by Bhatia et al. (2013).
Parameters
----------
pos : array_like, int, shape (n_items,)
Variant positions, using 1-based coordinates, in ascending order.
ac1 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the first population.
ac2 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the second population.
size : int, optional
The window size (number of bases).
start : int, optional
The position at which to start (1-based).
stop : int, optional
The position at which to stop (1-based).
step : int, optional
The distance between start positions of windows. If not given,
defaults to the window size, i.e., non-overlapping windows.
windows : array_like, int, shape (n_windows, 2), optional
Manually specify the windows to use as a sequence of (window_start,
window_stop) positions, using 1-based coordinates. Overrides the
size/start/stop/step parameters.
fill : object, optional
The value to use where there are no variants within a window.
Returns
-------
fst : ndarray, float, shape (n_windows,)
Average Fst in each window.
windows : ndarray, int, shape (n_windows, 2)
The windows used, as an array of (window_start, window_stop) positions,
using 1-based coordinates.
counts : ndarray, int, shape (n_windows,)
Number of variants in each window.
"""
# compute values per-variants
num, den = hudson_fst(ac1, ac2)
# define the statistic to compute within each window
def average_fst(wn, wd):
return np.nansum(wn) / np.nansum(wd)
# calculate average Fst in windows
fst, windows, counts = windowed_statistic(pos, values=(num, den),
statistic=average_fst,
size=size, start=start,
stop=stop, step=step,
windows=windows, fill=fill)
return fst, windows, counts | [
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following the method of Hudson (1992) elaborated by Bhatia et al. (2013).
Parameters
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pos : array_like, int, shape (n_items,)
Variant positions, using 1-based coordinates, in ascending order.
ac1 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the first population.
ac2 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the second population.
size : int, optional
The window size (number of bases).
start : int, optional
The position at which to start (1-based).
stop : int, optional
The position at which to stop (1-based).
step : int, optional
The distance between start positions of windows. If not given,
defaults to the window size, i.e., non-overlapping windows.
windows : array_like, int, shape (n_windows, 2), optional
Manually specify the windows to use as a sequence of (window_start,
window_stop) positions, using 1-based coordinates. Overrides the
size/start/stop/step parameters.
fill : object, optional
The value to use where there are no variants within a window.
Returns
-------
fst : ndarray, float, shape (n_windows,)
Average Fst in each window.
windows : ndarray, int, shape (n_windows, 2)
The windows used, as an array of (window_start, window_stop) positions,
using 1-based coordinates.
counts : ndarray, int, shape (n_windows,)
Number of variants in each window. | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/stats/fst.py#L424-L479 | train | Estimate average Fst in windows over a single chromosome or contig. | 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(0b101 + 0o152) + chr(50) + chr(52) + chr(50), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(50) + chr(1039 - 990) + '\061', ord("\x08")), nzTpIcepk0o8(chr(2277 - 2229) + '\x6f' + chr(0b1 + 0o65) + chr(0b10010 + 0o37), 23278 - 23270), nzTpIcepk0o8('\x30' + '\157' + chr(0b110111) + chr(0b100101 + 0o13), 20088 - 20080), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b101 + 0o56) + chr(1301 - 1249) + chr(0b110110), 5587 - 5579), nzTpIcepk0o8(chr(48) + '\157' + chr(0b100110 + 0o15) + '\064' + chr(0b110100), 64815 - 64807), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x32' + '\062' + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(1646 - 1535) + chr(0b100101 + 0o16) + chr(0b101101 + 0o4) + chr(53), 63091 - 63083), nzTpIcepk0o8(chr(0b10100 + 0o34) + '\x6f' + '\x32' + '\x35' + chr(0b11100 + 0o24), 0b1000), nzTpIcepk0o8(chr(2248 - 2200) + '\x6f' + '\062', 0o10), nzTpIcepk0o8('\x30' + chr(0b1101011 + 0o4) + '\063' + chr(0b10110 + 0o40) + '\x32', 52078 - 52070), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x31' + chr(0b101100 + 0o7) + '\x37', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\062' + chr(0b110101) + chr(0b101011 + 0o14), 44725 - 44717), nzTpIcepk0o8('\060' + chr(0b1001101 + 0o42) + chr(0b110011) + chr(50) + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(1313 - 1265) + chr(5501 - 5390) + chr(50) + chr(0b110011) + chr(0b10010 + 0o45), 64097 - 64089), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(2343 - 2294) + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(53) + chr(0b110111), 14492 - 14484), nzTpIcepk0o8(chr(48) + chr(2227 - 2116) + chr(1106 - 1056) + chr(0b110110) + '\067', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(1123 - 1074) + chr(0b110110) + chr(54), ord("\x08")), nzTpIcepk0o8(chr(1659 - 1611) + chr(0b110 + 0o151) + chr(769 - 718) + chr(0b110001), ord("\x08")), nzTpIcepk0o8(chr(1301 - 1253) + chr(0b1100000 + 0o17) + '\x31' + '\064' + '\x30', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\062' + chr(0b101000 + 0o13) + chr(1149 - 1097), 0b1000), nzTpIcepk0o8(chr(1631 - 1583) + '\x6f' + '\x32' + chr(0b110100) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110001) + chr(0b110111), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(50) + chr(541 - 491) + chr(0b111 + 0o53), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(10117 - 10006) + chr(0b110011) + '\064' + '\063', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110001) + chr(50) + chr(0b110000), ord("\x08")), nzTpIcepk0o8(chr(490 - 442) + '\157' + chr(51) + '\062' + chr(48), 0o10), nzTpIcepk0o8(chr(0b10011 + 0o35) + '\157' + chr(51) + chr(1135 - 1080) + chr(2314 - 2259), 35794 - 35786), nzTpIcepk0o8('\060' + chr(111) + chr(51) + chr(1382 - 1328) + chr(0b110011), 0o10), nzTpIcepk0o8(chr(2237 - 2189) + chr(0b11100 + 0o123) + chr(51) + chr(0b110011) + '\x37', 31349 - 31341), nzTpIcepk0o8(chr(582 - 534) + chr(111) + chr(0b110011) + chr(1041 - 993) + '\x33', 0b1000), nzTpIcepk0o8(chr(48) + '\157' + '\x33' + chr(2079 - 2027) + chr(0b10000 + 0o46), 8), nzTpIcepk0o8('\060' + chr(0b10010 + 0o135) + '\x31' + chr(52) + '\062', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1011110 + 0o21) + '\x33' + '\x32' + chr(0b110100 + 0o3), 45977 - 45969), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110001) + chr(0b1000 + 0o57) + chr(0b110001), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(1081 - 1030) + chr(1885 - 1833) + '\063', 8), nzTpIcepk0o8('\x30' + chr(111) + '\x31' + '\060' + '\x34', 11412 - 11404), nzTpIcepk0o8(chr(1282 - 1234) + chr(111) + chr(51) + '\062', 0o10), nzTpIcepk0o8('\060' + chr(4835 - 4724) + chr(0b111 + 0o52) + chr(0b110010), 13139 - 13131)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + chr(0b11100 + 0o123) + chr(67 - 14) + chr(0b110000), ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x8c'), chr(0b1100100) + '\145' + '\x63' + chr(11843 - 11732) + '\x64' + chr(101))('\x75' + chr(0b0 + 0o164) + chr(0b1111 + 0o127) + '\x2d' + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def si7vjvafrhev(IGIA_fu6MbaO, kqnbwhK0EBnP, S9W4ddqb2HVR, e1HrJaQHACnl=None, KQbHFTcl_LKy=None, dYJbBiYO_nGE=None, ZiKB99Xs91Lo=None, hVZaXHr1SthH=None, pPmkLCVA328e=roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'\xcc\xe8_'), chr(8476 - 8376) + chr(0b1100101) + '\x63' + '\157' + '\144' + chr(6820 - 6719))(chr(10929 - 10812) + chr(0b1110100) + chr(102) + chr(0b1010 + 0o43) + chr(143 - 87)))):
(o0eINMlvUImY, nlXsT_LUVPQ8) = NGz8qBsr3ohU(kqnbwhK0EBnP, S9W4ddqb2HVR)
def epK8bCqGWRjd(kU9f8JZiVl9F, YsvFHQUjJH1X):
return roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'\xcc\xe8_K\x93\x89'), chr(0b1100100) + chr(101) + chr(0b1001000 + 0o33) + chr(0b1101111) + '\x64' + chr(2429 - 2328))('\x75' + chr(0b1110100) + chr(102) + chr(1657 - 1612) + chr(56)))(kU9f8JZiVl9F) / roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'\xcc\xe8_K\x93\x89'), '\144' + chr(5804 - 5703) + chr(8581 - 8482) + chr(5076 - 4965) + chr(100) + chr(0b1100101))('\165' + chr(12581 - 12465) + chr(102) + '\055' + chr(388 - 332)))(YsvFHQUjJH1X)
(LXRrGYiwSV8C, hVZaXHr1SthH, gm2kNaWYNE_r) = JOnlY4qTZIKz(IGIA_fu6MbaO, values=(o0eINMlvUImY, nlXsT_LUVPQ8), statistic=epK8bCqGWRjd, size=e1HrJaQHACnl, start=KQbHFTcl_LKy, stop=dYJbBiYO_nGE, step=ZiKB99Xs91Lo, windows=hVZaXHr1SthH, fill=pPmkLCVA328e)
return (LXRrGYiwSV8C, hVZaXHr1SthH, gm2kNaWYNE_r) |
cggh/scikit-allel | allel/stats/fst.py | moving_weir_cockerham_fst | def moving_weir_cockerham_fst(g, subpops, size, start=0, stop=None, step=None,
max_allele=None):
"""Estimate average Fst in moving windows over a single chromosome/contig,
following the method of Weir and Cockerham (1984).
Parameters
----------
g : array_like, int, shape (n_variants, n_samples, ploidy)
Genotype array.
subpops : sequence of sequences of ints
Sample indices for each subpopulation.
size : int
The window size (number of variants).
start : int, optional
The index at which to start.
stop : int, optional
The index at which to stop.
step : int, optional
The number of variants between start positions of windows. If not
given, defaults to the window size, i.e., non-overlapping windows.
max_allele : int, optional
The highest allele index to consider.
Returns
-------
fst : ndarray, float, shape (n_windows,)
Average Fst in each window.
"""
# calculate per-variant values
a, b, c = weir_cockerham_fst(g, subpops, max_allele=max_allele)
# compute the numerator and denominator in moving windows
num = moving_statistic(a, statistic=np.nansum, size=size, start=start,
stop=stop, step=step)
den = moving_statistic(a + b + c, statistic=np.nansum, size=size,
start=start, stop=stop, step=step)
# calculate fst in each window
fst = num / den
return fst | python | def moving_weir_cockerham_fst(g, subpops, size, start=0, stop=None, step=None,
max_allele=None):
"""Estimate average Fst in moving windows over a single chromosome/contig,
following the method of Weir and Cockerham (1984).
Parameters
----------
g : array_like, int, shape (n_variants, n_samples, ploidy)
Genotype array.
subpops : sequence of sequences of ints
Sample indices for each subpopulation.
size : int
The window size (number of variants).
start : int, optional
The index at which to start.
stop : int, optional
The index at which to stop.
step : int, optional
The number of variants between start positions of windows. If not
given, defaults to the window size, i.e., non-overlapping windows.
max_allele : int, optional
The highest allele index to consider.
Returns
-------
fst : ndarray, float, shape (n_windows,)
Average Fst in each window.
"""
# calculate per-variant values
a, b, c = weir_cockerham_fst(g, subpops, max_allele=max_allele)
# compute the numerator and denominator in moving windows
num = moving_statistic(a, statistic=np.nansum, size=size, start=start,
stop=stop, step=step)
den = moving_statistic(a + b + c, statistic=np.nansum, size=size,
start=start, stop=stop, step=step)
# calculate fst in each window
fst = num / den
return fst | [
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Parameters
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g : array_like, int, shape (n_variants, n_samples, ploidy)
Genotype array.
subpops : sequence of sequences of ints
Sample indices for each subpopulation.
size : int
The window size (number of variants).
start : int, optional
The index at which to start.
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The index at which to stop.
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The number of variants between start positions of windows. If not
given, defaults to the window size, i.e., non-overlapping windows.
max_allele : int, optional
The highest allele index to consider.
Returns
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fst : ndarray, float, shape (n_windows,)
Average Fst in each window. | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/stats/fst.py#L540-L582 | train | Estimate average Fst in moving windows over a single chromosome or contig. | 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' + '\063' + '\066' + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(2086 - 2038) + chr(111) + '\x32' + chr(0b101 + 0o56) + chr(1495 - 1445), ord("\x08")), nzTpIcepk0o8(chr(0b11000 + 0o30) + chr(0b1101111) + '\063' + chr(0b110101) + '\066', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110000 + 0o2) + '\062' + chr(50), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1010100 + 0o33) + '\062' + chr(0b101001 + 0o10) + '\x31', 53715 - 53707), nzTpIcepk0o8(chr(1602 - 1554) + '\157' + chr(0b101100 + 0o6) + chr(0b110100) + chr(90 - 42), 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(53) + '\062', 0o10), nzTpIcepk0o8(chr(48) + chr(111) + '\061' + chr(1286 - 1236) + chr(0b110011), 0o10), nzTpIcepk0o8(chr(0b10010 + 0o36) + chr(0b1101111) + '\x33' + chr(0b110101) + '\x32', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1010010 + 0o35) + '\062' + '\x35' + chr(1076 - 1028), 41761 - 41753), nzTpIcepk0o8(chr(1483 - 1435) + '\157' + chr(2284 - 2235) + chr(0b110001) + '\063', 0o10), nzTpIcepk0o8(chr(0b100011 + 0o15) + chr(111) + chr(0b100010 + 0o21) + '\063' + chr(54), 0o10), nzTpIcepk0o8('\060' + chr(0b1000001 + 0o56) + chr(51) + '\x36', 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(0b110001) + chr(0b110001) + chr(0b111 + 0o51), 56383 - 56375), nzTpIcepk0o8('\x30' + '\x6f' + '\062' + chr(592 - 544) + chr(486 - 431), 0b1000), nzTpIcepk0o8(chr(0b10100 + 0o34) + chr(111) + chr(0b10010 + 0o37), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110010) + chr(1726 - 1673) + chr(0b110000), 8), nzTpIcepk0o8('\x30' + '\157' + '\063' + chr(0b110100) + chr(0b10000 + 0o40), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(49) + '\x30' + chr(0b110000), 0b1000), nzTpIcepk0o8('\060' + chr(0b110110 + 0o71) + chr(0b100000 + 0o23) + chr(48), 0o10), nzTpIcepk0o8(chr(0b10101 + 0o33) + chr(0b1000101 + 0o52) + '\x31' + chr(54) + '\060', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1010100 + 0o33) + '\061' + chr(2247 - 2193) + chr(938 - 888), 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(1381 - 1326) + chr(0b100101 + 0o20), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(2231 - 2180) + '\x33' + '\064', 13671 - 13663), nzTpIcepk0o8(chr(48) + '\157' + chr(1772 - 1722) + chr(0b110100) + chr(50), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b111 + 0o52) + chr(0b110100) + chr(2060 - 2005), 0b1000), nzTpIcepk0o8(chr(1043 - 995) + chr(9767 - 9656) + chr(1739 - 1685) + '\064', 0o10), nzTpIcepk0o8(chr(0b101111 + 0o1) + chr(0b1101111) + chr(55), 7163 - 7155), nzTpIcepk0o8(chr(204 - 156) + chr(0b1101111) + chr(0b110010) + chr(0b110101) + '\067', 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + '\x31' + '\066' + chr(53), 26963 - 26955), nzTpIcepk0o8(chr(48) + '\x6f' + chr(1876 - 1826) + chr(53) + chr(54), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b10 + 0o60) + '\x31' + '\064', 0b1000), nzTpIcepk0o8('\x30' + chr(111) + '\x34' + '\062', 12964 - 12956), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\061' + chr(0b101100 + 0o5) + '\063', 8), nzTpIcepk0o8(chr(48) + '\x6f' + chr(1391 - 1341) + '\062' + '\065', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + '\063' + chr(0b10011 + 0o43) + chr(1266 - 1211), 0o10), nzTpIcepk0o8(chr(0b100010 + 0o16) + chr(111) + '\062' + '\063' + '\062', 8), nzTpIcepk0o8(chr(1979 - 1931) + chr(0b1101111) + chr(0b110001) + chr(0b110110) + chr(755 - 705), 8), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b11111 + 0o24) + chr(0b100111 + 0o16) + chr(0b110010), 8), nzTpIcepk0o8(chr(0b1110 + 0o42) + chr(9938 - 9827) + '\x34' + chr(0b100110 + 0o16), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(965 - 917) + '\157' + '\065' + '\x30', 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xdb'), '\144' + chr(0b1100101) + '\x63' + chr(0b1101111) + '\144' + '\x65')('\165' + chr(0b1001101 + 0o47) + chr(5635 - 5533) + chr(0b11101 + 0o20) + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def NdxN8Rxn6Lae(KQq7Z9J63zv1, FsHH2qbtSh8t, e1HrJaQHACnl, KQbHFTcl_LKy=nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b10011 + 0o35), 60838 - 60830), dYJbBiYO_nGE=None, ZiKB99Xs91Lo=None, j75eupAGs_rK=None):
(AQ9ceR9AaoT1, xFDEVQn5qSdh, teUmM7cKWZUa) = HFXVdu3zdbXL(KQq7Z9J63zv1, FsHH2qbtSh8t, max_allele=j75eupAGs_rK)
o0eINMlvUImY = SvzAnntsMYgE(AQ9ceR9AaoT1, statistic=nDF4gVNx0u9Q.nansum, size=e1HrJaQHACnl, start=KQbHFTcl_LKy, stop=dYJbBiYO_nGE, step=ZiKB99Xs91Lo)
nlXsT_LUVPQ8 = SvzAnntsMYgE(AQ9ceR9AaoT1 + xFDEVQn5qSdh + teUmM7cKWZUa, statistic=nDF4gVNx0u9Q.nansum, size=e1HrJaQHACnl, start=KQbHFTcl_LKy, stop=dYJbBiYO_nGE, step=ZiKB99Xs91Lo)
LXRrGYiwSV8C = o0eINMlvUImY / nlXsT_LUVPQ8
return LXRrGYiwSV8C |
cggh/scikit-allel | allel/stats/fst.py | moving_hudson_fst | def moving_hudson_fst(ac1, ac2, size, start=0, stop=None, step=None):
"""Estimate average Fst in moving windows over a single chromosome/contig,
following the method of Hudson (1992) elaborated by Bhatia et al. (2013).
Parameters
----------
ac1 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the first population.
ac2 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the second population.
size : int
The window size (number of variants).
start : int, optional
The index at which to start.
stop : int, optional
The index at which to stop.
step : int, optional
The number of variants between start positions of windows. If not
given, defaults to the window size, i.e., non-overlapping windows.
Returns
-------
fst : ndarray, float, shape (n_windows,)
Average Fst in each window.
"""
# calculate per-variant values
num, den = hudson_fst(ac1, ac2, fill=np.nan)
# compute the numerator and denominator in moving windows
num_sum = moving_statistic(num, statistic=np.nansum, size=size,
start=start, stop=stop, step=step)
den_sum = moving_statistic(den, statistic=np.nansum, size=size,
start=start, stop=stop, step=step)
# calculate fst in each window
fst = num_sum / den_sum
return fst | python | def moving_hudson_fst(ac1, ac2, size, start=0, stop=None, step=None):
"""Estimate average Fst in moving windows over a single chromosome/contig,
following the method of Hudson (1992) elaborated by Bhatia et al. (2013).
Parameters
----------
ac1 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the first population.
ac2 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the second population.
size : int
The window size (number of variants).
start : int, optional
The index at which to start.
stop : int, optional
The index at which to stop.
step : int, optional
The number of variants between start positions of windows. If not
given, defaults to the window size, i.e., non-overlapping windows.
Returns
-------
fst : ndarray, float, shape (n_windows,)
Average Fst in each window.
"""
# calculate per-variant values
num, den = hudson_fst(ac1, ac2, fill=np.nan)
# compute the numerator and denominator in moving windows
num_sum = moving_statistic(num, statistic=np.nansum, size=size,
start=start, stop=stop, step=step)
den_sum = moving_statistic(den, statistic=np.nansum, size=size,
start=start, stop=stop, step=step)
# calculate fst in each window
fst = num_sum / den_sum
return fst | [
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Parameters
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ac1 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the first population.
ac2 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the second population.
size : int
The window size (number of variants).
start : int, optional
The index at which to start.
stop : int, optional
The index at which to stop.
step : int, optional
The number of variants between start positions of windows. If not
given, defaults to the window size, i.e., non-overlapping windows.
Returns
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fst : ndarray, float, shape (n_windows,)
Average Fst in each window. | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/stats/fst.py#L585-L624 | train | Estimate average Fst in moving windows over a single chromosome or contig. | 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(1654 - 1606) + chr(8010 - 7899) + '\067' + chr(1707 - 1656), 14941 - 14933), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110010) + '\x34' + '\064', 0o10), nzTpIcepk0o8(chr(450 - 402) + chr(3098 - 2987) + '\061' + chr(320 - 271) + chr(0b11001 + 0o27), 29193 - 29185), nzTpIcepk0o8(chr(48) + chr(2288 - 2177) + chr(0b100010 + 0o21) + chr(0b100101 + 0o14) + chr(0b110010), 0o10), nzTpIcepk0o8(chr(1435 - 1387) + chr(0b1101111) + '\x31' + chr(1794 - 1746) + '\060', 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x32' + chr(2118 - 2063) + chr(619 - 567), 50299 - 50291), nzTpIcepk0o8(chr(1016 - 968) + chr(111) + chr(0b110011) + chr(1275 - 1225) + chr(51), 0b1000), nzTpIcepk0o8(chr(0b1111 + 0o41) + chr(9402 - 9291) + chr(0b11001 + 0o32) + '\060' + chr(1474 - 1423), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(49) + '\x37' + '\x32', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x31' + '\x31', 0b1000), nzTpIcepk0o8(chr(0b10011 + 0o35) + chr(0b111000 + 0o67) + chr(50) + chr(926 - 872) + chr(54), 27854 - 27846), nzTpIcepk0o8(chr(761 - 713) + '\x6f' + chr(0b11011 + 0o26) + chr(48) + '\063', ord("\x08")), nzTpIcepk0o8(chr(0b11100 + 0o24) + chr(0b1101111) + chr(0b110111) + chr(53), ord("\x08")), nzTpIcepk0o8(chr(1591 - 1543) + '\157' + chr(0b110010) + '\061' + '\063', 23331 - 23323), nzTpIcepk0o8('\060' + '\157' + chr(0b100011 + 0o22) + '\x32', 0b1000), nzTpIcepk0o8('\x30' + chr(0b111110 + 0o61) + chr(0b11101 + 0o24) + chr(55) + chr(1844 - 1789), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110011) + '\x30' + chr(53), 40489 - 40481), nzTpIcepk0o8(chr(0b1110 + 0o42) + chr(0b1001011 + 0o44) + '\x33' + '\065' + chr(0b100101 + 0o14), 0b1000), nzTpIcepk0o8(chr(48) + chr(9093 - 8982) + '\x33' + chr(50) + '\x37', 33562 - 33554), nzTpIcepk0o8(chr(48) + chr(9431 - 9320) + chr(0b110011) + chr(0b11010 + 0o31) + chr(51), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(10745 - 10634) + chr(0b110001) + '\x31', 8), nzTpIcepk0o8('\x30' + '\157' + chr(0b110010) + chr(0b1101 + 0o50) + '\060', 0o10), nzTpIcepk0o8('\060' + chr(7776 - 7665) + chr(50) + chr(0b110 + 0o55) + chr(50), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + '\061' + chr(0b110111) + chr(50), 8), nzTpIcepk0o8('\x30' + chr(111) + '\062' + chr(0b110001) + '\x30', 0b1000), nzTpIcepk0o8(chr(1825 - 1777) + chr(111) + chr(0b1100 + 0o45) + chr(0b110110) + '\061', 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(98 - 50) + '\x6f' + '\x31' + chr(50) + chr(0b110010), 32108 - 32100), nzTpIcepk0o8(chr(48) + chr(5209 - 5098) + chr(0b110010) + chr(2668 - 2616) + chr(51), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b11 + 0o154) + '\061' + chr(54) + chr(51), 21440 - 21432), nzTpIcepk0o8(chr(0b110000) + chr(0b10010 + 0o135) + chr(0b110001) + '\065' + chr(2510 - 2457), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x31' + chr(0b100110 + 0o13) + chr(0b110011), 44326 - 44318), nzTpIcepk0o8('\x30' + '\157' + chr(0b100010 + 0o17) + chr(0b11011 + 0o27) + '\x32', 8), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x33' + chr(53) + chr(53), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(12269 - 12158) + chr(49) + chr(0b110000) + chr(0b100 + 0o60), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + '\067' + '\062', 0b1000), nzTpIcepk0o8(chr(1460 - 1412) + chr(0b1101111) + chr(50) + chr(48) + chr(0b110101), 26146 - 26138), nzTpIcepk0o8(chr(0b110000) + chr(4127 - 4016) + '\063' + chr(2915 - 2861) + chr(52), ord("\x08")), nzTpIcepk0o8(chr(0b10100 + 0o34) + '\x6f' + '\x31' + chr(1633 - 1585) + chr(0b110000), 8), nzTpIcepk0o8(chr(48) + '\x6f' + '\061' + '\061' + chr(0b11101 + 0o30), 39132 - 39124)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(0b1010011 + 0o34) + chr(0b110101) + chr(0b110000), 23382 - 23374)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x15'), chr(0b1111 + 0o125) + '\x65' + chr(0b1100011) + chr(0b11000 + 0o127) + '\x64' + chr(3436 - 3335))(chr(117) + chr(0b1111 + 0o145) + '\x66' + chr(299 - 254) + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def TwcmDEJLIPJU(kqnbwhK0EBnP, S9W4ddqb2HVR, e1HrJaQHACnl, KQbHFTcl_LKy=nzTpIcepk0o8(chr(1143 - 1095) + chr(0b1101111 + 0o0) + chr(0b110000), ord("\x08")), dYJbBiYO_nGE=None, ZiKB99Xs91Lo=None):
(o0eINMlvUImY, nlXsT_LUVPQ8) = NGz8qBsr3ohU(kqnbwhK0EBnP, S9W4ddqb2HVR, fill=nDF4gVNx0u9Q.nan)
YTsBFgoSfJ9r = SvzAnntsMYgE(o0eINMlvUImY, statistic=nDF4gVNx0u9Q.nansum, size=e1HrJaQHACnl, start=KQbHFTcl_LKy, stop=dYJbBiYO_nGE, step=ZiKB99Xs91Lo)
h6zhqTCtjKlT = SvzAnntsMYgE(nlXsT_LUVPQ8, statistic=nDF4gVNx0u9Q.nansum, size=e1HrJaQHACnl, start=KQbHFTcl_LKy, stop=dYJbBiYO_nGE, step=ZiKB99Xs91Lo)
LXRrGYiwSV8C = YTsBFgoSfJ9r / h6zhqTCtjKlT
return LXRrGYiwSV8C |
cggh/scikit-allel | allel/stats/fst.py | moving_patterson_fst | def moving_patterson_fst(ac1, ac2, size, start=0, stop=None, step=None):
"""Estimate average Fst in moving windows over a single chromosome/contig,
following the method of Patterson (2012).
Parameters
----------
ac1 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the first population.
ac2 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the second population.
size : int
The window size (number of variants).
start : int, optional
The index at which to start.
stop : int, optional
The index at which to stop.
step : int, optional
The number of variants between start positions of windows. If not
given, defaults to the window size, i.e., non-overlapping windows.
Returns
-------
fst : ndarray, float, shape (n_windows,)
Average Fst in each window.
"""
# calculate per-variant values
num, den = patterson_fst(ac1, ac2)
# compute the numerator and denominator in moving windows
num_sum = moving_statistic(num, statistic=np.nansum, size=size,
start=start, stop=stop, step=step)
den_sum = moving_statistic(den, statistic=np.nansum, size=size,
start=start, stop=stop, step=step)
# calculate fst in each window
fst = num_sum / den_sum
return fst | python | def moving_patterson_fst(ac1, ac2, size, start=0, stop=None, step=None):
"""Estimate average Fst in moving windows over a single chromosome/contig,
following the method of Patterson (2012).
Parameters
----------
ac1 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the first population.
ac2 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the second population.
size : int
The window size (number of variants).
start : int, optional
The index at which to start.
stop : int, optional
The index at which to stop.
step : int, optional
The number of variants between start positions of windows. If not
given, defaults to the window size, i.e., non-overlapping windows.
Returns
-------
fst : ndarray, float, shape (n_windows,)
Average Fst in each window.
"""
# calculate per-variant values
num, den = patterson_fst(ac1, ac2)
# compute the numerator and denominator in moving windows
num_sum = moving_statistic(num, statistic=np.nansum, size=size,
start=start, stop=stop, step=step)
den_sum = moving_statistic(den, statistic=np.nansum, size=size,
start=start, stop=stop, step=step)
# calculate fst in each window
fst = num_sum / den_sum
return fst | [
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Allele counts array from the first population.
ac2 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the second population.
size : int
The window size (number of variants).
start : int, optional
The index at which to start.
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The index at which to stop.
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The number of variants between start positions of windows. If not
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Returns
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fst : ndarray, float, shape (n_windows,)
Average Fst in each window. | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/stats/fst.py#L627-L666 | train | Estimate average Fst in moving windows over a single chromosome or contig. | 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(0b11011 + 0o25) + chr(111) + chr(55) + chr(0b10100 + 0o40), 0o10), nzTpIcepk0o8(chr(0b1 + 0o57) + '\x6f' + '\061' + chr(54) + '\062', 43483 - 43475), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b100010 + 0o20) + chr(0b101 + 0o55) + chr(0b100000 + 0o21), 35115 - 35107), nzTpIcepk0o8('\060' + '\157' + '\063' + chr(0b1000 + 0o53) + chr(0b11100 + 0o25), 17002 - 16994), nzTpIcepk0o8(chr(1549 - 1501) + chr(111) + '\061' + '\x32' + '\061', 0o10), nzTpIcepk0o8(chr(0b101101 + 0o3) + chr(0b111101 + 0o62) + chr(0b10111 + 0o32) + '\065' + chr(0b110000), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(0b110010) + chr(53) + chr(0b101101 + 0o7), ord("\x08")), nzTpIcepk0o8(chr(362 - 314) + '\157' + chr(0b11010 + 0o31) + chr(0b10111 + 0o32) + '\060', 64037 - 64029), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\063' + chr(1901 - 1847) + chr(51), 0b1000), nzTpIcepk0o8(chr(0b1001 + 0o47) + chr(111) + '\063' + chr(54) + chr(0b110011), 8), nzTpIcepk0o8('\x30' + chr(7255 - 7144) + chr(0b1100 + 0o47) + chr(0b110100) + chr(53), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b11101 + 0o122) + chr(0b10010 + 0o44) + chr(52), 11280 - 11272), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(49) + chr(0b110000) + chr(0b110001), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1100010 + 0o15) + '\x32' + chr(0b100110 + 0o13) + chr(0b110110), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + '\x31' + '\067' + chr(48), 52201 - 52193), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(50) + chr(48) + chr(923 - 868), 6673 - 6665), nzTpIcepk0o8(chr(0b110000) + chr(0b1101001 + 0o6) + '\x32' + '\067' + '\x36', 0b1000), nzTpIcepk0o8('\060' + chr(111) + '\x32' + chr(52) + chr(54), 61431 - 61423), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\061' + '\x35' + chr(0b10000 + 0o44), ord("\x08")), nzTpIcepk0o8(chr(1238 - 1190) + '\x6f' + chr(0b110011) + chr(0b11 + 0o60) + chr(0b110101), 16436 - 16428), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110001) + '\065' + chr(53), 0o10), nzTpIcepk0o8('\x30' + chr(0b111101 + 0o62) + chr(0b101111 + 0o2) + '\x33', 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(1847 - 1798) + chr(55), 2824 - 2816), nzTpIcepk0o8(chr(0b11110 + 0o22) + chr(111) + '\x31' + chr(54) + '\063', 48208 - 48200), nzTpIcepk0o8(chr(0b1100 + 0o44) + '\157' + '\x33' + '\x31' + chr(0b110010), 40110 - 40102), nzTpIcepk0o8(chr(529 - 481) + '\157' + '\x31' + chr(2179 - 2126) + chr(1411 - 1357), 0o10), nzTpIcepk0o8(chr(805 - 757) + chr(111) + '\x32' + chr(518 - 469) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(0b10100 + 0o34) + chr(0b1101111) + '\x37' + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(2218 - 2170) + '\x6f' + chr(2096 - 2047) + chr(54) + chr(1959 - 1907), 0b1000), nzTpIcepk0o8(chr(48) + chr(12282 - 12171) + '\x33' + chr(0b110010) + '\x37', 0b1000), nzTpIcepk0o8('\060' + chr(5790 - 5679) + '\063' + chr(0b100100 + 0o21), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b100011 + 0o20) + chr(0b110000) + '\065', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(51) + chr(0b11011 + 0o27) + chr(1992 - 1943), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b1011 + 0o50) + chr(314 - 265) + chr(1314 - 1264), 8), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110000), 48692 - 48684), nzTpIcepk0o8('\060' + '\157' + chr(0b110011) + chr(0b110 + 0o56) + '\x33', 2313 - 2305), nzTpIcepk0o8(chr(0b10110 + 0o32) + '\157' + '\061' + '\x30' + chr(55), 54827 - 54819), nzTpIcepk0o8('\x30' + chr(111) + '\067' + '\x36', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(928 - 877) + '\062' + '\066', 0o10), nzTpIcepk0o8(chr(0b11110 + 0o22) + chr(0b1101111) + chr(1671 - 1620) + chr(1798 - 1744) + chr(53), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + chr(111) + chr(0b1 + 0o64) + '\060', 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x12'), chr(0b1100100) + '\145' + chr(2182 - 2083) + chr(0b1100001 + 0o16) + '\x64' + chr(101))(chr(0b1110101) + chr(8517 - 8401) + chr(0b1100110) + chr(0b10000 + 0o35) + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def hdxAmGz28tnO(kqnbwhK0EBnP, S9W4ddqb2HVR, e1HrJaQHACnl, KQbHFTcl_LKy=nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(48), 8), dYJbBiYO_nGE=None, ZiKB99Xs91Lo=None):
(o0eINMlvUImY, nlXsT_LUVPQ8) = SRPucSlaq1kD(kqnbwhK0EBnP, S9W4ddqb2HVR)
YTsBFgoSfJ9r = SvzAnntsMYgE(o0eINMlvUImY, statistic=nDF4gVNx0u9Q.nansum, size=e1HrJaQHACnl, start=KQbHFTcl_LKy, stop=dYJbBiYO_nGE, step=ZiKB99Xs91Lo)
h6zhqTCtjKlT = SvzAnntsMYgE(nlXsT_LUVPQ8, statistic=nDF4gVNx0u9Q.nansum, size=e1HrJaQHACnl, start=KQbHFTcl_LKy, stop=dYJbBiYO_nGE, step=ZiKB99Xs91Lo)
LXRrGYiwSV8C = YTsBFgoSfJ9r / h6zhqTCtjKlT
return LXRrGYiwSV8C |
cggh/scikit-allel | allel/stats/fst.py | average_weir_cockerham_fst | def average_weir_cockerham_fst(g, subpops, blen, max_allele=None):
"""Estimate average Fst and standard error using the block-jackknife.
Parameters
----------
g : array_like, int, shape (n_variants, n_samples, ploidy)
Genotype array.
subpops : sequence of sequences of ints
Sample indices for each subpopulation.
blen : int
Block size (number of variants).
max_allele : int, optional
The highest allele index to consider.
Returns
-------
fst : float
Estimated value of the statistic using all data.
se : float
Estimated standard error.
vb : ndarray, float, shape (n_blocks,)
Value of the statistic in each block.
vj : ndarray, float, shape (n_blocks,)
Values of the statistic from block-jackknife resampling.
"""
# calculate per-variant values
a, b, c = weir_cockerham_fst(g, subpops, max_allele=max_allele)
# calculate overall estimate
a_sum = np.nansum(a)
b_sum = np.nansum(b)
c_sum = np.nansum(c)
fst = a_sum / (a_sum + b_sum + c_sum)
# compute the numerator and denominator within each block
num_bsum = moving_statistic(a, statistic=np.nansum, size=blen)
den_bsum = moving_statistic(a + b + c, statistic=np.nansum, size=blen)
# calculate the statistic values in each block
vb = num_bsum / den_bsum
# estimate standard error
_, se, vj = jackknife((num_bsum, den_bsum),
statistic=lambda n, d: np.sum(n) / np.sum(d))
return fst, se, vb, vj | python | def average_weir_cockerham_fst(g, subpops, blen, max_allele=None):
"""Estimate average Fst and standard error using the block-jackknife.
Parameters
----------
g : array_like, int, shape (n_variants, n_samples, ploidy)
Genotype array.
subpops : sequence of sequences of ints
Sample indices for each subpopulation.
blen : int
Block size (number of variants).
max_allele : int, optional
The highest allele index to consider.
Returns
-------
fst : float
Estimated value of the statistic using all data.
se : float
Estimated standard error.
vb : ndarray, float, shape (n_blocks,)
Value of the statistic in each block.
vj : ndarray, float, shape (n_blocks,)
Values of the statistic from block-jackknife resampling.
"""
# calculate per-variant values
a, b, c = weir_cockerham_fst(g, subpops, max_allele=max_allele)
# calculate overall estimate
a_sum = np.nansum(a)
b_sum = np.nansum(b)
c_sum = np.nansum(c)
fst = a_sum / (a_sum + b_sum + c_sum)
# compute the numerator and denominator within each block
num_bsum = moving_statistic(a, statistic=np.nansum, size=blen)
den_bsum = moving_statistic(a + b + c, statistic=np.nansum, size=blen)
# calculate the statistic values in each block
vb = num_bsum / den_bsum
# estimate standard error
_, se, vj = jackknife((num_bsum, den_bsum),
statistic=lambda n, d: np.sum(n) / np.sum(d))
return fst, se, vb, vj | [
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Parameters
----------
g : array_like, int, shape (n_variants, n_samples, ploidy)
Genotype array.
subpops : sequence of sequences of ints
Sample indices for each subpopulation.
blen : int
Block size (number of variants).
max_allele : int, optional
The highest allele index to consider.
Returns
-------
fst : float
Estimated value of the statistic using all data.
se : float
Estimated standard error.
vb : ndarray, float, shape (n_blocks,)
Value of the statistic in each block.
vj : ndarray, float, shape (n_blocks,)
Values of the statistic from block-jackknife resampling. | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/stats/fst.py#L669-L716 | train | Estimate average Fst and standard error using the block - jackknife resampling. | 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' + '\x31' + chr(0b110111) + '\x33', 0b1000), nzTpIcepk0o8('\x30' + chr(4318 - 4207) + chr(49) + chr(48) + chr(0b1100 + 0o50), 0o10), nzTpIcepk0o8(chr(77 - 29) + chr(111) + chr(0b111 + 0o53) + chr(0b110111) + chr(0b110011), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1110 + 0o141) + chr(786 - 735) + '\062' + chr(48), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110001), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x31' + '\061' + chr(0b10001 + 0o45), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(11898 - 11787) + chr(50) + '\x33' + '\063', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b111000 + 0o67) + '\061' + '\065' + chr(0b110000), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110001) + '\062' + chr(1974 - 1923), 6912 - 6904), nzTpIcepk0o8(chr(48) + chr(111) + '\061' + chr(0b101101 + 0o4) + '\063', ord("\x08")), nzTpIcepk0o8(chr(0b0 + 0o60) + chr(9520 - 9409) + '\x37' + chr(0b110110), 0b1000), nzTpIcepk0o8('\060' + '\157' + '\x33' + '\x31' + chr(0b110101), 56709 - 56701), nzTpIcepk0o8(chr(0b110000) + chr(6123 - 6012) + '\x35' + '\x35', 0o10), nzTpIcepk0o8(chr(48) + '\157' + '\x33' + '\066' + chr(54), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b100111 + 0o14) + '\x33' + chr(1015 - 965), 0b1000), nzTpIcepk0o8('\060' + '\x6f' + '\x36', 61789 - 61781), nzTpIcepk0o8('\x30' + '\157' + '\061' + '\061' + chr(50), 0o10), nzTpIcepk0o8(chr(0b100011 + 0o15) + chr(0b1101111) + chr(1970 - 1919) + '\x36', 0b1000), nzTpIcepk0o8('\060' + '\157' + '\062' + chr(107 - 52) + chr(0b110010), 0b1000), nzTpIcepk0o8(chr(0b1110 + 0o42) + chr(0b1101111) + chr(0b110011) + chr(835 - 782), 42125 - 42117), nzTpIcepk0o8(chr(0b1001 + 0o47) + '\x6f' + '\x36', 8), nzTpIcepk0o8(chr(2054 - 2006) + chr(0b1101111) + chr(0b110000 + 0o3) + chr(463 - 410) + chr(84 - 31), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(1376 - 1325) + '\066' + '\x37', 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(53) + chr(49), ord("\x08")), nzTpIcepk0o8(chr(0b10110 + 0o32) + chr(0b10000 + 0o137) + chr(1042 - 993) + chr(2449 - 2394) + chr(48), ord("\x08")), nzTpIcepk0o8(chr(0b101110 + 0o2) + '\157' + chr(53), 0o10), nzTpIcepk0o8('\060' + chr(0b1100100 + 0o13) + chr(55) + '\063', 0b1000), nzTpIcepk0o8('\060' + chr(541 - 430) + chr(1852 - 1802) + chr(0b101000 + 0o13) + chr(847 - 796), 8), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(420 - 370) + chr(50) + chr(0b111 + 0o51), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(2678 - 2624) + '\x35', 2914 - 2906), nzTpIcepk0o8(chr(509 - 461) + chr(111) + chr(0b110010) + chr(50) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x31' + chr(211 - 160) + chr(1928 - 1877), 0o10), nzTpIcepk0o8(chr(0b100001 + 0o17) + '\157' + chr(2031 - 1980) + chr(0b110001) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(1280 - 1231) + '\067' + chr(54), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\062' + chr(2473 - 2421) + chr(55), 0o10), nzTpIcepk0o8(chr(0b101111 + 0o1) + '\157' + '\x31' + chr(52) + chr(0b1 + 0o65), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1100011 + 0o14) + chr(1110 - 1061) + chr(2981 - 2926) + '\x37', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(158 - 47) + chr(0b0 + 0o63) + chr(1904 - 1854) + chr(459 - 405), 0o10), nzTpIcepk0o8('\x30' + chr(9065 - 8954) + chr(0b110100) + chr(48), 4037 - 4029), nzTpIcepk0o8(chr(0b101000 + 0o10) + chr(0b110100 + 0o73) + chr(0b11100 + 0o26) + '\060', 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(111) + chr(2710 - 2657) + '\060', ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'U'), chr(100) + '\145' + chr(0b1100011) + chr(111) + chr(0b1100100) + chr(5585 - 5484))('\x75' + '\x74' + '\x66' + '\x2d' + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def WBWws3mWB_1B(KQq7Z9J63zv1, FsHH2qbtSh8t, YRX9Ch4rysP9, j75eupAGs_rK=None):
(AQ9ceR9AaoT1, xFDEVQn5qSdh, teUmM7cKWZUa) = HFXVdu3zdbXL(KQq7Z9J63zv1, FsHH2qbtSh8t, max_allele=j75eupAGs_rK)
OQfuB_OLdoP0 = nDF4gVNx0u9Q.nansum(AQ9ceR9AaoT1)
QsQvRp3lxXFC = nDF4gVNx0u9Q.nansum(xFDEVQn5qSdh)
oVdDUflDlABQ = nDF4gVNx0u9Q.nansum(teUmM7cKWZUa)
LXRrGYiwSV8C = OQfuB_OLdoP0 / (OQfuB_OLdoP0 + QsQvRp3lxXFC + oVdDUflDlABQ)
HRz6j6oGoyDg = SvzAnntsMYgE(AQ9ceR9AaoT1, statistic=nDF4gVNx0u9Q.nansum, size=YRX9Ch4rysP9)
ET_bJLlHDdwW = SvzAnntsMYgE(AQ9ceR9AaoT1 + xFDEVQn5qSdh + teUmM7cKWZUa, statistic=nDF4gVNx0u9Q.nansum, size=YRX9Ch4rysP9)
LHLJNBZl6nbm = HRz6j6oGoyDg / ET_bJLlHDdwW
(zIqcgNgQ9U6F, pRpvet3n0tVT, IN8K3K6VL_Va) = E5TLp_nQkWxS((HRz6j6oGoyDg, ET_bJLlHDdwW), statistic=lambda NoZxuO7wjArS, vPPlOXQgR3SM: nDF4gVNx0u9Q.oclC8DLjA_lV(NoZxuO7wjArS) / nDF4gVNx0u9Q.oclC8DLjA_lV(vPPlOXQgR3SM))
return (LXRrGYiwSV8C, pRpvet3n0tVT, LHLJNBZl6nbm, IN8K3K6VL_Va) |
cggh/scikit-allel | allel/stats/fst.py | average_hudson_fst | def average_hudson_fst(ac1, ac2, blen):
"""Estimate average Fst between two populations and standard error using
the block-jackknife.
Parameters
----------
ac1 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the first population.
ac2 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the second population.
blen : int
Block size (number of variants).
Returns
-------
fst : float
Estimated value of the statistic using all data.
se : float
Estimated standard error.
vb : ndarray, float, shape (n_blocks,)
Value of the statistic in each block.
vj : ndarray, float, shape (n_blocks,)
Values of the statistic from block-jackknife resampling.
"""
# calculate per-variant values
num, den = hudson_fst(ac1, ac2, fill=np.nan)
# calculate overall estimate
fst = np.nansum(num) / np.nansum(den)
# compute the numerator and denominator within each block
num_bsum = moving_statistic(num, statistic=np.nansum, size=blen)
den_bsum = moving_statistic(den, statistic=np.nansum, size=blen)
# calculate the statistic values in each block
vb = num_bsum / den_bsum
# estimate standard error
_, se, vj = jackknife((num_bsum, den_bsum),
statistic=lambda n, d: np.sum(n) / np.sum(d))
return fst, se, vb, vj | python | def average_hudson_fst(ac1, ac2, blen):
"""Estimate average Fst between two populations and standard error using
the block-jackknife.
Parameters
----------
ac1 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the first population.
ac2 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the second population.
blen : int
Block size (number of variants).
Returns
-------
fst : float
Estimated value of the statistic using all data.
se : float
Estimated standard error.
vb : ndarray, float, shape (n_blocks,)
Value of the statistic in each block.
vj : ndarray, float, shape (n_blocks,)
Values of the statistic from block-jackknife resampling.
"""
# calculate per-variant values
num, den = hudson_fst(ac1, ac2, fill=np.nan)
# calculate overall estimate
fst = np.nansum(num) / np.nansum(den)
# compute the numerator and denominator within each block
num_bsum = moving_statistic(num, statistic=np.nansum, size=blen)
den_bsum = moving_statistic(den, statistic=np.nansum, size=blen)
# calculate the statistic values in each block
vb = num_bsum / den_bsum
# estimate standard error
_, se, vj = jackknife((num_bsum, den_bsum),
statistic=lambda n, d: np.sum(n) / np.sum(d))
return fst, se, vb, vj | [
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... | Estimate average Fst between two populations and standard error using
the block-jackknife.
Parameters
----------
ac1 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the first population.
ac2 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the second population.
blen : int
Block size (number of variants).
Returns
-------
fst : float
Estimated value of the statistic using all data.
se : float
Estimated standard error.
vb : ndarray, float, shape (n_blocks,)
Value of the statistic in each block.
vj : ndarray, float, shape (n_blocks,)
Values of the statistic from block-jackknife resampling. | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/stats/fst.py#L719-L762 | train | Estimate average Fst between two populations and standard error using the block - jackknife resampling algorithm. | 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(1466 - 1416) + chr(466 - 413) + '\x31', ord("\x08")), nzTpIcepk0o8(chr(238 - 190) + '\x6f' + '\x31' + '\x34' + chr(54), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(1233 - 1184) + '\062' + chr(1581 - 1532), 58511 - 58503), nzTpIcepk0o8(chr(649 - 601) + chr(111) + '\x32' + chr(0b101010 + 0o15) + chr(0b10000 + 0o46), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110001 + 0o1) + '\063' + chr(786 - 735), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110011) + chr(0b110010) + '\x31', 35056 - 35048), nzTpIcepk0o8(chr(0b10111 + 0o31) + chr(111) + chr(156 - 106) + chr(48) + '\066', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(7370 - 7259) + '\063' + chr(0b11111 + 0o21) + chr(0b11101 + 0o32), 0b1000), nzTpIcepk0o8('\060' + chr(9246 - 9135) + '\x31' + '\064' + chr(0b11100 + 0o25), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(2561 - 2510) + '\065', 0b1000), nzTpIcepk0o8(chr(1864 - 1816) + '\x6f' + chr(51) + chr(1905 - 1857) + '\065', 0o10), nzTpIcepk0o8(chr(0b101000 + 0o10) + chr(111) + chr(1716 - 1665) + chr(0b110000) + chr(0b101000 + 0o11), 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(50) + chr(0b110101 + 0o2) + chr(0b110010), 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(51) + chr(0b1010 + 0o50) + chr(49), 8), nzTpIcepk0o8('\x30' + '\x6f' + chr(51) + chr(1856 - 1808) + '\060', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b101111 + 0o100) + '\061' + chr(1140 - 1091) + chr(1485 - 1432), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b111010 + 0o65) + '\x33' + chr(1208 - 1156) + '\064', 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + '\063' + chr(0b100111 + 0o11) + '\x34', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b111111 + 0o60) + chr(0b101010 + 0o7) + chr(0b11000 + 0o30) + chr(0b110010), 0o10), nzTpIcepk0o8('\060' + chr(111) + '\x33' + chr(0b110010) + chr(0b110000), 21617 - 21609), nzTpIcepk0o8(chr(0b110000) + chr(7869 - 7758) + '\067' + chr(51), 0o10), nzTpIcepk0o8(chr(0b1100 + 0o44) + chr(0b1101111) + '\x32' + '\066' + chr(0b101011 + 0o13), 0o10), nzTpIcepk0o8(chr(0b1010 + 0o46) + chr(0b1111 + 0o140) + '\x36' + chr(0b110101), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(49) + chr(52) + chr(54), 8), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110010 + 0o0) + chr(0b110010) + chr(0b101011 + 0o10), 0o10), nzTpIcepk0o8(chr(48) + chr(8759 - 8648) + '\064' + chr(48), 22353 - 22345), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b1100 + 0o45) + '\067' + '\x36', 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(1487 - 1438) + '\062' + '\062', 42850 - 42842), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b100100 + 0o17) + chr(0b1101 + 0o51) + chr(0b110001), 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(277 - 226) + chr(2424 - 2369) + chr(0b110110), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + '\x31' + chr(0b110100) + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(0b100011 + 0o15) + chr(6147 - 6036) + chr(0b110001) + chr(0b110001) + chr(0b110110), 59927 - 59919), nzTpIcepk0o8('\060' + '\157' + '\x34' + chr(0b110110), 5942 - 5934), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(2264 - 2209) + chr(52), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(2319 - 2269) + chr(0b10010 + 0o44) + '\061', 38619 - 38611), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110011) + chr(0b101101 + 0o6) + '\x37', 17719 - 17711), nzTpIcepk0o8('\060' + chr(7789 - 7678) + chr(0b11100 + 0o26) + chr(0b1101 + 0o46), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(0b10010 + 0o41) + '\066' + chr(48), 0o10), nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(0b100000 + 0o117) + chr(51) + '\061', 7874 - 7866), nzTpIcepk0o8(chr(78 - 30) + '\157' + chr(202 - 147) + chr(0b110000), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(1086 - 1038) + chr(0b1101111) + chr(0b110000 + 0o5) + chr(0b110000), 64425 - 64417)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x87'), '\144' + chr(0b1011 + 0o132) + '\143' + '\x6f' + '\144' + '\x65')('\165' + chr(0b100 + 0o160) + '\146' + '\055' + chr(1109 - 1053)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def r9fVQlJOXjK4(kqnbwhK0EBnP, S9W4ddqb2HVR, YRX9Ch4rysP9):
(o0eINMlvUImY, nlXsT_LUVPQ8) = NGz8qBsr3ohU(kqnbwhK0EBnP, S9W4ddqb2HVR, fill=nDF4gVNx0u9Q.nan)
LXRrGYiwSV8C = nDF4gVNx0u9Q.nansum(o0eINMlvUImY) / nDF4gVNx0u9Q.nansum(nlXsT_LUVPQ8)
HRz6j6oGoyDg = SvzAnntsMYgE(o0eINMlvUImY, statistic=nDF4gVNx0u9Q.nansum, size=YRX9Ch4rysP9)
ET_bJLlHDdwW = SvzAnntsMYgE(nlXsT_LUVPQ8, statistic=nDF4gVNx0u9Q.nansum, size=YRX9Ch4rysP9)
LHLJNBZl6nbm = HRz6j6oGoyDg / ET_bJLlHDdwW
(zIqcgNgQ9U6F, pRpvet3n0tVT, IN8K3K6VL_Va) = E5TLp_nQkWxS((HRz6j6oGoyDg, ET_bJLlHDdwW), statistic=lambda NoZxuO7wjArS, vPPlOXQgR3SM: nDF4gVNx0u9Q.oclC8DLjA_lV(NoZxuO7wjArS) / nDF4gVNx0u9Q.oclC8DLjA_lV(vPPlOXQgR3SM))
return (LXRrGYiwSV8C, pRpvet3n0tVT, LHLJNBZl6nbm, IN8K3K6VL_Va) |
cggh/scikit-allel | allel/stats/fst.py | average_patterson_fst | def average_patterson_fst(ac1, ac2, blen):
"""Estimate average Fst between two populations and standard error using
the block-jackknife.
Parameters
----------
ac1 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the first population.
ac2 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the second population.
blen : int
Block size (number of variants).
Returns
-------
fst : float
Estimated value of the statistic using all data.
se : float
Estimated standard error.
vb : ndarray, float, shape (n_blocks,)
Value of the statistic in each block.
vj : ndarray, float, shape (n_blocks,)
Values of the statistic from block-jackknife resampling.
"""
# calculate per-variant values
num, den = patterson_fst(ac1, ac2)
# calculate overall estimate
fst = np.nansum(num) / np.nansum(den)
# compute the numerator and denominator within each block
num_bsum = moving_statistic(num, statistic=np.nansum, size=blen)
den_bsum = moving_statistic(den, statistic=np.nansum, size=blen)
# calculate the statistic values in each block
vb = num_bsum / den_bsum
# estimate standard error
_, se, vj = jackknife((num_bsum, den_bsum),
statistic=lambda n, d: np.sum(n) / np.sum(d))
return fst, se, vb, vj | python | def average_patterson_fst(ac1, ac2, blen):
"""Estimate average Fst between two populations and standard error using
the block-jackknife.
Parameters
----------
ac1 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the first population.
ac2 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the second population.
blen : int
Block size (number of variants).
Returns
-------
fst : float
Estimated value of the statistic using all data.
se : float
Estimated standard error.
vb : ndarray, float, shape (n_blocks,)
Value of the statistic in each block.
vj : ndarray, float, shape (n_blocks,)
Values of the statistic from block-jackknife resampling.
"""
# calculate per-variant values
num, den = patterson_fst(ac1, ac2)
# calculate overall estimate
fst = np.nansum(num) / np.nansum(den)
# compute the numerator and denominator within each block
num_bsum = moving_statistic(num, statistic=np.nansum, size=blen)
den_bsum = moving_statistic(den, statistic=np.nansum, size=blen)
# calculate the statistic values in each block
vb = num_bsum / den_bsum
# estimate standard error
_, se, vj = jackknife((num_bsum, den_bsum),
statistic=lambda n, d: np.sum(n) / np.sum(d))
return fst, se, vb, vj | [
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... | Estimate average Fst between two populations and standard error using
the block-jackknife.
Parameters
----------
ac1 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the first population.
ac2 : array_like, int, shape (n_variants, n_alleles)
Allele counts array from the second population.
blen : int
Block size (number of variants).
Returns
-------
fst : float
Estimated value of the statistic using all data.
se : float
Estimated standard error.
vb : ndarray, float, shape (n_blocks,)
Value of the statistic in each block.
vj : ndarray, float, shape (n_blocks,)
Values of the statistic from block-jackknife resampling. | [
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"jackknife",
"."
] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/stats/fst.py#L765-L808 | train | Estimate average Fst between two populations and standard error using the block - jackknife resampling algorithm. | 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(0b1000011 + 0o54) + chr(0b110010) + '\x37' + '\061', 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110001) + chr(0b110100) + '\x31', ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + chr(0b110011) + chr(0b11111 + 0o24) + chr(1481 - 1432), 23958 - 23950), nzTpIcepk0o8(chr(48) + '\x6f' + '\067', 8079 - 8071), nzTpIcepk0o8(chr(1152 - 1104) + chr(0b1001100 + 0o43) + '\063' + chr(0b100100 + 0o20) + '\066', 24421 - 24413), nzTpIcepk0o8('\x30' + chr(0b101111 + 0o100) + chr(49) + chr(55) + chr(0b110001), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b100110 + 0o13) + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + '\062' + '\x32' + '\x35', 23852 - 23844), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b1 + 0o64) + '\061', ord("\x08")), nzTpIcepk0o8(chr(1321 - 1273) + chr(0b1101111) + '\062' + chr(941 - 887) + chr(1874 - 1826), 0o10), nzTpIcepk0o8(chr(0b110000 + 0o0) + chr(111) + '\061' + '\x31' + '\067', 17824 - 17816), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\067' + '\x31', 15539 - 15531), nzTpIcepk0o8(chr(1188 - 1140) + '\x6f' + chr(902 - 852) + chr(286 - 234) + chr(1293 - 1245), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1001010 + 0o45) + chr(50) + '\x30' + '\x33', ord("\x08")), nzTpIcepk0o8(chr(645 - 597) + chr(111) + '\063' + chr(50) + '\060', 0b1000), nzTpIcepk0o8(chr(637 - 589) + chr(0b1100100 + 0o13) + chr(0b110011) + chr(0b1000 + 0o50) + '\x30', 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(49) + '\063' + chr(119 - 70), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(1416 - 1366) + chr(54) + '\x35', 0b1000), nzTpIcepk0o8(chr(2069 - 2021) + '\157' + '\x32' + chr(51) + chr(0b1100 + 0o52), ord("\x08")), nzTpIcepk0o8(chr(0b11 + 0o55) + '\157' + chr(0b100111 + 0o12) + '\x36' + '\x31', 0o10), nzTpIcepk0o8('\x30' + '\157' + '\x31' + chr(0b110101) + chr(0b11010 + 0o31), 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(0b10100 + 0o41) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(0b100110 + 0o12) + chr(111) + chr(863 - 813) + chr(0b11000 + 0o34) + '\065', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(11270 - 11159) + '\061' + '\060' + '\063', 0b1000), nzTpIcepk0o8(chr(1394 - 1346) + chr(0b1101111) + chr(0b110011) + '\x30' + chr(55), ord("\x08")), nzTpIcepk0o8(chr(0b11101 + 0o23) + chr(0b110 + 0o151) + '\x34' + chr(51), 55462 - 55454), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b101000 + 0o12) + '\x33' + chr(52), 0o10), nzTpIcepk0o8(chr(48) + chr(0b111101 + 0o62) + '\x36' + chr(0b1010 + 0o52), ord("\x08")), nzTpIcepk0o8(chr(0b100110 + 0o12) + chr(0b1010011 + 0o34) + chr(54) + '\061', 48217 - 48209), nzTpIcepk0o8(chr(48) + chr(7363 - 7252) + chr(0b10 + 0o60) + chr(50) + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b10010 + 0o37) + chr(0b110100) + '\067', ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1011110 + 0o21) + chr(165 - 110) + chr(0b11001 + 0o36), 36940 - 36932), nzTpIcepk0o8(chr(48) + '\157' + '\061' + '\x34', 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(0b110001) + '\062' + '\063', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x33' + chr(0b101011 + 0o5) + chr(53), 0o10), nzTpIcepk0o8(chr(1569 - 1521) + chr(0b111001 + 0o66) + chr(0b110010 + 0o0) + chr(0b110010) + chr(0b110010), 0b1000), nzTpIcepk0o8('\060' + chr(4697 - 4586) + chr(49) + chr(0b1001 + 0o55) + chr(53), 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(51) + chr(0b110000) + '\x37', 8), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b1001 + 0o56) + chr(53), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\061' + chr(0b110101 + 0o0) + chr(0b110101), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + chr(111) + chr(53) + '\x30', 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x97'), chr(100) + '\145' + chr(0b1100011) + chr(0b1000110 + 0o51) + chr(0b1100100) + '\145')(chr(0b1110010 + 0o3) + chr(0b1110100) + chr(0b101010 + 0o74) + chr(779 - 734) + chr(0b110010 + 0o6)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def MxZujHGX_GJD(kqnbwhK0EBnP, S9W4ddqb2HVR, YRX9Ch4rysP9):
(o0eINMlvUImY, nlXsT_LUVPQ8) = SRPucSlaq1kD(kqnbwhK0EBnP, S9W4ddqb2HVR)
LXRrGYiwSV8C = nDF4gVNx0u9Q.nansum(o0eINMlvUImY) / nDF4gVNx0u9Q.nansum(nlXsT_LUVPQ8)
HRz6j6oGoyDg = SvzAnntsMYgE(o0eINMlvUImY, statistic=nDF4gVNx0u9Q.nansum, size=YRX9Ch4rysP9)
ET_bJLlHDdwW = SvzAnntsMYgE(nlXsT_LUVPQ8, statistic=nDF4gVNx0u9Q.nansum, size=YRX9Ch4rysP9)
LHLJNBZl6nbm = HRz6j6oGoyDg / ET_bJLlHDdwW
(zIqcgNgQ9U6F, pRpvet3n0tVT, IN8K3K6VL_Va) = E5TLp_nQkWxS((HRz6j6oGoyDg, ET_bJLlHDdwW), statistic=lambda NoZxuO7wjArS, vPPlOXQgR3SM: nDF4gVNx0u9Q.oclC8DLjA_lV(NoZxuO7wjArS) / nDF4gVNx0u9Q.oclC8DLjA_lV(vPPlOXQgR3SM))
return (LXRrGYiwSV8C, pRpvet3n0tVT, LHLJNBZl6nbm, IN8K3K6VL_Va) |
cggh/scikit-allel | allel/stats/ld.py | rogers_huff_r | def rogers_huff_r(gn):
"""Estimate the linkage disequilibrium parameter *r* for each pair of
variants using the method of Rogers and Huff (2008).
Parameters
----------
gn : array_like, int8, shape (n_variants, n_samples)
Diploid genotypes at biallelic variants, coded as the number of
alternate alleles per call (i.e., 0 = hom ref, 1 = het, 2 = hom alt).
Returns
-------
r : ndarray, float, shape (n_variants * (n_variants - 1) // 2,)
Matrix in condensed form.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [1, 1], [0, 0]],
... [[0, 0], [1, 1], [0, 0]],
... [[1, 1], [0, 0], [1, 1]],
... [[0, 0], [0, 1], [-1, -1]]], dtype='i1')
>>> gn = g.to_n_alt(fill=-1)
>>> gn
array([[ 0, 2, 0],
[ 0, 2, 0],
[ 2, 0, 2],
[ 0, 1, -1]], dtype=int8)
>>> r = allel.rogers_huff_r(gn)
>>> r # doctest: +ELLIPSIS
array([ 1. , -1.0000001, 1. , -1.0000001, 1. ,
-1. ], dtype=float32)
>>> r ** 2 # doctest: +ELLIPSIS
array([1. , 1.0000002, 1. , 1.0000002, 1. , 1. ],
dtype=float32)
>>> from scipy.spatial.distance import squareform
>>> squareform(r ** 2)
array([[0. , 1. , 1.0000002, 1. ],
[1. , 0. , 1.0000002, 1. ],
[1.0000002, 1.0000002, 0. , 1. ],
[1. , 1. , 1. , 0. ]], dtype=float32)
"""
# check inputs
gn = asarray_ndim(gn, 2, dtype='i1')
gn = memoryview_safe(gn)
# compute correlation coefficients
r = gn_pairwise_corrcoef_int8(gn)
# convenience for singletons
if r.size == 1:
r = r[0]
return r | python | def rogers_huff_r(gn):
"""Estimate the linkage disequilibrium parameter *r* for each pair of
variants using the method of Rogers and Huff (2008).
Parameters
----------
gn : array_like, int8, shape (n_variants, n_samples)
Diploid genotypes at biallelic variants, coded as the number of
alternate alleles per call (i.e., 0 = hom ref, 1 = het, 2 = hom alt).
Returns
-------
r : ndarray, float, shape (n_variants * (n_variants - 1) // 2,)
Matrix in condensed form.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [1, 1], [0, 0]],
... [[0, 0], [1, 1], [0, 0]],
... [[1, 1], [0, 0], [1, 1]],
... [[0, 0], [0, 1], [-1, -1]]], dtype='i1')
>>> gn = g.to_n_alt(fill=-1)
>>> gn
array([[ 0, 2, 0],
[ 0, 2, 0],
[ 2, 0, 2],
[ 0, 1, -1]], dtype=int8)
>>> r = allel.rogers_huff_r(gn)
>>> r # doctest: +ELLIPSIS
array([ 1. , -1.0000001, 1. , -1.0000001, 1. ,
-1. ], dtype=float32)
>>> r ** 2 # doctest: +ELLIPSIS
array([1. , 1.0000002, 1. , 1.0000002, 1. , 1. ],
dtype=float32)
>>> from scipy.spatial.distance import squareform
>>> squareform(r ** 2)
array([[0. , 1. , 1.0000002, 1. ],
[1. , 0. , 1.0000002, 1. ],
[1.0000002, 1.0000002, 0. , 1. ],
[1. , 1. , 1. , 0. ]], dtype=float32)
"""
# check inputs
gn = asarray_ndim(gn, 2, dtype='i1')
gn = memoryview_safe(gn)
# compute correlation coefficients
r = gn_pairwise_corrcoef_int8(gn)
# convenience for singletons
if r.size == 1:
r = r[0]
return r | [
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"gn_pairwise_corrcoef_i... | Estimate the linkage disequilibrium parameter *r* for each pair of
variants using the method of Rogers and Huff (2008).
Parameters
----------
gn : array_like, int8, shape (n_variants, n_samples)
Diploid genotypes at biallelic variants, coded as the number of
alternate alleles per call (i.e., 0 = hom ref, 1 = het, 2 = hom alt).
Returns
-------
r : ndarray, float, shape (n_variants * (n_variants - 1) // 2,)
Matrix in condensed form.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [1, 1], [0, 0]],
... [[0, 0], [1, 1], [0, 0]],
... [[1, 1], [0, 0], [1, 1]],
... [[0, 0], [0, 1], [-1, -1]]], dtype='i1')
>>> gn = g.to_n_alt(fill=-1)
>>> gn
array([[ 0, 2, 0],
[ 0, 2, 0],
[ 2, 0, 2],
[ 0, 1, -1]], dtype=int8)
>>> r = allel.rogers_huff_r(gn)
>>> r # doctest: +ELLIPSIS
array([ 1. , -1.0000001, 1. , -1.0000001, 1. ,
-1. ], dtype=float32)
>>> r ** 2 # doctest: +ELLIPSIS
array([1. , 1.0000002, 1. , 1.0000002, 1. , 1. ],
dtype=float32)
>>> from scipy.spatial.distance import squareform
>>> squareform(r ** 2)
array([[0. , 1. , 1.0000002, 1. ],
[1. , 0. , 1.0000002, 1. ],
[1.0000002, 1.0000002, 0. , 1. ],
[1. , 1. , 1. , 0. ]], dtype=float32) | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/stats/ld.py#L16-L72 | train | Estimate the linkage disequilibrium parameter r for each pair of genotypes at biallelic variants using the method of Rogers and Huff. | 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) + '\061' + '\x33' + '\064', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b100101 + 0o112) + chr(0b110011) + chr(0b110001) + chr(0b110110), ord("\x08")), nzTpIcepk0o8(chr(0b1000 + 0o50) + '\157' + chr(50) + '\x33' + chr(54), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110011) + chr(0b110010), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(546 - 495) + chr(2335 - 2280) + chr(0b110110), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1010101 + 0o32) + chr(0b110010) + chr(0b110011) + chr(0b110010), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b101001 + 0o11) + '\x34' + chr(49), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\063' + chr(0b101011 + 0o5) + chr(0b1111 + 0o44), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b101010 + 0o11) + '\x35' + '\065', 0b1000), nzTpIcepk0o8(chr(1299 - 1251) + '\157' + '\062' + '\067' + chr(0b10100 + 0o37), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(342 - 291) + '\065' + '\066', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(4426 - 4315) + chr(0b110001) + chr(2003 - 1949), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(51) + '\x36' + chr(0b110101), 64328 - 64320), nzTpIcepk0o8('\x30' + '\x6f' + chr(2024 - 1974) + chr(1733 - 1684) + '\064', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(50) + chr(0b11001 + 0o34) + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(7037 - 6926) + chr(0b110001) + chr(54), 8), nzTpIcepk0o8(chr(48) + chr(6497 - 6386) + chr(0b11100 + 0o26) + chr(0b110100) + chr(628 - 574), 5363 - 5355), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\062' + '\064' + '\x37', 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + '\062' + '\064' + chr(0b1011 + 0o51), 49590 - 49582), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110001) + chr(296 - 243) + '\061', 0o10), nzTpIcepk0o8(chr(1930 - 1882) + chr(0b1111 + 0o140) + '\062' + chr(1438 - 1383) + '\063', 8), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110001) + chr(0b11000 + 0o33), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + '\x33' + '\x31' + chr(50), 55175 - 55167), nzTpIcepk0o8('\060' + '\157' + '\x31' + '\066' + chr(0b11 + 0o64), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(2260 - 2149) + '\x33' + chr(0b110011) + chr(0b110001), 56282 - 56274), nzTpIcepk0o8(chr(48) + '\157' + '\063' + chr(51) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b10111 + 0o130) + chr(54) + chr(0b11111 + 0o25), 23436 - 23428), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(1033 - 983) + '\x35' + chr(1918 - 1870), ord("\x08")), nzTpIcepk0o8(chr(1191 - 1143) + chr(111) + chr(0b1001 + 0o51) + chr(55) + chr(0b110001), 0o10), nzTpIcepk0o8(chr(48) + chr(10105 - 9994) + chr(185 - 135) + '\064' + chr(0b110001), 8), nzTpIcepk0o8('\060' + chr(0b1101001 + 0o6) + chr(2489 - 2439) + '\065' + chr(0b101001 + 0o7), 8), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111 + 0o0) + '\x32' + chr(48) + chr(0b101011 + 0o7), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b10001 + 0o136) + chr(50) + chr(55) + chr(2085 - 2034), 8), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110011) + '\062' + chr(1644 - 1590), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x31' + chr(0b110110) + '\060', 0o10), nzTpIcepk0o8(chr(296 - 248) + chr(0b1101111) + chr(0b110001) + '\066' + chr(51), 0o10), nzTpIcepk0o8('\x30' + chr(0b101111 + 0o100) + '\x33' + chr(0b110110), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110011 + 0o0) + '\x31' + chr(55), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + '\061' + chr(0b110111) + chr(0b110010), 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(1761 - 1711) + chr(0b1101 + 0o47) + '\060', 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(0b110 + 0o151) + chr(2685 - 2632) + chr(48), 9642 - 9634)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'r'), chr(100) + '\x65' + chr(99) + chr(0b1101111) + '\144' + '\145')(chr(117) + '\x74' + chr(0b1100110) + chr(0b10001 + 0o34) + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def TXw19gBXuonL(kABaul2JCreR):
kABaul2JCreR = EVVKPun88TqM(kABaul2JCreR, nzTpIcepk0o8(chr(0b110000) + '\157' + chr(50), 0o10), dtype=roI3spqORKae(ES5oEprVxulp(b'5\xff'), '\x64' + '\145' + '\x63' + '\x6f' + '\x64' + '\x65')('\165' + chr(0b101 + 0o157) + chr(102) + chr(1960 - 1915) + '\x38'))
kABaul2JCreR = ygMIbkSSXS59(kABaul2JCreR)
LCrwg7lcbmU9 = bKaC0Exo38E6(kABaul2JCreR)
if roI3spqORKae(LCrwg7lcbmU9, roI3spqORKae(ES5oEprVxulp(b'9\xff\xd6h\xb4\xfb\xf0\x8b\xac\xf8\x80b'), chr(3139 - 3039) + chr(2304 - 2203) + chr(0b1100011) + '\157' + '\144' + chr(2607 - 2506))(chr(7154 - 7037) + chr(0b1110100) + '\146' + chr(217 - 172) + '\070')) == nzTpIcepk0o8(chr(217 - 169) + '\x6f' + '\x31', 0b1000):
LCrwg7lcbmU9 = LCrwg7lcbmU9[nzTpIcepk0o8(chr(0b110000) + chr(7004 - 6893) + '\x30', 0o10)]
return LCrwg7lcbmU9 |
cggh/scikit-allel | allel/stats/ld.py | rogers_huff_r_between | def rogers_huff_r_between(gna, gnb):
"""Estimate the linkage disequilibrium parameter *r* for each pair of
variants between the two input arrays, using the method of Rogers and
Huff (2008).
Parameters
----------
gna, gnb : array_like, int8, shape (n_variants, n_samples)
Diploid genotypes at biallelic variants, coded as the number of
alternate alleles per call (i.e., 0 = hom ref, 1 = het, 2 = hom alt).
Returns
-------
r : ndarray, float, shape (m_variants, n_variants )
Matrix in rectangular form.
"""
# check inputs
gna = asarray_ndim(gna, 2, dtype='i1')
gnb = asarray_ndim(gnb, 2, dtype='i1')
gna = memoryview_safe(gna)
gnb = memoryview_safe(gnb)
# compute correlation coefficients
r = gn_pairwise2_corrcoef_int8(gna, gnb)
# convenience for singletons
if r.size == 1:
r = r[0, 0]
return r | python | def rogers_huff_r_between(gna, gnb):
"""Estimate the linkage disequilibrium parameter *r* for each pair of
variants between the two input arrays, using the method of Rogers and
Huff (2008).
Parameters
----------
gna, gnb : array_like, int8, shape (n_variants, n_samples)
Diploid genotypes at biallelic variants, coded as the number of
alternate alleles per call (i.e., 0 = hom ref, 1 = het, 2 = hom alt).
Returns
-------
r : ndarray, float, shape (m_variants, n_variants )
Matrix in rectangular form.
"""
# check inputs
gna = asarray_ndim(gna, 2, dtype='i1')
gnb = asarray_ndim(gnb, 2, dtype='i1')
gna = memoryview_safe(gna)
gnb = memoryview_safe(gnb)
# compute correlation coefficients
r = gn_pairwise2_corrcoef_int8(gna, gnb)
# convenience for singletons
if r.size == 1:
r = r[0, 0]
return r | [
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Parameters
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gna, gnb : array_like, int8, shape (n_variants, n_samples)
Diploid genotypes at biallelic variants, coded as the number of
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Returns
-------
r : ndarray, float, shape (m_variants, n_variants )
Matrix in rectangular form. | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/stats/ld.py#L75-L106 | train | Estimate the linkage disequilibrium parameter r for each pair of genotypes gna and gnb. | 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(0b100000 + 0o117) + '\x31' + chr(0b10011 + 0o42) + chr(53), 40823 - 40815), nzTpIcepk0o8(chr(403 - 355) + '\x6f' + '\x33' + chr(0b110010 + 0o1), ord("\x08")), nzTpIcepk0o8(chr(0b100110 + 0o12) + chr(0b1101011 + 0o4) + chr(0b110011) + chr(0b110010 + 0o1) + '\060', 0o10), nzTpIcepk0o8(chr(0b11010 + 0o26) + chr(111) + '\x31' + chr(1443 - 1391) + '\064', 0b1000), nzTpIcepk0o8('\x30' + chr(0b10010 + 0o135) + '\x32' + '\064' + '\062', 0b1000), nzTpIcepk0o8(chr(0b11011 + 0o25) + chr(0b1001101 + 0o42) + chr(0b10010 + 0o41) + chr(54) + chr(0b101000 + 0o14), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(521 - 470) + '\x35' + chr(52), 2668 - 2660), nzTpIcepk0o8('\060' + chr(0b1100010 + 0o15) + chr(0b110000), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b100110 + 0o111) + chr(49) + '\x36' + chr(265 - 211), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + '\x32' + '\x32' + '\x32', 59758 - 59750), nzTpIcepk0o8(chr(48) + chr(3694 - 3583) + chr(0b10110 + 0o33) + chr(0b110011) + '\067', 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(0b101001 + 0o12) + '\066' + chr(50), 0o10), nzTpIcepk0o8(chr(2111 - 2063) + '\157' + chr(0b110011) + chr(0b110111 + 0o0), 6610 - 6602), nzTpIcepk0o8('\060' + chr(2337 - 2226) + '\x33' + '\x35' + chr(55), 0b1000), nzTpIcepk0o8(chr(2216 - 2168) + '\x6f' + chr(0b110011) + chr(54) + chr(0b10001 + 0o37), 28620 - 28612), nzTpIcepk0o8(chr(0b10101 + 0o33) + '\157' + chr(1048 - 998) + chr(2235 - 2187) + chr(0b110110), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(49) + '\x32' + chr(48), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110011) + chr(0b110011) + '\x37', 0o10), nzTpIcepk0o8(chr(48) + chr(9169 - 9058) + '\x31' + chr(2150 - 2096) + chr(0b110111), 0o10), nzTpIcepk0o8('\060' + '\157' + '\x31' + chr(50) + chr(0b110011), 0b1000), nzTpIcepk0o8('\x30' + chr(1220 - 1109) + chr(50) + chr(50) + chr(0b100000 + 0o23), 0b1000), nzTpIcepk0o8(chr(223 - 175) + '\x6f' + chr(0b100011 + 0o16) + chr(50) + chr(0b100110 + 0o14), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110001) + chr(0b101000 + 0o11) + chr(1376 - 1327), 15035 - 15027), nzTpIcepk0o8(chr(48) + chr(111) + '\x31' + chr(51) + '\061', 0b1000), nzTpIcepk0o8('\x30' + chr(2957 - 2846) + chr(50) + chr(1735 - 1681) + chr(0b110000), 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(51) + chr(0b100 + 0o55) + '\061', 57703 - 57695), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(1568 - 1519) + '\066' + chr(0b110100), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b10000 + 0o41) + '\067' + '\x33', 15597 - 15589), nzTpIcepk0o8(chr(0b0 + 0o60) + chr(3374 - 3263) + '\063' + chr(0b110000) + chr(0b1011 + 0o51), 0o10), nzTpIcepk0o8(chr(1190 - 1142) + chr(111) + '\x33' + chr(0b110111) + '\x36', 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + '\063' + chr(2181 - 2133) + '\x34', 8), nzTpIcepk0o8(chr(48) + '\157' + chr(49) + '\x30', 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(0b100111 + 0o15) + '\x30', 5980 - 5972), nzTpIcepk0o8('\x30' + '\157' + chr(50) + '\x34', 0o10), nzTpIcepk0o8('\060' + '\157' + chr(848 - 799) + chr(53) + chr(0b100 + 0o57), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + '\063' + '\x32' + '\061', 36499 - 36491), nzTpIcepk0o8('\x30' + chr(7070 - 6959) + '\x31' + '\x30' + chr(0b110010), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + '\062' + chr(51) + '\066', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b100111 + 0o110) + chr(0b110011) + '\x32', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\063' + '\x32' + chr(0b11011 + 0o32), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + '\x6f' + '\x35' + chr(0b110000), 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'C'), '\x64' + chr(101) + chr(99) + chr(0b10100 + 0o133) + '\144' + chr(4416 - 4315))('\165' + chr(2552 - 2436) + chr(0b1100110) + chr(0b101101) + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def wWYyVnBJBTPI(hIebURTAQH4Y, L_Y5yNMvOgE8):
hIebURTAQH4Y = EVVKPun88TqM(hIebURTAQH4Y, nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110010), 20972 - 20964), dtype=roI3spqORKae(ES5oEprVxulp(b'\x04*'), chr(1396 - 1296) + chr(9290 - 9189) + chr(0b1100011) + chr(0b10010 + 0o135) + chr(0b1100100) + '\145')('\x75' + chr(116) + chr(102) + chr(1575 - 1530) + '\x38'))
L_Y5yNMvOgE8 = EVVKPun88TqM(L_Y5yNMvOgE8, nzTpIcepk0o8(chr(816 - 768) + chr(0b101111 + 0o100) + chr(0b101000 + 0o12), 8), dtype=roI3spqORKae(ES5oEprVxulp(b'\x04*'), '\144' + '\x65' + chr(99) + '\157' + chr(9418 - 9318) + chr(0b1100101))(chr(0b1010110 + 0o37) + '\164' + chr(0b101111 + 0o67) + chr(0b101001 + 0o4) + chr(1203 - 1147)))
hIebURTAQH4Y = ygMIbkSSXS59(hIebURTAQH4Y)
L_Y5yNMvOgE8 = ygMIbkSSXS59(L_Y5yNMvOgE8)
LCrwg7lcbmU9 = osHxEfKdl6Sv(hIebURTAQH4Y, L_Y5yNMvOgE8)
if roI3spqORKae(LCrwg7lcbmU9, roI3spqORKae(ES5oEprVxulp(b'\x08*\x90\x16\xe8\x95\xbdH7\xd11\x9e'), '\x64' + '\145' + '\143' + '\157' + '\144' + chr(0b1011100 + 0o11))(chr(117) + chr(116) + chr(3131 - 3029) + chr(0b10000 + 0o35) + chr(0b111000))) == nzTpIcepk0o8(chr(0b10010 + 0o36) + '\157' + '\x31', 8269 - 8261):
LCrwg7lcbmU9 = LCrwg7lcbmU9[nzTpIcepk0o8('\060' + '\x6f' + chr(1476 - 1428), 8), nzTpIcepk0o8(chr(48) + chr(111) + chr(48), 8)]
return LCrwg7lcbmU9 |
cggh/scikit-allel | allel/stats/ld.py | locate_unlinked | def locate_unlinked(gn, size=100, step=20, threshold=.1, blen=None):
"""Locate variants in approximate linkage equilibrium, where r**2 is
below the given `threshold`.
Parameters
----------
gn : array_like, int8, shape (n_variants, n_samples)
Diploid genotypes at biallelic variants, coded as the number of
alternate alleles per call (i.e., 0 = hom ref, 1 = het, 2 = hom alt).
size : int
Window size (number of variants).
step : int
Number of variants to advance to the next window.
threshold : float
Maximum value of r**2 to include variants.
blen : int, optional
Block length to use for chunked computation.
Returns
-------
loc : ndarray, bool, shape (n_variants)
Boolean array where True items locate variants in approximate
linkage equilibrium.
Notes
-----
The value of r**2 between each pair of variants is calculated using the
method of Rogers and Huff (2008).
"""
# check inputs
if not hasattr(gn, 'shape') or not hasattr(gn, 'dtype'):
gn = np.asarray(gn, dtype='i1')
if gn.ndim != 2:
raise ValueError('gn must have two dimensions')
# setup output
loc = np.ones(gn.shape[0], dtype='u1')
# compute in chunks to avoid loading big arrays into memory
blen = get_blen_array(gn, blen)
blen = max(blen, 10*size) # avoid too small chunks
n_variants = gn.shape[0]
for i in range(0, n_variants, blen):
# N.B., ensure overlap with next window
j = min(n_variants, i+blen+size)
gnb = np.asarray(gn[i:j], dtype='i1')
gnb = memoryview_safe(gnb)
locb = loc[i:j]
gn_locate_unlinked_int8(gnb, locb, size, step, threshold)
return loc.astype('b1') | python | def locate_unlinked(gn, size=100, step=20, threshold=.1, blen=None):
"""Locate variants in approximate linkage equilibrium, where r**2 is
below the given `threshold`.
Parameters
----------
gn : array_like, int8, shape (n_variants, n_samples)
Diploid genotypes at biallelic variants, coded as the number of
alternate alleles per call (i.e., 0 = hom ref, 1 = het, 2 = hom alt).
size : int
Window size (number of variants).
step : int
Number of variants to advance to the next window.
threshold : float
Maximum value of r**2 to include variants.
blen : int, optional
Block length to use for chunked computation.
Returns
-------
loc : ndarray, bool, shape (n_variants)
Boolean array where True items locate variants in approximate
linkage equilibrium.
Notes
-----
The value of r**2 between each pair of variants is calculated using the
method of Rogers and Huff (2008).
"""
# check inputs
if not hasattr(gn, 'shape') or not hasattr(gn, 'dtype'):
gn = np.asarray(gn, dtype='i1')
if gn.ndim != 2:
raise ValueError('gn must have two dimensions')
# setup output
loc = np.ones(gn.shape[0], dtype='u1')
# compute in chunks to avoid loading big arrays into memory
blen = get_blen_array(gn, blen)
blen = max(blen, 10*size) # avoid too small chunks
n_variants = gn.shape[0]
for i in range(0, n_variants, blen):
# N.B., ensure overlap with next window
j = min(n_variants, i+blen+size)
gnb = np.asarray(gn[i:j], dtype='i1')
gnb = memoryview_safe(gnb)
locb = loc[i:j]
gn_locate_unlinked_int8(gnb, locb, size, step, threshold)
return loc.astype('b1') | [
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Parameters
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gn : array_like, int8, shape (n_variants, n_samples)
Diploid genotypes at biallelic variants, coded as the number of
alternate alleles per call (i.e., 0 = hom ref, 1 = het, 2 = hom alt).
size : int
Window size (number of variants).
step : int
Number of variants to advance to the next window.
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Maximum value of r**2 to include variants.
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Block length to use for chunked computation.
Returns
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loc : ndarray, bool, shape (n_variants)
Boolean array where True items locate variants in approximate
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Notes
-----
The value of r**2 between each pair of variants is calculated using the
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"threshold",
"."
] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/stats/ld.py#L109-L161 | train | Locate unlinked genotypes in a given approximate linkage equilibrium. | 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(2288 - 2240) + chr(7667 - 7556) + chr(50) + chr(50) + chr(52), 36512 - 36504), nzTpIcepk0o8(chr(347 - 299) + '\157' + chr(0b0 + 0o63) + '\x32' + chr(0b101010 + 0o6), 0o10), nzTpIcepk0o8(chr(48) + chr(10453 - 10342) + chr(0b110010) + chr(0b110110) + '\x32', ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(0b1100 + 0o47) + chr(0b1111 + 0o42) + chr(52), 42493 - 42485), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b1001 + 0o51) + chr(2069 - 2018) + '\060', ord("\x08")), nzTpIcepk0o8(chr(0b0 + 0o60) + '\157' + '\x33' + chr(50) + chr(1720 - 1669), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(8691 - 8580) + chr(49) + chr(55) + chr(0b110011), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(51) + chr(535 - 484) + chr(0b110001), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(8951 - 8840) + chr(0b110011) + chr(0b110001) + chr(1210 - 1161), 26425 - 26417), nzTpIcepk0o8(chr(0b110000) + chr(0b1010000 + 0o37) + chr(0b1001 + 0o52) + chr(991 - 937) + '\x36', 0o10), nzTpIcepk0o8('\060' + chr(0b11 + 0o154) + '\063' + chr(53) + chr(0b11110 + 0o22), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(671 - 621) + '\x33' + chr(900 - 847), 45844 - 45836), nzTpIcepk0o8(chr(0b10010 + 0o36) + chr(111) + chr(0b10010 + 0o40) + chr(2115 - 2064) + chr(0b110101), 8), nzTpIcepk0o8('\060' + chr(0b1101111) + '\061' + chr(0b10011 + 0o41) + chr(0b110110), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(48), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(0b110001 + 0o2) + chr(0b10001 + 0o42) + '\x30', 8315 - 8307), nzTpIcepk0o8(chr(0b1001 + 0o47) + chr(0b1001011 + 0o44) + '\x33' + '\x32' + chr(1280 - 1225), 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(2277 - 2228) + chr(51) + chr(49), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\061' + '\064' + chr(0b101000 + 0o12), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110010) + '\x36' + chr(0b11 + 0o57), 8), nzTpIcepk0o8('\060' + chr(111) + chr(49) + '\060', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110101) + chr(1728 - 1676), 0b1000), nzTpIcepk0o8(chr(0b1 + 0o57) + '\157' + '\x35' + '\x35', 0o10), nzTpIcepk0o8(chr(48) + chr(1025 - 914) + chr(49) + chr(0b110110) + chr(0b11010 + 0o33), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1000001 + 0o56) + chr(2006 - 1957) + chr(173 - 123) + '\062', 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(55) + chr(0b101111 + 0o10), ord("\x08")), nzTpIcepk0o8('\060' + chr(6364 - 6253) + '\x31' + '\x35' + chr(1127 - 1078), 0o10), nzTpIcepk0o8(chr(48) + chr(3092 - 2981) + '\063' + '\x35', 11992 - 11984), nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(111) + chr(0b101110 + 0o3) + '\x37', 0b1000), nzTpIcepk0o8(chr(726 - 678) + '\x6f' + chr(2093 - 2044) + '\x35' + '\x35', 0b1000), nzTpIcepk0o8(chr(1698 - 1650) + '\157' + '\063' + chr(0b110001) + chr(616 - 564), 8), nzTpIcepk0o8('\060' + chr(111) + '\x37' + chr(55), 8), nzTpIcepk0o8(chr(48) + chr(4955 - 4844) + chr(50) + '\067' + chr(969 - 917), 36706 - 36698), nzTpIcepk0o8(chr(0b110000) + chr(0b110111 + 0o70) + '\x33' + chr(620 - 566) + chr(0b1101 + 0o46), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + '\x35' + '\x34', 8), nzTpIcepk0o8(chr(2301 - 2253) + '\157' + chr(0b10110 + 0o34) + chr(2734 - 2679) + chr(55), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b100010 + 0o115) + chr(50) + chr(0b110101) + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(969 - 920) + '\x33' + chr(50), 41334 - 41326), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x33' + '\x34' + chr(0b110001), 41979 - 41971), nzTpIcepk0o8(chr(0b11110 + 0o22) + chr(5199 - 5088) + chr(0b101101 + 0o4) + '\066' + chr(48), 45760 - 45752)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110101) + '\x30', 51338 - 51330)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xba'), chr(3516 - 3416) + '\145' + chr(0b1100011) + '\x6f' + '\144' + '\x65')(chr(117) + chr(0b1110100) + '\x66' + chr(0b1000 + 0o45) + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def JOeXNar5xd1W(kABaul2JCreR, e1HrJaQHACnl=nzTpIcepk0o8(chr(407 - 359) + chr(0b1101111) + chr(2361 - 2312) + chr(126 - 74) + chr(52), 39396 - 39388), ZiKB99Xs91Lo=nzTpIcepk0o8('\060' + '\x6f' + chr(0b101 + 0o55) + '\064', 38391 - 38383), klmSpxrzsw3P=0.1, YRX9Ch4rysP9=None):
if not dRKdVnHPFq7C(kABaul2JCreR, roI3spqORKae(ES5oEprVxulp(b'\xe7\xb8\xd3\xbc\xfd'), '\144' + chr(0b10101 + 0o120) + chr(0b1100011) + chr(8392 - 8281) + chr(2862 - 2762) + '\145')(chr(0b1010 + 0o153) + '\x74' + '\x66' + chr(45) + chr(1560 - 1504))) or not dRKdVnHPFq7C(kABaul2JCreR, roI3spqORKae(ES5oEprVxulp(b'\xf0\xa4\xcb\xbc\xfd'), chr(0b10011 + 0o121) + chr(0b110001 + 0o64) + chr(99) + '\157' + chr(0b1000 + 0o134) + chr(101))(chr(11453 - 11336) + '\x74' + chr(0b10001 + 0o125) + chr(203 - 158) + chr(0b111000))):
kABaul2JCreR = nDF4gVNx0u9Q.asarray(kABaul2JCreR, dtype=roI3spqORKae(ES5oEprVxulp(b'\xfd\xe1'), chr(0b1000111 + 0o35) + chr(5338 - 5237) + chr(0b1100011) + '\x6f' + chr(0b1100100) + chr(101))(chr(0b1110101) + '\x74' + chr(2865 - 2763) + chr(45) + chr(0b111000)))
if roI3spqORKae(kABaul2JCreR, roI3spqORKae(ES5oEprVxulp(b'\xde\x99\xea\x80\xd0\xe3I\x96\x8a\xc6\xbf\xdf'), chr(100) + chr(0b110000 + 0o65) + chr(99) + chr(0b0 + 0o157) + chr(0b110010 + 0o62) + chr(1522 - 1421))(chr(0b111100 + 0o71) + '\x74' + '\x66' + chr(1769 - 1724) + '\070')) != nzTpIcepk0o8(chr(0b110000) + '\157' + '\062', 0o10):
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'\xf3\xbe\x92\xa1\xed\xa0\x0f\xf9\xa1\x97\x9e\xf8\xbd\x12w\xb7\xf7=\x0b\xdfmB^\x1c=Q\x1a'), chr(4311 - 4211) + chr(9936 - 9835) + chr(0b100101 + 0o76) + chr(111) + chr(100) + chr(0b1100101))('\165' + '\164' + chr(0b1100110) + '\055' + chr(1535 - 1479)))
UQ8hRiBoHcn5 = nDF4gVNx0u9Q.rYPkZ8_2D0X1(kABaul2JCreR.lhbM092AFW8f[nzTpIcepk0o8('\x30' + '\157' + chr(2230 - 2182), 8)], dtype=roI3spqORKae(ES5oEprVxulp(b'\xe1\xe1'), chr(0b1100100) + chr(0b1100101) + '\143' + '\157' + '\x64' + '\x65')(chr(0b11000 + 0o135) + chr(0b1101111 + 0o5) + chr(102) + chr(1546 - 1501) + '\x38'))
YRX9Ch4rysP9 = nZgk6gh1b3dy(kABaul2JCreR, YRX9Ch4rysP9)
YRX9Ch4rysP9 = KV9ckIhroIia(YRX9Ch4rysP9, nzTpIcepk0o8(chr(48) + '\157' + chr(0b110001) + chr(0b101011 + 0o7), 48268 - 48260) * e1HrJaQHACnl)
J_Nfjz8pWxyQ = kABaul2JCreR.lhbM092AFW8f[nzTpIcepk0o8(chr(2015 - 1967) + '\x6f' + chr(48), 8)]
for ZlbFMSG8gCoF in bbT2xIe5pzk7(nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b101001 + 0o7), 8), J_Nfjz8pWxyQ, YRX9Ch4rysP9):
sChW4gUsXrIC = XURpmPuEWCNF(J_Nfjz8pWxyQ, ZlbFMSG8gCoF + YRX9Ch4rysP9 + e1HrJaQHACnl)
L_Y5yNMvOgE8 = nDF4gVNx0u9Q.asarray(kABaul2JCreR[ZlbFMSG8gCoF:sChW4gUsXrIC], dtype=roI3spqORKae(ES5oEprVxulp(b'\xfd\xe1'), chr(100) + chr(241 - 140) + '\x63' + '\157' + chr(0b1100100) + chr(0b1000011 + 0o42))(chr(0b1110101) + chr(116) + chr(102) + '\x2d' + chr(0b110000 + 0o10)))
L_Y5yNMvOgE8 = ygMIbkSSXS59(L_Y5yNMvOgE8)
TH6M9ncgGmPt = UQ8hRiBoHcn5[ZlbFMSG8gCoF:sChW4gUsXrIC]
XDFtlczPSU1e(L_Y5yNMvOgE8, TH6M9ncgGmPt, e1HrJaQHACnl, ZiKB99Xs91Lo, klmSpxrzsw3P)
return roI3spqORKae(UQ8hRiBoHcn5, roI3spqORKae(ES5oEprVxulp(b'\xec\xa1\xf3\x8f\xf0\xa3\x18\x9b\xa2\x85\x9b\xff'), '\x64' + '\x65' + chr(0b1100011) + '\x6f' + chr(0b1100100) + chr(6330 - 6229))('\x75' + '\164' + '\146' + chr(0b101101 + 0o0) + chr(56)))(roI3spqORKae(ES5oEprVxulp(b'\xf6\xe1'), '\144' + '\145' + chr(99) + chr(0b1101111) + '\144' + chr(2375 - 2274))('\165' + '\164' + chr(0b1100110) + '\055' + '\070')) |
cggh/scikit-allel | allel/stats/ld.py | windowed_r_squared | def windowed_r_squared(pos, gn, size=None, start=None, stop=None, step=None,
windows=None, fill=np.nan, percentile=50):
"""Summarise linkage disequilibrium in windows over a single
chromosome/contig.
Parameters
----------
pos : array_like, int, shape (n_items,)
The item positions in ascending order, using 1-based coordinates..
gn : array_like, int8, shape (n_variants, n_samples)
Diploid genotypes at biallelic variants, coded as the number of
alternate alleles per call (i.e., 0 = hom ref, 1 = het, 2 = hom alt).
size : int, optional
The window size (number of bases).
start : int, optional
The position at which to start (1-based).
stop : int, optional
The position at which to stop (1-based).
step : int, optional
The distance between start positions of windows. If not given,
defaults to the window size, i.e., non-overlapping windows.
windows : array_like, int, shape (n_windows, 2), optional
Manually specify the windows to use as a sequence of (window_start,
window_stop) positions, using 1-based coordinates. Overrides the
size/start/stop/step parameters.
fill : object, optional
The value to use where a window is empty, i.e., contains no items.
percentile : int or sequence of ints, optional
The percentile or percentiles to calculate within each window.
Returns
-------
out : ndarray, shape (n_windows,)
The value of the statistic for each window.
windows : ndarray, int, shape (n_windows, 2)
The windows used, as an array of (window_start, window_stop) positions,
using 1-based coordinates.
counts : ndarray, int, shape (n_windows,)
The number of items in each window.
Notes
-----
Linkage disequilibrium (r**2) is calculated using the method of Rogers
and Huff (2008).
See Also
--------
allel.stats.window.windowed_statistic
"""
# define the statistic function
if isinstance(percentile, (list, tuple)):
fill = [fill for _ in percentile]
def statistic(gnw):
r_squared = rogers_huff_r(gnw) ** 2
return [np.percentile(r_squared, p) for p in percentile]
else:
def statistic(gnw):
r_squared = rogers_huff_r(gnw) ** 2
return np.percentile(r_squared, percentile)
return windowed_statistic(pos, gn, statistic, size, start=start,
stop=stop, step=step, windows=windows, fill=fill) | python | def windowed_r_squared(pos, gn, size=None, start=None, stop=None, step=None,
windows=None, fill=np.nan, percentile=50):
"""Summarise linkage disequilibrium in windows over a single
chromosome/contig.
Parameters
----------
pos : array_like, int, shape (n_items,)
The item positions in ascending order, using 1-based coordinates..
gn : array_like, int8, shape (n_variants, n_samples)
Diploid genotypes at biallelic variants, coded as the number of
alternate alleles per call (i.e., 0 = hom ref, 1 = het, 2 = hom alt).
size : int, optional
The window size (number of bases).
start : int, optional
The position at which to start (1-based).
stop : int, optional
The position at which to stop (1-based).
step : int, optional
The distance between start positions of windows. If not given,
defaults to the window size, i.e., non-overlapping windows.
windows : array_like, int, shape (n_windows, 2), optional
Manually specify the windows to use as a sequence of (window_start,
window_stop) positions, using 1-based coordinates. Overrides the
size/start/stop/step parameters.
fill : object, optional
The value to use where a window is empty, i.e., contains no items.
percentile : int or sequence of ints, optional
The percentile or percentiles to calculate within each window.
Returns
-------
out : ndarray, shape (n_windows,)
The value of the statistic for each window.
windows : ndarray, int, shape (n_windows, 2)
The windows used, as an array of (window_start, window_stop) positions,
using 1-based coordinates.
counts : ndarray, int, shape (n_windows,)
The number of items in each window.
Notes
-----
Linkage disequilibrium (r**2) is calculated using the method of Rogers
and Huff (2008).
See Also
--------
allel.stats.window.windowed_statistic
"""
# define the statistic function
if isinstance(percentile, (list, tuple)):
fill = [fill for _ in percentile]
def statistic(gnw):
r_squared = rogers_huff_r(gnw) ** 2
return [np.percentile(r_squared, p) for p in percentile]
else:
def statistic(gnw):
r_squared = rogers_huff_r(gnw) ** 2
return np.percentile(r_squared, percentile)
return windowed_statistic(pos, gn, statistic, size, start=start,
stop=stop, step=step, windows=windows, fill=fill) | [
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... | Summarise linkage disequilibrium in windows over a single
chromosome/contig.
Parameters
----------
pos : array_like, int, shape (n_items,)
The item positions in ascending order, using 1-based coordinates..
gn : array_like, int8, shape (n_variants, n_samples)
Diploid genotypes at biallelic variants, coded as the number of
alternate alleles per call (i.e., 0 = hom ref, 1 = het, 2 = hom alt).
size : int, optional
The window size (number of bases).
start : int, optional
The position at which to start (1-based).
stop : int, optional
The position at which to stop (1-based).
step : int, optional
The distance between start positions of windows. If not given,
defaults to the window size, i.e., non-overlapping windows.
windows : array_like, int, shape (n_windows, 2), optional
Manually specify the windows to use as a sequence of (window_start,
window_stop) positions, using 1-based coordinates. Overrides the
size/start/stop/step parameters.
fill : object, optional
The value to use where a window is empty, i.e., contains no items.
percentile : int or sequence of ints, optional
The percentile or percentiles to calculate within each window.
Returns
-------
out : ndarray, shape (n_windows,)
The value of the statistic for each window.
windows : ndarray, int, shape (n_windows, 2)
The windows used, as an array of (window_start, window_stop) positions,
using 1-based coordinates.
counts : ndarray, int, shape (n_windows,)
The number of items in each window.
Notes
-----
Linkage disequilibrium (r**2) is calculated using the method of Rogers
and Huff (2008).
See Also
--------
allel.stats.window.windowed_statistic | [
"Summarise",
"linkage",
"disequilibrium",
"in",
"windows",
"over",
"a",
"single",
"chromosome",
"/",
"contig",
"."
] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/stats/ld.py#L164-L230 | train | Summarise linkage disequilibrium in windows over a single base. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b11011 + 0o25) + '\x6f' + chr(0b110001 + 0o2) + chr(2443 - 2391) + chr(52), 33377 - 33369), nzTpIcepk0o8(chr(0b1110 + 0o42) + chr(111) + chr(619 - 566), 0o10), nzTpIcepk0o8(chr(0b100000 + 0o20) + chr(0b1101111) + '\062' + '\063' + chr(0b110101), 0b1000), nzTpIcepk0o8('\060' + chr(0b1100111 + 0o10) + chr(0b110101) + chr(2151 - 2096), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x31' + '\063' + chr(2742 - 2688), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(55) + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(0b11110 + 0o22) + chr(111) + chr(0b110011) + chr(48) + chr(48), 0o10), nzTpIcepk0o8(chr(48) + chr(0b111010 + 0o65) + chr(0b11111 + 0o22) + '\063' + '\060', 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + '\063' + chr(1899 - 1851) + chr(53), ord("\x08")), nzTpIcepk0o8(chr(0b10111 + 0o31) + chr(8974 - 8863) + chr(2588 - 2536) + chr(1008 - 960), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(53) + chr(0b10110 + 0o35), 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(0b10010 + 0o37) + chr(0b101 + 0o60) + '\062', 0o10), nzTpIcepk0o8(chr(1952 - 1904) + '\x6f' + chr(0b110001) + chr(1125 - 1072) + chr(2532 - 2478), 14494 - 14486), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110010 + 0o0) + chr(1034 - 986) + chr(0b110011), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1100111 + 0o10) + chr(0b110011) + '\x30' + '\063', 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + '\x33' + chr(0b100011 + 0o15) + chr(0b110101 + 0o1), 20215 - 20207), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(53) + chr(52), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110100) + '\064', 0b1000), nzTpIcepk0o8(chr(0b10110 + 0o32) + chr(0b1101111) + chr(0b1 + 0o60) + chr(53) + chr(49), 0o10), nzTpIcepk0o8(chr(94 - 46) + '\157' + '\x31' + '\x33' + '\x32', 0b1000), nzTpIcepk0o8(chr(48) + chr(1224 - 1113) + chr(0b100101 + 0o14) + '\x34' + chr(0b1000 + 0o52), ord("\x08")), nzTpIcepk0o8(chr(1104 - 1056) + chr(342 - 231) + chr(0b110011) + '\x36' + chr(0b110001 + 0o6), 0o10), nzTpIcepk0o8(chr(0b101000 + 0o10) + chr(0b1101111) + chr(0b101011 + 0o10) + '\060' + chr(349 - 299), 0b1000), nzTpIcepk0o8('\x30' + chr(111) + '\060', 0o10), nzTpIcepk0o8(chr(0b11101 + 0o23) + '\x6f' + chr(0b110001) + '\064' + '\061', 34136 - 34128), nzTpIcepk0o8('\x30' + chr(0b101100 + 0o103) + chr(0b110001) + chr(53) + chr(1881 - 1831), 8), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b11 + 0o60) + '\x36' + '\064', 12304 - 12296), nzTpIcepk0o8(chr(0b100 + 0o54) + '\x6f' + chr(51) + chr(122 - 73) + chr(0b110001), 0b1000), nzTpIcepk0o8(chr(746 - 698) + chr(0b1100110 + 0o11) + chr(0b110001) + chr(49) + chr(0b110000), 55547 - 55539), nzTpIcepk0o8('\x30' + chr(0b101100 + 0o103) + chr(0b110011 + 0o0) + '\x37' + '\x36', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1100001 + 0o16) + chr(2127 - 2076) + chr(0b110101) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\065' + '\060', ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(52), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + chr(50) + chr(1060 - 1008), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110001) + chr(0b10100 + 0o36) + chr(0b1100 + 0o50), 0b1000), nzTpIcepk0o8(chr(48) + chr(552 - 441) + chr(49) + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(2222 - 2174) + chr(111) + chr(0b110011) + chr(54) + chr(49), 39545 - 39537), nzTpIcepk0o8(chr(1528 - 1480) + '\157' + '\062' + '\063' + chr(1306 - 1255), 35808 - 35800), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x34' + chr(230 - 181), 0b1000), nzTpIcepk0o8(chr(0b10011 + 0o35) + chr(0b1101111) + chr(0b110011) + chr(52) + chr(0b110110), 3998 - 3990)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + chr(4807 - 4696) + '\x35' + chr(48), 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xca'), chr(2865 - 2765) + '\145' + chr(99) + chr(0b1101111) + '\x64' + chr(0b11000 + 0o115))(chr(0b1000010 + 0o63) + '\164' + chr(0b11 + 0o143) + chr(0b101101) + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def TToeAMwvd3U1(IGIA_fu6MbaO, kABaul2JCreR, e1HrJaQHACnl=None, KQbHFTcl_LKy=None, dYJbBiYO_nGE=None, ZiKB99Xs91Lo=None, hVZaXHr1SthH=None, pPmkLCVA328e=roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'\x8ad\xf3'), chr(100) + chr(0b1000100 + 0o41) + chr(0b1010111 + 0o14) + chr(111) + '\144' + chr(101))(chr(117) + '\x74' + chr(2623 - 2521) + chr(0b101011 + 0o2) + '\070')), AnL2CONgwu6c=nzTpIcepk0o8(chr(2070 - 2022) + chr(0b101010 + 0o105) + '\x36' + chr(0b101011 + 0o7), 0b1000)):
if suIjIS24Zkqw(AnL2CONgwu6c, (H4NoA26ON7iG, nfNqtJL5aRaY)):
pPmkLCVA328e = [pPmkLCVA328e for zIqcgNgQ9U6F in AnL2CONgwu6c]
def oIEQLc5XDStf(gAjZi2ZmSSyq):
Nv5p5TQN_5ia = TXw19gBXuonL(gAjZi2ZmSSyq) ** nzTpIcepk0o8(chr(48) + '\157' + chr(50), 44174 - 44166)
return [roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'\x94`\xefL;U\xb41\xa9E'), chr(0b1100100) + '\145' + chr(99) + chr(4737 - 4626) + chr(0b1100100) + '\x65')('\x75' + '\x74' + '\146' + '\055' + chr(0b111000)))(Nv5p5TQN_5ia, fSdw5wwLo9MO) for fSdw5wwLo9MO in AnL2CONgwu6c]
else:
def oIEQLc5XDStf(gAjZi2ZmSSyq):
Nv5p5TQN_5ia = TXw19gBXuonL(gAjZi2ZmSSyq) ** nzTpIcepk0o8(chr(78 - 30) + chr(0b11100 + 0o123) + chr(50), 8)
return roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'\x94`\xefL;U\xb41\xa9E'), chr(100) + chr(7390 - 7289) + chr(0b1100011) + chr(111) + chr(0b1011001 + 0o13) + chr(0b1100101))(chr(0b11001 + 0o134) + '\x74' + chr(0b1011111 + 0o7) + chr(1098 - 1053) + chr(56)))(Nv5p5TQN_5ia, AnL2CONgwu6c)
return JOnlY4qTZIKz(IGIA_fu6MbaO, kABaul2JCreR, oIEQLc5XDStf, e1HrJaQHACnl, start=KQbHFTcl_LKy, stop=dYJbBiYO_nGE, step=ZiKB99Xs91Lo, windows=hVZaXHr1SthH, fill=pPmkLCVA328e) |
cggh/scikit-allel | allel/stats/ld.py | plot_pairwise_ld | def plot_pairwise_ld(m, colorbar=True, ax=None, imshow_kwargs=None):
"""Plot a matrix of genotype linkage disequilibrium values between
all pairs of variants.
Parameters
----------
m : array_like
Array of linkage disequilibrium values in condensed form.
colorbar : bool, optional
If True, add a colorbar to the current figure.
ax : axes, optional
The axes on which to draw. If not provided, a new figure will be
created.
imshow_kwargs : dict-like, optional
Additional keyword arguments passed through to
:func:`matplotlib.pyplot.imshow`.
Returns
-------
ax : axes
The axes on which the plot was drawn.
"""
import matplotlib.pyplot as plt
# check inputs
m_square = ensure_square(m)
# blank out lower triangle and flip up/down
m_square = np.tril(m_square)[::-1, :]
# set up axes
if ax is None:
# make a square figure with enough pixels to represent each variant
x = m_square.shape[0] / plt.rcParams['figure.dpi']
x = max(x, plt.rcParams['figure.figsize'][0])
fig, ax = plt.subplots(figsize=(x, x))
fig.tight_layout(pad=0)
# setup imshow arguments
if imshow_kwargs is None:
imshow_kwargs = dict()
imshow_kwargs.setdefault('interpolation', 'none')
imshow_kwargs.setdefault('cmap', 'Greys')
imshow_kwargs.setdefault('vmin', 0)
imshow_kwargs.setdefault('vmax', 1)
# plot as image
im = ax.imshow(m_square, **imshow_kwargs)
# tidy up
ax.set_xticks([])
ax.set_yticks([])
for s in 'bottom', 'right':
ax.spines[s].set_visible(False)
if colorbar:
plt.gcf().colorbar(im, shrink=.5, pad=0)
return ax | python | def plot_pairwise_ld(m, colorbar=True, ax=None, imshow_kwargs=None):
"""Plot a matrix of genotype linkage disequilibrium values between
all pairs of variants.
Parameters
----------
m : array_like
Array of linkage disequilibrium values in condensed form.
colorbar : bool, optional
If True, add a colorbar to the current figure.
ax : axes, optional
The axes on which to draw. If not provided, a new figure will be
created.
imshow_kwargs : dict-like, optional
Additional keyword arguments passed through to
:func:`matplotlib.pyplot.imshow`.
Returns
-------
ax : axes
The axes on which the plot was drawn.
"""
import matplotlib.pyplot as plt
# check inputs
m_square = ensure_square(m)
# blank out lower triangle and flip up/down
m_square = np.tril(m_square)[::-1, :]
# set up axes
if ax is None:
# make a square figure with enough pixels to represent each variant
x = m_square.shape[0] / plt.rcParams['figure.dpi']
x = max(x, plt.rcParams['figure.figsize'][0])
fig, ax = plt.subplots(figsize=(x, x))
fig.tight_layout(pad=0)
# setup imshow arguments
if imshow_kwargs is None:
imshow_kwargs = dict()
imshow_kwargs.setdefault('interpolation', 'none')
imshow_kwargs.setdefault('cmap', 'Greys')
imshow_kwargs.setdefault('vmin', 0)
imshow_kwargs.setdefault('vmax', 1)
# plot as image
im = ax.imshow(m_square, **imshow_kwargs)
# tidy up
ax.set_xticks([])
ax.set_yticks([])
for s in 'bottom', 'right':
ax.spines[s].set_visible(False)
if colorbar:
plt.gcf().colorbar(im, shrink=.5, pad=0)
return ax | [
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... | Plot a matrix of genotype linkage disequilibrium values between
all pairs of variants.
Parameters
----------
m : array_like
Array of linkage disequilibrium values in condensed form.
colorbar : bool, optional
If True, add a colorbar to the current figure.
ax : axes, optional
The axes on which to draw. If not provided, a new figure will be
created.
imshow_kwargs : dict-like, optional
Additional keyword arguments passed through to
:func:`matplotlib.pyplot.imshow`.
Returns
-------
ax : axes
The axes on which the plot was drawn. | [
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"variants",
"."
] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/stats/ld.py#L233-L292 | train | Plot a matrix of genotype linkage disequilibrium values between all pairs 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(chr(1565 - 1517) + '\x6f' + '\062' + '\x35' + chr(2522 - 2468), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(51) + '\x35' + '\065', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(6757 - 6646) + '\x31' + '\062' + chr(52), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(50) + chr(0b100001 + 0o23) + '\060', ord("\x08")), nzTpIcepk0o8(chr(492 - 444) + chr(8344 - 8233) + chr(55) + chr(0b100000 + 0o22), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110011) + '\x34' + chr(51), 0o10), nzTpIcepk0o8(chr(0b0 + 0o60) + chr(0b1101111) + chr(0b0 + 0o61) + chr(0b110010) + chr(0b110011 + 0o4), 48288 - 48280), nzTpIcepk0o8('\060' + '\x6f' + chr(0b10101 + 0o34) + chr(1808 - 1755) + chr(49), 44893 - 44885), nzTpIcepk0o8(chr(0b110000) + chr(0b11011 + 0o124) + chr(51) + '\x31' + '\065', 46114 - 46106), nzTpIcepk0o8(chr(48) + chr(0b11111 + 0o120) + chr(0b11111 + 0o22) + chr(0b110010) + chr(1989 - 1941), 9700 - 9692), nzTpIcepk0o8(chr(0b110000) + chr(6313 - 6202) + '\067' + chr(0b1010 + 0o53), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110111) + chr(0b101001 + 0o12), 0b1000), nzTpIcepk0o8(chr(952 - 904) + '\x6f' + chr(0b101010 + 0o7) + chr(50) + '\062', 56349 - 56341), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x32' + chr(53) + chr(0b110100 + 0o3), 28366 - 28358), nzTpIcepk0o8('\x30' + chr(111) + chr(1396 - 1341) + chr(50), 8), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110001) + chr(0b110001) + chr(0b11001 + 0o36), 5296 - 5288), nzTpIcepk0o8(chr(0b100100 + 0o14) + chr(3987 - 3876) + chr(0b110011) + chr(0b110110) + chr(54), 0b1000), nzTpIcepk0o8(chr(0b101111 + 0o1) + '\x6f' + '\x31' + '\064' + '\x32', 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(51) + '\x34' + chr(1438 - 1386), 0o10), nzTpIcepk0o8(chr(0b100010 + 0o16) + chr(0b1101111) + chr(49) + chr(0b110011) + '\064', 17415 - 17407), nzTpIcepk0o8('\x30' + chr(111) + chr(49) + chr(52) + '\x32', 8), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(989 - 939) + '\x32' + chr(1167 - 1116), 7569 - 7561), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b1100 + 0o45) + chr(0b110001) + chr(0b101100 + 0o4), 51678 - 51670), nzTpIcepk0o8(chr(293 - 245) + chr(0b1101111) + chr(0b1010 + 0o51) + '\x34' + '\x32', 24073 - 24065), nzTpIcepk0o8(chr(587 - 539) + '\157' + '\x32' + '\060' + '\061', 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + '\067' + '\x35', 8), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(50) + chr(1414 - 1361) + '\063', 0o10), nzTpIcepk0o8('\060' + chr(0b1001011 + 0o44) + chr(0b110011) + '\x30' + '\063', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1000010 + 0o55) + chr(0b110011) + chr(0b110001) + chr(0b110110), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110010) + chr(0b11101 + 0o25) + '\x37', 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b11000 + 0o33) + '\064', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b11001 + 0o126) + chr(49) + '\067' + chr(110 - 57), 0o10), nzTpIcepk0o8('\060' + '\157' + '\061' + chr(54) + chr(0b100010 + 0o16), 26296 - 26288), nzTpIcepk0o8('\060' + chr(0b1000011 + 0o54) + chr(0b110010) + '\060' + chr(0b101101 + 0o6), ord("\x08")), nzTpIcepk0o8(chr(1930 - 1882) + chr(0b1010101 + 0o32) + '\x33' + chr(0b110001) + '\061', 17668 - 17660), nzTpIcepk0o8('\060' + chr(111) + '\061' + chr(932 - 880) + '\067', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(4504 - 4393) + '\064' + '\x37', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\063' + chr(0b1111 + 0o46) + '\067', 52793 - 52785), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\062' + '\x31' + chr(52), 0b1000), nzTpIcepk0o8(chr(0b1101 + 0o43) + chr(0b1101111) + chr(49) + chr(0b110111) + chr(51), 1157 - 1149)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b11000 + 0o35) + '\060', 44398 - 44390)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x80'), chr(6235 - 6135) + '\x65' + chr(0b101111 + 0o64) + '\x6f' + chr(0b1011011 + 0o11) + '\145')(chr(0b110 + 0o157) + chr(0b1110100) + chr(0b100010 + 0o104) + chr(0b10011 + 0o32) + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def LrAfG6VPOniy(tF75nqoNENFL, G1nlXbDaI_wa=nzTpIcepk0o8('\060' + chr(9514 - 9403) + chr(0b110001), 49279 - 49271), ZtB7KOLCW2Hk=None, TbyqRkDRVs9Z=None):
(Z7HGgmIyegqz,) = (roI3spqORKae(rFFUeiYWzOhx(roI3spqORKae(ES5oEprVxulp(b'\xc3\x8c \xd0V\x8c#\x05\xa42\x13K+\xdfV \x82'), chr(0b1100100) + '\x65' + chr(99) + chr(111) + '\144' + chr(101))(chr(2409 - 2292) + chr(116) + chr(102) + chr(0b111 + 0o46) + chr(0b111000)), roI3spqORKae(ES5oEprVxulp(b'\xde\x94$\xccU\x97'), '\144' + chr(8567 - 8466) + '\x63' + chr(0b1101111) + '\144' + chr(101))('\x75' + chr(3406 - 3290) + chr(0b111001 + 0o55) + chr(45) + chr(56))), roI3spqORKae(ES5oEprVxulp(b'\xde\x94$\xccU\x97'), '\x64' + '\x65' + '\x63' + chr(111) + '\144' + '\x65')(chr(2044 - 1927) + chr(0b1110000 + 0o4) + '\146' + chr(1584 - 1539) + chr(0b111000))),)
Qy9XvLrWzdWE = m30P2_HbGN5v(tF75nqoNENFL)
Qy9XvLrWzdWE = nDF4gVNx0u9Q.tril(Qy9XvLrWzdWE)[::-nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b11000 + 0o31), 8), :]
if ZtB7KOLCW2Hk is None:
bI5jsQ9OkQtj = Qy9XvLrWzdWE.lhbM092AFW8f[nzTpIcepk0o8(chr(2162 - 2114) + chr(111) + '\060', 57511 - 57503)] / Z7HGgmIyegqz.Arpwt0FOuO5L[roI3spqORKae(ES5oEprVxulp(b'\xc8\x843\xd5H\x86y\r\xbd9'), '\x64' + chr(0b1100101) + chr(7107 - 7008) + '\157' + chr(0b100001 + 0o103) + chr(0b1001100 + 0o31))(chr(0b1110101) + '\164' + '\146' + chr(0b101101) + '\x38')]
bI5jsQ9OkQtj = KV9ckIhroIia(bI5jsQ9OkQtj, Z7HGgmIyegqz.Arpwt0FOuO5L[roI3spqORKae(ES5oEprVxulp(b'\xc8\x843\xd5H\x86y\x0f\xa47NR(\xca'), chr(0b1000110 + 0o36) + chr(3062 - 2961) + chr(7582 - 7483) + '\x6f' + chr(2592 - 2492) + '\x65')(chr(0b10010 + 0o143) + chr(6197 - 6081) + '\x66' + chr(1365 - 1320) + '\x38')][nzTpIcepk0o8('\060' + '\x6f' + chr(932 - 884), 8)])
(ux0XlXMUdKbX, ZtB7KOLCW2Hk) = Z7HGgmIyegqz.subplots(figsize=(bI5jsQ9OkQtj, bI5jsQ9OkQtj))
roI3spqORKae(ux0XlXMUdKbX, roI3spqORKae(ES5oEprVxulp(b'\xda\x843\xc8N\xbc;\x08\xb4?HO'), chr(0b101101 + 0o67) + chr(9606 - 9505) + '\143' + chr(6387 - 6276) + '\x64' + '\x65')(chr(0b101110 + 0o107) + '\164' + chr(0b1100110) + chr(0b101101) + chr(56)))(pad=nzTpIcepk0o8('\060' + '\157' + '\x30', 8))
if TbyqRkDRVs9Z is None:
TbyqRkDRVs9Z = znjnJWK64FDT()
roI3spqORKae(TbyqRkDRVs9Z, roI3spqORKae(ES5oEprVxulp(b'\xd4\x88d\xeaw\x96\x1cP\xbf?jh'), '\144' + '\x65' + chr(0b1100011) + '\x6f' + chr(0b1100100) + chr(8022 - 7921))(chr(117) + chr(0b1110100) + chr(7947 - 7845) + chr(1783 - 1738) + chr(56)))(roI3spqORKae(ES5oEprVxulp(b'\xc7\x83 \xc5H\x938\x05\xac$TT<'), '\144' + chr(646 - 545) + '\143' + '\x6f' + chr(9174 - 9074) + chr(10108 - 10007))('\x75' + chr(116) + chr(0b1100110) + '\055' + chr(0b111000)), roI3spqORKae(ES5oEprVxulp(b'\xc0\x82:\xc5'), '\144' + '\145' + '\143' + chr(0b111110 + 0o61) + '\144' + chr(101))(chr(0b1001101 + 0o50) + '\164' + chr(102) + chr(0b1100 + 0o41) + chr(0b111000)))
roI3spqORKae(TbyqRkDRVs9Z, roI3spqORKae(ES5oEprVxulp(b'\xd4\x88d\xeaw\x96\x1cP\xbf?jh'), chr(0b1100100) + chr(9602 - 9501) + '\143' + chr(111) + chr(0b1100100) + chr(0b1100101))('\x75' + chr(116) + chr(2329 - 2227) + '\055' + '\x38'))(roI3spqORKae(ES5oEprVxulp(b'\xcd\x805\xd0'), chr(100) + chr(101) + chr(0b1100011) + chr(0b110001 + 0o76) + '\144' + chr(0b1011010 + 0o13))('\x75' + '\164' + '\x66' + chr(0b1 + 0o54) + '\x38'), roI3spqORKae(ES5oEprVxulp(b'\xe9\x9f1\xd9I'), chr(0b1000100 + 0o40) + chr(0b1100101) + '\143' + chr(7371 - 7260) + '\x64' + '\x65')(chr(0b1110101) + '\164' + '\x66' + '\x2d' + '\070'))
roI3spqORKae(TbyqRkDRVs9Z, roI3spqORKae(ES5oEprVxulp(b'\xd4\x88d\xeaw\x96\x1cP\xbf?jh'), chr(0b1100100) + '\145' + chr(0b1000011 + 0o40) + '\157' + chr(100) + chr(101))(chr(0b1110101) + chr(0b1000010 + 0o62) + chr(0b1010110 + 0o20) + chr(0b10111 + 0o26) + '\070'))(roI3spqORKae(ES5oEprVxulp(b'\xd8\x80=\xce'), '\144' + '\x65' + '\143' + chr(923 - 812) + chr(100) + chr(101))('\165' + '\164' + chr(0b1100110) + chr(0b100110 + 0o7) + chr(2062 - 2006)), nzTpIcepk0o8(chr(101 - 53) + chr(518 - 407) + chr(2149 - 2101), 8))
roI3spqORKae(TbyqRkDRVs9Z, roI3spqORKae(ES5oEprVxulp(b'\xd4\x88d\xeaw\x96\x1cP\xbf?jh'), '\144' + '\145' + chr(2756 - 2657) + '\157' + chr(100) + chr(6538 - 6437))(chr(4957 - 4840) + chr(5514 - 5398) + '\x66' + chr(0b100101 + 0o10) + chr(0b100000 + 0o30)))(roI3spqORKae(ES5oEprVxulp(b'\xd8\x805\xd8'), '\x64' + chr(101) + chr(0b100001 + 0o102) + '\x6f' + chr(4999 - 4899) + chr(0b10000 + 0o125))(chr(0b1110101) + chr(116) + '\x66' + chr(1099 - 1054) + chr(207 - 151)), nzTpIcepk0o8('\x30' + chr(5612 - 5501) + chr(49), 8))
AreS5V4GZTfl = ZtB7KOLCW2Hk.imshow(Qy9XvLrWzdWE, **TbyqRkDRVs9Z)
roI3spqORKae(ZtB7KOLCW2Hk, roI3spqORKae(ES5oEprVxulp(b'\xdd\x88 \xffB\x97>\n\xa6#'), chr(0b1100100) + chr(4845 - 4744) + chr(0b1100011) + chr(2055 - 1944) + chr(5795 - 5695) + chr(0b1001010 + 0o33))(chr(7547 - 7430) + chr(0b1110 + 0o146) + '\x66' + '\055' + chr(0b111000)))([])
roI3spqORKae(ZtB7KOLCW2Hk, roI3spqORKae(ES5oEprVxulp(b'\xdd\x88 \xffC\x97>\n\xa6#'), '\x64' + chr(8187 - 8086) + chr(0b1100011) + chr(2577 - 2466) + chr(100) + chr(1944 - 1843))(chr(0b10010 + 0o143) + chr(0b1110100) + '\x66' + chr(0b101101) + chr(1130 - 1074)))([])
for PmE5_h409JAA in (roI3spqORKae(ES5oEprVxulp(b'\xcc\x82 \xd4U\x8e'), chr(0b1100100) + '\145' + chr(0b1100011) + chr(3986 - 3875) + chr(4413 - 4313) + '\x65')('\165' + chr(7945 - 7829) + '\x66' + '\055' + '\070'), roI3spqORKae(ES5oEprVxulp(b'\xdc\x843\xc8N'), chr(9667 - 9567) + chr(0b101010 + 0o73) + chr(0b1100011) + '\157' + '\144' + chr(101))(chr(117) + chr(116) + '\x66' + chr(0b101101) + chr(552 - 496))):
roI3spqORKae(ZtB7KOLCW2Hk.spines[PmE5_h409JAA], roI3spqORKae(ES5oEprVxulp(b'\xdd\x88 \xffL\x8a$\x00\xaf<X'), chr(0b1100100) + chr(7563 - 7462) + chr(99) + chr(0b1101111) + chr(100) + chr(101))(chr(0b1110101) + '\x74' + '\x66' + chr(0b101101) + chr(56)))(nzTpIcepk0o8(chr(1101 - 1053) + chr(0b1101111) + '\x30', 8))
if G1nlXbDaI_wa:
roI3spqORKae(Z7HGgmIyegqz.gcf(), roI3spqORKae(ES5oEprVxulp(b'\xe9\xdc:\xccb\x81\x13\x08\x84\x0fJZ'), chr(0b1100011 + 0o1) + chr(101) + '\x63' + '\x6f' + '\144' + chr(5655 - 5554))(chr(117) + chr(6528 - 6412) + chr(2559 - 2457) + '\x2d' + chr(0b111000)))(AreS5V4GZTfl, shrink=0.5, pad=nzTpIcepk0o8(chr(48) + chr(0b1000110 + 0o51) + chr(0b110000), 8))
return ZtB7KOLCW2Hk |
cggh/scikit-allel | allel/io/util.py | array_to_hdf5 | def array_to_hdf5(a, parent, name, **kwargs):
"""Write a Numpy array to an HDF5 dataset.
Parameters
----------
a : ndarray
Data to write.
parent : string or h5py group
Parent HDF5 file or group. If a string, will be treated as HDF5 file
name.
name : string
Name or path of dataset to write data into.
kwargs : keyword arguments
Passed through to h5py require_dataset() function.
Returns
-------
h5d : h5py dataset
"""
import h5py
h5f = None
if isinstance(parent, str):
h5f = h5py.File(parent, mode='a')
parent = h5f
try:
kwargs.setdefault('chunks', True) # auto-chunking
kwargs.setdefault('dtype', a.dtype)
kwargs.setdefault('compression', 'gzip')
h5d = parent.require_dataset(name, shape=a.shape, **kwargs)
h5d[...] = a
return h5d
finally:
if h5f is not None:
h5f.close() | python | def array_to_hdf5(a, parent, name, **kwargs):
"""Write a Numpy array to an HDF5 dataset.
Parameters
----------
a : ndarray
Data to write.
parent : string or h5py group
Parent HDF5 file or group. If a string, will be treated as HDF5 file
name.
name : string
Name or path of dataset to write data into.
kwargs : keyword arguments
Passed through to h5py require_dataset() function.
Returns
-------
h5d : h5py dataset
"""
import h5py
h5f = None
if isinstance(parent, str):
h5f = h5py.File(parent, mode='a')
parent = h5f
try:
kwargs.setdefault('chunks', True) # auto-chunking
kwargs.setdefault('dtype', a.dtype)
kwargs.setdefault('compression', 'gzip')
h5d = parent.require_dataset(name, shape=a.shape, **kwargs)
h5d[...] = a
return h5d
finally:
if h5f is not None:
h5f.close() | [
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Data to write.
parent : string or h5py group
Parent HDF5 file or group. If a string, will be treated as HDF5 file
name.
name : string
Name or path of dataset to write data into.
kwargs : keyword arguments
Passed through to h5py require_dataset() function.
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/io/util.py#L11-L51 | train | Write a Numpy array to an HDF5 dataset. | 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(0b1 + 0o57) + chr(0b1011 + 0o144) + chr(50) + chr(0b1010 + 0o47) + '\066', 25954 - 25946), nzTpIcepk0o8(chr(715 - 667) + chr(0b1101111) + chr(0b110001) + '\x35' + '\x35', 0o10), nzTpIcepk0o8(chr(0b11100 + 0o24) + chr(9860 - 9749) + chr(51) + chr(0b110011) + chr(0b10111 + 0o40), 57475 - 57467), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b111 + 0o54) + '\063' + '\067', 8), nzTpIcepk0o8(chr(585 - 537) + '\x6f' + '\x31' + '\x35' + chr(51), 0b1000), nzTpIcepk0o8(chr(0b100100 + 0o14) + chr(5121 - 5010) + chr(0b1010 + 0o47) + chr(0b110010) + '\066', 63296 - 63288), nzTpIcepk0o8(chr(1648 - 1600) + chr(111) + chr(0b110011) + '\061' + chr(54), 21053 - 21045), nzTpIcepk0o8(chr(1569 - 1521) + chr(111) + chr(50) + chr(980 - 932) + chr(52), 0b1000), nzTpIcepk0o8(chr(844 - 796) + '\157' + '\062' + '\064', ord("\x08")), nzTpIcepk0o8(chr(358 - 310) + chr(0b1101111) + chr(0b110010) + chr(55) + '\063', 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(2208 - 2159) + '\064' + chr(0b110010), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(51) + chr(53) + chr(0b101110 + 0o4), 0o10), nzTpIcepk0o8(chr(836 - 788) + chr(0b1101111) + chr(0b1010 + 0o51) + chr(48) + chr(48), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b101111 + 0o100) + '\063' + '\x37' + chr(1635 - 1582), 3710 - 3702), nzTpIcepk0o8(chr(1970 - 1922) + '\157' + '\x32' + '\060', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(2127 - 2072) + '\067', 10732 - 10724), nzTpIcepk0o8(chr(765 - 717) + chr(0b11111 + 0o120) + chr(0b110100), 62284 - 62276), nzTpIcepk0o8('\060' + '\157' + chr(0b110011) + chr(1364 - 1313) + '\x31', 50000 - 49992), nzTpIcepk0o8(chr(0b1111 + 0o41) + chr(111) + chr(0b110011) + '\062' + '\062', 65273 - 65265), nzTpIcepk0o8(chr(0b11010 + 0o26) + chr(0b1100100 + 0o13) + chr(0b110010 + 0o1) + chr(0b110011) + chr(54 - 6), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(51) + '\066' + chr(0b10101 + 0o41), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(5193 - 5082) + '\x35' + chr(2992 - 2937), 0o10), nzTpIcepk0o8(chr(48) + '\157' + '\x32' + '\062' + '\x37', ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110011) + chr(49) + chr(0b100011 + 0o16), 0b1000), nzTpIcepk0o8(chr(0b100 + 0o54) + '\157' + chr(2169 - 2119) + '\x31' + chr(48), 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(2316 - 2266) + chr(0b110000) + chr(51), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(1201 - 1151) + chr(0b100101 + 0o13) + '\x33', 8), nzTpIcepk0o8(chr(0b100011 + 0o15) + chr(11941 - 11830) + '\062' + chr(0b110010) + '\063', 0o10), nzTpIcepk0o8('\x30' + chr(12184 - 12073) + '\061' + '\x33' + chr(52), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + '\x32' + chr(49) + chr(0b110001), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(1411 - 1361) + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110010) + chr(52) + chr(224 - 176), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x31' + chr(0b11110 + 0o27) + '\x37', 0b1000), nzTpIcepk0o8(chr(0b1010 + 0o46) + chr(111) + '\x36', 43724 - 43716), nzTpIcepk0o8(chr(48) + chr(4828 - 4717) + chr(0b10100 + 0o36) + chr(0b110110) + chr(882 - 827), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110011) + '\064' + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(901 - 853) + '\x6f' + '\x32' + chr(0b11 + 0o57) + '\x31', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(50) + '\x30' + chr(48), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(50) + '\063' + chr(0b100000 + 0o23), 0b1000), nzTpIcepk0o8(chr(1803 - 1755) + chr(111) + chr(51) + chr(0b100000 + 0o27) + chr(2460 - 2406), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + 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'\xa0'), chr(6417 - 6317) + chr(0b1100101) + chr(5896 - 5797) + chr(111) + chr(0b100000 + 0o104) + chr(0b1100101))(chr(0b110001 + 0o104) + '\164' + '\x66' + chr(841 - 796) + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def SPJXnwIsQehF(AQ9ceR9AaoT1, aY0lxtg5akD2, SLVB2BPA_mIe, **q5n0sHDDTy90):
(RqFza2bfJyrc,) = (zGgTE_CdZfvi(roI3spqORKae(ES5oEprVxulp(b'\xe6X\xaf\xa6'), '\144' + chr(0b0 + 0o145) + chr(7675 - 7576) + chr(0b1010010 + 0o35) + '\144' + chr(0b110110 + 0o57))(chr(0b1010000 + 0o45) + chr(0b111100 + 0o70) + chr(102) + '\x2d' + chr(230 - 174))),)
uqjdddtgqsHt = None
if suIjIS24Zkqw(aY0lxtg5akD2, N9zlRy29S1SS):
uqjdddtgqsHt = RqFza2bfJyrc.File(aY0lxtg5akD2, mode=roI3spqORKae(ES5oEprVxulp(b'\xef'), '\x64' + chr(0b1001100 + 0o31) + '\143' + chr(111) + chr(8435 - 8335) + chr(0b1100101))(chr(0b1110101) + chr(0b1110100) + chr(10398 - 10296) + chr(0b100111 + 0o6) + chr(0b111000)))
aY0lxtg5akD2 = uqjdddtgqsHt
try:
roI3spqORKae(q5n0sHDDTy90, roI3spqORKae(ES5oEprVxulp(b'\xf4\x08\xef\x95&#\x85\xbdf\xd45\xb9'), chr(100) + chr(8924 - 8823) + chr(0b1100011) + '\x6f' + chr(100) + chr(0b1100101))(chr(11470 - 11353) + '\164' + '\146' + chr(0b101101) + chr(1860 - 1804)))(roI3spqORKae(ES5oEprVxulp(b'\xed\x05\xaa\xb1\x00%'), chr(0b1011110 + 0o6) + chr(8851 - 8750) + chr(0b1100011) + chr(0b1101111) + '\144' + chr(0b1010110 + 0o17))(chr(11374 - 11257) + chr(0b1110100) + chr(0b1100010 + 0o4) + '\x2d' + chr(784 - 728)), nzTpIcepk0o8('\x30' + chr(0b1 + 0o156) + chr(0b110000 + 0o1), ord("\x08")))
roI3spqORKae(q5n0sHDDTy90, roI3spqORKae(ES5oEprVxulp(b'\xf4\x08\xef\x95&#\x85\xbdf\xd45\xb9'), chr(0b100000 + 0o104) + chr(6277 - 6176) + chr(0b1100011) + '\x6f' + '\x64' + chr(0b1100101))('\165' + chr(0b1110100) + chr(102) + chr(0b100 + 0o51) + chr(0b110011 + 0o5)))(roI3spqORKae(ES5oEprVxulp(b'\xea\x19\xa6\xaf\x0e'), '\144' + chr(0b10011 + 0o122) + chr(0b1100011) + '\x6f' + chr(0b1100100) + '\145')(chr(3807 - 3690) + chr(0b1110100) + chr(3229 - 3127) + '\x2d' + '\070'), roI3spqORKae(AQ9ceR9AaoT1, roI3spqORKae(ES5oEprVxulp(b'\xdc\x0e\x87\xe6\t4\xbb\xcbn\xd3W\xa6'), '\144' + chr(7048 - 6947) + chr(0b1100011) + chr(0b1101111) + '\144' + chr(101))(chr(117) + chr(0b101 + 0o157) + '\x66' + chr(0b101101) + chr(0b111000))))
roI3spqORKae(q5n0sHDDTy90, roI3spqORKae(ES5oEprVxulp(b'\xf4\x08\xef\x95&#\x85\xbdf\xd45\xb9'), chr(100) + '\145' + chr(0b1001110 + 0o25) + chr(0b1010110 + 0o31) + '\x64' + chr(0b1100101))(chr(12130 - 12013) + '\164' + chr(6143 - 6041) + chr(316 - 271) + chr(56)))(roI3spqORKae(ES5oEprVxulp(b'\xed\x02\xb2\xaf\x193\xbd\xf7}\xd4\x0c'), chr(0b1100100) + chr(0b10100 + 0o121) + '\143' + chr(0b1000110 + 0o51) + '\144' + chr(2215 - 2114))(chr(0b101 + 0o160) + chr(116) + chr(102) + chr(0b101101) + '\x38'), roI3spqORKae(ES5oEprVxulp(b'\xe9\x17\xb6\xaf'), chr(9122 - 9022) + '\145' + chr(0b1100011) + chr(111) + chr(100) + '\x65')(chr(117) + '\x74' + '\146' + '\055' + chr(56)))
DA7YDEtVFHsF = aY0lxtg5akD2.require_dataset(SLVB2BPA_mIe, shape=AQ9ceR9AaoT1.lhbM092AFW8f, **q5n0sHDDTy90)
DA7YDEtVFHsF[...] = AQ9ceR9AaoT1
return DA7YDEtVFHsF
finally:
if uqjdddtgqsHt is not None:
roI3spqORKae(uqjdddtgqsHt, roI3spqORKae(ES5oEprVxulp(b'\xd4\x08\xae\xe8(5\xa8\xbdA\xdfZ\x80'), '\144' + chr(7141 - 7040) + chr(0b1100011) + '\x6f' + chr(0b1100100) + chr(0b111011 + 0o52))(chr(0b1011001 + 0o34) + chr(3109 - 2993) + '\146' + '\055' + chr(56)))() |
cggh/scikit-allel | allel/io/util.py | recarray_from_hdf5_group | def recarray_from_hdf5_group(*args, **kwargs):
"""Load a recarray from columns stored as separate datasets with an
HDF5 group.
Either provide an h5py group as a single positional argument,
or provide two positional arguments giving the HDF5 file path and the
group node path within the file.
The following optional parameters may be given.
Parameters
----------
start : int, optional
Index to start loading from.
stop : int, optional
Index to finish loading at.
condition : array_like, bool, optional
A 1-dimensional boolean array of the same length as the columns of the
table to load, indicating a selection of rows to load.
"""
import h5py
h5f = None
if len(args) == 1:
group = args[0]
elif len(args) == 2:
file_path, node_path = args
h5f = h5py.File(file_path, mode='r')
try:
group = h5f[node_path]
except Exception as e:
h5f.close()
raise e
else:
raise ValueError('bad arguments; expected group or (file_path, '
'node_path), found %s' % repr(args))
try:
if not isinstance(group, h5py.Group):
raise ValueError('expected group, found %r' % group)
# determine dataset names to load
available_dataset_names = [n for n in group.keys()
if isinstance(group[n], h5py.Dataset)]
names = kwargs.pop('names', available_dataset_names)
names = [str(n) for n in names] # needed for PY2
for n in names:
if n not in set(group.keys()):
raise ValueError('name not found: %s' % n)
if not isinstance(group[n], h5py.Dataset):
raise ValueError('name does not refer to a dataset: %s, %r'
% (n, group[n]))
# check datasets are aligned
datasets = [group[n] for n in names]
length = datasets[0].shape[0]
for d in datasets[1:]:
if d.shape[0] != length:
raise ValueError('datasets must be of equal length')
# determine start and stop parameters for load
start = kwargs.pop('start', 0)
stop = kwargs.pop('stop', length)
# check condition
condition = kwargs.pop('condition', None) # type: np.ndarray
condition = asarray_ndim(condition, 1, allow_none=True)
if condition is not None and condition.size != length:
raise ValueError('length of condition does not match length '
'of datasets')
# setup output data
dtype = [(n, d.dtype, d.shape[1:]) for n, d in zip(names, datasets)]
ra = np.empty(length, dtype=dtype)
for n, d in zip(names, datasets):
a = d[start:stop]
if condition is not None:
a = np.compress(condition[start:stop], a, axis=0)
ra[n] = a
return ra
finally:
if h5f is not None:
h5f.close() | python | def recarray_from_hdf5_group(*args, **kwargs):
"""Load a recarray from columns stored as separate datasets with an
HDF5 group.
Either provide an h5py group as a single positional argument,
or provide two positional arguments giving the HDF5 file path and the
group node path within the file.
The following optional parameters may be given.
Parameters
----------
start : int, optional
Index to start loading from.
stop : int, optional
Index to finish loading at.
condition : array_like, bool, optional
A 1-dimensional boolean array of the same length as the columns of the
table to load, indicating a selection of rows to load.
"""
import h5py
h5f = None
if len(args) == 1:
group = args[0]
elif len(args) == 2:
file_path, node_path = args
h5f = h5py.File(file_path, mode='r')
try:
group = h5f[node_path]
except Exception as e:
h5f.close()
raise e
else:
raise ValueError('bad arguments; expected group or (file_path, '
'node_path), found %s' % repr(args))
try:
if not isinstance(group, h5py.Group):
raise ValueError('expected group, found %r' % group)
# determine dataset names to load
available_dataset_names = [n for n in group.keys()
if isinstance(group[n], h5py.Dataset)]
names = kwargs.pop('names', available_dataset_names)
names = [str(n) for n in names] # needed for PY2
for n in names:
if n not in set(group.keys()):
raise ValueError('name not found: %s' % n)
if not isinstance(group[n], h5py.Dataset):
raise ValueError('name does not refer to a dataset: %s, %r'
% (n, group[n]))
# check datasets are aligned
datasets = [group[n] for n in names]
length = datasets[0].shape[0]
for d in datasets[1:]:
if d.shape[0] != length:
raise ValueError('datasets must be of equal length')
# determine start and stop parameters for load
start = kwargs.pop('start', 0)
stop = kwargs.pop('stop', length)
# check condition
condition = kwargs.pop('condition', None) # type: np.ndarray
condition = asarray_ndim(condition, 1, allow_none=True)
if condition is not None and condition.size != length:
raise ValueError('length of condition does not match length '
'of datasets')
# setup output data
dtype = [(n, d.dtype, d.shape[1:]) for n, d in zip(names, datasets)]
ra = np.empty(length, dtype=dtype)
for n, d in zip(names, datasets):
a = d[start:stop]
if condition is not None:
a = np.compress(condition[start:stop], a, axis=0)
ra[n] = a
return ra
finally:
if h5f is not None:
h5f.close() | [
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"==... | Load a recarray from columns stored as separate datasets with an
HDF5 group.
Either provide an h5py group as a single positional argument,
or provide two positional arguments giving the HDF5 file path and the
group node path within the file.
The following optional parameters may be given.
Parameters
----------
start : int, optional
Index to start loading from.
stop : int, optional
Index to finish loading at.
condition : array_like, bool, optional
A 1-dimensional boolean array of the same length as the columns of the
table to load, indicating a selection of rows to load. | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/io/util.py#L55-L146 | train | Load a recarray from columns stored as separate datasets with an HDF5 group. | 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(5897 - 5786) + '\061' + chr(0b110111) + chr(0b110001 + 0o3), 0b1000), nzTpIcepk0o8(chr(0b110 + 0o52) + chr(111) + chr(0b110111) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\063' + chr(0b110100) + '\x30', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1010000 + 0o37) + chr(0b11100 + 0o30) + chr(51), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(50) + '\064' + chr(0b110111), 7665 - 7657), nzTpIcepk0o8(chr(1826 - 1778) + '\157' + chr(49) + chr(2224 - 2175) + '\060', 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110001) + '\061' + chr(2581 - 2530), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b101111 + 0o3) + chr(0b110110) + '\x31', ord("\x08")), nzTpIcepk0o8('\060' + '\157' + '\x33' + chr(531 - 483) + chr(1625 - 1576), ord("\x08")), nzTpIcepk0o8(chr(0b1100 + 0o44) + chr(111) + chr(0b100000 + 0o22) + '\067' + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b11110 + 0o121) + '\062' + '\062' + '\063', ord("\x08")), nzTpIcepk0o8('\060' + chr(9447 - 9336) + chr(0b1110 + 0o44) + chr(0b11101 + 0o30) + chr(1961 - 1907), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\061' + '\067' + chr(0b101101 + 0o10), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + chr(55) + chr(0b110110), 0o10), nzTpIcepk0o8(chr(421 - 373) + chr(0b1101111) + chr(2277 - 2228) + '\x30' + chr(2740 - 2686), 0o10), nzTpIcepk0o8(chr(48) + chr(1222 - 1111) + '\062' + '\065' + '\060', 0o10), nzTpIcepk0o8('\060' + '\x6f' + '\062' + '\060' + '\060', 54462 - 54454), nzTpIcepk0o8('\x30' + '\157' + '\x31' + '\x34' + chr(2135 - 2087), 0b1000), nzTpIcepk0o8(chr(0b100001 + 0o17) + '\157' + chr(965 - 916) + chr(0b110111), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(175 - 121) + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\062' + chr(51) + chr(1091 - 1042), 3170 - 3162), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110001) + chr(0b110001) + '\062', 2134 - 2126), nzTpIcepk0o8('\x30' + chr(791 - 680) + '\061' + chr(0b110001) + '\065', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(1875 - 1824) + chr(0b110000) + chr(1295 - 1240), ord("\x08")), nzTpIcepk0o8(chr(709 - 661) + chr(0b1101111) + '\x33' + chr(54) + chr(2585 - 2531), 3767 - 3759), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b100010 + 0o17) + chr(0b110010) + '\062', 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(55) + '\x37', 0o10), nzTpIcepk0o8(chr(0b100111 + 0o11) + chr(0b1101111) + chr(0b110010) + chr(49) + chr(49), ord("\x08")), nzTpIcepk0o8(chr(0b1111 + 0o41) + '\x6f' + chr(52) + chr(54), ord("\x08")), nzTpIcepk0o8(chr(0b101100 + 0o4) + '\157' + '\x32' + chr(0b110000), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(123 - 74) + chr(1458 - 1409) + chr(2199 - 2147), 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110011) + '\x33' + '\x31', 0o10), nzTpIcepk0o8(chr(584 - 536) + chr(1459 - 1348) + chr(0b11101 + 0o26) + chr(66 - 13) + chr(0b10101 + 0o40), 0b1000), nzTpIcepk0o8('\060' + chr(0b10011 + 0o134) + '\061' + chr(0b10101 + 0o41) + chr(55), 0o10), nzTpIcepk0o8(chr(0b1011 + 0o45) + '\157' + chr(577 - 528) + '\066' + chr(0b1111 + 0o44), 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b11000 + 0o31) + chr(298 - 248) + chr(1332 - 1283), 0o10), nzTpIcepk0o8(chr(0b10011 + 0o35) + '\157' + '\x32' + '\063' + '\x32', ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(2444 - 2390) + chr(52), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(51) + '\065' + chr(55), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110100) + chr(0b1010 + 0o52), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b11101 + 0o23) + '\157' + chr(0b100011 + 0o22) + chr(0b110000), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'R'), '\x64' + '\x65' + chr(0b101001 + 0o72) + chr(0b1111 + 0o140) + '\x64' + '\x65')(chr(820 - 703) + chr(0b11001 + 0o133) + '\x66' + chr(85 - 40) + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def mvjuhqUAhrHC(*eemPYp2vtTSr, **q5n0sHDDTy90):
(RqFza2bfJyrc,) = (zGgTE_CdZfvi(roI3spqORKae(ES5oEprVxulp(b'\x14\x0e\x90Z'), '\x64' + chr(4480 - 4379) + chr(0b1100011) + '\157' + chr(1991 - 1891) + chr(0b1100101))(chr(0b1001010 + 0o53) + '\164' + chr(2179 - 2077) + chr(0b101101) + '\070')),)
uqjdddtgqsHt = None
if ftfygxgFas5X(eemPYp2vtTSr) == nzTpIcepk0o8(chr(48) + chr(111) + '\061', 0o10):
F9lJ8RbIonqb = eemPYp2vtTSr[nzTpIcepk0o8('\060' + chr(0b1101111) + chr(1739 - 1691), 0o10)]
elif ftfygxgFas5X(eemPYp2vtTSr) == nzTpIcepk0o8('\x30' + '\157' + chr(0b11111 + 0o23), 0o10):
(FQgy_W0Nc99x, RDWD_OZuE4Cl) = eemPYp2vtTSr
uqjdddtgqsHt = RqFza2bfJyrc.File(FQgy_W0Nc99x, mode=roI3spqORKae(ES5oEprVxulp(b'\x0e'), '\144' + chr(101) + chr(0b1100011) + '\157' + chr(0b1100100) + chr(0b10000 + 0o125))(chr(4745 - 4628) + '\x74' + chr(0b1100000 + 0o6) + chr(1056 - 1011) + '\x38'))
try:
F9lJ8RbIonqb = uqjdddtgqsHt[RDWD_OZuE4Cl]
except zfo2Sgkz3IVJ as wgf0sgcu_xPL:
roI3spqORKae(uqjdddtgqsHt, roI3spqORKae(ES5oEprVxulp(b'&^\x91\x14\xe4+-\x88\x94\xd9\xab\xc4'), '\144' + chr(5615 - 5514) + '\x63' + '\157' + '\144' + chr(101))(chr(0b1101010 + 0o13) + '\x74' + '\x66' + chr(0b10100 + 0o31) + chr(56)))()
raise wgf0sgcu_xPL
else:
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'\x1eZ\x84\x03\xc6:,\xc4\xac\xd8\xfd\xda\x0e\x05f\xcd\xf8\x10jQ\xed/)\xe7\x91 P\xfcV0#\xab\xcd_\x158\xf6Q\xb0T\x1dO\x88\x0f\x87&$\xd5\xa4\xe2\xe3\xcf\tVo\x84\xa0\x06`G\xf7.m\xe2\x85'), chr(3146 - 3046) + '\x65' + chr(4037 - 3938) + chr(111) + chr(0b1100100) + '\145')('\x75' + chr(0b10010 + 0o142) + chr(938 - 836) + chr(45) + '\070') % VWshwTzZfwvC(eemPYp2vtTSr))
try:
if not suIjIS24Zkqw(F9lJ8RbIonqb, roI3spqORKae(RqFza2bfJyrc, roI3spqORKae(ES5oEprVxulp(b';I\x8fV\xd7'), '\x64' + '\x65' + chr(0b1001001 + 0o32) + '\x6f' + '\x64' + '\145')('\165' + chr(116) + '\x66' + chr(0b100001 + 0o14) + chr(0b111000)))):
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'\x19C\x90F\xc4<.\xd5\xe1\xda\xe1\xc1\x08Nj\x88\xe6\x0fz\\\xfdjh\xb5'), chr(0b111001 + 0o53) + '\x65' + chr(0b1000111 + 0o34) + '\157' + '\144' + chr(0b110010 + 0o63))(chr(0b101011 + 0o112) + chr(0b1110100) + chr(0b1100110) + chr(1876 - 1831) + chr(56)) % F9lJ8RbIonqb)
ArS_gOheLibH = [NoZxuO7wjArS for NoZxuO7wjArS in F9lJ8RbIonqb.keys() if suIjIS24Zkqw(F9lJ8RbIonqb[NoZxuO7wjArS], RqFza2bfJyrc.Dataset)]
TMMrjsiU6eED = q5n0sHDDTy90.uC_Yoybx7J0I(roI3spqORKae(ES5oEprVxulp(b'\x12Z\x8dF\xd4'), '\x64' + '\x65' + '\x63' + chr(0b1001011 + 0o44) + '\x64' + chr(0b1100101))('\x75' + chr(6656 - 6540) + chr(7525 - 7423) + chr(45) + '\070'), ArS_gOheLibH)
TMMrjsiU6eED = [N9zlRy29S1SS(NoZxuO7wjArS) for NoZxuO7wjArS in TMMrjsiU6eED]
for NoZxuO7wjArS in TMMrjsiU6eED:
if NoZxuO7wjArS not in Bvi71nNyvlqO(roI3spqORKae(F9lJ8RbIonqb, roI3spqORKae(ES5oEprVxulp(b'\x17^\x99P'), chr(0b1100100) + chr(3215 - 3114) + chr(0b1011 + 0o130) + chr(111) + chr(7804 - 7704) + '\x65')('\x75' + chr(10080 - 9964) + '\146' + '\x2d' + chr(2175 - 2119)))()):
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'\x12Z\x8dF\x87&$\xc5\xe1\xdb\xfc\xdb\x13Z|\x88\xa5\x13'), '\144' + chr(101) + '\x63' + '\157' + chr(3233 - 3133) + chr(0b101001 + 0o74))(chr(0b1110101) + '\x74' + chr(0b11000 + 0o116) + chr(45) + chr(0b1010 + 0o56)) % NoZxuO7wjArS)
if not suIjIS24Zkqw(F9lJ8RbIonqb[NoZxuO7wjArS], roI3spqORKae(RqFza2bfJyrc, roI3spqORKae(ES5oEprVxulp(b'8Z\x94B\xd4-?'), chr(0b110001 + 0o63) + chr(0b1100101) + chr(5022 - 4923) + chr(111) + '\x64' + '\145')(chr(117) + chr(2532 - 2416) + '\x66' + chr(0b101001 + 0o4) + chr(56)))):
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'\x12Z\x8dF\x87,$\xd4\xb2\x9d\xfd\xc1\t\x1e4\xcd\xe6\x05}\x12\xed%m\xa6\xd66^\xfdGc)\xad\xd7WV"\xb6\x14\xcaV'), '\x64' + chr(5384 - 5283) + chr(7156 - 7057) + chr(0b1001100 + 0o43) + '\x64' + chr(0b1100101))(chr(0b1110101) + chr(0b111110 + 0o66) + chr(0b11000 + 0o116) + '\055' + chr(56)) % (NoZxuO7wjArS, F9lJ8RbIonqb[NoZxuO7wjArS]))
OeaqGM6C910S = [F9lJ8RbIonqb[NoZxuO7wjArS] for NoZxuO7wjArS in TMMrjsiU6eED]
a1RCQZREo3Kd = OeaqGM6C910S[nzTpIcepk0o8(chr(48) + chr(0b100100 + 0o113) + chr(48), 8)].lhbM092AFW8f[nzTpIcepk0o8(chr(1896 - 1848) + chr(111) + chr(1492 - 1444), 8)]
for vPPlOXQgR3SM in OeaqGM6C910S[nzTpIcepk0o8(chr(0b110000) + chr(7104 - 6993) + chr(49), 8):]:
if roI3spqORKae(vPPlOXQgR3SM, roI3spqORKae(ES5oEprVxulp(b'\x10S\x82n\x97qy\xf0\x87\xea\xab\xc8'), chr(0b11011 + 0o111) + chr(0b1100101) + chr(0b10100 + 0o117) + chr(0b1101 + 0o142) + chr(0b110 + 0o136) + '\x65')(chr(2174 - 2057) + chr(116) + '\146' + '\x2d' + chr(0b111000)))[nzTpIcepk0o8('\x30' + '\157' + chr(90 - 42), 8)] != a1RCQZREo3Kd:
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'\x18Z\x94B\xd4-?\xc2\xe1\xd0\xe6\xdd\t\x1e$\xcd\xa0\x0fi\x12\xfc;8\xa6\x9arS\xecHw8\xb1'), chr(0b1100100) + chr(101) + '\143' + chr(7362 - 7251) + chr(100) + chr(0b1100101))('\165' + chr(8547 - 8431) + '\146' + chr(0b101101) + '\070'))
KQbHFTcl_LKy = q5n0sHDDTy90.uC_Yoybx7J0I(roI3spqORKae(ES5oEprVxulp(b'\x0fO\x81Q\xd3'), '\x64' + chr(0b111010 + 0o53) + chr(0b1100011) + '\x6f' + chr(100) + chr(537 - 436))(chr(117) + '\164' + chr(0b1100000 + 0o6) + '\055' + '\x38'), nzTpIcepk0o8(chr(712 - 664) + '\157' + chr(0b110000), 8))
dYJbBiYO_nGE = q5n0sHDDTy90.uC_Yoybx7J0I(roI3spqORKae(ES5oEprVxulp(b'\x0fO\x8fS'), chr(100) + '\145' + '\143' + chr(0b1101111) + '\x64' + chr(442 - 341))('\165' + chr(11023 - 10907) + '\x66' + '\x2d' + chr(0b1010 + 0o56)), a1RCQZREo3Kd)
ihXi_REa_8XA = q5n0sHDDTy90.uC_Yoybx7J0I(roI3spqORKae(ES5oEprVxulp(b'\x1fT\x8eG\xce<"\xde\xaf'), chr(0b1100100) + chr(8413 - 8312) + chr(0b1100011) + chr(111) + '\x64' + '\145')(chr(5712 - 5595) + chr(0b1110100) + '\146' + chr(45) + chr(56)), None)
ihXi_REa_8XA = EVVKPun88TqM(ihXi_REa_8XA, nzTpIcepk0o8(chr(48) + '\157' + chr(0b110001), 8), allow_none=nzTpIcepk0o8(chr(1108 - 1060) + '\157' + chr(0b110001), 8))
if ihXi_REa_8XA is not None and roI3spqORKae(ihXi_REa_8XA, roI3spqORKae(ES5oEprVxulp(b'\x19\n\xa8Q\xed)\x1a\xf9\x80\xfe\xfd\xc2'), '\144' + '\145' + chr(0b1010111 + 0o14) + '\157' + '\x64' + chr(0b1100101))(chr(0b101000 + 0o115) + '\164' + chr(0b11110 + 0o110) + chr(158 - 113) + '\070')) != a1RCQZREo3Kd:
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'\x10^\x8eD\xd3 k\xde\xa7\x9d\xf0\xc1\x13Z/\xdc\xe9\x0fa\x12\xfd%(\xb4\xd6<P\xfd\x06}-\xad\x8e\x1fS=\xffZ\x88P\x14\x1b\x8fE\x87,*\xc5\xa0\xce\xf6\xda\x0e'), chr(0b1100010 + 0o2) + chr(6808 - 6707) + '\x63' + chr(111) + '\x64' + chr(101))(chr(11694 - 11577) + '\164' + '\146' + chr(207 - 162) + chr(56)))
RcX9bbuOzh5L = [(NoZxuO7wjArS, vPPlOXQgR3SM.RcX9bbuOzh5L, vPPlOXQgR3SM.lhbM092AFW8f[nzTpIcepk0o8('\x30' + chr(0b1100010 + 0o15) + chr(49), 8):]) for (NoZxuO7wjArS, vPPlOXQgR3SM) in TxMFWa_Xzviv(TMMrjsiU6eED, OeaqGM6C910S)]
vGclg_aQYHuN = nDF4gVNx0u9Q.EEl0Pry8vzTp(a1RCQZREo3Kd, dtype=RcX9bbuOzh5L)
for (NoZxuO7wjArS, vPPlOXQgR3SM) in TxMFWa_Xzviv(TMMrjsiU6eED, OeaqGM6C910S):
AQ9ceR9AaoT1 = vPPlOXQgR3SM[KQbHFTcl_LKy:dYJbBiYO_nGE]
if ihXi_REa_8XA is not None:
AQ9ceR9AaoT1 = nDF4gVNx0u9Q.compress(ihXi_REa_8XA[KQbHFTcl_LKy:dYJbBiYO_nGE], AQ9ceR9AaoT1, axis=nzTpIcepk0o8(chr(2042 - 1994) + chr(7867 - 7756) + chr(0b110000), 8))
vGclg_aQYHuN[NoZxuO7wjArS] = AQ9ceR9AaoT1
return vGclg_aQYHuN
finally:
if uqjdddtgqsHt is not None:
roI3spqORKae(uqjdddtgqsHt, roI3spqORKae(ES5oEprVxulp(b'&^\x91\x14\xe4+-\x88\x94\xd9\xab\xc4'), chr(3690 - 3590) + chr(7316 - 7215) + chr(0b1100011) + '\157' + '\x64' + chr(101))('\165' + '\x74' + chr(0b1100110) + chr(0b101101) + chr(56)))() |
cggh/scikit-allel | allel/io/util.py | recarray_to_hdf5_group | def recarray_to_hdf5_group(ra, parent, name, **kwargs):
"""Write each column in a recarray to a dataset in an HDF5 group.
Parameters
----------
ra : recarray
Numpy recarray to store.
parent : string or h5py group
Parent HDF5 file or group. If a string, will be treated as HDF5 file
name.
name : string
Name or path of group to write data into.
kwargs : keyword arguments
Passed through to h5py require_dataset() function.
Returns
-------
h5g : h5py group
"""
import h5py
h5f = None
if isinstance(parent, str):
h5f = h5py.File(parent, mode='a')
parent = h5f
try:
h5g = parent.require_group(name)
for n in ra.dtype.names:
array_to_hdf5(ra[n], h5g, n, **kwargs)
return h5g
finally:
if h5f is not None:
h5f.close() | python | def recarray_to_hdf5_group(ra, parent, name, **kwargs):
"""Write each column in a recarray to a dataset in an HDF5 group.
Parameters
----------
ra : recarray
Numpy recarray to store.
parent : string or h5py group
Parent HDF5 file or group. If a string, will be treated as HDF5 file
name.
name : string
Name or path of group to write data into.
kwargs : keyword arguments
Passed through to h5py require_dataset() function.
Returns
-------
h5g : h5py group
"""
import h5py
h5f = None
if isinstance(parent, str):
h5f = h5py.File(parent, mode='a')
parent = h5f
try:
h5g = parent.require_group(name)
for n in ra.dtype.names:
array_to_hdf5(ra[n], h5g, n, **kwargs)
return h5g
finally:
if h5f is not None:
h5f.close() | [
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Numpy recarray to store.
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Parent HDF5 file or group. If a string, will be treated as HDF5 file
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name : string
Name or path of group to write data into.
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Passed through to h5py require_dataset() function.
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/io/util.py#L149-L188 | train | Write each column in a recarray to an HDF5 group. | 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' + '\x33' + '\x30', 65214 - 65206), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b11000 + 0o32) + chr(0b110001) + chr(0b110110), 52072 - 52064), nzTpIcepk0o8('\x30' + chr(111) + chr(0b101000 + 0o12) + chr(0b110100) + chr(48), 0o10), nzTpIcepk0o8(chr(2023 - 1975) + '\x6f' + chr(0b10111 + 0o32) + '\062' + '\x33', 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(1446 - 1392) + '\x31', ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(0b100111 + 0o13) + chr(49) + chr(0b1111 + 0o44), ord("\x08")), nzTpIcepk0o8(chr(0b1000 + 0o50) + '\157' + chr(51) + chr(0b111 + 0o54) + chr(1175 - 1127), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(49) + '\x37' + '\x37', 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(1453 - 1404) + chr(0b100000 + 0o26) + chr(55), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(0b1111 + 0o43) + chr(1004 - 951) + chr(0b11001 + 0o30), 0b1000), nzTpIcepk0o8(chr(48) + chr(1503 - 1392) + chr(51) + chr(0b110001) + chr(0b110 + 0o52), 28912 - 28904), nzTpIcepk0o8(chr(0b100011 + 0o15) + chr(111) + chr(0b101011 + 0o7) + chr(0b110111) + chr(52), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + '\x34' + '\x37', ord("\x08")), nzTpIcepk0o8(chr(0b1010 + 0o46) + chr(111) + chr(50) + chr(649 - 594), 0b1000), nzTpIcepk0o8(chr(83 - 35) + chr(9342 - 9231) + '\x34' + '\x33', 0b1000), nzTpIcepk0o8(chr(1444 - 1396) + chr(0b1101111) + '\061' + chr(0b110110) + chr(51), 0o10), nzTpIcepk0o8('\060' + chr(0b1000001 + 0o56) + '\x32' + chr(1910 - 1856) + chr(0b110100), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + '\062' + '\x35' + chr(0b10 + 0o60), 41873 - 41865), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b101011 + 0o7) + chr(0b101010 + 0o10) + '\x32', 22702 - 22694), nzTpIcepk0o8('\060' + chr(0b1101111) + '\061' + '\066' + chr(0b101000 + 0o17), 8), nzTpIcepk0o8(chr(0b110000) + chr(0b10011 + 0o134) + '\063' + chr(52) + chr(1511 - 1460), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x33' + chr(0b1011 + 0o47) + chr(426 - 377), ord("\x08")), nzTpIcepk0o8(chr(0b100 + 0o54) + chr(12072 - 11961) + '\062' + '\x31' + chr(48), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + '\x32' + chr(0b10001 + 0o44) + '\x36', 53111 - 53103), nzTpIcepk0o8(chr(0b101111 + 0o1) + chr(0b1101111) + '\063' + chr(0b10101 + 0o42) + chr(0b100001 + 0o24), 32993 - 32985), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\062' + chr(0b110010) + chr(456 - 405), 41267 - 41259), nzTpIcepk0o8(chr(1059 - 1011) + '\x6f' + chr(0b110011 + 0o1) + chr(0b100001 + 0o22), 8), nzTpIcepk0o8(chr(0b1001 + 0o47) + '\157' + chr(49) + chr(48) + chr(323 - 269), 17115 - 17107), nzTpIcepk0o8(chr(1759 - 1711) + chr(0b1000011 + 0o54) + '\062' + chr(0b110111) + chr(52), 8), nzTpIcepk0o8(chr(839 - 791) + chr(8026 - 7915) + chr(229 - 179) + chr(0b110100), 0o10), nzTpIcepk0o8(chr(0b100101 + 0o13) + chr(111) + '\x32' + chr(0b110100) + chr(54), 0o10), nzTpIcepk0o8('\x30' + chr(111) + '\063' + chr(48) + chr(1359 - 1310), 0b1000), nzTpIcepk0o8(chr(1548 - 1500) + '\157' + chr(49) + chr(0b111 + 0o54) + chr(0b110010 + 0o2), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1010101 + 0o32) + '\062' + chr(709 - 656) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(0b100110 + 0o12) + chr(0b1101111) + chr(0b11000 + 0o33) + chr(1681 - 1631), 0b1000), nzTpIcepk0o8(chr(48) + chr(10912 - 10801) + chr(0b110011) + chr(0b110111), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101110 + 0o1) + '\062' + '\x33' + chr(0b10101 + 0o41), 3071 - 3063), nzTpIcepk0o8(chr(0b100 + 0o54) + '\157' + '\065' + chr(1339 - 1284), 12118 - 12110), nzTpIcepk0o8(chr(434 - 386) + '\157' + chr(1299 - 1249) + chr(50) + '\066', 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110011) + chr(311 - 259) + chr(49), 42819 - 42811)][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + '\157' + '\x35' + chr(0b10101 + 0o33), 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'6'), '\x64' + '\145' + '\x63' + chr(8162 - 8051) + chr(6800 - 6700) + '\145')('\x75' + '\x74' + chr(0b1100110) + '\x2d' + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def twAGqmjW8gOQ(vGclg_aQYHuN, aY0lxtg5akD2, SLVB2BPA_mIe, **q5n0sHDDTy90):
(RqFza2bfJyrc,) = (zGgTE_CdZfvi(roI3spqORKae(ES5oEprVxulp(b'p\xbb\xd0*'), chr(0b111100 + 0o50) + '\x65' + chr(0b101 + 0o136) + '\x6f' + chr(100) + '\x65')(chr(117) + chr(116) + chr(102) + chr(45) + '\x38')),)
uqjdddtgqsHt = None
if suIjIS24Zkqw(aY0lxtg5akD2, N9zlRy29S1SS):
uqjdddtgqsHt = RqFza2bfJyrc.File(aY0lxtg5akD2, mode=roI3spqORKae(ES5oEprVxulp(b'y'), chr(0b1100100) + chr(0b1100101) + chr(99) + chr(0b1101111) + chr(0b1100100) + chr(0b1100101))(chr(0b1110101) + chr(0b1110100) + '\x66' + chr(0b101101) + chr(0b11100 + 0o34)))
aY0lxtg5akD2 = uqjdddtgqsHt
try:
klut_3MNLz4d = aY0lxtg5akD2.require_group(SLVB2BPA_mIe)
for NoZxuO7wjArS in roI3spqORKae(vGclg_aQYHuN.dtype, roI3spqORKae(ES5oEprVxulp(b'L\xc3\xed![\xf8\xb1*A\xcc\x8d\xf8'), '\144' + '\x65' + chr(9542 - 9443) + chr(111) + chr(5270 - 5170) + '\x65')(chr(11118 - 11001) + chr(116) + '\x66' + chr(0b101101) + chr(0b111000))):
SPJXnwIsQehF(vGclg_aQYHuN[NoZxuO7wjArS], klut_3MNLz4d, NoZxuO7wjArS, **q5n0sHDDTy90)
return klut_3MNLz4d
finally:
if uqjdddtgqsHt is not None:
roI3spqORKae(uqjdddtgqsHt, roI3spqORKae(ES5oEprVxulp(b'B\xeb\xd1dr\xe8\xbeF"\xcd\xf0\xd6'), chr(0b111011 + 0o51) + '\x65' + '\143' + chr(0b1010 + 0o145) + '\x64' + chr(4596 - 4495))('\165' + chr(0b1110100) + '\146' + '\x2d' + '\070'))() |
cggh/scikit-allel | allel/model/ndarray.py | subset | def subset(data, sel0, sel1):
"""Apply selections on first and second axes."""
# check inputs
data = np.asarray(data)
if data.ndim < 2:
raise ValueError('data must have 2 or more dimensions')
sel0 = asarray_ndim(sel0, 1, allow_none=True)
sel1 = asarray_ndim(sel1, 1, allow_none=True)
# ensure indices
if sel0 is not None and sel0.dtype.kind == 'b':
sel0, = np.nonzero(sel0)
if sel1 is not None and sel1.dtype.kind == 'b':
sel1, = np.nonzero(sel1)
# ensure leading dimension indices can be broadcast correctly
if sel0 is not None and sel1 is not None:
sel0 = sel0[:, np.newaxis]
# deal with None arguments
if sel0 is None:
sel0 = _total_slice
if sel1 is None:
sel1 = _total_slice
return data[sel0, sel1] | python | def subset(data, sel0, sel1):
"""Apply selections on first and second axes."""
# check inputs
data = np.asarray(data)
if data.ndim < 2:
raise ValueError('data must have 2 or more dimensions')
sel0 = asarray_ndim(sel0, 1, allow_none=True)
sel1 = asarray_ndim(sel1, 1, allow_none=True)
# ensure indices
if sel0 is not None and sel0.dtype.kind == 'b':
sel0, = np.nonzero(sel0)
if sel1 is not None and sel1.dtype.kind == 'b':
sel1, = np.nonzero(sel1)
# ensure leading dimension indices can be broadcast correctly
if sel0 is not None and sel1 is not None:
sel0 = sel0[:, np.newaxis]
# deal with None arguments
if sel0 is None:
sel0 = _total_slice
if sel1 is None:
sel1 = _total_slice
return data[sel0, sel1] | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/model/ndarray.py#L43-L69 | train | Apply selections on first and second axes. | 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(10063 - 9952) + chr(55) + '\062', ord("\x08")), nzTpIcepk0o8(chr(0b11010 + 0o26) + '\x6f' + chr(0b10000 + 0o42) + chr(344 - 296) + '\x34', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1010101 + 0o32) + chr(0b101 + 0o56) + chr(748 - 693) + '\060', ord("\x08")), nzTpIcepk0o8(chr(1971 - 1923) + '\x6f' + '\x33' + chr(2139 - 2091) + chr(0b11110 + 0o26), 0b1000), nzTpIcepk0o8(chr(48) + chr(6444 - 6333) + chr(49) + chr(0b11011 + 0o27) + chr(0b1001 + 0o55), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1111 + 0o140) + chr(49) + chr(0b110101) + chr(569 - 516), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + '\x32' + chr(2764 - 2709) + chr(212 - 161), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b10 + 0o155) + chr(1818 - 1768) + chr(0b0 + 0o67) + '\x33', 8), nzTpIcepk0o8(chr(48) + chr(1028 - 917) + '\x32' + '\x32' + chr(184 - 132), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(1442 - 1331) + '\x33' + chr(998 - 943) + '\065', 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(49) + chr(0b110110) + '\x30', 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(51) + '\x36' + chr(0b110010), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110100) + chr(0b110111), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(900 - 849) + chr(0b110101 + 0o0) + chr(0b110110), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b100110 + 0o14) + chr(191 - 137) + '\061', 51074 - 51066), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110010) + chr(0b100011 + 0o22) + chr(518 - 464), 21179 - 21171), nzTpIcepk0o8('\060' + chr(0b10101 + 0o132) + '\065' + chr(0b110110), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(1719 - 1666) + chr(0b110000 + 0o3), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x33' + chr(0b110001) + chr(2019 - 1969), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(0b110011) + '\062' + '\065', 17060 - 17052), nzTpIcepk0o8(chr(0b11001 + 0o27) + '\x6f' + chr(0b110011) + chr(0b101100 + 0o6) + '\x36', 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(210 - 155) + chr(55), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(5694 - 5583) + '\x35' + chr(51), 8), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b10100 + 0o36) + chr(0b110 + 0o54) + chr(0b101010 + 0o13), 60923 - 60915), nzTpIcepk0o8(chr(1772 - 1724) + chr(111) + chr(50) + chr(0b11110 + 0o26) + chr(79 - 31), 32682 - 32674), nzTpIcepk0o8(chr(48) + chr(0b1011111 + 0o20) + chr(0b100001 + 0o22) + chr(0b110001) + chr(54), 22583 - 22575), nzTpIcepk0o8(chr(48) + '\x6f' + chr(49) + '\x30' + chr(0b11 + 0o61), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b111001 + 0o66) + chr(1583 - 1533) + chr(50) + chr(0b110000), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(629 - 578) + '\x36' + '\062', 8), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x34', 0o10), nzTpIcepk0o8('\x30' + chr(10354 - 10243) + '\061' + '\060' + '\062', ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + '\063' + chr(53) + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(54) + '\067', 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(1696 - 1647) + chr(49) + '\x31', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(50) + '\066' + '\x36', ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(606 - 556) + '\066', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1000010 + 0o55) + chr(1843 - 1792) + chr(54) + '\x33', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b110 + 0o151) + chr(2292 - 2241) + chr(888 - 835) + chr(50), ord("\x08")), nzTpIcepk0o8(chr(440 - 392) + '\x6f' + chr(0b11100 + 0o26) + '\061' + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + chr(51) + chr(0b110001) + chr(55), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + chr(9572 - 9461) + chr(0b100111 + 0o16) + chr(0b1101 + 0o43), 27046 - 27038)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x14'), '\144' + chr(0b1100010 + 0o3) + chr(99) + chr(111) + '\x64' + chr(1151 - 1050))(chr(0b1110101) + chr(116) + '\x66' + '\055' + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def kw37P8hgNdNY(FfKOThdpoDTb, xIIxKLhLgM7X, OjBOFYa5buna):
FfKOThdpoDTb = nDF4gVNx0u9Q.asarray(FfKOThdpoDTb)
if roI3spqORKae(FfKOThdpoDTb, roI3spqORKae(ES5oEprVxulp(b"p\xcd\xa0\x88\x1e]\x89\xf4\xd7\xcd'\xb0"), chr(0b1100100) + chr(0b1011000 + 0o15) + chr(0b1100011) + '\157' + chr(0b1100100) + '\x65')(chr(117) + chr(0b1110100) + '\x66' + '\055' + chr(0b11111 + 0o31))) < nzTpIcepk0o8('\060' + '\157' + '\062', 0o10):
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b"^\xe5\x8c\xa5v\x00\xce\xc8\xe0\xdd\x18\x93Q\x8b\x91\x9c\x0eD\xb8\xf5\xbbPY\xf0\x80\xaa-\xfd\x97j1\x84X'\xc5"), chr(4200 - 4100) + '\145' + chr(99) + chr(3502 - 3391) + chr(0b1100100) + chr(0b1000001 + 0o44))('\165' + '\164' + '\x66' + chr(45) + '\x38'))
xIIxKLhLgM7X = EVVKPun88TqM(xIIxKLhLgM7X, nzTpIcepk0o8(chr(291 - 243) + '\x6f' + chr(0b110001), 0o10), allow_none=nzTpIcepk0o8(chr(570 - 522) + '\157' + chr(0b10100 + 0o35), 8))
OjBOFYa5buna = EVVKPun88TqM(OjBOFYa5buna, nzTpIcepk0o8(chr(48) + '\157' + '\061', 8), allow_none=nzTpIcepk0o8(chr(48) + '\x6f' + '\x31', 8))
if xIIxKLhLgM7X is not None and roI3spqORKae(xIIxKLhLgM7X.dtype, roI3spqORKae(ES5oEprVxulp(b'o\xe5\x82\x82b_\x8d\xd9\xe1\xbf\x15\xa1'), '\x64' + chr(101) + chr(0b1100011) + chr(111) + chr(0b1100100) + chr(101))(chr(117) + chr(0b1110100) + chr(0b1100110) + chr(1570 - 1525) + chr(0b111000))) == roI3spqORKae(ES5oEprVxulp(b'X'), chr(5333 - 5233) + chr(8405 - 8304) + chr(0b101001 + 0o72) + chr(111) + '\144' + chr(10152 - 10051))(chr(117) + chr(1290 - 1174) + chr(102) + chr(493 - 448) + chr(56)):
(xIIxKLhLgM7X,) = nDF4gVNx0u9Q.B3vb9auQy6eX(xIIxKLhLgM7X)
if OjBOFYa5buna is not None and roI3spqORKae(OjBOFYa5buna.dtype, roI3spqORKae(ES5oEprVxulp(b'o\xe5\x82\x82b_\x8d\xd9\xe1\xbf\x15\xa1'), chr(0b1100100) + '\x65' + chr(0b100111 + 0o74) + chr(0b1101111) + '\144' + chr(101))(chr(117) + '\x74' + chr(0b1100110) + chr(500 - 455) + chr(0b110100 + 0o4))) == roI3spqORKae(ES5oEprVxulp(b'X'), '\144' + chr(0b1000000 + 0o45) + chr(99) + chr(0b1001010 + 0o45) + '\x64' + '\145')('\165' + chr(0b1110100) + chr(102) + chr(0b1101 + 0o40) + chr(56)):
(OjBOFYa5buna,) = nDF4gVNx0u9Q.B3vb9auQy6eX(OjBOFYa5buna)
if xIIxKLhLgM7X is not None and OjBOFYa5buna is not None:
xIIxKLhLgM7X = xIIxKLhLgM7X[:, nDF4gVNx0u9Q.newaxis]
if xIIxKLhLgM7X is None:
xIIxKLhLgM7X = yWddyZgrrkTx
if OjBOFYa5buna is None:
OjBOFYa5buna = yWddyZgrrkTx
return FfKOThdpoDTb[xIIxKLhLgM7X, OjBOFYa5buna] |
cggh/scikit-allel | allel/model/ndarray.py | NumpyRecArrayWrapper.eval | def eval(self, expression, vm='python'):
"""Evaluate an expression against the table columns.
Parameters
----------
expression : string
Expression to evaluate.
vm : {'numexpr', 'python'}
Virtual machine to use.
Returns
-------
result : ndarray
"""
if vm == 'numexpr':
import numexpr as ne
return ne.evaluate(expression, local_dict=self)
else:
if PY2:
# locals must be a mapping
m = {k: self[k] for k in self.dtype.names}
else:
m = self
return eval(expression, dict(), m) | python | def eval(self, expression, vm='python'):
"""Evaluate an expression against the table columns.
Parameters
----------
expression : string
Expression to evaluate.
vm : {'numexpr', 'python'}
Virtual machine to use.
Returns
-------
result : ndarray
"""
if vm == 'numexpr':
import numexpr as ne
return ne.evaluate(expression, local_dict=self)
else:
if PY2:
# locals must be a mapping
m = {k: self[k] for k in self.dtype.names}
else:
m = self
return eval(expression, dict(), m) | [
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expression : string
Expression to evaluate.
vm : {'numexpr', 'python'}
Virtual machine to use.
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result : ndarray | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/model/ndarray.py#L129-L154 | train | Evaluate an expression against the table columns. | 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(0b110011 + 0o0) + chr(53) + '\x34', 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(0b1111 + 0o44) + chr(0b10011 + 0o42) + chr(0b11 + 0o61), 8), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x33' + chr(1642 - 1588) + '\066', 0b1000), nzTpIcepk0o8(chr(1012 - 964) + '\157' + chr(2209 - 2155) + chr(1999 - 1945), 0o10), nzTpIcepk0o8(chr(0b100101 + 0o13) + '\x6f' + chr(750 - 699) + chr(52) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(1100 - 1051) + chr(0b1111 + 0o47) + chr(53), 0b1000), nzTpIcepk0o8(chr(2227 - 2179) + chr(0b1000001 + 0o56) + chr(50) + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(0b11110 + 0o22) + chr(0b1100001 + 0o16) + '\061' + '\066' + chr(0b110101), 8), nzTpIcepk0o8(chr(48) + chr(0b1010101 + 0o32) + chr(349 - 300) + chr(1577 - 1526) + '\061', 0o10), nzTpIcepk0o8(chr(48) + chr(0b110 + 0o151) + chr(0b110001) + '\065' + '\x37', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b100111 + 0o110) + chr(0b11111 + 0o23) + '\065' + chr(0b110010), 0o10), nzTpIcepk0o8(chr(889 - 841) + chr(0b10011 + 0o134) + chr(52) + chr(0b101001 + 0o13), 0o10), nzTpIcepk0o8(chr(0b10100 + 0o34) + '\157' + '\061' + chr(50) + chr(50), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x32' + chr(0b11000 + 0o30) + chr(0b11 + 0o63), ord("\x08")), nzTpIcepk0o8(chr(322 - 274) + chr(0b1101111) + chr(0b10010 + 0o41) + '\x33' + '\x34', 0o10), nzTpIcepk0o8('\060' + chr(3597 - 3486) + chr(0b110000 + 0o3) + chr(50) + '\x33', 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b100001 + 0o20) + '\x36' + chr(0b110111), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(0b10101 + 0o34) + chr(0b110010) + chr(54), 8889 - 8881), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x31' + chr(0b1110 + 0o51) + chr(2704 - 2652), 34020 - 34012), nzTpIcepk0o8(chr(48) + '\x6f' + '\063' + chr(310 - 256) + chr(0b11101 + 0o27), 0o10), nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(2372 - 2261) + chr(0b11 + 0o57) + '\x30' + '\067', 0b1000), nzTpIcepk0o8(chr(0b100011 + 0o15) + '\x6f' + '\066' + '\x30', 0o10), nzTpIcepk0o8('\060' + '\157' + chr(1672 - 1623) + '\x31' + chr(55), 0o10), nzTpIcepk0o8(chr(0b11111 + 0o21) + chr(111) + chr(1784 - 1733) + chr(1028 - 976), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1010010 + 0o35) + '\062' + chr(798 - 749) + chr(0b10 + 0o61), 0o10), nzTpIcepk0o8(chr(0b100011 + 0o15) + chr(0b1101111) + '\062' + chr(0b101100 + 0o13) + chr(819 - 766), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x31' + chr(2748 - 2693) + chr(54), 35484 - 35476), nzTpIcepk0o8(chr(988 - 940) + chr(11043 - 10932) + '\x34' + '\065', 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(750 - 700) + chr(0b110000) + chr(113 - 65), 61636 - 61628), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(51) + chr(0b1011 + 0o45) + '\x36', 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(50) + chr(0b10001 + 0o44) + chr(0b101 + 0o55), 8), nzTpIcepk0o8(chr(0b111 + 0o51) + chr(9397 - 9286) + chr(50) + '\x34' + '\x37', 48052 - 48044), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(50) + '\061' + chr(0b10010 + 0o41), 8), nzTpIcepk0o8(chr(1425 - 1377) + chr(11341 - 11230) + chr(799 - 750) + chr(0b110011) + '\x37', 51834 - 51826), nzTpIcepk0o8('\x30' + chr(111) + '\x31' + '\062' + chr(0b110001), 0o10), nzTpIcepk0o8(chr(0b110 + 0o52) + chr(0b101000 + 0o107) + chr(49) + chr(53), 0o10), nzTpIcepk0o8(chr(0b100010 + 0o16) + chr(4496 - 4385) + chr(55), 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110011) + chr(2284 - 2235) + '\060', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(1774 - 1725) + chr(0b100000 + 0o23), ord("\x08")), nzTpIcepk0o8(chr(2059 - 2011) + chr(0b1001101 + 0o42) + chr(0b10011 + 0o36) + chr(0b110100) + chr(48), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + chr(1634 - 1523) + chr(0b110101) + '\060', 45805 - 45797)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xc2'), chr(0b1100100) + chr(0b111110 + 0o47) + '\143' + chr(0b1000 + 0o147) + chr(100) + chr(101))(chr(7777 - 7660) + '\164' + chr(0b1100110) + chr(45) + '\070') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def Z5xOfqIptFuc(hXMPsSrOQzbh, Jni_E12Y8D3Y, jfR8qmy1vJ8o=roI3spqORKae(ES5oEprVxulp(b'\x9c\x95\x82^\x8b\x1b'), chr(3625 - 3525) + '\145' + chr(9438 - 9339) + chr(0b1101111) + chr(159 - 59) + '\x65')(chr(7914 - 7797) + chr(0b1110100) + chr(0b111 + 0o137) + '\055' + chr(333 - 277))):
if jfR8qmy1vJ8o == roI3spqORKae(ES5oEprVxulp(b'\x82\x99\x9bS\x9c\x05g'), chr(100) + chr(101) + '\x63' + chr(9661 - 9550) + chr(2405 - 2305) + chr(101))('\165' + chr(0b1101111 + 0o5) + chr(102) + chr(0b101101) + '\x38'):
(tYLZOe66Tw0a,) = (zGgTE_CdZfvi(roI3spqORKae(ES5oEprVxulp(b'\x82\x99\x9bS\x9c\x05g'), chr(8657 - 8557) + chr(0b110100 + 0o61) + chr(0b11110 + 0o105) + chr(0b1101111) + chr(100) + chr(101))('\165' + chr(4027 - 3911) + chr(0b1100110) + chr(45) + '\070')),)
return roI3spqORKae(tYLZOe66Tw0a, roI3spqORKae(ES5oEprVxulp(b'\xbf\xba\xbdX\x81\x17O 1\x1f\xdbH'), chr(1620 - 1520) + chr(0b1100101) + chr(0b1011110 + 0o5) + chr(111) + '\x64' + chr(0b1010 + 0o133))('\x75' + chr(0b11100 + 0o130) + chr(0b100111 + 0o77) + chr(0b101101) + '\070'))(Jni_E12Y8D3Y, local_dict=hXMPsSrOQzbh)
else:
if rd1Zt5ggQ4Ye:
tF75nqoNENFL = {B6UAF1zReOyJ: hXMPsSrOQzbh[B6UAF1zReOyJ] for B6UAF1zReOyJ in hXMPsSrOQzbh.dtype.TMMrjsiU6eED}
else:
tF75nqoNENFL = hXMPsSrOQzbh
return Z5xOfqIptFuc(Jni_E12Y8D3Y, znjnJWK64FDT(), tF75nqoNENFL) |
cggh/scikit-allel | allel/model/ndarray.py | NumpyRecArrayWrapper.query | def query(self, expression, vm='python'):
"""Evaluate expression and then use it to extract rows from the table.
Parameters
----------
expression : string
Expression to evaluate.
vm : {'numexpr', 'python'}
Virtual machine to use.
Returns
-------
result : structured array
"""
condition = self.eval(expression, vm=vm)
return self.compress(condition) | python | def query(self, expression, vm='python'):
"""Evaluate expression and then use it to extract rows from the table.
Parameters
----------
expression : string
Expression to evaluate.
vm : {'numexpr', 'python'}
Virtual machine to use.
Returns
-------
result : structured array
"""
condition = self.eval(expression, vm=vm)
return self.compress(condition) | [
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Parameters
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expression : string
Expression to evaluate.
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Virtual machine to use.
Returns
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result : structured array | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/model/ndarray.py#L156-L173 | train | Evaluate expression and then use it to extract rows from the 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('\x30' + chr(1540 - 1429) + '\063', 24232 - 24224), nzTpIcepk0o8(chr(0b100010 + 0o16) + '\x6f' + chr(55), ord("\x08")), nzTpIcepk0o8('\060' + chr(5785 - 5674) + '\061' + '\x36' + chr(0b100011 + 0o20), 0o10), nzTpIcepk0o8(chr(0b100110 + 0o12) + '\x6f' + '\063' + '\066' + chr(53), 0b1000), nzTpIcepk0o8(chr(0b11001 + 0o27) + chr(111) + '\063' + '\x32' + chr(2204 - 2154), 0b1000), nzTpIcepk0o8(chr(967 - 919) + chr(111) + chr(0b110010) + '\063' + chr(2030 - 1981), ord("\x08")), nzTpIcepk0o8(chr(0b10011 + 0o35) + '\x6f' + chr(0b1100 + 0o45) + '\067' + '\067', 0b1000), nzTpIcepk0o8(chr(858 - 810) + chr(0b1101111) + chr(50) + chr(0b1110 + 0o43) + chr(846 - 797), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(10518 - 10407) + '\062' + '\060', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x31' + chr(50) + chr(0b110100), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(49) + chr(0b110011) + chr(0b110100), 47538 - 47530), nzTpIcepk0o8('\060' + '\157' + '\062' + chr(53) + chr(2207 - 2157), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(688 - 639) + chr(52), ord("\x08")), nzTpIcepk0o8(chr(2073 - 2025) + chr(0b1101111) + chr(0b10100 + 0o35) + chr(0b110101) + chr(0b110110), 0b1000), nzTpIcepk0o8(chr(0b11001 + 0o27) + '\x6f' + chr(751 - 700) + chr(2319 - 2269) + chr(0b110001), 8672 - 8664), nzTpIcepk0o8('\060' + '\157' + chr(0b110010) + chr(48) + chr(0b110000), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + chr(51) + '\062' + chr(0b1000 + 0o56), ord("\x08")), nzTpIcepk0o8(chr(1515 - 1467) + '\x6f' + chr(0b110011) + chr(2135 - 2082) + chr(1815 - 1761), 38052 - 38044), nzTpIcepk0o8('\060' + '\x6f' + '\066' + '\065', 0b1000), nzTpIcepk0o8(chr(48) + chr(3360 - 3249) + chr(49) + chr(0b110100) + '\062', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b11011 + 0o26) + '\x35' + chr(48), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\063' + chr(1677 - 1627) + chr(50), 8), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(774 - 725) + chr(0b0 + 0o63) + chr(0b101101 + 0o5), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(51) + chr(0b110100) + '\066', 18307 - 18299), nzTpIcepk0o8(chr(675 - 627) + '\x6f' + '\063' + chr(0b101001 + 0o12) + chr(50), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\061' + '\063' + chr(0b11010 + 0o32), 8), nzTpIcepk0o8('\060' + '\x6f' + chr(0b10010 + 0o41) + chr(50) + '\x37', 0o10), nzTpIcepk0o8('\060' + '\157' + chr(51) + chr(580 - 532) + chr(201 - 151), 20308 - 20300), nzTpIcepk0o8('\x30' + chr(0b1001011 + 0o44) + chr(0b110011) + chr(0b110110) + '\065', 8), nzTpIcepk0o8(chr(557 - 509) + chr(0b1101111) + chr(1153 - 1103) + chr(0b110010) + '\x36', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b101011 + 0o6) + '\066' + chr(0b100101 + 0o21), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b100110 + 0o111) + chr(0b110010) + chr(649 - 601) + '\063', 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(49) + '\x34' + chr(49), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\061' + '\x30' + chr(55), 0b1000), nzTpIcepk0o8('\060' + chr(4534 - 4423) + chr(49) + '\060', 0b1000), nzTpIcepk0o8(chr(2091 - 2043) + chr(0b1101111 + 0o0) + chr(0b110011) + chr(52) + '\060', 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110010) + chr(0b110111) + '\x35', 27768 - 27760), nzTpIcepk0o8(chr(2150 - 2102) + '\x6f' + chr(55) + chr(0b110100), 0o10), nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(0b1101111) + chr(0b110010) + chr(51) + chr(0b11111 + 0o25), 59338 - 59330), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(49) + chr(0b110001) + chr(52), 10181 - 10173)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110101) + '\060', 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'-'), '\x64' + chr(0b1100101) + '\143' + chr(0b1101111) + '\x64' + chr(3107 - 3006))('\x75' + chr(8625 - 8509) + '\x66' + chr(994 - 949) + chr(0b110101 + 0o3)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def wKKXKFBlqW0G(hXMPsSrOQzbh, Jni_E12Y8D3Y, jfR8qmy1vJ8o=roI3spqORKae(ES5oEprVxulp(b's~\x07\x9d\xbd\xf7'), chr(0b1100001 + 0o3) + '\x65' + '\x63' + chr(111) + chr(0b1100100) + chr(101))('\165' + chr(0b1110100) + chr(0b1100110) + chr(45) + '\x38')):
ihXi_REa_8XA = hXMPsSrOQzbh.Z5xOfqIptFuc(Jni_E12Y8D3Y, vm=jfR8qmy1vJ8o)
return roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'`h\x1e\x85\xa0\xfc\x0c\xfa'), chr(0b10010 + 0o122) + '\x65' + '\x63' + '\x6f' + chr(8065 - 7965) + chr(0b1100101))(chr(13430 - 13313) + chr(0b110 + 0o156) + '\146' + chr(45) + '\070'))(ihXi_REa_8XA) |
cggh/scikit-allel | allel/model/ndarray.py | NumpyRecArrayWrapper.concatenate | def concatenate(self, others):
"""Concatenate arrays."""
if not isinstance(others, (list, tuple)):
others = others,
tup = (self.values,) + tuple(o.values for o in others)
out = np.concatenate(tup, axis=0)
out = type(self)(out)
return out | python | def concatenate(self, others):
"""Concatenate arrays."""
if not isinstance(others, (list, tuple)):
others = others,
tup = (self.values,) + tuple(o.values for o in others)
out = np.concatenate(tup, axis=0)
out = type(self)(out)
return out | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/model/ndarray.py#L192-L199 | train | Concatenate arrays. | 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(0b100110 + 0o12) + chr(0b11111 + 0o120) + chr(50) + chr(55) + chr(0b10 + 0o63), 56001 - 55993), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110001) + '\x37' + chr(559 - 511), 54297 - 54289), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110011) + chr(0b110011) + chr(0b1100 + 0o50), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1 + 0o156) + chr(2272 - 2220) + chr(2145 - 2090), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(2083 - 2034) + chr(54) + '\063', 20043 - 20035), nzTpIcepk0o8('\x30' + chr(111) + '\x32' + chr(53) + chr(2415 - 2361), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + '\x32' + '\065' + '\064', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x32' + chr(0b10000 + 0o42), 0b1000), nzTpIcepk0o8(chr(0b101000 + 0o10) + '\157' + '\x33' + chr(781 - 730) + '\x33', 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b11001 + 0o31) + chr(0b110011 + 0o2) + chr(599 - 550), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(49) + chr(0b110011) + chr(0b110001 + 0o0), 9466 - 9458), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(50) + chr(1248 - 1194), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101 + 0o142) + chr(53) + '\066', 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b11010 + 0o35) + chr(55), 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(0b101010 + 0o11) + chr(55) + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(48) + chr(6336 - 6225) + chr(63 - 12) + chr(1382 - 1332) + chr(506 - 458), 63638 - 63630), nzTpIcepk0o8(chr(0b1000 + 0o50) + chr(6509 - 6398) + '\063' + chr(52) + chr(2369 - 2319), 0o10), nzTpIcepk0o8(chr(0b11011 + 0o25) + chr(0b1101111) + '\064' + chr(0b110110), 0o10), nzTpIcepk0o8(chr(0b101000 + 0o10) + '\x6f' + chr(1978 - 1923) + '\x35', 0b1000), nzTpIcepk0o8('\x30' + chr(0b1100000 + 0o17) + chr(849 - 800) + chr(70 - 18), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + '\x31' + '\x34', 8), nzTpIcepk0o8(chr(0b10110 + 0o32) + '\x6f' + '\x33' + '\x30' + chr(103 - 52), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b1101 + 0o47) + chr(0b101000 + 0o13), 51220 - 51212), nzTpIcepk0o8('\x30' + '\157' + chr(610 - 559) + '\x35', 0b1000), nzTpIcepk0o8(chr(48) + chr(7102 - 6991) + '\x31' + chr(51) + '\067', 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(1170 - 1119) + chr(0b11 + 0o57) + '\x33', 16154 - 16146), nzTpIcepk0o8('\060' + chr(8710 - 8599) + chr(51) + '\x32' + '\x33', 8), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\062', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x31' + '\x34' + chr(0b1101 + 0o51), 0o10), nzTpIcepk0o8(chr(48) + chr(10413 - 10302) + chr(49) + chr(0b110101), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1100 + 0o143) + '\061' + chr(0b110110) + '\062', ord("\x08")), nzTpIcepk0o8(chr(0b100011 + 0o15) + chr(0b1101111) + chr(125 - 74) + '\060' + chr(0b110001), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + '\x32' + '\x34' + '\x36', 6766 - 6758), nzTpIcepk0o8(chr(1944 - 1896) + chr(0b10111 + 0o130) + chr(0b1111 + 0o44) + chr(0b110011) + chr(0b11111 + 0o24), 8), nzTpIcepk0o8('\x30' + '\x6f' + '\062' + chr(0b110011) + chr(55), 4890 - 4882), nzTpIcepk0o8('\060' + '\157' + chr(885 - 834) + chr(2928 - 2873) + '\x37', 0b1000), nzTpIcepk0o8(chr(0b11101 + 0o23) + chr(3791 - 3680) + chr(861 - 812) + chr(50) + '\x32', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(6855 - 6744) + chr(0b110001) + '\064' + chr(0b10 + 0o56), 0b1000), nzTpIcepk0o8(chr(48) + chr(4129 - 4018) + chr(0b110111) + chr(0b101110 + 0o5), 65095 - 65087), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\063' + chr(0b110110) + chr(1376 - 1325), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(1783 - 1735) + '\x6f' + chr(53) + chr(0b1110 + 0o42), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x93'), '\x64' + '\145' + '\143' + '\x6f' + chr(9167 - 9067) + '\145')('\x75' + chr(5442 - 5326) + chr(0b1110 + 0o130) + '\x2d' + chr(2361 - 2305)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def cNUMWjTSOBqD(hXMPsSrOQzbh, XlJQggBAVmIr):
if not suIjIS24Zkqw(XlJQggBAVmIr, (H4NoA26ON7iG, nfNqtJL5aRaY)):
XlJQggBAVmIr = (XlJQggBAVmIr,)
WRQDInte8Ztr = (hXMPsSrOQzbh.CsodZJH6x9Tx,) + nfNqtJL5aRaY((WgZUEOuIyTUO.CsodZJH6x9Tx for WgZUEOuIyTUO in XlJQggBAVmIr))
VwOu8WkJ9cpc = nDF4gVNx0u9Q.concatenate(WRQDInte8Ztr, axis=nzTpIcepk0o8(chr(847 - 799) + chr(111) + chr(1582 - 1534), 18032 - 18024))
VwOu8WkJ9cpc = MJ07XsN5uFgW(hXMPsSrOQzbh)(VwOu8WkJ9cpc)
return VwOu8WkJ9cpc |
cggh/scikit-allel | allel/model/ndarray.py | Genotypes.fill_masked | def fill_masked(self, value=-1, copy=True):
"""Fill masked genotype calls with a given value.
Parameters
----------
value : int, optional
The fill value.
copy : bool, optional
If False, modify the array in place.
Returns
-------
g : GenotypeArray
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 1]],
... [[0, 1], [1, 1]],
... [[0, 2], [-1, -1]]], dtype='i1')
>>> mask = [[True, False], [False, True], [False, False]]
>>> g.mask = mask
>>> g.fill_masked().values
array([[[-1, -1],
[ 0, 1]],
[[ 0, 1],
[-1, -1]],
[[ 0, 2],
[-1, -1]]], dtype=int8)
"""
if self.mask is None:
raise ValueError('no mask is set')
# apply the mask
data = np.array(self.values, copy=copy)
data[self.mask, ...] = value
if copy:
out = type(self)(data) # wrap
out.is_phased = self.is_phased
# don't set mask because it has been filled in
else:
out = self
out.mask = None # reset mask
return out | python | def fill_masked(self, value=-1, copy=True):
"""Fill masked genotype calls with a given value.
Parameters
----------
value : int, optional
The fill value.
copy : bool, optional
If False, modify the array in place.
Returns
-------
g : GenotypeArray
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 1]],
... [[0, 1], [1, 1]],
... [[0, 2], [-1, -1]]], dtype='i1')
>>> mask = [[True, False], [False, True], [False, False]]
>>> g.mask = mask
>>> g.fill_masked().values
array([[[-1, -1],
[ 0, 1]],
[[ 0, 1],
[-1, -1]],
[[ 0, 2],
[-1, -1]]], dtype=int8)
"""
if self.mask is None:
raise ValueError('no mask is set')
# apply the mask
data = np.array(self.values, copy=copy)
data[self.mask, ...] = value
if copy:
out = type(self)(data) # wrap
out.is_phased = self.is_phased
# don't set mask because it has been filled in
else:
out = self
out.mask = None # reset mask
return out | [
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... | Fill masked genotype calls with a given value.
Parameters
----------
value : int, optional
The fill value.
copy : bool, optional
If False, modify the array in place.
Returns
-------
g : GenotypeArray
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 1]],
... [[0, 1], [1, 1]],
... [[0, 2], [-1, -1]]], dtype='i1')
>>> mask = [[True, False], [False, True], [False, False]]
>>> g.mask = mask
>>> g.fill_masked().values
array([[[-1, -1],
[ 0, 1]],
[[ 0, 1],
[-1, -1]],
[[ 0, 2],
[-1, -1]]], dtype=int8) | [
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"."
] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/model/ndarray.py#L332-L380 | train | Fill the masked genotype calls with a given 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(2050 - 2002) + chr(111) + '\x35' + '\061', 0o10), nzTpIcepk0o8(chr(0b100011 + 0o15) + chr(111) + chr(0b100000 + 0o22) + chr(1327 - 1273) + chr(0b100 + 0o55), 0o10), nzTpIcepk0o8(chr(1358 - 1310) + '\157' + chr(51) + chr(52) + chr(53), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b110010 + 0o75) + chr(0b1001 + 0o52) + chr(0b101001 + 0o11) + chr(0b110100 + 0o2), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + '\061' + chr(51) + '\064', 5170 - 5162), nzTpIcepk0o8(chr(2175 - 2127) + '\x6f' + chr(0b111 + 0o53) + '\062' + '\067', 0o10), nzTpIcepk0o8(chr(0b11 + 0o55) + '\x6f' + chr(0b100001 + 0o22) + chr(1883 - 1832) + chr(53), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(49) + chr(0b110101) + chr(0b110010), 24020 - 24012), nzTpIcepk0o8(chr(0b110000) + chr(0b100101 + 0o112) + chr(0b110011) + '\064' + '\x37', 52753 - 52745), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(2206 - 2156), 11566 - 11558), nzTpIcepk0o8(chr(0b110000) + chr(0b111111 + 0o60) + '\x31' + chr(50) + chr(0b10011 + 0o43), 8876 - 8868), nzTpIcepk0o8(chr(0b101010 + 0o6) + chr(0b11111 + 0o120) + chr(0b110010) + chr(242 - 188) + '\060', 0o10), nzTpIcepk0o8('\060' + chr(0b10010 + 0o135) + chr(0b11011 + 0o26) + chr(1971 - 1918) + chr(0b1110 + 0o51), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110001) + '\060' + chr(0b110100), 43130 - 43122), nzTpIcepk0o8(chr(0b110000) + chr(2893 - 2782) + chr(0b101011 + 0o7) + '\x35' + '\x35', 0b1000), nzTpIcepk0o8(chr(1797 - 1749) + chr(0b1100011 + 0o14) + chr(0b110010) + chr(0b110010) + '\061', 26340 - 26332), nzTpIcepk0o8('\x30' + chr(111) + chr(1086 - 1035) + '\060', 0o10), nzTpIcepk0o8(chr(502 - 454) + chr(0b1101111) + chr(0b10001 + 0o41) + '\x30' + chr(0b110000), 0b1000), nzTpIcepk0o8(chr(821 - 773) + chr(0b1101111) + chr(118 - 66) + '\x37', ord("\x08")), nzTpIcepk0o8(chr(2098 - 2050) + '\x6f' + '\x37' + '\067', ord("\x08")), nzTpIcepk0o8(chr(0b1101 + 0o43) + '\157' + chr(0b11101 + 0o26) + chr(50), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\061' + '\x34' + chr(0b110010), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(51) + '\x34' + '\x35', 8), nzTpIcepk0o8('\060' + chr(10598 - 10487) + '\x32' + '\x33' + chr(0b110110), 0o10), nzTpIcepk0o8(chr(229 - 181) + chr(0b1101111) + '\x32' + '\067' + chr(0b100101 + 0o16), ord("\x08")), nzTpIcepk0o8(chr(0b11101 + 0o23) + chr(6948 - 6837) + '\062' + chr(0b10011 + 0o40) + chr(2321 - 2266), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b101011 + 0o7) + '\065' + chr(0b101111 + 0o3), 0o10), nzTpIcepk0o8(chr(0b1000 + 0o50) + chr(10269 - 10158) + chr(0b110001) + chr(50) + chr(1601 - 1547), 8), nzTpIcepk0o8('\060' + '\157' + '\x33' + chr(0b101001 + 0o13) + chr(2306 - 2253), 8), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110010) + chr(2282 - 2228), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b10110 + 0o34) + chr(0b1011 + 0o52), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\067' + '\066', 41224 - 41216), nzTpIcepk0o8(chr(0b1010 + 0o46) + chr(0b1101111) + '\061' + chr(327 - 274) + '\064', 318 - 310), nzTpIcepk0o8('\060' + chr(0b1101 + 0o142) + chr(863 - 814) + '\x32' + '\x31', 0o10), nzTpIcepk0o8(chr(0b100010 + 0o16) + chr(3189 - 3078) + chr(615 - 566) + chr(2309 - 2255) + chr(978 - 926), 15966 - 15958), nzTpIcepk0o8(chr(416 - 368) + chr(111) + '\x36' + chr(52), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1000000 + 0o57) + chr(0b100 + 0o57) + chr(55) + chr(0b100011 + 0o23), 0b1000), nzTpIcepk0o8('\060' + chr(671 - 560) + chr(49) + chr(0b110110) + chr(0b110010), 53232 - 53224), nzTpIcepk0o8(chr(48) + chr(7330 - 7219) + '\x33' + chr(0b110111) + chr(55), 0b1000), nzTpIcepk0o8(chr(0b101001 + 0o7) + '\x6f' + chr(702 - 652) + '\x35' + chr(0b110001), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + chr(6252 - 6141) + chr(1503 - 1450) + chr(48), ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x07'), '\144' + chr(0b1000111 + 0o36) + '\143' + chr(712 - 601) + '\144' + chr(2576 - 2475))(chr(0b1110101) + '\164' + chr(0b1100110) + chr(0b101101) + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def g9XHcd1rm5UU(hXMPsSrOQzbh, uV9iBiw0y_Mp=-nzTpIcepk0o8('\x30' + chr(10082 - 9971) + chr(0b110001), 0o10), aZTCj4v5QdfO=nzTpIcepk0o8(chr(0b0 + 0o60) + '\x6f' + '\061', 8)):
if roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'k\xf3\xa8\xee8\xef\xb0]\xbeU1\xd5'), '\x64' + '\145' + '\143' + '\x6f' + '\144' + '\145')('\x75' + chr(0b1110100) + chr(102) + chr(45) + '\070')) is None:
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'G\xde\xc5\xbb=\xe4\xb6J\x8eqv\xc3\n0'), chr(100) + chr(0b1100101) + chr(0b111011 + 0o50) + chr(0b100011 + 0o114) + '\x64' + chr(101))(chr(0b1110101) + chr(116) + '\146' + '\x2d' + '\070'))
FfKOThdpoDTb = nDF4gVNx0u9Q.Tn6rGr7XTM7t(hXMPsSrOQzbh.CsodZJH6x9Tx, copy=aZTCj4v5QdfO)
FfKOThdpoDTb[hXMPsSrOQzbh.BBM8dxm7YWge, ...] = uV9iBiw0y_Mp
if aZTCj4v5QdfO:
VwOu8WkJ9cpc = MJ07XsN5uFgW(hXMPsSrOQzbh)(FfKOThdpoDTb)
VwOu8WkJ9cpc.fUab2YaX8axD = hXMPsSrOQzbh.fUab2YaX8axD
else:
VwOu8WkJ9cpc = hXMPsSrOQzbh
VwOu8WkJ9cpc.BBM8dxm7YWge = None
return VwOu8WkJ9cpc |
cggh/scikit-allel | allel/model/ndarray.py | Genotypes.is_called | def is_called(self):
"""Find non-missing genotype calls.
Returns
-------
out : ndarray, bool, shape (n_variants, n_samples)
Array where elements are True if the genotype call matches the
condition.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 1]],
... [[0, 1], [1, 1]],
... [[0, 2], [-1, -1]]])
>>> g.is_called()
array([[ True, True],
[ True, True],
[ True, False]])
>>> v = g[:, 1]
>>> v
<GenotypeVector shape=(3, 2) dtype=int64>
0/1 1/1 ./.
>>> v.is_called()
array([ True, True, False])
"""
out = np.all(self.values >= 0, axis=-1)
# handle mask
if self.mask is not None:
out &= ~self.mask
return out | python | def is_called(self):
"""Find non-missing genotype calls.
Returns
-------
out : ndarray, bool, shape (n_variants, n_samples)
Array where elements are True if the genotype call matches the
condition.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 1]],
... [[0, 1], [1, 1]],
... [[0, 2], [-1, -1]]])
>>> g.is_called()
array([[ True, True],
[ True, True],
[ True, False]])
>>> v = g[:, 1]
>>> v
<GenotypeVector shape=(3, 2) dtype=int64>
0/1 1/1 ./.
>>> v.is_called()
array([ True, True, False])
"""
out = np.all(self.values >= 0, axis=-1)
# handle mask
if self.mask is not None:
out &= ~self.mask
return out | [
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Returns
-------
out : ndarray, bool, shape (n_variants, n_samples)
Array where elements are True if the genotype call matches the
condition.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 1]],
... [[0, 1], [1, 1]],
... [[0, 2], [-1, -1]]])
>>> g.is_called()
array([[ True, True],
[ True, True],
[ True, False]])
>>> v = g[:, 1]
>>> v
<GenotypeVector shape=(3, 2) dtype=int64>
0/1 1/1 ./.
>>> v.is_called()
array([ True, True, False]) | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/model/ndarray.py#L382-L417 | train | Find non - missing genotype calls. | 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(430 - 382) + '\x6f' + chr(0b101011 + 0o6) + '\065' + chr(996 - 946), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(51) + chr(55) + chr(0b1011 + 0o52), ord("\x08")), nzTpIcepk0o8(chr(1504 - 1456) + '\x6f' + chr(50) + chr(0b11011 + 0o34) + chr(0b101010 + 0o10), 0o10), nzTpIcepk0o8(chr(0b1111 + 0o41) + chr(5004 - 4893) + '\064', ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(695 - 645) + chr(1052 - 998), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(7618 - 7507) + chr(0b110001) + chr(0b110111) + chr(0b101010 + 0o10), 9288 - 9280), nzTpIcepk0o8(chr(0b100101 + 0o13) + chr(0b1101111) + chr(0b1110 + 0o43) + '\064' + chr(0b110010), 62260 - 62252), nzTpIcepk0o8(chr(48) + '\157' + chr(1626 - 1573) + chr(606 - 557), ord("\x08")), nzTpIcepk0o8(chr(1221 - 1173) + chr(0b1101111) + '\061' + chr(0b11 + 0o63) + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(2257 - 2209) + chr(0b1101111) + chr(0b110001) + '\067' + chr(2147 - 2095), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b100 + 0o55) + chr(1077 - 1023) + '\060', 0o10), nzTpIcepk0o8(chr(48) + chr(111) + '\063' + chr(0b110110) + chr(1921 - 1872), 0o10), nzTpIcepk0o8(chr(429 - 381) + chr(0b1011 + 0o144) + chr(0b110011) + '\066' + '\067', ord("\x08")), nzTpIcepk0o8('\x30' + chr(1743 - 1632) + chr(0b1010 + 0o50) + chr(0b110011) + chr(0b110011 + 0o1), 31902 - 31894), nzTpIcepk0o8('\x30' + '\157' + chr(0b101101 + 0o6) + '\x34' + chr(0b110101), ord("\x08")), nzTpIcepk0o8('\060' + chr(7447 - 7336) + '\x32' + chr(0b1111 + 0o50) + chr(689 - 638), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b111100 + 0o63) + chr(49) + chr(0b111 + 0o51) + chr(0b110001), 0b1000), nzTpIcepk0o8(chr(1382 - 1334) + chr(111) + '\060', 40096 - 40088), nzTpIcepk0o8('\060' + chr(0b100011 + 0o114) + chr(0b110010 + 0o0) + '\x31' + '\067', 62164 - 62156), nzTpIcepk0o8('\x30' + '\x6f' + chr(803 - 752) + chr(53) + '\x33', 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(2181 - 2131) + chr(0b110111) + chr(51), 8), nzTpIcepk0o8('\x30' + '\x6f' + '\061' + chr(50) + chr(701 - 651), 33740 - 33732), nzTpIcepk0o8(chr(0b110000) + '\157' + '\061' + '\x32' + chr(54), 42446 - 42438), nzTpIcepk0o8('\060' + '\157' + chr(0b110001) + chr(0b110101) + chr(0b110010), 8), nzTpIcepk0o8('\x30' + chr(0b1001000 + 0o47) + '\x33' + chr(802 - 750) + chr(1902 - 1850), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\062' + chr(0b1101 + 0o43) + chr(0b110101), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + '\062' + '\062' + chr(0b110010 + 0o0), ord("\x08")), nzTpIcepk0o8(chr(0b11010 + 0o26) + '\157' + chr(50) + chr(50) + '\x34', 33105 - 33097), nzTpIcepk0o8(chr(0b110000) + chr(0b1010100 + 0o33) + chr(0b101010 + 0o11) + '\063' + '\x34', 0b1000), nzTpIcepk0o8(chr(0b10010 + 0o36) + '\x6f' + chr(0b1110 + 0o44) + chr(0b110100) + chr(55), 0o10), nzTpIcepk0o8('\x30' + chr(0b1000 + 0o147) + chr(0b1010 + 0o47) + '\x36' + '\x37', 4119 - 4111), nzTpIcepk0o8(chr(0b110000) + chr(0b1011010 + 0o25) + chr(0b110010) + chr(0b110001) + chr(53), 47296 - 47288), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b110011) + chr(0b110000) + chr(1583 - 1531), 60686 - 60678), nzTpIcepk0o8(chr(0b110000 + 0o0) + '\x6f' + chr(0b110011) + chr(0b110111) + chr(0b101101 + 0o11), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + '\x31' + chr(54) + chr(0b110010), 32002 - 31994), nzTpIcepk0o8(chr(0b100011 + 0o15) + chr(1740 - 1629) + chr(0b11101 + 0o24) + chr(2238 - 2190) + '\066', 45633 - 45625), nzTpIcepk0o8('\060' + chr(10150 - 10039) + '\062' + '\064', 0o10), nzTpIcepk0o8(chr(2130 - 2082) + chr(0b1001100 + 0o43) + '\x31' + '\061' + '\065', 0o10), nzTpIcepk0o8('\x30' + '\157' + '\061' + chr(0b110111) + '\064', 8), nzTpIcepk0o8('\x30' + '\x6f' + chr(1901 - 1850) + chr(0b110011) + chr(0b11011 + 0o26), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + '\x6f' + chr(0b110100 + 0o1) + chr(0b110000), 52489 - 52481)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'D'), '\x64' + chr(0b1100101) + chr(0b1100000 + 0o3) + chr(1754 - 1643) + chr(1689 - 1589) + chr(0b100111 + 0o76))(chr(0b1110101) + '\164' + '\146' + '\055' + chr(2759 - 2703)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def YQUHQlRSVoh_(hXMPsSrOQzbh):
VwOu8WkJ9cpc = nDF4gVNx0u9Q.qX60lO1lgHA5(hXMPsSrOQzbh.CsodZJH6x9Tx >= nzTpIcepk0o8('\060' + '\157' + chr(0b1010 + 0o46), 8), axis=-nzTpIcepk0o8('\060' + chr(111) + '\061', 0b1000))
if roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'(\xbf\xf7<r\x02\x0f\x1e*+\x17\x94'), '\x64' + chr(101) + chr(4684 - 4585) + '\157' + chr(0b1100100) + '\x65')(chr(117) + chr(116) + chr(0b1100110) + chr(224 - 179) + chr(0b111000))) is not None:
VwOu8WkJ9cpc &= ~hXMPsSrOQzbh.BBM8dxm7YWge
return VwOu8WkJ9cpc |
cggh/scikit-allel | allel/model/ndarray.py | Genotypes.is_missing | def is_missing(self):
"""Find missing genotype calls.
Returns
-------
out : ndarray, bool, shape (n_variants, n_samples)
Array where elements are True if the genotype call matches the
condition.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 1]],
... [[0, 1], [1, 1]],
... [[0, 2], [-1, -1]]])
>>> g.is_missing()
array([[False, False],
[False, False],
[False, True]])
>>> v = g[:, 1]
>>> v
<GenotypeVector shape=(3, 2) dtype=int64>
0/1 1/1 ./.
>>> v.is_missing()
array([False, False, True])
"""
out = np.any(self.values < 0, axis=-1)
# handle mask
if self.mask is not None:
out |= self.mask
return out | python | def is_missing(self):
"""Find missing genotype calls.
Returns
-------
out : ndarray, bool, shape (n_variants, n_samples)
Array where elements are True if the genotype call matches the
condition.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 1]],
... [[0, 1], [1, 1]],
... [[0, 2], [-1, -1]]])
>>> g.is_missing()
array([[False, False],
[False, False],
[False, True]])
>>> v = g[:, 1]
>>> v
<GenotypeVector shape=(3, 2) dtype=int64>
0/1 1/1 ./.
>>> v.is_missing()
array([False, False, True])
"""
out = np.any(self.values < 0, axis=-1)
# handle mask
if self.mask is not None:
out |= self.mask
return out | [
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"ma... | Find missing genotype calls.
Returns
-------
out : ndarray, bool, shape (n_variants, n_samples)
Array where elements are True if the genotype call matches the
condition.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 1]],
... [[0, 1], [1, 1]],
... [[0, 2], [-1, -1]]])
>>> g.is_missing()
array([[False, False],
[False, False],
[False, True]])
>>> v = g[:, 1]
>>> v
<GenotypeVector shape=(3, 2) dtype=int64>
0/1 1/1 ./.
>>> v.is_missing()
array([False, False, True]) | [
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"."
] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/model/ndarray.py#L419-L454 | train | Find missing genotype calls. | 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(51) + chr(1493 - 1445) + chr(51), ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + '\063' + '\066' + '\x35', 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b101011 + 0o6) + '\061' + chr(443 - 389), ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(1174 - 1126) + chr(0b1101111) + chr(0b100100 + 0o15) + '\060' + chr(54), 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(52) + chr(0b110000), 57645 - 57637), nzTpIcepk0o8(chr(0b1111 + 0o41) + '\157' + '\x32' + chr(51) + chr(0b11101 + 0o32), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(51) + chr(0b110111) + '\x36', 0b1000), nzTpIcepk0o8(chr(244 - 196) + '\157' + '\x32' + chr(54) + chr(0b11 + 0o57), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\062' + chr(0b110011), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110010) + '\x35' + '\x37', 0o10), nzTpIcepk0o8(chr(0b11110 + 0o22) + '\x6f' + chr(49) + chr(0b100011 + 0o16) + '\062', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b1110 + 0o44) + '\x30' + '\x35', ord("\x08")), nzTpIcepk0o8(chr(1152 - 1104) + '\x6f' + '\x32' + '\x37' + chr(0b100101 + 0o17), 0o10), nzTpIcepk0o8(chr(1340 - 1292) + chr(7402 - 7291) + chr(0b100100 + 0o17) + chr(0b101101 + 0o4) + '\x33', 30374 - 30366), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b11100 + 0o25) + '\066' + chr(0b110001), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(49) + chr(55) + '\x37', 22761 - 22753), nzTpIcepk0o8('\x30' + chr(111) + '\062' + chr(54) + chr(0b11000 + 0o33), 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(0b110010) + chr(51) + chr(0b110100), 57260 - 57252), nzTpIcepk0o8(chr(48) + '\x6f' + '\067' + chr(49), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(0b110010 + 0o4) + '\x35', 0b1000), nzTpIcepk0o8(chr(0b10011 + 0o35) + chr(111) + chr(0b110011) + chr(1536 - 1488) + chr(1228 - 1177), 8), nzTpIcepk0o8(chr(1097 - 1049) + '\x6f' + chr(0b110101 + 0o2) + '\x33', ord("\x08")), nzTpIcepk0o8('\x30' + chr(10223 - 10112) + chr(0b11110 + 0o24) + chr(2348 - 2296) + chr(2367 - 2313), 34739 - 34731), nzTpIcepk0o8('\x30' + '\x6f' + '\062' + chr(2614 - 2562), 0b1000), nzTpIcepk0o8('\x30' + chr(10303 - 10192) + chr(50) + '\060' + '\060', 55565 - 55557), nzTpIcepk0o8('\x30' + chr(4736 - 4625) + '\x31' + chr(0b110111) + chr(1174 - 1122), ord("\x08")), nzTpIcepk0o8(chr(701 - 653) + chr(0b1101111) + '\067' + chr(0b100111 + 0o15), 0b1000), nzTpIcepk0o8(chr(0b100 + 0o54) + chr(111) + '\060', 15219 - 15211), nzTpIcepk0o8(chr(0b110 + 0o52) + chr(0b10011 + 0o134) + '\067' + chr(51), 8), nzTpIcepk0o8(chr(692 - 644) + chr(111) + chr(204 - 154) + '\062' + chr(0b1011 + 0o54), 0b1000), nzTpIcepk0o8(chr(930 - 882) + chr(0b1101111) + chr(2541 - 2490) + chr(52), 0o10), nzTpIcepk0o8(chr(0b101111 + 0o1) + '\157' + chr(0b110010) + chr(0b1111 + 0o41) + chr(0b110000), 8), nzTpIcepk0o8('\060' + '\157' + chr(0b110010) + chr(0b110011) + '\064', 8), nzTpIcepk0o8('\x30' + chr(111) + '\x36' + chr(54), 0o10), nzTpIcepk0o8(chr(453 - 405) + chr(111) + chr(50) + chr(0b110001) + '\063', 0o10), nzTpIcepk0o8(chr(0b1101 + 0o43) + '\x6f' + chr(0b101100 + 0o5) + chr(51) + '\067', 55165 - 55157), nzTpIcepk0o8('\060' + chr(0b1101111 + 0o0) + '\065' + chr(0b110100), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1011010 + 0o25) + chr(0b110010) + '\065' + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(11202 - 11091) + chr(0b100000 + 0o22) + '\x31' + '\x33', 8)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x35' + chr(48), 21937 - 21929)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xed'), '\x64' + chr(101) + chr(1394 - 1295) + chr(0b1101111) + chr(5450 - 5350) + chr(0b1100101))(chr(0b1011001 + 0o34) + '\x74' + chr(0b1100110) + chr(0b11101 + 0o20) + chr(154 - 98)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def zYFtC4_vxWk9(hXMPsSrOQzbh):
VwOu8WkJ9cpc = nDF4gVNx0u9Q.VF4pKOObtlPc(hXMPsSrOQzbh.CsodZJH6x9Tx < nzTpIcepk0o8(chr(0b110000) + chr(10115 - 10004) + chr(674 - 626), 8), axis=-nzTpIcepk0o8('\x30' + chr(111) + '\061', 55052 - 55044))
if roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x81\xb7\x03<"X\xf2\xc9\xebD\xc8/'), chr(3748 - 3648) + chr(7907 - 7806) + chr(9160 - 9061) + chr(0b1010011 + 0o34) + '\144' + chr(8376 - 8275))(chr(0b1110101) + chr(0b11110 + 0o126) + chr(102) + '\055' + chr(2966 - 2910))) is not None:
VwOu8WkJ9cpc |= hXMPsSrOQzbh.BBM8dxm7YWge
return VwOu8WkJ9cpc |
cggh/scikit-allel | allel/model/ndarray.py | Genotypes.is_hom | def is_hom(self, allele=None):
"""Find genotype calls that are homozygous.
Parameters
----------
allele : int, optional
Allele index.
Returns
-------
out : ndarray, bool, shape (n_variants, n_samples)
Array where elements are True if the genotype call matches the
condition.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 1]],
... [[0, 1], [1, 1]],
... [[2, 2], [-1, -1]]])
>>> g.is_hom()
array([[ True, False],
[False, True],
[ True, False]])
>>> g.is_hom(allele=1)
array([[False, False],
[False, True],
[False, False]])
>>> v = g[:, 0]
>>> v
<GenotypeVector shape=(3, 2) dtype=int64>
0/0 0/1 2/2
>>> v.is_hom()
array([ True, False, True])
"""
if allele is None:
allele1 = self.values[..., 0, np.newaxis]
other_alleles = self.values[..., 1:]
tmp = (allele1 >= 0) & (allele1 == other_alleles)
out = np.all(tmp, axis=-1)
else:
out = np.all(self.values == allele, axis=-1)
# handle mask
if self.mask is not None:
out &= ~self.mask
return out | python | def is_hom(self, allele=None):
"""Find genotype calls that are homozygous.
Parameters
----------
allele : int, optional
Allele index.
Returns
-------
out : ndarray, bool, shape (n_variants, n_samples)
Array where elements are True if the genotype call matches the
condition.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 1]],
... [[0, 1], [1, 1]],
... [[2, 2], [-1, -1]]])
>>> g.is_hom()
array([[ True, False],
[False, True],
[ True, False]])
>>> g.is_hom(allele=1)
array([[False, False],
[False, True],
[False, False]])
>>> v = g[:, 0]
>>> v
<GenotypeVector shape=(3, 2) dtype=int64>
0/0 0/1 2/2
>>> v.is_hom()
array([ True, False, True])
"""
if allele is None:
allele1 = self.values[..., 0, np.newaxis]
other_alleles = self.values[..., 1:]
tmp = (allele1 >= 0) & (allele1 == other_alleles)
out = np.all(tmp, axis=-1)
else:
out = np.all(self.values == allele, axis=-1)
# handle mask
if self.mask is not None:
out &= ~self.mask
return out | [
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... | Find genotype calls that are homozygous.
Parameters
----------
allele : int, optional
Allele index.
Returns
-------
out : ndarray, bool, shape (n_variants, n_samples)
Array where elements are True if the genotype call matches the
condition.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 1]],
... [[0, 1], [1, 1]],
... [[2, 2], [-1, -1]]])
>>> g.is_hom()
array([[ True, False],
[False, True],
[ True, False]])
>>> g.is_hom(allele=1)
array([[False, False],
[False, True],
[False, False]])
>>> v = g[:, 0]
>>> v
<GenotypeVector shape=(3, 2) dtype=int64>
0/0 0/1 2/2
>>> v.is_hom()
array([ True, False, True]) | [
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"homozygous",
"."
] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/model/ndarray.py#L456-L506 | train | Find genotype calls that are homozygous. | 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(1364 - 1316) + chr(111) + chr(0b110001) + '\x36' + chr(1823 - 1775), ord("\x08")), nzTpIcepk0o8(chr(0b101 + 0o53) + chr(0b10010 + 0o135) + chr(0b110010) + '\x37', 0b1000), nzTpIcepk0o8(chr(512 - 464) + '\x6f' + chr(0b1111 + 0o43) + '\x32' + chr(52), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(2301 - 2250), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1001101 + 0o42) + chr(0b101001 + 0o11) + chr(49) + '\064', 0b1000), nzTpIcepk0o8('\060' + chr(5313 - 5202) + '\067' + chr(55), 26348 - 26340), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x33' + chr(55) + chr(100 - 49), 0o10), nzTpIcepk0o8(chr(0b110000 + 0o0) + '\157' + '\x31' + '\062' + '\x30', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b10010 + 0o41) + '\x35' + chr(52), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + '\062' + chr(0b110010 + 0o1) + chr(0b100001 + 0o21), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(49) + '\060' + chr(0b110110), 0b1000), nzTpIcepk0o8(chr(0b11011 + 0o25) + chr(111) + chr(0b10110 + 0o34) + chr(0b110010 + 0o5) + chr(2158 - 2104), 64403 - 64395), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(54) + chr(0b100101 + 0o16), 0o10), nzTpIcepk0o8('\060' + '\157' + '\x31' + chr(0b110101) + chr(50), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110101) + '\x35', ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(0b100110 + 0o14) + '\060' + '\067', 56801 - 56793), nzTpIcepk0o8(chr(2095 - 2047) + chr(0b11010 + 0o125) + chr(0b110111) + chr(2000 - 1950), 0o10), nzTpIcepk0o8(chr(48) + chr(367 - 256) + chr(0b110001) + chr(54) + chr(872 - 822), ord("\x08")), nzTpIcepk0o8(chr(574 - 526) + chr(0b101011 + 0o104) + '\x36' + chr(0b110001), 0o10), nzTpIcepk0o8('\060' + chr(10692 - 10581) + chr(869 - 818) + '\x31' + '\x32', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(51) + '\x33' + chr(0b110011), 3801 - 3793), nzTpIcepk0o8(chr(0b10110 + 0o32) + chr(0b1011011 + 0o24) + '\x33' + chr(48), 0b1000), nzTpIcepk0o8('\060' + chr(0b100011 + 0o114) + chr(0b110010) + '\x35', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\x31' + '\063' + chr(0b11111 + 0o27), 0b1000), nzTpIcepk0o8('\060' + chr(111) + '\x33' + chr(0b1101 + 0o46) + chr(0b110011), 8), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110001) + chr(0b110000) + chr(824 - 771), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x31' + chr(52) + chr(49), ord("\x08")), nzTpIcepk0o8(chr(0b11011 + 0o25) + chr(0b1101111) + chr(2328 - 2278) + chr(2331 - 2281) + chr(1923 - 1868), 40756 - 40748), nzTpIcepk0o8('\x30' + '\x6f' + '\061' + chr(49), 0o10), nzTpIcepk0o8(chr(48) + chr(4073 - 3962) + chr(810 - 760) + chr(52) + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(0b11111 + 0o21) + '\x6f' + '\066' + '\064', ord("\x08")), nzTpIcepk0o8(chr(0b101111 + 0o1) + chr(0b1101111) + '\x31' + '\x35' + chr(0b1010 + 0o52), 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(903 - 852) + chr(53) + chr(1077 - 1027), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(5433 - 5322) + '\x32' + chr(2176 - 2126) + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(2201 - 2149) + chr(616 - 565), ord("\x08")), nzTpIcepk0o8('\060' + chr(5705 - 5594) + chr(1630 - 1581) + chr(692 - 640), ord("\x08")), nzTpIcepk0o8(chr(0b1111 + 0o41) + '\157' + '\x32' + chr(53) + '\065', ord("\x08")), nzTpIcepk0o8(chr(50 - 2) + chr(8864 - 8753) + chr(49) + '\066' + chr(0b100 + 0o61), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(2195 - 2145) + '\x37' + chr(53), 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(0b10000 + 0o41) + '\x35' + '\x30', ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b11101 + 0o23) + chr(0b1101111) + chr(0b110101) + '\x30', ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'^'), chr(354 - 254) + '\x65' + '\143' + chr(6833 - 6722) + '\144' + chr(101))(chr(0b1110101) + '\x74' + '\146' + chr(0b101101) + chr(0b101110 + 0o12)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def Q_8M8cVbDjwn(hXMPsSrOQzbh, A94c267WMRU1=None):
if A94c267WMRU1 is None:
qO6cEDA0xZYf = hXMPsSrOQzbh.CsodZJH6x9Tx[..., nzTpIcepk0o8(chr(0b101010 + 0o6) + '\x6f' + '\x30', 3299 - 3291), nDF4gVNx0u9Q.newaxis]
DQZxlnhQweEZ = hXMPsSrOQzbh.CsodZJH6x9Tx[..., nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b111 + 0o52), ord("\x08")):]
PT32xG247TS3 = (qO6cEDA0xZYf >= nzTpIcepk0o8(chr(1260 - 1212) + chr(111) + '\060', 8)) & (qO6cEDA0xZYf == DQZxlnhQweEZ)
VwOu8WkJ9cpc = nDF4gVNx0u9Q.qX60lO1lgHA5(PT32xG247TS3, axis=-nzTpIcepk0o8(chr(48) + '\x6f' + chr(1664 - 1615), 8))
else:
VwOu8WkJ9cpc = nDF4gVNx0u9Q.qX60lO1lgHA5(hXMPsSrOQzbh.CsodZJH6x9Tx == A94c267WMRU1, axis=-nzTpIcepk0o8(chr(48) + chr(0b1001 + 0o146) + chr(49), 8))
if roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'2U\xd9;\xe8G\x96g\xb5\xcd!\xdb'), '\144' + chr(5757 - 5656) + '\143' + chr(9866 - 9755) + chr(0b1100100) + chr(101))('\165' + chr(409 - 293) + chr(102) + '\x2d' + '\070')) is not None:
VwOu8WkJ9cpc &= ~hXMPsSrOQzbh.BBM8dxm7YWge
return VwOu8WkJ9cpc |
cggh/scikit-allel | allel/model/ndarray.py | Genotypes.is_hom_alt | def is_hom_alt(self):
"""Find genotype calls that are homozygous for any alternate (i.e.,
non-reference) allele.
Returns
-------
out : ndarray, bool, shape (n_variants, n_samples)
Array where elements are True if the genotype call matches the
condition.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 1]],
... [[0, 1], [1, 1]],
... [[2, 2], [-1, -1]]])
>>> g.is_hom_alt()
array([[False, False],
[False, True],
[ True, False]])
>>> v = g[:, 1]
>>> v
<GenotypeVector shape=(3, 2) dtype=int64>
0/1 1/1 ./.
>>> v.is_hom_alt()
array([False, True, False])
"""
allele1 = self.values[..., 0, np.newaxis]
other_alleles = self.values[..., 1:]
tmp = (allele1 > 0) & (allele1 == other_alleles)
out = np.all(tmp, axis=-1)
# handle mask
if self.mask is not None:
out &= ~self.mask
return out | python | def is_hom_alt(self):
"""Find genotype calls that are homozygous for any alternate (i.e.,
non-reference) allele.
Returns
-------
out : ndarray, bool, shape (n_variants, n_samples)
Array where elements are True if the genotype call matches the
condition.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 1]],
... [[0, 1], [1, 1]],
... [[2, 2], [-1, -1]]])
>>> g.is_hom_alt()
array([[False, False],
[False, True],
[ True, False]])
>>> v = g[:, 1]
>>> v
<GenotypeVector shape=(3, 2) dtype=int64>
0/1 1/1 ./.
>>> v.is_hom_alt()
array([False, True, False])
"""
allele1 = self.values[..., 0, np.newaxis]
other_alleles = self.values[..., 1:]
tmp = (allele1 > 0) & (allele1 == other_alleles)
out = np.all(tmp, axis=-1)
# handle mask
if self.mask is not None:
out &= ~self.mask
return out | [
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">",... | Find genotype calls that are homozygous for any alternate (i.e.,
non-reference) allele.
Returns
-------
out : ndarray, bool, shape (n_variants, n_samples)
Array where elements are True if the genotype call matches the
condition.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 1]],
... [[0, 1], [1, 1]],
... [[2, 2], [-1, -1]]])
>>> g.is_hom_alt()
array([[False, False],
[False, True],
[ True, False]])
>>> v = g[:, 1]
>>> v
<GenotypeVector shape=(3, 2) dtype=int64>
0/1 1/1 ./.
>>> v.is_hom_alt()
array([False, True, False]) | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/model/ndarray.py#L539-L578 | train | Find genotype calls that are homozygous for any alternate allele. | 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(7917 - 7806) + '\061' + '\x37' + chr(801 - 746), 0b1000), nzTpIcepk0o8('\060' + '\157' + '\x32' + chr(822 - 774) + chr(1845 - 1796), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(51) + '\066' + chr(0b1 + 0o65), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + '\x35', 33408 - 33400), nzTpIcepk0o8(chr(48) + '\157' + chr(50) + chr(0b110000) + chr(1311 - 1263), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(50) + '\067' + chr(326 - 275), 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + '\066' + chr(0b110001), 0o10), nzTpIcepk0o8(chr(48) + '\157' + chr(1398 - 1347) + chr(1927 - 1874) + chr(0b110101), 64451 - 64443), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b111 + 0o54) + chr(0b110111) + '\x34', ord("\x08")), nzTpIcepk0o8(chr(0b100001 + 0o17) + '\157' + chr(0b11100 + 0o27) + chr(1860 - 1808) + '\x30', 0b1000), nzTpIcepk0o8('\x30' + chr(0b110 + 0o151) + '\x31' + chr(1940 - 1885) + '\063', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(11789 - 11678) + '\x31', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1011100 + 0o23) + chr(51) + '\061' + chr(51), 12523 - 12515), nzTpIcepk0o8(chr(48) + '\157' + chr(49) + '\x33' + chr(0b110010), ord("\x08")), nzTpIcepk0o8('\060' + chr(10107 - 9996) + chr(0b10111 + 0o40) + '\062', 0o10), nzTpIcepk0o8('\x30' + chr(547 - 436) + chr(0b110010) + '\x35' + chr(0b1001 + 0o47), 54774 - 54766), nzTpIcepk0o8(chr(0b10111 + 0o31) + chr(111) + chr(51) + chr(49) + chr(52), 0b1000), nzTpIcepk0o8(chr(0b10110 + 0o32) + '\x6f' + '\x33' + chr(0b1101 + 0o52) + chr(1753 - 1700), 0o10), nzTpIcepk0o8('\060' + '\157' + '\062' + chr(1673 - 1622) + chr(1895 - 1841), 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110011) + chr(0b110010 + 0o1) + chr(0b110110), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b10111 + 0o130) + '\063' + chr(422 - 372) + chr(0b110110), 32502 - 32494), nzTpIcepk0o8(chr(1949 - 1901) + '\157' + chr(0b0 + 0o62) + chr(0b110110) + '\066', 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(488 - 439) + chr(0b110110) + '\x34', 1681 - 1673), nzTpIcepk0o8('\060' + '\x6f' + chr(2178 - 2125) + chr(0b110100), 0o10), nzTpIcepk0o8('\060' + chr(111) + '\061' + chr(0b110 + 0o55) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(0b11 + 0o55) + chr(111) + chr(2353 - 2302) + chr(0b11 + 0o63) + chr(1506 - 1454), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110010) + '\061' + '\x37', 0b1000), nzTpIcepk0o8(chr(48) + chr(4025 - 3914) + chr(1200 - 1149) + '\x33' + '\067', ord("\x08")), nzTpIcepk0o8(chr(0b1111 + 0o41) + chr(0b0 + 0o157) + chr(1151 - 1100) + chr(48) + chr(225 - 173), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(0b100010 + 0o17) + chr(1600 - 1551) + chr(0b110111), 4707 - 4699), nzTpIcepk0o8('\x30' + chr(9443 - 9332) + chr(50) + chr(53) + chr(0b111 + 0o55), 24849 - 24841), nzTpIcepk0o8(chr(1002 - 954) + '\x6f' + chr(0b101001 + 0o12) + '\x35' + '\063', ord("\x08")), nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(111) + chr(0b110010) + chr(0b11110 + 0o30) + chr(49), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101101 + 0o2) + chr(49) + chr(48) + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(2201 - 2153) + chr(2607 - 2496) + chr(0b110010) + chr(0b1001 + 0o55) + '\x31', 8), nzTpIcepk0o8('\x30' + chr(4429 - 4318) + '\062' + chr(1310 - 1255) + chr(50), 0o10), nzTpIcepk0o8(chr(808 - 760) + '\157' + chr(0b110010) + chr(0b10001 + 0o41) + chr(0b110011), 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(0b110001 + 0o0) + chr(2579 - 2525) + '\x32', 9738 - 9730), nzTpIcepk0o8('\060' + chr(111) + chr(1102 - 1053) + chr(0b10011 + 0o44) + chr(111 - 56), 8), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b11010 + 0o31) + chr(0b110100) + '\x36', ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + chr(0b100001 + 0o116) + chr(2329 - 2276) + chr(0b110000), 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'Q'), '\x64' + chr(2852 - 2751) + chr(99) + chr(0b1101111) + '\x64' + chr(0b10100 + 0o121))(chr(0b1000110 + 0o57) + chr(0b1110100) + '\x66' + chr(0b100110 + 0o7) + chr(0b100001 + 0o27)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def gxwZLOQCmuwc(hXMPsSrOQzbh):
qO6cEDA0xZYf = hXMPsSrOQzbh.CsodZJH6x9Tx[..., nzTpIcepk0o8(chr(1410 - 1362) + chr(111) + chr(0b110000), 29997 - 29989), nDF4gVNx0u9Q.newaxis]
DQZxlnhQweEZ = hXMPsSrOQzbh.CsodZJH6x9Tx[..., nzTpIcepk0o8(chr(743 - 695) + chr(1118 - 1007) + chr(0b110001), 8):]
PT32xG247TS3 = (qO6cEDA0xZYf > nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(1335 - 1287), 8)) & (qO6cEDA0xZYf == DQZxlnhQweEZ)
VwOu8WkJ9cpc = nDF4gVNx0u9Q.qX60lO1lgHA5(PT32xG247TS3, axis=-nzTpIcepk0o8(chr(48) + chr(0b1001011 + 0o44) + '\061', 8))
if roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'=\xc3\xbb=\xe4\xc3\\\xda\xa5\xb7\x1cd'), chr(100) + chr(101) + chr(0b1100011) + chr(0b1101111) + chr(0b1100100) + chr(0b1100101))('\165' + chr(0b1110100) + chr(102) + '\055' + chr(0b1000 + 0o60))) is not None:
VwOu8WkJ9cpc &= ~hXMPsSrOQzbh.BBM8dxm7YWge
return VwOu8WkJ9cpc |
cggh/scikit-allel | allel/model/ndarray.py | Genotypes.is_het | def is_het(self, allele=None):
"""Find genotype calls that are heterozygous.
Returns
-------
out : ndarray, bool, shape (n_variants, n_samples)
Array where elements are True if the genotype call matches the
condition.
allele : int, optional
Heterozygous allele.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 1]],
... [[0, 1], [1, 1]],
... [[0, 2], [-1, -1]]])
>>> g.is_het()
array([[False, True],
[ True, False],
[ True, False]])
>>> g.is_het(2)
array([[False, False],
[False, False],
[ True, False]])
>>> v = g[:, 0]
>>> v
<GenotypeVector shape=(3, 2) dtype=int64>
0/0 0/1 0/2
>>> v.is_het()
array([False, True, True])
"""
allele1 = self.values[..., 0, np.newaxis] # type: np.ndarray
other_alleles = self.values[..., 1:] # type: np.ndarray
out = np.all(self.values >= 0, axis=-1) & np.any(allele1 != other_alleles, axis=-1)
if allele is not None:
out &= np.any(self.values == allele, axis=-1)
# handle mask
if self.mask is not None:
out &= ~self.mask
return out | python | def is_het(self, allele=None):
"""Find genotype calls that are heterozygous.
Returns
-------
out : ndarray, bool, shape (n_variants, n_samples)
Array where elements are True if the genotype call matches the
condition.
allele : int, optional
Heterozygous allele.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 1]],
... [[0, 1], [1, 1]],
... [[0, 2], [-1, -1]]])
>>> g.is_het()
array([[False, True],
[ True, False],
[ True, False]])
>>> g.is_het(2)
array([[False, False],
[False, False],
[ True, False]])
>>> v = g[:, 0]
>>> v
<GenotypeVector shape=(3, 2) dtype=int64>
0/0 0/1 0/2
>>> v.is_het()
array([False, True, True])
"""
allele1 = self.values[..., 0, np.newaxis] # type: np.ndarray
other_alleles = self.values[..., 1:] # type: np.ndarray
out = np.all(self.values >= 0, axis=-1) & np.any(allele1 != other_alleles, axis=-1)
if allele is not None:
out &= np.any(self.values == allele, axis=-1)
# handle mask
if self.mask is not None:
out &= ~self.mask
return out | [
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... | Find genotype calls that are heterozygous.
Returns
-------
out : ndarray, bool, shape (n_variants, n_samples)
Array where elements are True if the genotype call matches the
condition.
allele : int, optional
Heterozygous allele.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 1]],
... [[0, 1], [1, 1]],
... [[0, 2], [-1, -1]]])
>>> g.is_het()
array([[False, True],
[ True, False],
[ True, False]])
>>> g.is_het(2)
array([[False, False],
[False, False],
[ True, False]])
>>> v = g[:, 0]
>>> v
<GenotypeVector shape=(3, 2) dtype=int64>
0/0 0/1 0/2
>>> v.is_het()
array([False, True, True]) | [
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"heterozygous",
"."
] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/model/ndarray.py#L580-L625 | train | Find genotype calls that are heterozygous. | 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(0b10111 + 0o33) + chr(0b111 + 0o52) + '\x35', 46186 - 46178), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110 + 0o53) + '\x35', 24795 - 24787), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b10001 + 0o44) + chr(48), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b101100 + 0o5) + chr(48), 63734 - 63726), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(1909 - 1860) + '\x31' + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110011) + '\062' + chr(0b1011 + 0o45), 0o10), nzTpIcepk0o8('\060' + chr(0b1100 + 0o143) + '\065', 199 - 191), nzTpIcepk0o8('\x30' + '\157' + chr(2001 - 1952) + chr(55) + '\065', 60485 - 60477), nzTpIcepk0o8(chr(2081 - 2033) + chr(0b1011100 + 0o23) + chr(0b10110 + 0o34) + chr(0b10 + 0o63) + chr(52), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(326 - 277) + chr(0b10100 + 0o42) + chr(0b101110 + 0o5), ord("\x08")), nzTpIcepk0o8(chr(1925 - 1877) + '\157' + '\063', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(2084 - 2033) + chr(50) + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(49) + chr(295 - 240), 60963 - 60955), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(49) + '\062' + '\066', 0o10), nzTpIcepk0o8('\060' + '\157' + '\x35' + '\062', 0o10), nzTpIcepk0o8(chr(1204 - 1156) + '\157' + chr(0b110111) + chr(0b1100 + 0o45), 0o10), nzTpIcepk0o8(chr(0b1010 + 0o46) + chr(3222 - 3111) + '\x34' + chr(0b110 + 0o56), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(2399 - 2350) + chr(0b1100 + 0o47) + '\066', ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + '\061' + chr(0b100101 + 0o17), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110010) + '\067' + chr(0b110111), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1000000 + 0o57) + chr(0b110011) + '\067' + '\066', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(328 - 278) + chr(0b100001 + 0o21) + '\065', 429 - 421), nzTpIcepk0o8('\060' + chr(0b1110 + 0o141) + chr(1356 - 1307) + chr(0b1 + 0o65) + '\061', 0o10), nzTpIcepk0o8(chr(48) + chr(7610 - 7499) + chr(51) + '\x30' + chr(1935 - 1886), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(1441 - 1391) + '\x34' + chr(247 - 199), 0b1000), nzTpIcepk0o8('\x30' + chr(2326 - 2215) + chr(51) + chr(0b110110) + '\062', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(49) + chr(52) + '\063', 36251 - 36243), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b100110 + 0o21) + chr(0b11 + 0o64), 0b1000), nzTpIcepk0o8(chr(0b10001 + 0o37) + chr(0b1101111) + '\x31' + '\x37' + chr(1735 - 1686), 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(50) + '\x31' + chr(0b110001), 65154 - 65146), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\062' + '\064' + '\061', 0b1000), nzTpIcepk0o8('\060' + chr(8689 - 8578) + chr(54) + chr(0b101111 + 0o5), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + '\062' + '\x31', ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(0b100000 + 0o21) + '\067' + '\x31', 8), nzTpIcepk0o8(chr(48) + '\x6f' + '\063' + chr(51) + chr(0b11010 + 0o33), 9440 - 9432), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110010) + '\061' + chr(0b110011), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(51) + '\x35' + '\x33', 8303 - 8295), nzTpIcepk0o8(chr(0b110000) + chr(0b110001 + 0o76) + '\065' + '\x36', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1000011 + 0o54) + chr(0b110111) + chr(0b110001), 8), nzTpIcepk0o8('\x30' + chr(2725 - 2614) + chr(0b11011 + 0o26) + '\x36' + chr(0b110000), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(1624 - 1576) + chr(0b101110 + 0o101) + chr(0b110101) + chr(48), 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xa3'), '\x64' + chr(0b1100101) + '\x63' + chr(0b1101111) + chr(100) + '\145')(chr(117) + chr(10313 - 10197) + '\x66' + '\x2d' + chr(0b10110 + 0o42)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def CIhdTuaykgHR(hXMPsSrOQzbh, A94c267WMRU1=None):
qO6cEDA0xZYf = hXMPsSrOQzbh.CsodZJH6x9Tx[..., nzTpIcepk0o8('\060' + chr(0b11011 + 0o124) + '\x30', 16341 - 16333), nDF4gVNx0u9Q.newaxis]
DQZxlnhQweEZ = hXMPsSrOQzbh.CsodZJH6x9Tx[..., nzTpIcepk0o8(chr(1730 - 1682) + '\157' + '\061', ord("\x08")):]
VwOu8WkJ9cpc = nDF4gVNx0u9Q.qX60lO1lgHA5(hXMPsSrOQzbh.CsodZJH6x9Tx >= nzTpIcepk0o8(chr(0b110000) + chr(3751 - 3640) + chr(0b1101 + 0o43), 8), axis=-nzTpIcepk0o8(chr(0b110000) + chr(0b11101 + 0o122) + chr(298 - 249), 8)) & nDF4gVNx0u9Q.VF4pKOObtlPc(qO6cEDA0xZYf != DQZxlnhQweEZ, axis=-nzTpIcepk0o8(chr(0b101101 + 0o3) + chr(0b1011000 + 0o27) + '\061', 8))
if A94c267WMRU1 is not None:
VwOu8WkJ9cpc &= nDF4gVNx0u9Q.VF4pKOObtlPc(hXMPsSrOQzbh.CsodZJH6x9Tx == A94c267WMRU1, axis=-nzTpIcepk0o8('\060' + chr(111) + chr(49), 8))
if roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xcfOe0(\xa8hJ\xf5$d\xb1'), '\144' + chr(101) + '\x63' + chr(0b10010 + 0o135) + '\144' + chr(0b1100101))(chr(0b1001000 + 0o55) + chr(0b1100001 + 0o23) + chr(4862 - 4760) + chr(0b101101) + chr(1777 - 1721))) is not None:
VwOu8WkJ9cpc &= ~hXMPsSrOQzbh.BBM8dxm7YWge
return VwOu8WkJ9cpc |
cggh/scikit-allel | allel/model/ndarray.py | Genotypes.is_call | def is_call(self, call):
"""Locate genotypes with a given call.
Parameters
----------
call : array_like, int, shape (ploidy,)
The genotype call to find.
Returns
-------
out : ndarray, bool, shape (n_variants, n_samples)
Array where elements are True if the genotype is `call`.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 1]],
... [[0, 1], [1, 1]],
... [[0, 2], [-1, -1]]])
>>> g.is_call((0, 2))
array([[False, False],
[False, False],
[ True, False]])
>>> v = g[:, 0]
>>> v
<GenotypeVector shape=(3, 2) dtype=int64>
0/0 0/1 0/2
>>> v.is_call((0, 2))
array([False, False, True])
"""
# guard conditions
if not len(call) == self.shape[-1]:
raise ValueError('invalid call ploidy: %s', repr(call))
if self.ndim == 2:
call = np.asarray(call)[np.newaxis, :]
else:
call = np.asarray(call)[np.newaxis, np.newaxis, :]
out = np.all(self.values == call, axis=-1)
# handle mask
if self.mask is not None:
out &= ~self.mask
return out | python | def is_call(self, call):
"""Locate genotypes with a given call.
Parameters
----------
call : array_like, int, shape (ploidy,)
The genotype call to find.
Returns
-------
out : ndarray, bool, shape (n_variants, n_samples)
Array where elements are True if the genotype is `call`.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 1]],
... [[0, 1], [1, 1]],
... [[0, 2], [-1, -1]]])
>>> g.is_call((0, 2))
array([[False, False],
[False, False],
[ True, False]])
>>> v = g[:, 0]
>>> v
<GenotypeVector shape=(3, 2) dtype=int64>
0/0 0/1 0/2
>>> v.is_call((0, 2))
array([False, False, True])
"""
# guard conditions
if not len(call) == self.shape[-1]:
raise ValueError('invalid call ploidy: %s', repr(call))
if self.ndim == 2:
call = np.asarray(call)[np.newaxis, :]
else:
call = np.asarray(call)[np.newaxis, np.newaxis, :]
out = np.all(self.values == call, axis=-1)
# handle mask
if self.mask is not None:
out &= ~self.mask
return out | [
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Parameters
----------
call : array_like, int, shape (ploidy,)
The genotype call to find.
Returns
-------
out : ndarray, bool, shape (n_variants, n_samples)
Array where elements are True if the genotype is `call`.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 1]],
... [[0, 1], [1, 1]],
... [[0, 2], [-1, -1]]])
>>> g.is_call((0, 2))
array([[False, False],
[False, False],
[ True, False]])
>>> v = g[:, 0]
>>> v
<GenotypeVector shape=(3, 2) dtype=int64>
0/0 0/1 0/2
>>> v.is_call((0, 2))
array([False, False, True]) | [
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"call",
"."
] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/model/ndarray.py#L627-L674 | train | Return True if the genotype with a given call is present in the local cache. | 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(11314 - 11203) + chr(0b110100) + '\064', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(51) + '\x30' + chr(0b110100), 64194 - 64186), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\061' + chr(0b110001) + chr(0b11010 + 0o26), 0o10), nzTpIcepk0o8(chr(1927 - 1879) + chr(111) + '\x31' + '\x35' + chr(48), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x31' + chr(826 - 774) + '\067', 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(0b110010) + '\067' + chr(679 - 625), 48786 - 48778), nzTpIcepk0o8(chr(0b1101 + 0o43) + chr(0b1101111) + '\067' + chr(53), ord("\x08")), nzTpIcepk0o8(chr(0b100100 + 0o14) + chr(0b1101111) + chr(0b100010 + 0o20) + '\x37' + chr(0b101001 + 0o15), 8), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110001) + '\x32' + chr(50), 51516 - 51508), nzTpIcepk0o8(chr(1903 - 1855) + chr(11133 - 11022) + chr(0b100010 + 0o17) + chr(0b1010 + 0o55) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x33' + chr(0b10010 + 0o45) + chr(0b110011), 0o10), nzTpIcepk0o8(chr(97 - 49) + chr(111) + '\063' + chr(55) + chr(305 - 252), 0o10), nzTpIcepk0o8(chr(680 - 632) + chr(111) + chr(0b110111) + chr(1143 - 1089), 0o10), nzTpIcepk0o8(chr(81 - 33) + '\157' + chr(1237 - 1187) + chr(0b101001 + 0o12) + chr(0b110010 + 0o3), 24400 - 24392), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(51) + chr(0b110111) + '\x36', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(1817 - 1765) + chr(0b101101 + 0o11), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(51) + chr(0b110010) + '\x36', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(6898 - 6787) + chr(49) + '\066', 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x32' + '\x34' + chr(1198 - 1148), ord("\x08")), nzTpIcepk0o8('\060' + chr(4348 - 4237) + '\x31' + chr(387 - 332) + chr(0b110000), 0b1000), nzTpIcepk0o8(chr(399 - 351) + chr(111) + '\x32' + chr(0b110100 + 0o3) + chr(51), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b101101 + 0o102) + chr(1504 - 1449) + '\x32', 0o10), nzTpIcepk0o8('\060' + chr(0b1100101 + 0o12) + '\x36' + '\x35', 0b1000), nzTpIcepk0o8(chr(0b11110 + 0o22) + chr(0b1010100 + 0o33) + '\062' + '\x32' + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(0b101111 + 0o1) + chr(8712 - 8601) + chr(0b110010) + chr(367 - 314) + chr(0b11000 + 0o35), 23313 - 23305), nzTpIcepk0o8(chr(0b101010 + 0o6) + '\157' + chr(0b110010) + chr(0b1100 + 0o45) + chr(54), 28739 - 28731), nzTpIcepk0o8(chr(48) + chr(0b1011001 + 0o26) + chr(0b100001 + 0o20) + '\063' + chr(0b11001 + 0o34), 20222 - 20214), nzTpIcepk0o8('\060' + chr(1051 - 940) + '\x35' + '\x37', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b10100 + 0o35) + '\x36' + chr(52), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\x33' + chr(0b110011 + 0o3) + '\x30', ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + '\063' + '\x35' + chr(0b110011), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + '\061' + chr(0b101 + 0o55) + chr(0b10 + 0o60), 8), nzTpIcepk0o8('\x30' + '\x6f' + chr(2322 - 2272) + chr(0b110001) + '\x33', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(538 - 487) + chr(0b110000) + chr(0b101 + 0o53), ord("\x08")), nzTpIcepk0o8(chr(0b11 + 0o55) + chr(111) + chr(50) + chr(0b10001 + 0o40) + '\x32', 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + '\x32' + chr(54) + '\x36', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1100101 + 0o12) + '\063' + chr(0b110100) + '\060', 30920 - 30912), nzTpIcepk0o8(chr(48) + '\x6f' + '\062' + chr(267 - 217) + chr(0b1011 + 0o46), 0b1000), nzTpIcepk0o8(chr(954 - 906) + '\x6f' + chr(0b110001 + 0o4) + chr(0b100101 + 0o13), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x31' + chr(573 - 521) + '\x31', 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(1823 - 1770) + chr(0b110000), 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\n'), chr(100) + '\145' + '\143' + chr(692 - 581) + '\144' + '\x65')(chr(5894 - 5777) + '\164' + chr(102) + chr(993 - 948) + chr(2744 - 2688)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def qF_0SkS7TtlQ(hXMPsSrOQzbh, c76Yf40Q6MeM):
if not ftfygxgFas5X(c76Yf40Q6MeM) == roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'H\xac*%W\x87\x0f\xff\x14,\xc3\x9b'), chr(100) + chr(101) + chr(0b1100011) + chr(0b110111 + 0o70) + chr(0b1100100) + '\x65')(chr(1595 - 1478) + '\x74' + chr(102) + chr(45) + '\070'))[-nzTpIcepk0o8(chr(48) + '\157' + chr(2206 - 2157), 1892 - 1884)]:
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'M\xaa>\t\x0b\xd7Y\x9e1\x1a\x97\x91\x1e\xed\x92I\xbfj\xdbB\x9b\x1fF'), chr(0b1001000 + 0o34) + '\x65' + '\143' + chr(0b1101111) + '\x64' + chr(0b1100101))(chr(117) + chr(116) + chr(5886 - 5784) + chr(150 - 105) + '\070'), VWshwTzZfwvC(c76Yf40Q6MeM))
if roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'n\x8d\x10$/\x8e\x0f\xf1\x11K\xac\xbf'), chr(100) + '\x65' + '\143' + '\x6f' + chr(0b111111 + 0o45) + chr(0b111101 + 0o50))(chr(0b10010 + 0o143) + '\164' + chr(102) + chr(1232 - 1187) + chr(0b110001 + 0o7))) == nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(1800 - 1750), ord("\x08")):
c76Yf40Q6MeM = nDF4gVNx0u9Q.asarray(c76Yf40Q6MeM)[nDF4gVNx0u9Q.newaxis, :]
else:
c76Yf40Q6MeM = nDF4gVNx0u9Q.asarray(c76Yf40Q6MeM)[nDF4gVNx0u9Q.newaxis, nDF4gVNx0u9Q.newaxis, :]
VwOu8WkJ9cpc = nDF4gVNx0u9Q.qX60lO1lgHA5(hXMPsSrOQzbh.CsodZJH6x9Tx == c76Yf40Q6MeM, axis=-nzTpIcepk0o8(chr(48) + chr(0b1111 + 0o140) + chr(0b100 + 0o55), 8))
if roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'f\x86\x05P\x03\xc6P\x89\x0b,\x9c\x98'), '\x64' + chr(0b1110 + 0o127) + chr(0b1010110 + 0o15) + chr(0b1101111) + '\144' + chr(0b1100101))(chr(13343 - 13226) + chr(1696 - 1580) + chr(0b101001 + 0o75) + '\055' + '\070')) is not None:
VwOu8WkJ9cpc &= ~hXMPsSrOQzbh.BBM8dxm7YWge
return VwOu8WkJ9cpc |
cggh/scikit-allel | allel/model/ndarray.py | Genotypes.count_called | def count_called(self, axis=None):
"""Count called genotypes.
Parameters
----------
axis : int, optional
Axis over which to count, or None to perform overall count.
"""
b = self.is_called()
return np.sum(b, axis=axis) | python | def count_called(self, axis=None):
"""Count called genotypes.
Parameters
----------
axis : int, optional
Axis over which to count, or None to perform overall count.
"""
b = self.is_called()
return np.sum(b, axis=axis) | [
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Parameters
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axis : int, optional
Axis over which to count, or None to perform overall count. | [
"Count",
"called",
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"."
] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/model/ndarray.py#L676-L686 | train | Count the number of genotypes called over a given axis. | 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(1194 - 1144) + chr(52) + chr(2383 - 2334), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(49) + '\x34' + chr(0b1111 + 0o45), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\061' + chr(1177 - 1128) + '\x37', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1010010 + 0o35) + chr(1997 - 1947) + chr(0b110111) + '\063', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1010010 + 0o35) + chr(0b110111), 0o10), nzTpIcepk0o8(chr(48) + '\157' + '\x31' + chr(0b110101) + '\x32', 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + '\062' + chr(2924 - 2869) + chr(54), 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(0b10011 + 0o36) + chr(48), 0b1000), nzTpIcepk0o8(chr(2004 - 1956) + '\157' + chr(1552 - 1501) + chr(0b100000 + 0o20) + chr(0b10111 + 0o37), 0b1000), nzTpIcepk0o8('\x30' + chr(111) + '\x32' + chr(1331 - 1283) + '\x32', 0b1000), nzTpIcepk0o8(chr(0b0 + 0o60) + chr(0b111101 + 0o62) + chr(55) + chr(1940 - 1892), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + '\x33' + chr(0b101100 + 0o12) + '\062', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110011) + chr(519 - 469) + '\x35', 0b1000), nzTpIcepk0o8(chr(0b10010 + 0o36) + '\157' + chr(1041 - 992) + chr(0b101 + 0o55) + '\063', 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(711 - 662) + chr(0b110011), 35663 - 35655), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110011) + chr(52) + '\x30', 50354 - 50346), nzTpIcepk0o8(chr(48) + chr(9879 - 9768) + chr(0b110001) + '\061' + chr(1353 - 1305), 0b1000), nzTpIcepk0o8(chr(48) + chr(10522 - 10411) + '\061' + chr(0b101111 + 0o5) + '\064', 8), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b10011 + 0o37) + chr(938 - 887), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + '\063' + '\x32' + chr(1288 - 1240), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(2477 - 2423) + chr(0b110011), 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(887 - 836) + chr(433 - 383) + chr(0b10011 + 0o36), 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(49) + chr(0b110101) + '\x30', 53505 - 53497), nzTpIcepk0o8('\x30' + chr(111) + chr(0b101110 + 0o3) + chr(0b110010) + chr(0b101101 + 0o11), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\061' + '\x30' + chr(2137 - 2082), 14826 - 14818), nzTpIcepk0o8(chr(48) + chr(3946 - 3835) + chr(0b101100 + 0o6) + chr(0b0 + 0o64) + chr(0b11 + 0o55), 0b1000), nzTpIcepk0o8(chr(0b101000 + 0o10) + chr(0b1011011 + 0o24) + chr(0b110010) + '\064' + chr(453 - 405), 8), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b101110 + 0o3) + '\065' + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(2121 - 2073) + '\157' + chr(49) + '\x30' + chr(0b110001), 0b1000), nzTpIcepk0o8(chr(447 - 399) + '\157' + '\063' + '\062' + chr(50), 55619 - 55611), nzTpIcepk0o8('\060' + '\x6f' + chr(51) + chr(0b110001) + chr(54), ord("\x08")), nzTpIcepk0o8(chr(0b110000 + 0o0) + chr(0b10010 + 0o135) + chr(1722 - 1672) + chr(50) + chr(2500 - 2448), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(50) + chr(0b110100) + '\060', 8), nzTpIcepk0o8('\060' + chr(1839 - 1728) + chr(0b110001) + '\x30' + '\066', 39129 - 39121), nzTpIcepk0o8(chr(0b10101 + 0o33) + chr(0b1101111) + chr(0b110010) + chr(51) + '\x33', 0b1000), nzTpIcepk0o8(chr(1469 - 1421) + chr(0b1101111) + '\061' + '\061' + '\066', 30173 - 30165), nzTpIcepk0o8(chr(2115 - 2067) + chr(4040 - 3929) + '\062' + '\060' + '\062', 8), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x32' + chr(0b1110 + 0o43) + '\x37', 0b1000), nzTpIcepk0o8(chr(0b11001 + 0o27) + chr(0b1001110 + 0o41) + '\x31' + '\063', 8), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x31' + '\065' + '\x36', ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + chr(4891 - 4780) + '\x35' + '\060', 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x8f'), chr(0b1001011 + 0o31) + '\x65' + chr(1726 - 1627) + chr(0b1101111) + '\144' + chr(101))(chr(11722 - 11605) + chr(116) + chr(102) + chr(0b11110 + 0o17) + chr(0b111 + 0o61)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def Q3asjtWwVKPZ(hXMPsSrOQzbh, JD902pvyCLH1=None):
xFDEVQn5qSdh = hXMPsSrOQzbh.is_called()
return roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'\xce\x07#\xf8?.\xf2b\x87\xddT\xa4'), '\x64' + chr(101) + chr(99) + chr(111) + chr(0b1100100) + '\145')('\x75' + chr(116) + chr(8743 - 8641) + chr(45) + '\x38'))(xFDEVQn5qSdh, axis=JD902pvyCLH1) |
cggh/scikit-allel | allel/model/ndarray.py | Genotypes.count_missing | def count_missing(self, axis=None):
"""Count missing genotypes.
Parameters
----------
axis : int, optional
Axis over which to count, or None to perform overall count.
"""
b = self.is_missing()
return np.sum(b, axis=axis) | python | def count_missing(self, axis=None):
"""Count missing genotypes.
Parameters
----------
axis : int, optional
Axis over which to count, or None to perform overall count.
"""
b = self.is_missing()
return np.sum(b, axis=axis) | [
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Parameters
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axis : int, optional
Axis over which to count, or None to perform overall count. | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/model/ndarray.py#L688-L698 | train | Count missing genotypes. | 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(0b1010011 + 0o34) + chr(1431 - 1381) + '\x31' + chr(1850 - 1802), 59114 - 59106), nzTpIcepk0o8(chr(0b1111 + 0o41) + '\157' + chr(1617 - 1565) + chr(0b1010 + 0o55), 0b1000), nzTpIcepk0o8(chr(0b11 + 0o55) + chr(10369 - 10258) + chr(1919 - 1870) + chr(2190 - 2142) + chr(0b100000 + 0o26), 0b1000), nzTpIcepk0o8(chr(748 - 700) + '\157' + '\x32' + '\x32' + chr(48), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110010) + chr(50) + '\067', 0b1000), nzTpIcepk0o8(chr(0b101111 + 0o1) + chr(0b100010 + 0o115) + '\062' + chr(49) + '\066', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110001) + chr(644 - 592) + chr(0b10001 + 0o45), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b111000 + 0o67) + '\x37' + '\x36', 58062 - 58054), nzTpIcepk0o8(chr(0b11011 + 0o25) + chr(111) + '\x33' + chr(0b110100) + chr(0b10111 + 0o35), 0b1000), nzTpIcepk0o8(chr(1723 - 1675) + chr(0b1101111) + chr(1529 - 1479) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(0b1000 + 0o50) + chr(0b110010 + 0o75) + chr(0b10001 + 0o41) + chr(55) + chr(0b100011 + 0o20), 19861 - 19853), nzTpIcepk0o8('\060' + chr(8780 - 8669) + chr(0b110011) + chr(0b1011 + 0o53) + '\067', 0b1000), nzTpIcepk0o8(chr(664 - 616) + chr(10805 - 10694) + '\x35' + '\061', 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(53) + chr(0b110101), 0o10), nzTpIcepk0o8(chr(264 - 216) + chr(10023 - 9912) + chr(50) + chr(0b1100 + 0o51) + '\x30', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110011) + chr(0b110100) + '\065', 0o10), nzTpIcepk0o8(chr(0b100100 + 0o14) + chr(0b101101 + 0o102) + chr(0b101101 + 0o5) + chr(0b110011) + '\061', 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b1 + 0o60) + '\067' + '\062', 0b1000), nzTpIcepk0o8(chr(981 - 933) + chr(111) + chr(49) + '\062' + chr(0b110001), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101010 + 0o5) + chr(1420 - 1369) + chr(0b10101 + 0o37) + '\x35', 8), nzTpIcepk0o8(chr(150 - 102) + chr(0b1101111) + chr(51) + '\x36' + '\066', 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(1750 - 1698) + chr(55), 8), nzTpIcepk0o8('\060' + chr(0b1101011 + 0o4) + '\x33' + chr(0b101001 + 0o7) + '\062', ord("\x08")), nzTpIcepk0o8(chr(0b1110 + 0o42) + chr(3208 - 3097) + '\063' + chr(0b100010 + 0o25) + '\x30', 54680 - 54672), nzTpIcepk0o8(chr(48) + chr(0b1001101 + 0o42) + chr(0b110010 + 0o1) + chr(0b110110) + '\065', 37204 - 37196), nzTpIcepk0o8(chr(48) + chr(7981 - 7870) + '\x33' + chr(51) + chr(1683 - 1629), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110010) + chr(0b110000) + chr(1100 - 1050), 0o10), nzTpIcepk0o8(chr(138 - 90) + '\x6f' + chr(0b101011 + 0o7) + '\x32' + '\x33', 44852 - 44844), nzTpIcepk0o8('\x30' + chr(10315 - 10204) + chr(0b11100 + 0o25) + chr(1065 - 1011) + chr(0b101 + 0o53), 0o10), nzTpIcepk0o8(chr(1169 - 1121) + '\x6f' + chr(51) + chr(52) + chr(1356 - 1306), ord("\x08")), nzTpIcepk0o8(chr(1068 - 1020) + chr(5178 - 5067) + chr(0b11100 + 0o25) + chr(0b110100), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110001) + '\x35' + '\064', 60215 - 60207), nzTpIcepk0o8(chr(0b11011 + 0o25) + chr(3870 - 3759) + '\x31' + '\066' + '\x36', 52609 - 52601), nzTpIcepk0o8('\x30' + chr(0b100100 + 0o113) + chr(51) + chr(2330 - 2276) + chr(0b110001), 0o10), nzTpIcepk0o8(chr(0b101110 + 0o2) + chr(11703 - 11592) + '\x33' + chr(630 - 578) + '\x33', 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + '\x33' + chr(0b110010) + chr(492 - 444), 39465 - 39457), nzTpIcepk0o8(chr(1713 - 1665) + chr(0b1101111) + '\062' + '\x31' + '\x32', 0b1000), nzTpIcepk0o8('\060' + chr(4814 - 4703) + chr(0b110011) + chr(1997 - 1946), 0o10), nzTpIcepk0o8('\x30' + chr(5867 - 5756) + '\x37' + chr(1110 - 1055), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\062' + chr(0b10100 + 0o43) + '\x33', 8)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b110000) + chr(0b1010101 + 0o32) + '\x35' + chr(1545 - 1497), ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xa6'), '\144' + chr(2110 - 2009) + '\x63' + chr(5580 - 5469) + chr(0b100100 + 0o100) + '\145')(chr(117) + chr(116) + chr(0b1100110) + chr(0b101101) + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def iZDsTn5abbAQ(hXMPsSrOQzbh, JD902pvyCLH1=None):
xFDEVQn5qSdh = hXMPsSrOQzbh.zYFtC4_vxWk9()
return roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'\xe7D*\xd3\xaf\xca*T\xa5K\xd7\xa1'), chr(3646 - 3546) + '\x65' + chr(0b11111 + 0o104) + chr(0b1101111) + chr(0b101101 + 0o67) + '\145')(chr(13191 - 13074) + chr(116) + '\146' + '\055' + '\x38'))(xFDEVQn5qSdh, axis=JD902pvyCLH1) |
cggh/scikit-allel | allel/model/ndarray.py | Genotypes.count_hom | def count_hom(self, allele=None, axis=None):
"""Count homozygous genotypes.
Parameters
----------
allele : int, optional
Allele index.
axis : int, optional
Axis over which to count, or None to perform overall count.
"""
b = self.is_hom(allele=allele)
return np.sum(b, axis=axis) | python | def count_hom(self, allele=None, axis=None):
"""Count homozygous genotypes.
Parameters
----------
allele : int, optional
Allele index.
axis : int, optional
Axis over which to count, or None to perform overall count.
"""
b = self.is_hom(allele=allele)
return np.sum(b, axis=axis) | [
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Parameters
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allele : int, optional
Allele index.
axis : int, optional
Axis over which to count, or None to perform overall count. | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/model/ndarray.py#L700-L712 | train | Count homozygous genotypes. | 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(10172 - 10061) + '\x33' + chr(52) + '\061', 0o10), nzTpIcepk0o8(chr(1400 - 1352) + chr(4377 - 4266) + '\x33' + '\x33' + chr(0b110111), 11964 - 11956), nzTpIcepk0o8(chr(1108 - 1060) + '\x6f' + chr(0b110001) + '\064' + chr(51), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(8599 - 8488) + chr(1100 - 1045) + chr(51 - 3), 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(0b110010) + '\x32' + chr(0b110110), ord("\x08")), nzTpIcepk0o8(chr(1700 - 1652) + chr(111) + '\x33' + chr(0b1010 + 0o55) + chr(51), 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(49) + '\x33' + chr(941 - 886), 0o10), nzTpIcepk0o8('\x30' + chr(6978 - 6867) + '\x33' + '\x30' + chr(1176 - 1121), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110001) + chr(1119 - 1070) + chr(0b101001 + 0o15), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(50) + chr(51) + '\061', 6340 - 6332), nzTpIcepk0o8(chr(48) + '\157' + chr(54) + chr(0b110001 + 0o3), 0b1000), nzTpIcepk0o8(chr(0b111 + 0o51) + chr(0b1101111) + '\x33' + chr(0b1101 + 0o46) + '\066', 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(51) + chr(673 - 623) + chr(0b11001 + 0o32), 0o10), nzTpIcepk0o8(chr(0b10100 + 0o34) + chr(111) + '\x32' + chr(0b10001 + 0o45) + chr(1285 - 1235), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(49) + chr(915 - 867) + chr(0b110000), 0o10), nzTpIcepk0o8(chr(1975 - 1927) + '\x6f' + chr(0b110011) + chr(0b1010 + 0o55) + chr(0b110100), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(0b1110 + 0o45) + chr(51) + chr(0b110000), 0o10), nzTpIcepk0o8(chr(0b10 + 0o56) + chr(0b1001000 + 0o47) + chr(0b110011) + '\x36' + '\064', 0o10), nzTpIcepk0o8(chr(48) + chr(11306 - 11195) + chr(0b101001 + 0o16) + chr(0b100110 + 0o15), 0o10), nzTpIcepk0o8(chr(520 - 472) + chr(111) + chr(0b110110) + '\060', 6433 - 6425), nzTpIcepk0o8('\060' + chr(111) + chr(49) + chr(1727 - 1679) + chr(0b11000 + 0o32), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(10430 - 10319) + '\x31' + chr(0b1110 + 0o50) + '\062', 31399 - 31391), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b1000 + 0o52) + chr(52) + chr(0b110101 + 0o2), 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(0b110011), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x32' + chr(50) + chr(0b11100 + 0o32), 8), nzTpIcepk0o8(chr(0b10000 + 0o40) + chr(111) + '\x31' + '\061' + chr(0b1110 + 0o45), 40197 - 40189), nzTpIcepk0o8(chr(318 - 270) + '\157' + '\x32' + chr(0b10110 + 0o36) + chr(0b110011 + 0o1), 53693 - 53685), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b101011 + 0o13), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + '\x31' + chr(0b110100) + '\x33', 8), nzTpIcepk0o8(chr(48) + chr(0b1001 + 0o146) + '\063' + chr(0b11100 + 0o27), 2126 - 2118), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(49) + chr(54) + chr(0b1010 + 0o52), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\063' + chr(50) + '\x32', 0o10), nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(111) + '\x31' + chr(48) + '\064', 55075 - 55067), nzTpIcepk0o8(chr(48) + chr(6107 - 5996) + '\061' + chr(0b100000 + 0o21) + chr(0b110111), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110001) + chr(0b11101 + 0o27) + '\x32', 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(49) + chr(0b10100 + 0o42) + chr(0b10000 + 0o46), 6425 - 6417), nzTpIcepk0o8(chr(48) + chr(0b1 + 0o156) + '\x33' + chr(0b110110) + chr(55), 0o10), nzTpIcepk0o8(chr(673 - 625) + chr(111) + chr(0b1011 + 0o51) + chr(0b110111), 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(0b100100 + 0o15) + '\x35' + chr(50), 0b1000), nzTpIcepk0o8(chr(0b100000 + 0o20) + '\157' + chr(0b11111 + 0o22) + chr(2349 - 2297), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + chr(0b1100000 + 0o17) + '\x35' + chr(48), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xcf'), '\144' + chr(0b1010000 + 0o25) + chr(0b1100011) + chr(0b111011 + 0o64) + chr(5970 - 5870) + chr(3324 - 3223))('\165' + chr(116) + '\x66' + '\055' + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def JsZ76TY_stj3(hXMPsSrOQzbh, A94c267WMRU1=None, JD902pvyCLH1=None):
xFDEVQn5qSdh = hXMPsSrOQzbh.is_hom(allele=A94c267WMRU1)
return roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'\x8e\xbc\x0f{\xae\xbf\x13\xad\x0f\xc6X\x88'), chr(4305 - 4205) + '\145' + '\143' + chr(0b1100010 + 0o15) + '\x64' + chr(0b1100101))(chr(117) + chr(5582 - 5466) + '\x66' + '\055' + chr(0b111000)))(xFDEVQn5qSdh, axis=JD902pvyCLH1) |
cggh/scikit-allel | allel/model/ndarray.py | Genotypes.count_hom_ref | def count_hom_ref(self, axis=None):
"""Count homozygous reference genotypes.
Parameters
----------
axis : int, optional
Axis over which to count, or None to perform overall count.
"""
b = self.is_hom_ref()
return np.sum(b, axis=axis) | python | def count_hom_ref(self, axis=None):
"""Count homozygous reference genotypes.
Parameters
----------
axis : int, optional
Axis over which to count, or None to perform overall count.
"""
b = self.is_hom_ref()
return np.sum(b, axis=axis) | [
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axis : int, optional
Axis over which to count, or None to perform overall count. | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/model/ndarray.py#L714-L724 | train | Count homozygous reference genotypes. | 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(1697 - 1648) + '\061' + chr(596 - 541), 0b1000), nzTpIcepk0o8(chr(0b11111 + 0o21) + '\x6f' + chr(54), 41756 - 41748), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(1120 - 1071) + '\x36' + '\x37', 0b1000), nzTpIcepk0o8('\060' + '\x6f' + '\x36' + chr(1813 - 1762), 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\061' + chr(53) + '\x35', 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(50) + chr(0b111 + 0o53) + '\063', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b101101 + 0o102) + chr(2304 - 2253) + chr(1242 - 1191) + '\063', 0o10), nzTpIcepk0o8('\060' + '\157' + chr(49) + chr(0b1111 + 0o42) + chr(50), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(7597 - 7486) + chr(50) + chr(0b110111) + chr(50), 0o10), nzTpIcepk0o8(chr(0b10010 + 0o36) + '\x6f' + chr(0b11011 + 0o27) + chr(50) + '\x34', 0b1000), nzTpIcepk0o8(chr(0b101011 + 0o5) + chr(0b1010110 + 0o31) + chr(0b110010) + chr(2465 - 2414) + '\063', 0o10), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x33' + chr(0b11000 + 0o33) + '\x31', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1100100 + 0o13) + chr(0b110011) + chr(0b110100 + 0o2) + chr(0b11011 + 0o34), 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(49) + chr(0b110000) + chr(317 - 268), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(6153 - 6042) + '\062' + '\066' + chr(736 - 685), 62852 - 62844), nzTpIcepk0o8('\x30' + '\157' + '\x31' + '\x37' + chr(0b110110), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101101 + 0o2) + '\061' + '\x37' + chr(0b10110 + 0o32), 14124 - 14116), nzTpIcepk0o8(chr(396 - 348) + '\157' + chr(1738 - 1688) + '\067', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\063' + '\065' + chr(819 - 770), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101101 + 0o2) + '\x31' + chr(735 - 684), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(508 - 458) + chr(51) + '\061', ord("\x08")), nzTpIcepk0o8('\x30' + '\157' + chr(49) + chr(0b110101) + '\067', 0o10), nzTpIcepk0o8(chr(476 - 428) + chr(0b1011100 + 0o23) + chr(0b110011 + 0o0) + '\x36' + chr(1859 - 1810), 0b1000), nzTpIcepk0o8(chr(382 - 334) + chr(0b1101111) + '\x34' + '\x32', ord("\x08")), nzTpIcepk0o8(chr(1758 - 1710) + '\x6f' + chr(2176 - 2125) + chr(0b110001) + chr(0b11110 + 0o26), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x31' + chr(0b110101) + chr(0b10001 + 0o46), 8), nzTpIcepk0o8(chr(48) + chr(111) + chr(51) + '\062' + chr(53), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b110101 + 0o72) + chr(0b110001) + chr(0b110001) + '\065', 0b1000), nzTpIcepk0o8(chr(48) + chr(4826 - 4715) + '\x31' + chr(0b10010 + 0o41) + chr(0b110001), 4032 - 4024), nzTpIcepk0o8(chr(1447 - 1399) + chr(0b1101111) + chr(2209 - 2159) + chr(0b110 + 0o57) + '\061', 0b1000), nzTpIcepk0o8(chr(0b11110 + 0o22) + '\157' + chr(2508 - 2457) + chr(49) + chr(53), ord("\x08")), nzTpIcepk0o8(chr(0b10010 + 0o36) + chr(0b11100 + 0o123) + chr(1040 - 990) + chr(0b110111), 8), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110101) + '\063', 0b1000), nzTpIcepk0o8('\x30' + '\157' + chr(0b110111) + chr(0b11010 + 0o34), 0b1000), nzTpIcepk0o8(chr(1063 - 1015) + chr(0b1101111) + chr(1910 - 1859) + chr(1864 - 1809) + '\067', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110010) + chr(571 - 522) + '\x36', 0o10), nzTpIcepk0o8(chr(0b10011 + 0o35) + chr(0b1100001 + 0o16) + '\063' + chr(55) + '\x36', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110001) + chr(0b110111) + chr(0b1100 + 0o52), 8), nzTpIcepk0o8(chr(0b1100 + 0o44) + chr(0b1111 + 0o140) + '\x33' + '\x34' + chr(1262 - 1211), 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(49) + chr(48) + chr(0b110111), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + '\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'a'), '\x64' + '\145' + chr(0b1100011) + chr(0b1101111) + chr(6268 - 6168) + chr(101))(chr(117) + chr(0b1010100 + 0o40) + chr(0b11011 + 0o113) + '\055' + chr(56)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def X6cNGUNyQ5ir(hXMPsSrOQzbh, JD902pvyCLH1=None):
xFDEVQn5qSdh = hXMPsSrOQzbh.is_hom_ref()
return roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b' e\x1bpU\xd7\x97 \xfb\xcb\xf7\x8f'), chr(100) + chr(101) + '\x63' + chr(111) + chr(100) + chr(0b1100101))('\x75' + chr(1250 - 1134) + chr(2955 - 2853) + chr(1835 - 1790) + chr(56)))(xFDEVQn5qSdh, axis=JD902pvyCLH1) |
cggh/scikit-allel | allel/model/ndarray.py | Genotypes.count_hom_alt | def count_hom_alt(self, axis=None):
"""Count homozygous alternate genotypes.
Parameters
----------
axis : int, optional
Axis over which to count, or None to perform overall count.
"""
b = self.is_hom_alt()
return np.sum(b, axis=axis) | python | def count_hom_alt(self, axis=None):
"""Count homozygous alternate genotypes.
Parameters
----------
axis : int, optional
Axis over which to count, or None to perform overall count.
"""
b = self.is_hom_alt()
return np.sum(b, axis=axis) | [
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Axis over which to count, or None to perform overall count. | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/model/ndarray.py#L726-L736 | train | Count homozygous alternate genotypes. | 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(1553 - 1505) + '\157' + chr(0b110010) + chr(51) + chr(49), 32137 - 32129), nzTpIcepk0o8('\060' + chr(0b10101 + 0o132) + '\066' + chr(0b110100), 0b1000), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x31' + '\x36' + chr(0b110001), 0o10), nzTpIcepk0o8(chr(0b10010 + 0o36) + '\x6f' + '\x32' + '\x32' + chr(53), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\062' + '\060' + '\x34', 0o10), nzTpIcepk0o8('\x30' + chr(111) + chr(0b10111 + 0o32) + chr(0b110010 + 0o4) + '\x35', 0o10), nzTpIcepk0o8(chr(2219 - 2171) + '\157' + chr(50) + chr(0b11101 + 0o26) + chr(0b100101 + 0o17), 49974 - 49966), nzTpIcepk0o8(chr(0b110000) + chr(3091 - 2980) + chr(329 - 276) + '\067', ord("\x08")), nzTpIcepk0o8(chr(0b100 + 0o54) + chr(0b1101111) + chr(0b110101) + chr(53), 0b1000), nzTpIcepk0o8('\x30' + chr(11629 - 11518) + '\x32' + '\x34' + chr(54), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(4451 - 4340) + '\x32' + '\067' + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(741 - 693) + '\157' + chr(1908 - 1858) + chr(52) + chr(2776 - 2722), 8), nzTpIcepk0o8(chr(2161 - 2113) + '\157' + '\x32' + chr(0b110110 + 0o1) + chr(0b110001), 0o10), nzTpIcepk0o8(chr(1522 - 1474) + chr(0b101100 + 0o103) + chr(51) + '\x33', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\061' + '\064', 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(55) + chr(1795 - 1745), 0o10), nzTpIcepk0o8(chr(48) + chr(7158 - 7047) + chr(0b110010) + chr(0b110011) + '\x31', 8), nzTpIcepk0o8(chr(0b110000) + chr(11786 - 11675) + chr(252 - 198) + chr(2392 - 2339), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\064' + '\064', 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110001) + '\067' + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(49) + chr(0b11011 + 0o25) + chr(52), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110011) + chr(0b1 + 0o61) + chr(55), 59379 - 59371), nzTpIcepk0o8(chr(0b1101 + 0o43) + '\x6f' + chr(51) + chr(0b1010 + 0o51) + '\x33', 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x31' + '\067' + chr(0b11110 + 0o30), 4094 - 4086), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\063' + '\065', 0o10), nzTpIcepk0o8(chr(0b0 + 0o60) + chr(3584 - 3473) + chr(55) + '\x34', 0o10), nzTpIcepk0o8(chr(0b10 + 0o56) + chr(0b1101011 + 0o4) + '\x32' + chr(0b101110 + 0o6) + chr(1682 - 1634), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(49) + chr(0b110101) + chr(51), ord("\x08")), nzTpIcepk0o8(chr(0b101100 + 0o4) + '\x6f' + chr(0b110110) + '\064', 8), nzTpIcepk0o8(chr(949 - 901) + '\157' + chr(0b110011) + '\066' + chr(2389 - 2334), 41272 - 41264), nzTpIcepk0o8(chr(350 - 302) + '\x6f' + '\062' + chr(197 - 147) + chr(0b101001 + 0o13), 0o10), nzTpIcepk0o8(chr(1770 - 1722) + '\157' + chr(0b110001) + chr(0b110011) + chr(0b10 + 0o61), ord("\x08")), nzTpIcepk0o8(chr(0b1001 + 0o47) + chr(111) + chr(0b10110 + 0o34) + chr(0b110011 + 0o1) + chr(0b10111 + 0o36), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1010100 + 0o33) + chr(0b110010) + chr(0b111 + 0o57) + '\x30', 0o10), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(49) + '\060' + '\x37', 0b1000), nzTpIcepk0o8(chr(2270 - 2222) + chr(0b100001 + 0o116) + chr(0b110011) + chr(0b110101 + 0o1), ord("\x08")), nzTpIcepk0o8('\x30' + chr(5526 - 5415) + '\x31' + '\x32' + chr(0b1110 + 0o44), ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + chr(49) + '\065' + chr(49), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(51) + chr(521 - 470) + '\x35', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110001) + chr(0b110110) + chr(185 - 132), 8)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + chr(0b1010100 + 0o33) + chr(0b11001 + 0o34) + chr(0b110000), 14982 - 14974)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xb7'), '\x64' + chr(0b1000011 + 0o42) + chr(0b1100011) + chr(111) + '\144' + chr(0b111011 + 0o52))('\x75' + chr(116) + chr(0b1100110) + chr(1405 - 1360) + chr(0b101100 + 0o14)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def N2SfjBOPDplP(hXMPsSrOQzbh, JD902pvyCLH1=None):
xFDEVQn5qSdh = hXMPsSrOQzbh.is_hom_alt()
return roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'\xf6W\x1d\xd6\xbc1\xd0El\xf9\xd1\xf0'), '\x64' + chr(0b1100101) + chr(9294 - 9195) + '\x6f' + '\144' + chr(2291 - 2190))('\x75' + chr(0b111100 + 0o70) + chr(102) + '\x2d' + '\x38'))(xFDEVQn5qSdh, axis=JD902pvyCLH1) |
cggh/scikit-allel | allel/model/ndarray.py | Genotypes.count_het | def count_het(self, allele=None, axis=None):
"""Count heterozygous genotypes.
Parameters
----------
allele : int, optional
Allele index.
axis : int, optional
Axis over which to count, or None to perform overall count.
"""
b = self.is_het(allele=allele)
return np.sum(b, axis=axis) | python | def count_het(self, allele=None, axis=None):
"""Count heterozygous genotypes.
Parameters
----------
allele : int, optional
Allele index.
axis : int, optional
Axis over which to count, or None to perform overall count.
"""
b = self.is_het(allele=allele)
return np.sum(b, axis=axis) | [
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Parameters
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allele : int, optional
Allele index.
axis : int, optional
Axis over which to count, or None to perform overall count. | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/model/ndarray.py#L738-L750 | train | Count heterozygous genotypes. | 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(0b100010 + 0o16) + chr(0b1001 + 0o146) + '\x33' + chr(2135 - 2085) + chr(51), 37909 - 37901), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b10110 + 0o33) + chr(51) + chr(48), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(0b1011 + 0o47) + chr(50) + chr(0b101000 + 0o14), ord("\x08")), nzTpIcepk0o8(chr(161 - 113) + chr(111) + '\062' + chr(0b1101 + 0o45) + chr(0b100101 + 0o15), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b11100 + 0o123) + '\062' + '\065' + chr(49), 41960 - 41952), nzTpIcepk0o8('\x30' + '\157' + chr(1536 - 1486) + '\x32' + chr(0b110111), 0b1000), nzTpIcepk0o8(chr(1159 - 1111) + chr(111) + chr(0b110111), 57672 - 57664), nzTpIcepk0o8(chr(0b101 + 0o53) + chr(0b10011 + 0o134) + chr(2380 - 2329) + chr(0b110100) + '\x33', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(11319 - 11208) + '\061' + chr(0b10011 + 0o44) + chr(0b110100), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\061' + '\x32' + '\067', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b110010) + chr(0b10000 + 0o43) + chr(1644 - 1596), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b11000 + 0o32) + chr(0b110011) + chr(53), 15788 - 15780), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(2726 - 2672) + chr(0b11110 + 0o24), 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110010 + 0o0) + '\x31' + chr(0b1010 + 0o55), 9103 - 9095), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110001 + 0o6) + '\066', ord("\x08")), nzTpIcepk0o8(chr(520 - 472) + '\x6f' + chr(49) + chr(0b110111) + chr(0b110000), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + '\x32' + chr(0b101110 + 0o4) + chr(0b110111), 8), nzTpIcepk0o8(chr(1416 - 1368) + chr(0b1101111) + '\x31' + chr(48) + chr(2253 - 2203), 0o10), nzTpIcepk0o8(chr(0b100000 + 0o20) + chr(8118 - 8007) + '\x32' + chr(0b110111) + '\x33', 8708 - 8700), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x31' + chr(55) + chr(2871 - 2817), 0o10), nzTpIcepk0o8('\x30' + chr(4373 - 4262) + chr(51) + chr(0b110100) + '\x32', 0o10), nzTpIcepk0o8(chr(0b101010 + 0o6) + '\157' + chr(0b11001 + 0o31) + '\x32' + '\x33', 0o10), nzTpIcepk0o8(chr(1033 - 985) + chr(0b10101 + 0o132) + '\x35' + '\066', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b101110 + 0o11) + chr(0b10100 + 0o35), 8040 - 8032), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110110) + chr(54), 0o10), nzTpIcepk0o8(chr(0b101 + 0o53) + chr(0b1101111) + '\x31' + chr(193 - 143) + chr(0b110110), 55645 - 55637), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b10000 + 0o43) + '\x31' + chr(749 - 700), ord("\x08")), nzTpIcepk0o8(chr(1141 - 1093) + chr(4143 - 4032) + chr(0b10101 + 0o40) + chr(0b110000), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(2758 - 2704) + chr(0b110110), 8), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(576 - 522) + '\x37', ord("\x08")), nzTpIcepk0o8(chr(0b1 + 0o57) + chr(0b1101111) + '\062' + chr(0b100011 + 0o22) + chr(54), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110001) + chr(55), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + chr(0b100001 + 0o21) + chr(70 - 20), 0b1000), nzTpIcepk0o8(chr(0b1011 + 0o45) + chr(10681 - 10570) + chr(1141 - 1091) + chr(55) + chr(54), 61592 - 61584), nzTpIcepk0o8(chr(0b101101 + 0o3) + chr(7785 - 7674) + chr(51) + chr(296 - 245) + chr(1909 - 1854), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b111010 + 0o65) + '\x32' + chr(777 - 723) + '\062', 59545 - 59537), nzTpIcepk0o8(chr(0b110000) + chr(3704 - 3593) + chr(0b11 + 0o60) + chr(55) + '\x36', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1000001 + 0o56) + chr(0b110011) + '\067' + chr(0b110000), 8786 - 8778), nzTpIcepk0o8(chr(48) + chr(6470 - 6359) + '\063' + '\x34' + chr(0b100001 + 0o25), 0b1000), nzTpIcepk0o8(chr(0b101010 + 0o6) + chr(0b1010000 + 0o37) + '\065' + chr(51), ord("\x08"))][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(111) + chr(371 - 318) + chr(0b110000), 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xfd'), '\144' + chr(5016 - 4915) + chr(1197 - 1098) + chr(5398 - 5287) + chr(958 - 858) + chr(2527 - 2426))('\165' + '\164' + chr(0b1100110) + chr(1256 - 1211) + chr(0b1000 + 0o60)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def e8mtxPZiFN3E(hXMPsSrOQzbh, A94c267WMRU1=None, JD902pvyCLH1=None):
xFDEVQn5qSdh = hXMPsSrOQzbh.is_het(allele=A94c267WMRU1)
return roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'\xbc;\xf8\xd1\x91\xd3K\x89=\x08\xf4\xcb'), chr(0b1100100) + chr(0b1000101 + 0o40) + '\143' + chr(0b100011 + 0o114) + chr(0b1100100) + chr(0b11001 + 0o114))('\x75' + chr(0b1110100) + chr(102) + chr(0b101101) + chr(0b110000 + 0o10)))(xFDEVQn5qSdh, axis=JD902pvyCLH1) |
cggh/scikit-allel | allel/model/ndarray.py | Genotypes.count_call | def count_call(self, call, axis=None):
"""Count genotypes with a given call.
Parameters
----------
call : array_like, int, shape (ploidy,)
The genotype call to find.
axis : int, optional
Axis over which to count, or None to perform overall count.
"""
b = self.is_call(call=call)
return np.sum(b, axis=axis) | python | def count_call(self, call, axis=None):
"""Count genotypes with a given call.
Parameters
----------
call : array_like, int, shape (ploidy,)
The genotype call to find.
axis : int, optional
Axis over which to count, or None to perform overall count.
"""
b = self.is_call(call=call)
return np.sum(b, axis=axis) | [
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Parameters
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call : array_like, int, shape (ploidy,)
The genotype call to find.
axis : int, optional
Axis over which to count, or None to perform overall count. | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/model/ndarray.py#L752-L764 | train | Count the number of genotypes with a given call. | 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(0b1011001 + 0o26) + chr(1268 - 1214) + '\064', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(2895 - 2784) + chr(53) + chr(54), ord("\x08")), nzTpIcepk0o8(chr(0b110 + 0o52) + chr(0b1101111) + chr(0b100100 + 0o15) + chr(52) + chr(307 - 254), 0o10), nzTpIcepk0o8(chr(2158 - 2110) + chr(0b1101111) + chr(0b110010 + 0o0) + chr(48) + chr(0b101101 + 0o5), 0b1000), nzTpIcepk0o8(chr(0b101000 + 0o10) + '\157' + '\x32' + '\x32' + chr(0b11 + 0o57), 53137 - 53129), nzTpIcepk0o8(chr(1490 - 1442) + chr(0b1011011 + 0o24) + '\063' + '\x30' + '\x32', 0o10), nzTpIcepk0o8(chr(0b101010 + 0o6) + chr(111) + chr(0b110010) + chr(1770 - 1721) + chr(1640 - 1592), ord("\x08")), nzTpIcepk0o8('\x30' + chr(3580 - 3469) + '\062' + chr(467 - 414) + '\062', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(49) + chr(1193 - 1138) + '\x32', 18210 - 18202), nzTpIcepk0o8(chr(48) + chr(3561 - 3450) + chr(0b110001) + chr(0b10100 + 0o34) + chr(829 - 780), 63107 - 63099), nzTpIcepk0o8(chr(48) + '\x6f' + chr(49) + '\061' + chr(276 - 223), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(762 - 707) + chr(0b100101 + 0o20), 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(51) + '\x37' + chr(0b110100), 45812 - 45804), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110001) + chr(0b110111) + chr(2157 - 2109), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b110010 + 0o75) + '\061' + chr(0b110111) + '\061', 0b1000), nzTpIcepk0o8(chr(1012 - 964) + '\x6f' + chr(0b101101 + 0o4) + chr(53) + chr(48), 0b1000), nzTpIcepk0o8(chr(0b1110 + 0o42) + '\157' + '\x31' + chr(0b110000 + 0o6) + '\067', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b100000 + 0o117) + chr(50) + '\064' + '\x36', 65041 - 65033), nzTpIcepk0o8(chr(0b11111 + 0o21) + chr(8021 - 7910) + chr(0b110011) + chr(1200 - 1151) + chr(2242 - 2191), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110010) + chr(0b110101) + chr(1156 - 1102), 37555 - 37547), nzTpIcepk0o8('\060' + '\157' + chr(0b110010) + chr(237 - 185) + chr(940 - 886), 8), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\061' + chr(54) + '\063', 2018 - 2010), nzTpIcepk0o8(chr(1989 - 1941) + '\157' + chr(0b110001 + 0o2) + chr(50) + '\x32', ord("\x08")), nzTpIcepk0o8('\060' + chr(1655 - 1544) + chr(217 - 167) + '\061' + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + '\061' + '\065' + '\062', 18226 - 18218), nzTpIcepk0o8(chr(48) + '\157' + '\x31' + chr(0b101100 + 0o11) + '\060', 8), nzTpIcepk0o8(chr(0b110000) + chr(9202 - 9091) + chr(1635 - 1584) + chr(50) + '\x31', 0b1000), nzTpIcepk0o8(chr(0b1100 + 0o44) + chr(111) + chr(52) + chr(0b101011 + 0o7), 27426 - 27418), nzTpIcepk0o8('\x30' + chr(7808 - 7697) + chr(0b110011) + chr(1800 - 1752) + chr(52), 0o10), nzTpIcepk0o8(chr(2108 - 2060) + chr(111) + chr(0b100001 + 0o23) + chr(1010 - 956), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\062' + chr(0b110101) + chr(0b10010 + 0o40), 8), nzTpIcepk0o8(chr(0b11 + 0o55) + '\x6f' + '\x31' + '\x33' + '\x30', 41873 - 41865), nzTpIcepk0o8('\x30' + chr(6260 - 6149) + chr(51) + chr(0b110101) + chr(1109 - 1060), 0o10), nzTpIcepk0o8(chr(269 - 221) + '\x6f' + chr(49) + chr(0b11010 + 0o26) + chr(0b110011), 18199 - 18191), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110010) + chr(2548 - 2496) + '\065', ord("\x08")), nzTpIcepk0o8(chr(0b1010 + 0o46) + '\x6f' + chr(0b1001 + 0o55) + chr(0b110101), ord("\x08")), nzTpIcepk0o8('\x30' + chr(4758 - 4647) + '\062' + '\067' + chr(52), 28406 - 28398), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x36' + '\063', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b100011 + 0o114) + chr(0b110001) + chr(0b110101 + 0o2) + '\060', 8), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x32' + '\061' + '\x37', 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + chr(0b1101111) + '\065' + chr(1953 - 1905), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x1a'), '\x64' + chr(0b1100001 + 0o4) + '\143' + chr(2363 - 2252) + '\x64' + '\x65')(chr(9874 - 9757) + '\164' + chr(0b1100110) + '\055' + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def cFxU5RS3YVGZ(hXMPsSrOQzbh, c76Yf40Q6MeM, JD902pvyCLH1=None):
xFDEVQn5qSdh = hXMPsSrOQzbh.is_call(call=c76Yf40Q6MeM)
return roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'[M\t\xc1\xaa\x86\xc4\xc0;\x1e!k'), '\x64' + chr(9265 - 9164) + chr(0b1100011) + chr(5031 - 4920) + '\144' + chr(0b1100101))('\165' + chr(0b1001101 + 0o47) + chr(102) + chr(0b101101) + chr(1684 - 1628)))(xFDEVQn5qSdh, axis=JD902pvyCLH1) |
cggh/scikit-allel | allel/model/ndarray.py | Genotypes.to_n_ref | def to_n_ref(self, fill=0, dtype='i1'):
"""Transform each genotype call into the number of
reference alleles.
Parameters
----------
fill : int, optional
Use this value to represent missing calls.
dtype : dtype, optional
Output dtype.
Returns
-------
out : ndarray, int8, shape (n_variants, n_samples)
Array of ref alleles per genotype call.
Notes
-----
By default this function returns 0 for missing genotype calls
**and** for homozygous non-reference genotype calls. Use the
`fill` argument to change how missing calls are represented.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 1]],
... [[0, 2], [1, 1]],
... [[2, 2], [-1, -1]]])
>>> g.to_n_ref()
array([[2, 1],
[1, 0],
[0, 0]], dtype=int8)
>>> g.to_n_ref(fill=-1)
array([[ 2, 1],
[ 1, 0],
[ 0, -1]], dtype=int8)
>>> v = g[:, 0]
>>> v
<GenotypeVector shape=(3, 2) dtype=int64>
0/0 0/2 2/2
>>> v.to_n_ref()
array([2, 1, 0], dtype=int8)
"""
# count number of alternate alleles
out = np.empty(self.shape[:-1], dtype=dtype)
np.sum(self.values == 0, axis=-1, out=out)
# fill missing calls
if fill != 0:
m = self.is_missing()
out[m] = fill
# handle mask
if self.mask is not None:
out[self.mask] = fill
return out | python | def to_n_ref(self, fill=0, dtype='i1'):
"""Transform each genotype call into the number of
reference alleles.
Parameters
----------
fill : int, optional
Use this value to represent missing calls.
dtype : dtype, optional
Output dtype.
Returns
-------
out : ndarray, int8, shape (n_variants, n_samples)
Array of ref alleles per genotype call.
Notes
-----
By default this function returns 0 for missing genotype calls
**and** for homozygous non-reference genotype calls. Use the
`fill` argument to change how missing calls are represented.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 1]],
... [[0, 2], [1, 1]],
... [[2, 2], [-1, -1]]])
>>> g.to_n_ref()
array([[2, 1],
[1, 0],
[0, 0]], dtype=int8)
>>> g.to_n_ref(fill=-1)
array([[ 2, 1],
[ 1, 0],
[ 0, -1]], dtype=int8)
>>> v = g[:, 0]
>>> v
<GenotypeVector shape=(3, 2) dtype=int64>
0/0 0/2 2/2
>>> v.to_n_ref()
array([2, 1, 0], dtype=int8)
"""
# count number of alternate alleles
out = np.empty(self.shape[:-1], dtype=dtype)
np.sum(self.values == 0, axis=-1, out=out)
# fill missing calls
if fill != 0:
m = self.is_missing()
out[m] = fill
# handle mask
if self.mask is not None:
out[self.mask] = fill
return out | [
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... | Transform each genotype call into the number of
reference alleles.
Parameters
----------
fill : int, optional
Use this value to represent missing calls.
dtype : dtype, optional
Output dtype.
Returns
-------
out : ndarray, int8, shape (n_variants, n_samples)
Array of ref alleles per genotype call.
Notes
-----
By default this function returns 0 for missing genotype calls
**and** for homozygous non-reference genotype calls. Use the
`fill` argument to change how missing calls are represented.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 1]],
... [[0, 2], [1, 1]],
... [[2, 2], [-1, -1]]])
>>> g.to_n_ref()
array([[2, 1],
[1, 0],
[0, 0]], dtype=int8)
>>> g.to_n_ref(fill=-1)
array([[ 2, 1],
[ 1, 0],
[ 0, -1]], dtype=int8)
>>> v = g[:, 0]
>>> v
<GenotypeVector shape=(3, 2) dtype=int64>
0/0 0/2 2/2
>>> v.to_n_ref()
array([2, 1, 0], dtype=int8) | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/model/ndarray.py#L766-L825 | train | Transform each genotype call into the number of reference alleles. | 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(1916 - 1868) + chr(111) + '\x34' + chr(51), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101011 + 0o4) + chr(0b110000), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(1728 - 1678) + chr(0b110101), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b11 + 0o56) + chr(0b101111 + 0o7) + chr(0b1111 + 0o45), 6259 - 6251), nzTpIcepk0o8('\060' + chr(0b1000100 + 0o53) + '\x32' + '\x35' + chr(0b101 + 0o53), 0b1000), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110010) + chr(739 - 684) + '\063', 0o10), nzTpIcepk0o8('\060' + chr(2129 - 2018) + chr(795 - 745) + chr(405 - 355) + chr(0b110010), 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + '\062' + chr(0b1101 + 0o44) + chr(48), ord("\x08")), nzTpIcepk0o8(chr(0b11101 + 0o23) + chr(0b1101111) + chr(322 - 273) + chr(0b10010 + 0o37) + '\x35', 0b1000), nzTpIcepk0o8(chr(967 - 919) + chr(0b1100110 + 0o11) + '\062' + chr(52) + '\067', 0o10), nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(6604 - 6493) + chr(1679 - 1630) + chr(711 - 660) + '\x34', 12182 - 12174), nzTpIcepk0o8('\x30' + '\157' + chr(0b10100 + 0o37) + chr(0b110001) + chr(54), 0o10), nzTpIcepk0o8('\060' + chr(3351 - 3240) + '\063' + chr(0b10110 + 0o36) + chr(0b10011 + 0o42), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(50) + '\x31' + chr(0b101111 + 0o6), 31217 - 31209), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(49) + chr(52) + chr(0b110111), 0o10), nzTpIcepk0o8(chr(2186 - 2138) + chr(0b1101111) + chr(0b110010) + chr(0b100111 + 0o13) + chr(695 - 640), 10521 - 10513), nzTpIcepk0o8(chr(221 - 173) + chr(111) + chr(50) + chr(0b110111) + chr(0b110000), 48819 - 48811), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(1897 - 1848) + chr(0b110101) + chr(0b100011 + 0o20), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(51) + '\x34', 0b1000), nzTpIcepk0o8('\060' + '\157' + chr(0b100001 + 0o17), 8), nzTpIcepk0o8(chr(0b10010 + 0o36) + '\157' + chr(0b1100 + 0o47) + chr(0b1001 + 0o55) + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1010111 + 0o30) + chr(51) + chr(2107 - 2057) + chr(0b11110 + 0o31), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(6124 - 6013) + '\x31' + chr(0b110100) + '\064', 0b1000), nzTpIcepk0o8(chr(373 - 325) + '\x6f' + '\x34' + chr(55), 0b1000), nzTpIcepk0o8('\060' + chr(0b1000001 + 0o56) + chr(0b100010 + 0o17) + '\x32' + chr(0b10111 + 0o37), 0b1000), nzTpIcepk0o8(chr(0b101 + 0o53) + chr(0b1101111) + chr(1377 - 1328) + chr(0b10010 + 0o41) + chr(53), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1010001 + 0o36) + '\x32' + chr(0b110000) + chr(1689 - 1635), 10432 - 10424), nzTpIcepk0o8('\x30' + chr(111) + '\x31' + chr(0b11101 + 0o27) + '\066', 0o10), nzTpIcepk0o8('\x30' + '\157' + chr(0b11 + 0o56) + '\064', 0o10), nzTpIcepk0o8(chr(995 - 947) + chr(111) + chr(1662 - 1613) + chr(0b110010) + chr(0b100 + 0o55), 0o10), nzTpIcepk0o8('\060' + chr(7172 - 7061) + '\x33' + chr(0b110110) + chr(1190 - 1142), 0o10), nzTpIcepk0o8(chr(1702 - 1654) + '\157' + chr(1504 - 1455) + chr(1687 - 1639) + '\063', 0b1000), nzTpIcepk0o8(chr(48) + '\x6f' + chr(51) + chr(55), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + '\062' + chr(52) + chr(52), 0o10), nzTpIcepk0o8('\060' + '\157' + chr(0b110011) + '\064' + chr(52), 46694 - 46686), nzTpIcepk0o8('\x30' + chr(7355 - 7244) + chr(49) + '\x35' + chr(53), ord("\x08")), nzTpIcepk0o8('\060' + chr(9415 - 9304) + chr(49) + '\065' + '\x33', 8), nzTpIcepk0o8('\060' + '\157' + chr(2062 - 2013) + '\062' + chr(2613 - 2560), 33521 - 33513), nzTpIcepk0o8(chr(0b100011 + 0o15) + '\x6f' + chr(1296 - 1243) + '\x31', 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + '\x33' + chr(0b110111) + chr(0b110 + 0o54), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(1421 - 1373) + '\157' + chr(0b110101) + '\x30', ord("\x08"))] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\r'), chr(5403 - 5303) + '\145' + chr(99) + chr(7369 - 7258) + '\144' + '\145')(chr(0b1110101) + chr(994 - 878) + chr(0b1011011 + 0o13) + '\x2d' + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def _Sm9Q23tv3Lr(hXMPsSrOQzbh, pPmkLCVA328e=nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110000), 8), RcX9bbuOzh5L=roI3spqORKae(ES5oEprVxulp(b'J1'), '\144' + '\145' + '\x63' + '\157' + chr(0b1100100) + chr(0b111101 + 0o50))(chr(0b1110101) + chr(0b1110100) + '\x66' + chr(1633 - 1588) + chr(824 - 768))):
VwOu8WkJ9cpc = nDF4gVNx0u9Q.EEl0Pry8vzTp(hXMPsSrOQzbh.lhbM092AFW8f[:-nzTpIcepk0o8('\060' + chr(0b1101111) + '\061', 0b1000)], dtype=RcX9bbuOzh5L)
roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'Lcy7\x90\xff\xde\xe2\x0c\xf80\x98'), chr(7332 - 7232) + '\x65' + chr(0b1100011) + chr(111) + '\x64' + chr(101))('\165' + chr(0b101000 + 0o114) + chr(0b1100110) + '\055' + chr(0b111000)))(roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'`sz\x10\xf2\xf1\xda\xbe5\x9e\x08\xb6'), chr(7095 - 6995) + '\145' + chr(2509 - 2410) + '\x6f' + chr(100) + '\145')('\x75' + '\x74' + chr(1174 - 1072) + chr(2005 - 1960) + chr(0b111000))) == nzTpIcepk0o8('\060' + chr(0b111101 + 0o62) + '\x30', 8), axis=-nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(49), 8), out=VwOu8WkJ9cpc)
if pPmkLCVA328e != nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110000), 8):
tF75nqoNENFL = hXMPsSrOQzbh.zYFtC4_vxWk9()
VwOu8WkJ9cpc[tF75nqoNENFL] = pPmkLCVA328e
if roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'aBXL\xcc\xc3\xff\xbf\x14\xf0;\xab'), '\x64' + chr(0b1100101) + chr(7691 - 7592) + chr(1728 - 1617) + chr(0b10010 + 0o122) + '\145')('\165' + chr(0b1110100) + chr(7370 - 7268) + chr(45) + '\x38')) is not None:
VwOu8WkJ9cpc[hXMPsSrOQzbh.BBM8dxm7YWge] = pPmkLCVA328e
return VwOu8WkJ9cpc |
cggh/scikit-allel | allel/model/ndarray.py | Genotypes.to_allele_counts | def to_allele_counts(self, max_allele=None, dtype='u1'):
"""Transform genotype calls into allele counts per call.
Parameters
----------
max_allele : int, optional
Highest allele index. Provide this value to speed up computation.
dtype : dtype, optional
Output dtype.
Returns
-------
out : ndarray, uint8, shape (n_variants, n_samples, len(alleles))
Array of allele counts per call.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 1]],
... [[0, 2], [1, 1]],
... [[2, 2], [-1, -1]]])
>>> g.to_allele_counts()
<GenotypeAlleleCountsArray shape=(3, 2, 3) dtype=uint8>
2:0:0 1:1:0
1:0:1 0:2:0
0:0:2 0:0:0
>>> v = g[:, 0]
>>> v
<GenotypeVector shape=(3, 2) dtype=int64>
0/0 0/2 2/2
>>> v.to_allele_counts()
<GenotypeAlleleCountsVector shape=(3, 3) dtype=uint8>
2:0:0 1:0:1 0:0:2
"""
# determine alleles to count
if max_allele is None:
max_allele = self.max()
alleles = list(range(max_allele + 1))
# set up output array
outshape = self.shape[:-1] + (len(alleles),)
out = np.zeros(outshape, dtype=dtype)
for allele in alleles:
# count alleles along ploidy dimension
allele_match = self.values == allele
if self.mask is not None:
allele_match &= ~self.mask[..., np.newaxis]
np.sum(allele_match, axis=-1, out=out[..., allele])
if self.ndim == 2:
out = GenotypeAlleleCountsVector(out)
elif self.ndim == 3:
out = GenotypeAlleleCountsArray(out)
return out | python | def to_allele_counts(self, max_allele=None, dtype='u1'):
"""Transform genotype calls into allele counts per call.
Parameters
----------
max_allele : int, optional
Highest allele index. Provide this value to speed up computation.
dtype : dtype, optional
Output dtype.
Returns
-------
out : ndarray, uint8, shape (n_variants, n_samples, len(alleles))
Array of allele counts per call.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 1]],
... [[0, 2], [1, 1]],
... [[2, 2], [-1, -1]]])
>>> g.to_allele_counts()
<GenotypeAlleleCountsArray shape=(3, 2, 3) dtype=uint8>
2:0:0 1:1:0
1:0:1 0:2:0
0:0:2 0:0:0
>>> v = g[:, 0]
>>> v
<GenotypeVector shape=(3, 2) dtype=int64>
0/0 0/2 2/2
>>> v.to_allele_counts()
<GenotypeAlleleCountsVector shape=(3, 3) dtype=uint8>
2:0:0 1:0:1 0:0:2
"""
# determine alleles to count
if max_allele is None:
max_allele = self.max()
alleles = list(range(max_allele + 1))
# set up output array
outshape = self.shape[:-1] + (len(alleles),)
out = np.zeros(outshape, dtype=dtype)
for allele in alleles:
# count alleles along ploidy dimension
allele_match = self.values == allele
if self.mask is not None:
allele_match &= ~self.mask[..., np.newaxis]
np.sum(allele_match, axis=-1, out=out[..., allele])
if self.ndim == 2:
out = GenotypeAlleleCountsVector(out)
elif self.ndim == 3:
out = GenotypeAlleleCountsArray(out)
return out | [
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"("... | Transform genotype calls into allele counts per call.
Parameters
----------
max_allele : int, optional
Highest allele index. Provide this value to speed up computation.
dtype : dtype, optional
Output dtype.
Returns
-------
out : ndarray, uint8, shape (n_variants, n_samples, len(alleles))
Array of allele counts per call.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 1]],
... [[0, 2], [1, 1]],
... [[2, 2], [-1, -1]]])
>>> g.to_allele_counts()
<GenotypeAlleleCountsArray shape=(3, 2, 3) dtype=uint8>
2:0:0 1:1:0
1:0:1 0:2:0
0:0:2 0:0:0
>>> v = g[:, 0]
>>> v
<GenotypeVector shape=(3, 2) dtype=int64>
0/0 0/2 2/2
>>> v.to_allele_counts()
<GenotypeAlleleCountsVector shape=(3, 3) dtype=uint8>
2:0:0 1:0:1 0:0:2 | [
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"call",
"."
] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/model/ndarray.py#L892-L950 | train | Transform genotype calls into allele counts per call. | 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(2936 - 2825) + '\062' + chr(0b101000 + 0o10) + chr(0b11 + 0o62), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b100101 + 0o16) + chr(52), 0b1000), nzTpIcepk0o8('\060' + chr(1238 - 1127) + '\x33' + '\x32' + chr(0b100110 + 0o13), 0b1000), nzTpIcepk0o8('\060' + chr(0b1011011 + 0o24) + '\x35' + '\063', 40319 - 40311), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110010) + '\x37' + chr(48), 0b1000), nzTpIcepk0o8(chr(1223 - 1175) + chr(111) + '\062' + chr(2240 - 2189), 42369 - 42361), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(0b110010) + chr(0b110011) + '\062', 34784 - 34776), nzTpIcepk0o8(chr(48) + '\157' + chr(0b110010) + chr(0b11000 + 0o36) + chr(0b110101), 55462 - 55454), nzTpIcepk0o8(chr(2292 - 2244) + chr(0b1101111) + '\061' + '\x30' + '\x35', 0o10), nzTpIcepk0o8(chr(1948 - 1900) + '\x6f' + chr(51) + chr(0b11101 + 0o23) + chr(2330 - 2280), 28974 - 28966), nzTpIcepk0o8('\x30' + chr(111) + '\061' + chr(2488 - 2434) + chr(50), 0o10), nzTpIcepk0o8(chr(487 - 439) + chr(111) + '\x31' + chr(2181 - 2127) + chr(1242 - 1188), 0o10), nzTpIcepk0o8(chr(0b11111 + 0o21) + chr(0b1011 + 0o144) + '\x32' + chr(0b110111) + chr(243 - 195), 8), nzTpIcepk0o8(chr(0b1001 + 0o47) + chr(111) + chr(78 - 27) + chr(0b11001 + 0o36) + '\x36', 0b1000), nzTpIcepk0o8(chr(0b10101 + 0o33) + chr(0b1101111) + chr(50) + chr(809 - 760) + chr(1453 - 1398), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b101000 + 0o13) + chr(51) + chr(48), 35497 - 35489), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(50) + chr(0b110011) + chr(55), 0o10), nzTpIcepk0o8(chr(48) + chr(0b110001 + 0o76) + chr(0b110001 + 0o2) + chr(52) + '\x32', 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(49) + chr(0b110110) + chr(0b110010), 8), nzTpIcepk0o8(chr(0b110000) + chr(2563 - 2452) + '\061' + chr(1289 - 1234) + chr(0b110000), 0o10), nzTpIcepk0o8(chr(0b1010 + 0o46) + '\157' + chr(0b11001 + 0o31) + '\064' + chr(0b10000 + 0o47), ord("\x08")), nzTpIcepk0o8(chr(48) + '\157' + '\x33' + chr(52) + chr(53), ord("\x08")), nzTpIcepk0o8(chr(0b1001 + 0o47) + chr(7670 - 7559) + chr(0b11100 + 0o27) + '\067' + '\x36', 8), nzTpIcepk0o8(chr(993 - 945) + chr(0b1011101 + 0o22) + chr(51) + chr(48), 763 - 755), nzTpIcepk0o8(chr(146 - 98) + chr(0b0 + 0o157) + '\x33' + chr(0b101011 + 0o13) + chr(49), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(5671 - 5560) + '\x31' + '\061' + '\x34', 0o10), nzTpIcepk0o8('\060' + chr(1235 - 1124) + chr(50) + chr(0b110111) + chr(0b10010 + 0o37), 55480 - 55472), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x31' + chr(0b11100 + 0o33) + '\060', 8), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\063' + chr(2435 - 2380) + chr(55), 0b1000), nzTpIcepk0o8(chr(215 - 167) + chr(111) + chr(51) + '\x33' + chr(244 - 190), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b10 + 0o155) + '\x32' + chr(93 - 41), 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(0b11011 + 0o30) + chr(0b110100) + chr(0b101101 + 0o6), 18014 - 18006), nzTpIcepk0o8(chr(0b10001 + 0o37) + chr(0b1101111) + chr(0b110001 + 0o6) + chr(0b10011 + 0o35), 0b1000), nzTpIcepk0o8('\x30' + chr(111) + '\x33' + chr(52) + '\067', 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + '\063' + chr(0b100011 + 0o15), 8), nzTpIcepk0o8(chr(0b110000) + '\157' + '\061' + '\062' + '\064', ord("\x08")), nzTpIcepk0o8('\060' + '\157' + '\062' + chr(0b10101 + 0o35) + chr(48), ord("\x08")), nzTpIcepk0o8('\060' + chr(3172 - 3061) + chr(49) + chr(1077 - 1026), 19019 - 19011), nzTpIcepk0o8(chr(48) + chr(5269 - 5158) + chr(49) + '\x31' + '\x30', 43081 - 43073), nzTpIcepk0o8(chr(0b1100 + 0o44) + chr(0b1101111) + '\x32' + chr(52) + chr(0b110101), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110101) + chr(0b110000), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xab'), chr(5663 - 5563) + chr(0b1100000 + 0o5) + chr(0b1100011) + chr(0b1101111) + chr(0b1000100 + 0o40) + chr(0b10001 + 0o124))(chr(11919 - 11802) + chr(0b1110100) + '\x66' + chr(0b101101) + chr(0b111000)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def cBa7OWQ_054B(hXMPsSrOQzbh, j75eupAGs_rK=None, RcX9bbuOzh5L=roI3spqORKae(ES5oEprVxulp(b'\xf0-'), '\x64' + chr(101) + chr(7701 - 7602) + '\157' + '\144' + '\x65')('\x75' + '\164' + chr(0b1100110) + '\x2d' + '\x38')):
if j75eupAGs_rK is None:
j75eupAGs_rK = hXMPsSrOQzbh.KV9ckIhroIia()
ZP51d81mJGUO = H4NoA26ON7iG(bbT2xIe5pzk7(j75eupAGs_rK + nzTpIcepk0o8('\x30' + chr(111) + '\061', 22611 - 22603)))
Jd0a_ViNmtjm = hXMPsSrOQzbh.lhbM092AFW8f[:-nzTpIcepk0o8('\060' + chr(0b1001110 + 0o41) + chr(49), 8)] + (ftfygxgFas5X(ZP51d81mJGUO),)
VwOu8WkJ9cpc = nDF4gVNx0u9Q.UmwwEp7MzR6q(Jd0a_ViNmtjm, dtype=RcX9bbuOzh5L)
for A94c267WMRU1 in ZP51d81mJGUO:
lj9JYdS6ffjO = hXMPsSrOQzbh.CsodZJH6x9Tx == A94c267WMRU1
if roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xc7^\x9c\x13\xdck\xf7\x82\x1c\x95\x15\x13'), '\x64' + chr(0b100100 + 0o101) + chr(99) + chr(0b1010000 + 0o37) + chr(0b1100100) + '\145')('\165' + chr(11159 - 11043) + chr(1904 - 1802) + '\055' + chr(0b111000))) is not None:
lj9JYdS6ffjO &= ~hXMPsSrOQzbh.BBM8dxm7YWge[..., nDF4gVNx0u9Q.newaxis]
roI3spqORKae(nDF4gVNx0u9Q, roI3spqORKae(ES5oEprVxulp(b'\xea\x7f\xbdh\x80W\xd6\xdf\x04\x9d\x1e '), chr(0b1010111 + 0o15) + chr(0b1001001 + 0o34) + '\x63' + chr(10378 - 10267) + chr(0b1100100) + chr(0b1100101))('\x75' + chr(0b1101010 + 0o12) + chr(0b1100110) + chr(0b101101) + '\070'))(lj9JYdS6ffjO, axis=-nzTpIcepk0o8(chr(48) + '\157' + chr(49), 8), out=VwOu8WkJ9cpc[..., A94c267WMRU1])
if roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xcfU\x89g\xf0#\xa8\xfa\x06\xf2%4'), chr(0b1100100) + chr(0b1100101) + chr(99) + '\x6f' + chr(0b101101 + 0o67) + '\x65')(chr(0b1110000 + 0o5) + chr(0b1110100) + chr(8229 - 8127) + chr(1194 - 1149) + chr(0b110101 + 0o3))) == nzTpIcepk0o8(chr(466 - 418) + chr(0b1011111 + 0o20) + '\x32', 0b1000):
VwOu8WkJ9cpc = vU72xo7aGHxQ(VwOu8WkJ9cpc)
elif roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xcfU\x89g\xf0#\xa8\xfa\x06\xf2%4'), chr(6757 - 6657) + chr(0b100000 + 0o105) + '\x63' + '\x6f' + '\x64' + '\x65')(chr(0b100001 + 0o124) + chr(0b110001 + 0o103) + chr(0b1100110) + chr(0b1100 + 0o41) + '\x38')) == nzTpIcepk0o8(chr(0b1101 + 0o43) + chr(0b1101111) + '\x33', 58179 - 58171):
VwOu8WkJ9cpc = XcLwziDbAMWx(VwOu8WkJ9cpc)
return VwOu8WkJ9cpc |
cggh/scikit-allel | allel/model/ndarray.py | Genotypes.to_gt | def to_gt(self, max_allele=None):
"""Convert genotype calls to VCF-style string representation.
Returns
-------
gt : ndarray, string, shape (n_variants, n_samples)
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 1]],
... [[0, 2], [1, 1]],
... [[1, 2], [2, 1]],
... [[2, 2], [-1, -1]]])
>>> g.to_gt()
chararray([[b'0/0', b'0/1'],
[b'0/2', b'1/1'],
[b'1/2', b'2/1'],
[b'2/2', b'./.']],
dtype='|S3')
>>> v = g[:, 0]
>>> v
<GenotypeVector shape=(4, 2) dtype=int64>
0/0 0/2 1/2 2/2
>>> v.to_gt()
chararray([b'0/0', b'0/2', b'1/2', b'2/2'],
dtype='|S3')
>>> g.is_phased = np.ones(g.shape[:-1])
>>> g.to_gt()
chararray([[b'0|0', b'0|1'],
[b'0|2', b'1|1'],
[b'1|2', b'2|1'],
[b'2|2', b'.|.']],
dtype='|S3')
>>> v = g[:, 0]
>>> v
<GenotypeVector shape=(4, 2) dtype=int64>
0|0 0|2 1|2 2|2
>>> v.to_gt()
chararray([b'0|0', b'0|2', b'1|2', b'2|2'],
dtype='|S3')
"""
# how many characters needed per allele call?
if max_allele is None:
max_allele = np.max(self)
if max_allele <= 0:
max_allele = 1
nchar = int(np.floor(np.log10(max_allele))) + 1
# convert to string
a = self.astype((np.string_, nchar)).view(np.chararray)
# recode missing alleles
a[self < 0] = b'.'
if self.mask is not None:
a[self.mask] = b'.'
# determine allele call separator
if self.is_phased is None:
sep = b'/'
else:
sep = np.empty(self.shape[:-1], dtype='S1').view(np.chararray)
sep[self.is_phased] = b'|'
sep[~self.is_phased] = b'/'
# join via separator, coping with any ploidy
gt = a[..., 0]
for i in range(1, self.ploidy):
gt = gt + sep + a[..., i]
return gt | python | def to_gt(self, max_allele=None):
"""Convert genotype calls to VCF-style string representation.
Returns
-------
gt : ndarray, string, shape (n_variants, n_samples)
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 1]],
... [[0, 2], [1, 1]],
... [[1, 2], [2, 1]],
... [[2, 2], [-1, -1]]])
>>> g.to_gt()
chararray([[b'0/0', b'0/1'],
[b'0/2', b'1/1'],
[b'1/2', b'2/1'],
[b'2/2', b'./.']],
dtype='|S3')
>>> v = g[:, 0]
>>> v
<GenotypeVector shape=(4, 2) dtype=int64>
0/0 0/2 1/2 2/2
>>> v.to_gt()
chararray([b'0/0', b'0/2', b'1/2', b'2/2'],
dtype='|S3')
>>> g.is_phased = np.ones(g.shape[:-1])
>>> g.to_gt()
chararray([[b'0|0', b'0|1'],
[b'0|2', b'1|1'],
[b'1|2', b'2|1'],
[b'2|2', b'.|.']],
dtype='|S3')
>>> v = g[:, 0]
>>> v
<GenotypeVector shape=(4, 2) dtype=int64>
0|0 0|2 1|2 2|2
>>> v.to_gt()
chararray([b'0|0', b'0|2', b'1|2', b'2|2'],
dtype='|S3')
"""
# how many characters needed per allele call?
if max_allele is None:
max_allele = np.max(self)
if max_allele <= 0:
max_allele = 1
nchar = int(np.floor(np.log10(max_allele))) + 1
# convert to string
a = self.astype((np.string_, nchar)).view(np.chararray)
# recode missing alleles
a[self < 0] = b'.'
if self.mask is not None:
a[self.mask] = b'.'
# determine allele call separator
if self.is_phased is None:
sep = b'/'
else:
sep = np.empty(self.shape[:-1], dtype='S1').view(np.chararray)
sep[self.is_phased] = b'|'
sep[~self.is_phased] = b'/'
# join via separator, coping with any ploidy
gt = a[..., 0]
for i in range(1, self.ploidy):
gt = gt + sep + a[..., i]
return gt | [
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Returns
-------
gt : ndarray, string, shape (n_variants, n_samples)
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 1]],
... [[0, 2], [1, 1]],
... [[1, 2], [2, 1]],
... [[2, 2], [-1, -1]]])
>>> g.to_gt()
chararray([[b'0/0', b'0/1'],
[b'0/2', b'1/1'],
[b'1/2', b'2/1'],
[b'2/2', b'./.']],
dtype='|S3')
>>> v = g[:, 0]
>>> v
<GenotypeVector shape=(4, 2) dtype=int64>
0/0 0/2 1/2 2/2
>>> v.to_gt()
chararray([b'0/0', b'0/2', b'1/2', b'2/2'],
dtype='|S3')
>>> g.is_phased = np.ones(g.shape[:-1])
>>> g.to_gt()
chararray([[b'0|0', b'0|1'],
[b'0|2', b'1|1'],
[b'1|2', b'2|1'],
[b'2|2', b'.|.']],
dtype='|S3')
>>> v = g[:, 0]
>>> v
<GenotypeVector shape=(4, 2) dtype=int64>
0|0 0|2 1|2 2|2
>>> v.to_gt()
chararray([b'0|0', b'0|2', b'1|2', b'2|2'],
dtype='|S3') | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/model/ndarray.py#L952-L1025 | train | Convert genotype calls to VCF - style string representation. | 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(2091 - 2043) + '\x6f' + '\x32' + chr(0b110100) + chr(0b101100 + 0o11), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + '\061' + chr(0b11011 + 0o25) + chr(876 - 824), 0b1000), nzTpIcepk0o8(chr(2245 - 2197) + chr(0b1101111) + '\063' + chr(0b110100) + chr(2223 - 2174), 0o10), nzTpIcepk0o8(chr(0b10011 + 0o35) + '\x6f' + '\x32' + chr(0b110010) + '\x30', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b1101 + 0o44) + chr(54) + chr(0b110000), 0b1000), nzTpIcepk0o8('\x30' + '\157' + '\062' + chr(0b110010) + chr(169 - 120), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1001000 + 0o47) + chr(49) + '\x34' + '\062', 0o10), nzTpIcepk0o8(chr(885 - 837) + chr(0b111100 + 0o63) + chr(0b110010) + '\065' + '\063', 0b1000), nzTpIcepk0o8(chr(48) + chr(962 - 851) + '\x35' + '\061', 22812 - 22804), nzTpIcepk0o8(chr(0b110000) + chr(6017 - 5906) + '\063' + chr(255 - 204) + chr(222 - 172), 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + '\062' + chr(2427 - 2375) + chr(55), 0o10), nzTpIcepk0o8(chr(0b100100 + 0o14) + chr(0b1101111) + chr(49) + chr(0b11111 + 0o26) + chr(0b110000), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(49) + '\065' + chr(49), 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110011) + '\061' + chr(53), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + '\063' + '\060' + chr(611 - 560), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(10295 - 10184) + '\x31' + '\x35' + '\062', 0b1000), nzTpIcepk0o8(chr(48) + chr(111) + '\062' + '\x35' + '\064', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x31' + chr(0b110010), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(50) + '\x37' + '\x32', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\061' + chr(52) + '\x30', 0o10), nzTpIcepk0o8(chr(270 - 222) + chr(760 - 649) + chr(0b10010 + 0o41) + '\065' + chr(0b110111), 7550 - 7542), nzTpIcepk0o8(chr(1920 - 1872) + chr(1254 - 1143) + chr(0b1000 + 0o52) + chr(49) + chr(2319 - 2270), 28379 - 28371), nzTpIcepk0o8(chr(0b110 + 0o52) + '\x6f' + chr(52) + chr(2221 - 2169), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x31' + chr(2370 - 2319) + chr(0b11111 + 0o30), 39548 - 39540), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\062' + chr(1733 - 1685) + chr(2182 - 2132), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(55) + chr(0b110000), 0o10), nzTpIcepk0o8('\x30' + chr(0b111 + 0o150) + chr(2405 - 2354) + '\x36' + '\x36', 0o10), nzTpIcepk0o8(chr(2068 - 2020) + '\157' + '\065' + chr(49), 8), nzTpIcepk0o8(chr(0b1110 + 0o42) + chr(0b1101111) + chr(0b100010 + 0o20) + chr(55) + chr(781 - 733), 59452 - 59444), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110011) + '\x32' + chr(55), ord("\x08")), nzTpIcepk0o8('\060' + chr(9844 - 9733) + chr(51) + '\x33' + chr(0b110010), 8), nzTpIcepk0o8(chr(0b100110 + 0o12) + '\157' + chr(1878 - 1827) + '\x33' + chr(0b100001 + 0o21), 8), nzTpIcepk0o8('\060' + chr(0b1101111) + '\x32' + chr(53) + chr(548 - 495), 0o10), nzTpIcepk0o8(chr(48) + chr(0b11010 + 0o125) + chr(49) + chr(0b1011 + 0o47) + '\066', 0o10), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(0b110 + 0o55) + '\x32' + chr(53), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b10000 + 0o43) + '\x34' + chr(0b110010), 1608 - 1600), nzTpIcepk0o8(chr(48) + chr(0b1000011 + 0o54) + chr(51) + chr(0b101110 + 0o5) + chr(68 - 19), 0b1000), nzTpIcepk0o8('\060' + chr(111) + '\x32' + '\x36' + chr(0b110000), ord("\x08")), nzTpIcepk0o8('\060' + '\157' + chr(0b110011) + '\x35', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(0b10011 + 0o37) + chr(0b100000 + 0o26), 55029 - 55021)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + '\x6f' + chr(53) + chr(0b110000), 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x8b'), chr(0b101101 + 0o67) + chr(0b1100101) + chr(99) + '\x6f' + chr(0b1100100) + chr(4205 - 4104))('\165' + chr(116) + '\x66' + chr(696 - 651) + '\x38') + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def eV2fwdc8_nOA(hXMPsSrOQzbh, j75eupAGs_rK=None):
if j75eupAGs_rK is None:
j75eupAGs_rK = nDF4gVNx0u9Q.KV9ckIhroIia(hXMPsSrOQzbh)
if j75eupAGs_rK <= nzTpIcepk0o8('\060' + '\x6f' + chr(1392 - 1344), 0o10):
j75eupAGs_rK = nzTpIcepk0o8('\060' + '\x6f' + '\x31', 0b1000)
ynH_7ocTE_Z8 = nzTpIcepk0o8(nDF4gVNx0u9Q.floor(nDF4gVNx0u9Q.log10(j75eupAGs_rK))) + nzTpIcepk0o8(chr(0b1001 + 0o47) + '\157' + '\x31', 8)
AQ9ceR9AaoT1 = hXMPsSrOQzbh.astype((nDF4gVNx0u9Q.string_, ynH_7ocTE_Z8)).mJI8h1w8YmYz(nDF4gVNx0u9Q.chararray)
AQ9ceR9AaoT1[hXMPsSrOQzbh < nzTpIcepk0o8(chr(0b0 + 0o60) + chr(111) + chr(48), 8)] = ES5oEprVxulp(b'\x8b')
if roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xe7\x06\xac\xa8\x14\xe9\x0f\x9cp\x8d\xc0\r'), chr(100) + chr(0b1100101) + '\x63' + '\x6f' + '\x64' + chr(101))(chr(117) + chr(116) + chr(0b1100110) + '\055' + chr(2071 - 2015))) is not None:
AQ9ceR9AaoT1[hXMPsSrOQzbh.BBM8dxm7YWge] = ES5oEprVxulp(b'\x8b')
if roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xc3\x11\x80\xf2B\xc8\x03\xf3\x11\xbb\xdf,'), '\144' + chr(1286 - 1185) + '\143' + chr(0b1000101 + 0o52) + chr(0b1100100) + chr(0b110111 + 0o56))(chr(117) + '\x74' + chr(0b11101 + 0o111) + '\055' + chr(0b110001 + 0o7))) is None:
EAvVzGIvS3lY = ES5oEprVxulp(b'\x8a')
else:
EAvVzGIvS3lY = nDF4gVNx0u9Q.empty(hXMPsSrOQzbh.shape[:-nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\061', 8)], dtype=roI3spqORKae(ES5oEprVxulp(b'\xf6u'), chr(4695 - 4595) + chr(6504 - 6403) + chr(99) + chr(0b1101111) + '\x64' + chr(0b1 + 0o144))(chr(0b1110101) + chr(0b1110100) + chr(0b1100110) + '\x2d' + chr(0b11101 + 0o33))).mJI8h1w8YmYz(nDF4gVNx0u9Q.chararray)
EAvVzGIvS3lY[hXMPsSrOQzbh.fUab2YaX8axD] = ES5oEprVxulp(b'\xd9')
EAvVzGIvS3lY[~hXMPsSrOQzbh.fUab2YaX8axD] = ES5oEprVxulp(b'\x8a')
li4jbl7JOSjv = AQ9ceR9AaoT1[..., nzTpIcepk0o8(chr(48) + '\157' + chr(457 - 409), 8)]
for ZlbFMSG8gCoF in bbT2xIe5pzk7(nzTpIcepk0o8(chr(0b101100 + 0o4) + chr(0b111010 + 0o65) + '\x31', 8), roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xd5(\x8e\xf9\x14\xe8'), '\144' + chr(0b1100101) + chr(0b1100011) + chr(0b1101111) + chr(9420 - 9320) + chr(0b1100101))(chr(0b1110101) + chr(12522 - 12406) + '\146' + chr(45) + '\070'))):
li4jbl7JOSjv = li4jbl7JOSjv + EAvVzGIvS3lY + AQ9ceR9AaoT1[..., ZlbFMSG8gCoF]
return li4jbl7JOSjv |
cggh/scikit-allel | allel/model/ndarray.py | Genotypes.map_alleles | def map_alleles(self, mapping, copy=True):
"""Transform alleles via a mapping.
Parameters
----------
mapping : ndarray, int8, shape (n_variants, max_allele)
An array defining the allele mapping for each variant.
copy : bool, optional
If True, return a new array; if False, apply mapping in place
(only applies for arrays with dtype int8; all other dtypes
require a copy).
Returns
-------
gm : GenotypeArray
Examples
--------
>>> import allel
>>> import numpy as np
>>> g = allel.GenotypeArray([[[0, 0], [0, 1]],
... [[0, 2], [1, 1]],
... [[1, 2], [2, 1]],
... [[2, 2], [-1, -1]]], dtype='i1')
>>> mapping = np.array([[1, 2, 0],
... [2, 0, 1],
... [2, 1, 0],
... [0, 2, 1]], dtype='i1')
>>> g.map_alleles(mapping)
<GenotypeArray shape=(4, 2, 2) dtype=int8>
1/1 1/2
2/1 0/0
1/0 0/1
1/1 ./.
>>> v = g[:, 0]
>>> v
<GenotypeVector shape=(4, 2) dtype=int8>
0/0 0/2 1/2 2/2
>>> v.map_alleles(mapping)
<GenotypeVector shape=(4, 2) dtype=int8>
1/1 2/1 1/0 1/1
Notes
-----
If a mask has been set, it is ignored by this function.
For arrays with dtype int8 an optimised implementation is used which is
faster and uses far less memory. It is recommended to convert arrays to
dtype int8 where possible before calling this method.
See Also
--------
create_allele_mapping
"""
h = self.to_haplotypes()
hm = h.map_alleles(mapping, copy=copy)
if self.ndim == 2:
gm = GenotypeVector(hm)
else:
gm = hm.to_genotypes(ploidy=self.ploidy)
return gm | python | def map_alleles(self, mapping, copy=True):
"""Transform alleles via a mapping.
Parameters
----------
mapping : ndarray, int8, shape (n_variants, max_allele)
An array defining the allele mapping for each variant.
copy : bool, optional
If True, return a new array; if False, apply mapping in place
(only applies for arrays with dtype int8; all other dtypes
require a copy).
Returns
-------
gm : GenotypeArray
Examples
--------
>>> import allel
>>> import numpy as np
>>> g = allel.GenotypeArray([[[0, 0], [0, 1]],
... [[0, 2], [1, 1]],
... [[1, 2], [2, 1]],
... [[2, 2], [-1, -1]]], dtype='i1')
>>> mapping = np.array([[1, 2, 0],
... [2, 0, 1],
... [2, 1, 0],
... [0, 2, 1]], dtype='i1')
>>> g.map_alleles(mapping)
<GenotypeArray shape=(4, 2, 2) dtype=int8>
1/1 1/2
2/1 0/0
1/0 0/1
1/1 ./.
>>> v = g[:, 0]
>>> v
<GenotypeVector shape=(4, 2) dtype=int8>
0/0 0/2 1/2 2/2
>>> v.map_alleles(mapping)
<GenotypeVector shape=(4, 2) dtype=int8>
1/1 2/1 1/0 1/1
Notes
-----
If a mask has been set, it is ignored by this function.
For arrays with dtype int8 an optimised implementation is used which is
faster and uses far less memory. It is recommended to convert arrays to
dtype int8 where possible before calling this method.
See Also
--------
create_allele_mapping
"""
h = self.to_haplotypes()
hm = h.map_alleles(mapping, copy=copy)
if self.ndim == 2:
gm = GenotypeVector(hm)
else:
gm = hm.to_genotypes(ploidy=self.ploidy)
return gm | [
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... | Transform alleles via a mapping.
Parameters
----------
mapping : ndarray, int8, shape (n_variants, max_allele)
An array defining the allele mapping for each variant.
copy : bool, optional
If True, return a new array; if False, apply mapping in place
(only applies for arrays with dtype int8; all other dtypes
require a copy).
Returns
-------
gm : GenotypeArray
Examples
--------
>>> import allel
>>> import numpy as np
>>> g = allel.GenotypeArray([[[0, 0], [0, 1]],
... [[0, 2], [1, 1]],
... [[1, 2], [2, 1]],
... [[2, 2], [-1, -1]]], dtype='i1')
>>> mapping = np.array([[1, 2, 0],
... [2, 0, 1],
... [2, 1, 0],
... [0, 2, 1]], dtype='i1')
>>> g.map_alleles(mapping)
<GenotypeArray shape=(4, 2, 2) dtype=int8>
1/1 1/2
2/1 0/0
1/0 0/1
1/1 ./.
>>> v = g[:, 0]
>>> v
<GenotypeVector shape=(4, 2) dtype=int8>
0/0 0/2 1/2 2/2
>>> v.map_alleles(mapping)
<GenotypeVector shape=(4, 2) dtype=int8>
1/1 2/1 1/0 1/1
Notes
-----
If a mask has been set, it is ignored by this function.
For arrays with dtype int8 an optimised implementation is used which is
faster and uses far less memory. It is recommended to convert arrays to
dtype int8 where possible before calling this method.
See Also
--------
create_allele_mapping | [
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"."
] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/model/ndarray.py#L1036-L1099 | train | Transform alleles via a mapping. | 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' + '\x33' + chr(0b110101) + chr(0b11011 + 0o34), 34375 - 34367), nzTpIcepk0o8('\060' + chr(0b101111 + 0o100) + chr(0b110 + 0o53) + chr(0b10001 + 0o41) + chr(557 - 504), 32466 - 32458), nzTpIcepk0o8(chr(1101 - 1053) + '\x6f' + '\062' + chr(50) + chr(55), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(6845 - 6734) + chr(0b110001) + '\x30' + chr(51), 0o10), nzTpIcepk0o8(chr(515 - 467) + chr(0b1101111) + '\061' + chr(0b110001) + chr(49), 53259 - 53251), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(211 - 162) + chr(0b110100), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + chr(1139 - 1089) + chr(0b110111) + '\060', 11471 - 11463), nzTpIcepk0o8(chr(48) + chr(111) + chr(51) + chr(1377 - 1323) + chr(0b110110), 14735 - 14727), nzTpIcepk0o8(chr(0b10011 + 0o35) + chr(0b111100 + 0o63) + chr(0b101100 + 0o6) + chr(0b110000) + chr(0b110100), 39710 - 39702), nzTpIcepk0o8('\060' + '\x6f' + '\x32' + '\x35' + chr(52), 0b1000), nzTpIcepk0o8('\060' + '\157' + '\061' + chr(0b1110 + 0o42) + '\062', 0o10), nzTpIcepk0o8(chr(921 - 873) + chr(111) + chr(53) + chr(50), ord("\x08")), nzTpIcepk0o8(chr(738 - 690) + chr(0b1101111) + '\063' + '\x35', 0o10), nzTpIcepk0o8('\060' + chr(11967 - 11856) + '\063' + chr(0b1101 + 0o44) + chr(50), ord("\x08")), nzTpIcepk0o8('\x30' + chr(7817 - 7706) + chr(183 - 133) + chr(52) + '\060', 45307 - 45299), nzTpIcepk0o8('\x30' + '\157' + '\063' + chr(1963 - 1911), 51912 - 51904), nzTpIcepk0o8('\060' + chr(2931 - 2820) + chr(55) + '\x31', 4113 - 4105), nzTpIcepk0o8('\060' + chr(0b1101001 + 0o6) + '\x33' + chr(54) + chr(0b110111), 57897 - 57889), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b101111 + 0o2) + chr(268 - 217) + '\067', 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(49) + chr(51) + '\x33', 29447 - 29439), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110011) + '\060' + '\064', 52658 - 52650), nzTpIcepk0o8('\060' + chr(0b100001 + 0o116) + '\062' + chr(0b110001) + '\067', 0o10), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b10101 + 0o36) + chr(0b110001) + '\x35', 40596 - 40588), nzTpIcepk0o8(chr(1796 - 1748) + chr(111) + '\x31' + '\065' + chr(0b11110 + 0o30), 0o10), nzTpIcepk0o8(chr(496 - 448) + chr(0b11011 + 0o124) + chr(0b110011) + chr(530 - 476) + '\x37', 8), nzTpIcepk0o8('\x30' + chr(0b100101 + 0o112) + chr(0b10011 + 0o37) + '\x37' + chr(0b10100 + 0o41), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + '\x37' + chr(2614 - 2561), 0o10), nzTpIcepk0o8(chr(48) + '\157' + '\061' + chr(2471 - 2417) + chr(0b110111), 49327 - 49319), nzTpIcepk0o8('\060' + '\157' + '\x31' + '\060' + chr(0b100000 + 0o20), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(49) + chr(54) + chr(0b100000 + 0o22), 55755 - 55747), nzTpIcepk0o8('\x30' + chr(111) + chr(0b11100 + 0o31) + chr(223 - 175), 0b1000), nzTpIcepk0o8('\060' + chr(111) + '\061' + chr(0b110101) + chr(0b100 + 0o62), 8), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110010) + chr(1479 - 1424) + chr(49), 0o10), nzTpIcepk0o8('\060' + chr(11327 - 11216) + '\x32' + '\067' + '\x35', 8), nzTpIcepk0o8(chr(1589 - 1541) + '\x6f' + chr(0b100010 + 0o22) + '\x32', 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(1650 - 1596) + '\x33', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\063' + chr(0b110110) + '\062', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1010101 + 0o32) + chr(53) + chr(0b110000), 8), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(51), 0o10), nzTpIcepk0o8(chr(133 - 85) + chr(0b11101 + 0o122) + chr(0b110010) + '\x31' + chr(2708 - 2655), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(1131 - 1083) + chr(0b1101111) + chr(0b10010 + 0o43) + chr(0b11110 + 0o22), 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xc1'), chr(0b1100100) + chr(0b1100101) + chr(99) + '\x6f' + '\x64' + chr(0b11000 + 0o115))(chr(8256 - 8139) + chr(0b1110100) + chr(1693 - 1591) + chr(45) + chr(1704 - 1648)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def fU7qW8bb7J43(hXMPsSrOQzbh, lq9M6RYMdyT1, aZTCj4v5QdfO=nzTpIcepk0o8(chr(0b100101 + 0o13) + chr(0b10111 + 0o130) + '\x31', ord("\x08"))):
_9ve2uheHd6a = hXMPsSrOQzbh.to_haplotypes()
nBb88_Egavh_ = _9ve2uheHd6a.map_alleles(lq9M6RYMdyT1, copy=aZTCj4v5QdfO)
if roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\xa5\x1c\xcf\x0f\x01<\x8a\xb9\xc7\x9c\x15h'), chr(100) + chr(7923 - 7822) + chr(0b1100011) + chr(111) + chr(0b1100100) + '\145')(chr(0b1110101) + chr(5614 - 5498) + chr(0b110111 + 0o57) + chr(0b100011 + 0o12) + chr(0b111000))) == nzTpIcepk0o8('\060' + '\157' + chr(0b110010), ord("\x08")):
AGmAas3CjOkD = HdHc7d8bC2af(nBb88_Egavh_)
else:
AGmAas3CjOkD = nBb88_Egavh_.to_genotypes(ploidy=hXMPsSrOQzbh.ploidy)
return AGmAas3CjOkD |
cggh/scikit-allel | allel/model/ndarray.py | GenotypeArray.to_packed | def to_packed(self, boundscheck=True):
"""Pack diploid genotypes into a single byte for each genotype,
using the left-most 4 bits for the first allele and the right-most 4
bits for the second allele. Allows single byte encoding of diploid
genotypes for variants with up to 15 alleles.
Parameters
----------
boundscheck : bool, optional
If False, do not check that minimum and maximum alleles are
compatible with bit-packing.
Returns
-------
packed : ndarray, uint8, shape (n_variants, n_samples)
Bit-packed genotype array.
Notes
-----
If a mask has been set, it is ignored by this function.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 1]],
... [[0, 2], [1, 1]],
... [[2, 2], [-1, -1]]], dtype='i1')
>>> g.to_packed()
array([[ 0, 1],
[ 2, 17],
[ 34, 239]], dtype=uint8)
"""
check_ploidy(self.ploidy, 2)
if boundscheck:
amx = self.max()
if amx > 14:
raise ValueError('max allele for packing is 14, found %s' % amx)
amn = self.min()
if amn < -1:
raise ValueError('min allele for packing is -1, found %s' % amn)
# pack data
values = memoryview_safe(self.values)
packed = genotype_array_pack_diploid(values)
return packed | python | def to_packed(self, boundscheck=True):
"""Pack diploid genotypes into a single byte for each genotype,
using the left-most 4 bits for the first allele and the right-most 4
bits for the second allele. Allows single byte encoding of diploid
genotypes for variants with up to 15 alleles.
Parameters
----------
boundscheck : bool, optional
If False, do not check that minimum and maximum alleles are
compatible with bit-packing.
Returns
-------
packed : ndarray, uint8, shape (n_variants, n_samples)
Bit-packed genotype array.
Notes
-----
If a mask has been set, it is ignored by this function.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 1]],
... [[0, 2], [1, 1]],
... [[2, 2], [-1, -1]]], dtype='i1')
>>> g.to_packed()
array([[ 0, 1],
[ 2, 17],
[ 34, 239]], dtype=uint8)
"""
check_ploidy(self.ploidy, 2)
if boundscheck:
amx = self.max()
if amx > 14:
raise ValueError('max allele for packing is 14, found %s' % amx)
amn = self.min()
if amn < -1:
raise ValueError('min allele for packing is -1, found %s' % amn)
# pack data
values = memoryview_safe(self.values)
packed = genotype_array_pack_diploid(values)
return packed | [
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bits for the second allele. Allows single byte encoding of diploid
genotypes for variants with up to 15 alleles.
Parameters
----------
boundscheck : bool, optional
If False, do not check that minimum and maximum alleles are
compatible with bit-packing.
Returns
-------
packed : ndarray, uint8, shape (n_variants, n_samples)
Bit-packed genotype array.
Notes
-----
If a mask has been set, it is ignored by this function.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 1]],
... [[0, 2], [1, 1]],
... [[2, 2], [-1, -1]]], dtype='i1')
>>> g.to_packed()
array([[ 0, 1],
[ 2, 17],
[ 34, 239]], dtype=uint8) | [
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"allele"... | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/model/ndarray.py#L1553-L1602 | train | Pack the diploid genotypes into a single byte array. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJUSN6g,Awc2QmWaiVq8,fPFTJxVnGShv,Kqv3Zaj1M9P0,uKsHT175xV8E,ah0DLMBSEU5j,EsFcqWRT9elq,d9st0HqZDng1,knUxyjfq07F9,Fc8q2OvvlH7d,KSw3AkHkJy1a,JD7LadPikpPw,VwkB9reRDydR,aHxuT4bIDdeg,Qn0k4xGfJpuL,NfwEQ1VKf5DV,WdoB9EK8ABTr,Y1otPTwLRJvi,zsedrPqY_EmW,CJFGX4uBWMak,DB9Ra8FNEf7o,DHq8A6v2Wg4n,Migy1gLCcYvQ,IAGRfZDRyjN_,ze1AhR_jfpze,ej204HIOxzoZ,_1qUu0gKi9gH,Wa8JM2k53wi5,aFaxROHyT7UJ,ZOdpVDJPWn4I,LqOf4dRsAg72,K3alqetBMgas,ZtIuyIq3ta7g,UIHY5MV5X5uS,C60ELahXqfKV,FB4_7GjVy3pW,wXIYU_4UfQFa,jZIjKu8IFANs,REazVyvp6OIp,pZy5DBJ8WJod,aP29ipGsOVzf,YikXQdxs3VoO,UBvEeZympYSz,mRTjFWUmjlQA,QhZRiM1qvaW7,WbNHlDKpyPtQ,z18h6aCn31dg,oxjHmqoBrCHG,GA4ANb_Tki5v,LdFlJR2ssk3y,gCu7Qd75URN1,yfEeqQiUoqWT,zGgTE_CdZfvi,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2,zQBGwUT7UU8L,DvlSWc3qeAuL,qX60lO1lgHA5,ZQUt7vS8_3kI,VF4pKOObtlPc,D6JeCyjJUA8O,fBqfYi7uj_uC,TVUhqOt5_BbS,WtdkIpFeYozM,MdkNqd1bagO6,QNQS9e6tJqMV,typojWN5Phrq,gufQJgTAhMnI,uPAcezIXzQNA,i739myaCTbWD,AtYHTsImz86v,pWZq9QOaZbhU,lI5UiuqoXdKZ,qZ4DivK_Doaa,znjnJWK64FDT,iJbw0iNQ06Xw,Jq33HEV_XqZE,_kV_Bomx8PZ4,Z5xOfqIptFuc,_9cznYtBZk6k,ZurjcUL1ssA8,qEahrGEDF7Tq,jLW6pRf2DSRk,q33KG3foQ_CJ,PNaRkv8AjHWU,roI3spqORKae,CFUos7dinCa7,dRKdVnHPFq7C,dMJNtLk2mncQ,Mq8h41ilRngb,vgO67Nkl7Kt9,maLnLg8O5zPT,QnTXOd5N96r1,nzTpIcepk0o8,suIjIS24Zkqw,CmsH_0IVxIiZ,b8MSkfijeeBr,ftfygxgFas5X,xM0vTMWcJQBa,H4NoA26ON7iG,y0cCpS6dh4OT,VVP82lOIz6CD,KV9ckIhroIia,D2M3XQk26HKr,XURpmPuEWCNF,ltB3XhPy2rYf,mxgO6GAb3Xup,llEg6op6Lr8F,DnU3Rq9N5ala,RmKXV0QRcrJP,JEroPXRTriYU,v8jsMqaYV6U2,X1QyyvXSAOQt,PWTqT_PKIfuW,bbT2xIe5pzk7,VWshwTzZfwvC,DoS4vLAglV8A,sOS7b2Ofrbne,Bvi71nNyvlqO,lCf1uzpaIUMv,nDEnDEV3Lc5Z,V3OlOVg98A85,WsP3Nc3n6e0b,N9zlRy29S1SS,oclC8DLjA_lV,CO2YiXoIEhJY,nfNqtJL5aRaY,MJ07XsN5uFgW,cL4sFo6RhVJa,TxMFWa_Xzviv,bpTSxj4JFQ8o,zL_YcxPEZPhm,yfEeqQiUoqWT,OHWDi_URd_WF,NKGkaWkPPkT2,AYtDRlqeP0tq,vQqJeSQfHM0X,FUdwyfT9sfj2=ArithmeticError,AssertionError,AttributeError,BaseException,BlockingIOError,BrokenPipeError,BufferError,BytesWarning,ChildProcessError,ConnectionAbortedError,ConnectionError,ConnectionRefusedError,ConnectionResetError,DeprecationWarning,EOFError,Ellipsis,EncodingWarning,EnvironmentError,Exception,False,FileExistsError,FileNotFoundError,FloatingPointError,FutureWarning,GeneratorExit,IOError,ImportError,ImportWarning,IndentationError,IndexError,InterruptedError,IsADirectoryError,KeyError,KeyboardInterrupt,LookupError,MemoryError,ModuleNotFoundError,NameError,None,NotADirectoryError,NotImplemented,NotImplementedError,OSError,OverflowError,PendingDeprecationWarning,PermissionError,ProcessLookupError,RecursionError,ReferenceError,ResourceWarning,RuntimeError,RuntimeWarning,StopAsyncIteration,StopIteration,SyntaxError,SyntaxWarning,SystemError,SystemExit,TabError,TimeoutError,True,TypeError,UnboundLocalError,UnicodeDecodeError,UnicodeEncodeError,UnicodeError,UnicodeTranslateError,UnicodeWarning,UserWarning,ValueError,Warning,WindowsError,ZeroDivisionError,__build_class__,__debug__,__doc__,__import__,__loader__,__name__,__package__,__spec__,abs,aiter,all,anext,any,ascii,bin,bool,breakpoint,bytearray,bytes,callable,chr,classmethod,compile,complex,copyright,credits,delattr,dict,dir,divmod,enumerate,eval,exec,exit,filter,float,format,frozenset,getattr,globals,hasattr,hash,help,hex,id,input,int,isinstance,issubclass,iter,len,license,list,locals,map,max,memoryview,min,next,object,oct,open,ord,pow,print,property,quit,range,repr,reversed,round,set,setattr,slice,sorted,staticmethod,str,sum,super,tuple,type,vars,zip,__builtins__,__cached__,__doc__,__file__,__loader__,__name__,__package__,__spec__
ES5oEprVxulp = lambda R7ltlgvcKSD4: QNQS9e6tJqMV([bI5jsQ9OkQtj ^ [nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110011) + chr(55) + '\x32', 55870 - 55862), nzTpIcepk0o8(chr(0b1111 + 0o41) + '\157' + chr(49) + chr(50), 21202 - 21194), nzTpIcepk0o8('\x30' + chr(111) + '\063' + chr(0b110101) + '\065', ord("\x08")), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110011) + chr(0b110011) + chr(0b100000 + 0o21), 54555 - 54547), nzTpIcepk0o8('\x30' + '\157' + chr(51) + '\x35', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(0b110001) + '\063', 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110001) + chr(53) + '\064', 38646 - 38638), nzTpIcepk0o8('\060' + chr(0b1101111) + '\063' + chr(820 - 768) + chr(2365 - 2311), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(9603 - 9492) + '\x32' + chr(945 - 892) + chr(52), 0b1000), nzTpIcepk0o8(chr(0b1011 + 0o45) + chr(8320 - 8209) + chr(0b110011) + chr(0b110111) + chr(889 - 836), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\062' + '\064', ord("\x08")), nzTpIcepk0o8('\x30' + chr(10972 - 10861) + '\x37' + chr(756 - 703), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + chr(0b110001) + chr(48) + '\066', 25010 - 25002), nzTpIcepk0o8(chr(1570 - 1522) + '\157' + chr(2221 - 2170) + chr(51) + chr(1521 - 1472), 8), nzTpIcepk0o8('\060' + chr(0b101001 + 0o106) + chr(0b110011) + '\064' + chr(54), 8), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(51) + chr(108 - 55) + chr(50), 0b1000), nzTpIcepk0o8('\x30' + chr(111) + chr(1239 - 1190) + chr(1969 - 1915) + '\061', 0o10), nzTpIcepk0o8(chr(0b11110 + 0o22) + '\157' + chr(0b11 + 0o60) + '\x36' + chr(0b110000), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(6225 - 6114) + chr(49) + '\x31' + '\x35', 0o10), nzTpIcepk0o8('\060' + '\x6f' + chr(0b10110 + 0o35) + chr(1778 - 1728) + chr(0b110101), 46394 - 46386), nzTpIcepk0o8(chr(48) + chr(0b1101111) + chr(49) + '\066' + '\063', 57733 - 57725), nzTpIcepk0o8(chr(363 - 315) + '\157' + chr(1652 - 1602) + chr(0b110101) + chr(52), 8), nzTpIcepk0o8(chr(48) + chr(111) + '\063' + chr(0b110000), 10145 - 10137), nzTpIcepk0o8(chr(0b10000 + 0o40) + chr(0b111101 + 0o62) + '\062' + chr(52) + chr(882 - 831), 16954 - 16946), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b110000 + 0o5) + chr(1555 - 1504), ord("\x08")), nzTpIcepk0o8(chr(1440 - 1392) + chr(10475 - 10364) + chr(354 - 305) + chr(50) + '\064', 0o10), nzTpIcepk0o8(chr(2278 - 2230) + '\157' + '\065' + chr(53), 0o10), nzTpIcepk0o8('\060' + chr(111) + '\061' + chr(744 - 693) + '\x35', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(4846 - 4735) + '\063' + chr(48) + chr(740 - 687), 0o10), nzTpIcepk0o8('\x30' + chr(0b1000111 + 0o50) + chr(0b100000 + 0o21) + chr(53) + chr(0b100111 + 0o11), 30150 - 30142), nzTpIcepk0o8(chr(48) + chr(4055 - 3944) + '\x32' + chr(0b110001) + '\063', 0o10), nzTpIcepk0o8(chr(48) + chr(111) + chr(50) + chr(53), 0b1000), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\062' + chr(242 - 191) + chr(0b110011), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b110111 + 0o70) + chr(55) + chr(979 - 927), 0b1000), nzTpIcepk0o8(chr(1128 - 1080) + '\x6f' + chr(0b110011 + 0o0) + '\x31' + chr(1958 - 1910), 0b1000), nzTpIcepk0o8('\060' + chr(111) + chr(0b110 + 0o53) + chr(2860 - 2805) + '\x31', 0o10), nzTpIcepk0o8(chr(0b10110 + 0o32) + '\157' + '\x35' + chr(54), 14795 - 14787), nzTpIcepk0o8(chr(48) + chr(2682 - 2571) + '\x33' + chr(0b101000 + 0o10) + chr(2021 - 1973), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b110010 + 0o75) + chr(49) + '\x35' + '\x34', 8), nzTpIcepk0o8('\060' + chr(0b1011101 + 0o22) + chr(51) + chr(0b110000) + chr(0b110101), 8)][ZlbFMSG8gCoF % nzTpIcepk0o8('\060' + chr(0b10011 + 0o134) + chr(53) + chr(0b101010 + 0o6), 0o10)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\xd4'), '\144' + chr(0b1100101) + chr(0b1100011) + chr(1582 - 1471) + chr(7558 - 7458) + chr(0b1100101))(chr(0b1011101 + 0o30) + '\164' + chr(4523 - 4421) + chr(1247 - 1202) + chr(0b101110 + 0o12)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def n0lotMdPTHC2(hXMPsSrOQzbh, VUUqHTa_4DJs=nzTpIcepk0o8('\x30' + chr(0b1000000 + 0o57) + '\061', 0o10)):
S0Uypoo4zSP9(roI3spqORKae(hXMPsSrOQzbh, roI3spqORKae(ES5oEprVxulp(b'\x8af\x82\xb0yr'), chr(8833 - 8733) + chr(101) + chr(0b1100011) + chr(10669 - 10558) + chr(630 - 530) + chr(5609 - 5508))(chr(0b101001 + 0o114) + chr(0b1110100) + '\x66' + chr(0b1110 + 0o37) + chr(0b11010 + 0o36))), nzTpIcepk0o8('\x30' + chr(1794 - 1683) + chr(50), 17125 - 17117))
if VUUqHTa_4DJs:
bLk08MwP6Edd = hXMPsSrOQzbh.KV9ckIhroIia()
if bLk08MwP6Edd > nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(1910 - 1861) + chr(0b10 + 0o64), 0b1000):
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'\x97k\x95\xf9|g\x00\x83\xc0\x984[)\xab\xc6\x9a\x10\x93&\xbc\x1d\xcb8\xcaXt\x1ci\xe9H\xedz\xeeR\xacY\x0b\xb3'), chr(100) + '\x65' + chr(0b1100011) + '\157' + '\x64' + '\145')(chr(0b1110101) + '\164' + chr(0b1100110) + chr(45) + '\x38') % bLk08MwP6Edd)
EgSn6oPcp2mr = hXMPsSrOQzbh.XURpmPuEWCNF()
if EgSn6oPcp2mr < -nzTpIcepk0o8('\060' + chr(0b1101111) + chr(1839 - 1790), 8):
raise WbNHlDKpyPtQ(roI3spqORKae(ES5oEprVxulp(b'\x97c\x83\xf9|g\x00\x83\xc0\x984[)\xab\xc6\x9a\x10\x93&\xbc\x1d\xcb8\xcaXt\x00l\xe9H\xedz\xeeR\xacY\x0b\xb3'), chr(0b100000 + 0o104) + '\145' + chr(0b1000010 + 0o41) + '\x6f' + '\x64' + '\145')(chr(8805 - 8688) + chr(116) + chr(0b111 + 0o137) + chr(0b101101) + chr(0b110001 + 0o7)) % EgSn6oPcp2mr)
CsodZJH6x9Tx = ygMIbkSSXS59(hXMPsSrOQzbh.CsodZJH6x9Tx)
V9B3HFEeYb08 = Ue2EXSQRAQPb(CsodZJH6x9Tx)
return V9B3HFEeYb08 |
cggh/scikit-allel | allel/model/ndarray.py | GenotypeArray.from_packed | def from_packed(cls, packed):
"""Unpack diploid genotypes that have been bit-packed into single
bytes.
Parameters
----------
packed : ndarray, uint8, shape (n_variants, n_samples)
Bit-packed diploid genotype array.
Returns
-------
g : GenotypeArray, shape (n_variants, n_samples, 2)
Genotype array.
Examples
--------
>>> import allel
>>> import numpy as np
>>> packed = np.array([[0, 1],
... [2, 17],
... [34, 239]], dtype='u1')
>>> allel.GenotypeArray.from_packed(packed)
<GenotypeArray shape=(3, 2, 2) dtype=int8>
0/0 0/1
0/2 1/1
2/2 ./.
"""
# check arguments
packed = np.asarray(packed)
check_ndim(packed, 2)
check_dtype(packed, 'u1')
packed = memoryview_safe(packed)
data = genotype_array_unpack_diploid(packed)
return cls(data) | python | def from_packed(cls, packed):
"""Unpack diploid genotypes that have been bit-packed into single
bytes.
Parameters
----------
packed : ndarray, uint8, shape (n_variants, n_samples)
Bit-packed diploid genotype array.
Returns
-------
g : GenotypeArray, shape (n_variants, n_samples, 2)
Genotype array.
Examples
--------
>>> import allel
>>> import numpy as np
>>> packed = np.array([[0, 1],
... [2, 17],
... [34, 239]], dtype='u1')
>>> allel.GenotypeArray.from_packed(packed)
<GenotypeArray shape=(3, 2, 2) dtype=int8>
0/0 0/1
0/2 1/1
2/2 ./.
"""
# check arguments
packed = np.asarray(packed)
check_ndim(packed, 2)
check_dtype(packed, 'u1')
packed = memoryview_safe(packed)
data = genotype_array_unpack_diploid(packed)
return cls(data) | [
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bytes.
Parameters
----------
packed : ndarray, uint8, shape (n_variants, n_samples)
Bit-packed diploid genotype array.
Returns
-------
g : GenotypeArray, shape (n_variants, n_samples, 2)
Genotype array.
Examples
--------
>>> import allel
>>> import numpy as np
>>> packed = np.array([[0, 1],
... [2, 17],
... [34, 239]], dtype='u1')
>>> allel.GenotypeArray.from_packed(packed)
<GenotypeArray shape=(3, 2, 2) dtype=int8>
0/0 0/1
0/2 1/1
2/2 ./. | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/model/ndarray.py#L1605-L1642 | train | Unpack diploid genotypes that have been bit - packed into single
bytes. | 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(7223 - 7112) + chr(0b110010) + chr(0b110111) + chr(50), 0o10), nzTpIcepk0o8(chr(48) + chr(111) + '\x32' + '\x34', 31849 - 31841), nzTpIcepk0o8('\x30' + chr(0b1101111) + '\x33' + chr(0b110010 + 0o0) + chr(0b110010), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(111) + '\063' + chr(48) + '\063', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b110100 + 0o73) + chr(0b110001) + chr(0b110110) + chr(0b110011), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(54) + chr(0b110010), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(741 - 691) + '\x35' + chr(1658 - 1604), 23225 - 23217), nzTpIcepk0o8('\060' + chr(111) + '\063' + chr(0b11111 + 0o25) + '\062', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1010100 + 0o33) + chr(0b110001 + 0o3) + chr(49), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\063' + chr(1570 - 1517) + chr(2388 - 2333), 0o10), nzTpIcepk0o8(chr(1172 - 1124) + chr(8349 - 8238) + '\x32' + '\061', 0b1000), nzTpIcepk0o8(chr(0b101000 + 0o10) + chr(111) + chr(0b11101 + 0o25) + '\062' + '\x36', ord("\x08")), nzTpIcepk0o8('\060' + chr(111) + chr(0b100010 + 0o24) + '\x35', ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + '\066', ord("\x08")), nzTpIcepk0o8(chr(0b101111 + 0o1) + chr(0b1101111) + chr(0b110011) + chr(0b10110 + 0o40) + chr(1128 - 1078), 51604 - 51596), nzTpIcepk0o8('\060' + '\157' + chr(0b100011 + 0o16) + '\x36' + chr(0b110011), 8), nzTpIcepk0o8('\x30' + '\157' + '\062' + chr(54) + chr(0b110010), 26353 - 26345), nzTpIcepk0o8('\060' + chr(111) + '\063' + '\063' + chr(0b110010), 18039 - 18031), nzTpIcepk0o8(chr(1954 - 1906) + chr(111) + chr(49) + '\062' + chr(0b110010), 38549 - 38541), nzTpIcepk0o8(chr(0b110000) + chr(9028 - 8917) + chr(0b110010) + chr(0b110101) + chr(0b110101), 44496 - 44488), nzTpIcepk0o8(chr(1631 - 1583) + chr(0b110001 + 0o76) + '\x31' + '\x37' + '\x36', 0o10), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(0b10101 + 0o40) + chr(50), 1006 - 998), nzTpIcepk0o8(chr(0b1100 + 0o44) + chr(0b1101111) + chr(0b110010) + chr(1535 - 1481), 0b1000), nzTpIcepk0o8(chr(48) + chr(5220 - 5109) + chr(0b100100 + 0o22) + chr(53), 8), nzTpIcepk0o8(chr(496 - 448) + '\157' + chr(49) + chr(1497 - 1449) + chr(0b110001), 0o10), nzTpIcepk0o8(chr(0b11111 + 0o21) + chr(0b1101111) + chr(0b100011 + 0o20) + chr(50) + chr(0b110 + 0o61), 0o10), nzTpIcepk0o8('\060' + chr(3693 - 3582) + chr(0b10011 + 0o37) + '\063' + '\062', 64124 - 64116), nzTpIcepk0o8(chr(48) + chr(0b1010011 + 0o34) + '\x31' + chr(48) + chr(0b110000), ord("\x08")), nzTpIcepk0o8('\060' + '\x6f' + '\063' + '\x35' + chr(0b100 + 0o54), 0o10), nzTpIcepk0o8(chr(0b11010 + 0o26) + '\157' + chr(49) + '\x37' + chr(0b110011), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + '\x33' + chr(0b110001) + chr(0b110110), 19543 - 19535), nzTpIcepk0o8(chr(1912 - 1864) + chr(0b111010 + 0o65) + '\067' + chr(51), 18754 - 18746), nzTpIcepk0o8(chr(2221 - 2173) + '\157' + chr(0b101001 + 0o12) + chr(53) + '\065', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(9947 - 9836) + '\061' + chr(0b101111 + 0o2) + '\064', ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(51) + chr(52) + '\062', 8), nzTpIcepk0o8('\060' + '\x6f' + chr(0b100001 + 0o20) + chr(0b100000 + 0o24) + chr(52), ord("\x08")), nzTpIcepk0o8('\x30' + chr(111) + chr(51) + chr(990 - 938) + chr(2100 - 2048), 0b1000), nzTpIcepk0o8(chr(1688 - 1640) + '\157' + '\066', 8), nzTpIcepk0o8(chr(0b110000) + chr(5508 - 5397) + '\x31' + chr(0b110 + 0o61) + chr(1796 - 1746), 11080 - 11072), nzTpIcepk0o8('\x30' + chr(0b1100011 + 0o14) + '\x32' + chr(475 - 423), 8)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(0b101011 + 0o5) + chr(0b1100100 + 0o13) + chr(53) + chr(48), 0b1000)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x94'), chr(0b1000110 + 0o36) + chr(3893 - 3792) + chr(99) + chr(541 - 430) + chr(0b1011010 + 0o12) + '\x65')('\x75' + chr(116) + '\146' + chr(45) + chr(0b1 + 0o67)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def XxJzYF28MPKA(_1vzISbJ_R2i, V9B3HFEeYb08):
V9B3HFEeYb08 = nDF4gVNx0u9Q.asarray(V9B3HFEeYb08)
MBVsA6X06TUz(V9B3HFEeYb08, nzTpIcepk0o8('\060' + chr(12240 - 12129) + chr(2150 - 2100), 60014 - 60006))
u2kL2hIrgS6F(V9B3HFEeYb08, roI3spqORKae(ES5oEprVxulp(b'\xcf%'), chr(100) + chr(101) + '\143' + chr(0b1101111) + '\144' + chr(0b1100101))('\x75' + chr(116) + chr(1364 - 1262) + chr(0b101101) + '\x38'))
V9B3HFEeYb08 = ygMIbkSSXS59(V9B3HFEeYb08)
FfKOThdpoDTb = RpRYAq7o6JNB(V9B3HFEeYb08)
return _1vzISbJ_R2i(FfKOThdpoDTb) |
cggh/scikit-allel | allel/model/ndarray.py | GenotypeArray.to_sparse | def to_sparse(self, format='csr', **kwargs):
"""Convert into a sparse matrix.
Parameters
----------
format : {'coo', 'csc', 'csr', 'dia', 'dok', 'lil'}
Sparse matrix format.
kwargs : keyword arguments
Passed through to sparse matrix constructor.
Returns
-------
m : scipy.sparse.spmatrix
Sparse matrix
Notes
-----
If a mask has been set, it is ignored by this function.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 0]],
... [[0, 1], [0, 1]],
... [[1, 1], [0, 0]],
... [[0, 0], [-1, -1]]], dtype='i1')
>>> m = g.to_sparse(format='csr')
>>> m
<4x4 sparse matrix of type '<class 'numpy.int8'>'
with 6 stored elements in Compressed Sparse Row format>
>>> m.data
array([ 1, 1, 1, 1, -1, -1], dtype=int8)
>>> m.indices
array([1, 3, 0, 1, 2, 3], dtype=int32)
>>> m.indptr
array([0, 0, 2, 4, 6], dtype=int32)
"""
h = self.to_haplotypes()
m = h.to_sparse(format=format, **kwargs)
return m | python | def to_sparse(self, format='csr', **kwargs):
"""Convert into a sparse matrix.
Parameters
----------
format : {'coo', 'csc', 'csr', 'dia', 'dok', 'lil'}
Sparse matrix format.
kwargs : keyword arguments
Passed through to sparse matrix constructor.
Returns
-------
m : scipy.sparse.spmatrix
Sparse matrix
Notes
-----
If a mask has been set, it is ignored by this function.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 0]],
... [[0, 1], [0, 1]],
... [[1, 1], [0, 0]],
... [[0, 0], [-1, -1]]], dtype='i1')
>>> m = g.to_sparse(format='csr')
>>> m
<4x4 sparse matrix of type '<class 'numpy.int8'>'
with 6 stored elements in Compressed Sparse Row format>
>>> m.data
array([ 1, 1, 1, 1, -1, -1], dtype=int8)
>>> m.indices
array([1, 3, 0, 1, 2, 3], dtype=int32)
>>> m.indptr
array([0, 0, 2, 4, 6], dtype=int32)
"""
h = self.to_haplotypes()
m = h.to_sparse(format=format, **kwargs)
return m | [
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Parameters
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format : {'coo', 'csc', 'csr', 'dia', 'dok', 'lil'}
Sparse matrix format.
kwargs : keyword arguments
Passed through to sparse matrix constructor.
Returns
-------
m : scipy.sparse.spmatrix
Sparse matrix
Notes
-----
If a mask has been set, it is ignored by this function.
Examples
--------
>>> import allel
>>> g = allel.GenotypeArray([[[0, 0], [0, 0]],
... [[0, 1], [0, 1]],
... [[1, 1], [0, 0]],
... [[0, 0], [-1, -1]]], dtype='i1')
>>> m = g.to_sparse(format='csr')
>>> m
<4x4 sparse matrix of type '<class 'numpy.int8'>'
with 6 stored elements in Compressed Sparse Row format>
>>> m.data
array([ 1, 1, 1, 1, -1, -1], dtype=int8)
>>> m.indices
array([1, 3, 0, 1, 2, 3], dtype=int32)
>>> m.indptr
array([0, 0, 2, 4, 6], dtype=int32) | [
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] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/model/ndarray.py#L1645-L1688 | train | Convert the current object into a sparse matrix. | 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) + '\066' + chr(0b110011 + 0o4), 0b1000), nzTpIcepk0o8(chr(48) + '\157' + chr(49) + chr(0b110110) + chr(0b10110 + 0o40), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\062' + '\x32', 0o10), nzTpIcepk0o8(chr(2124 - 2076) + '\157' + '\x32' + '\x36' + chr(2088 - 2040), 0o10), nzTpIcepk0o8('\x30' + '\x6f' + chr(0b110001) + chr(2022 - 1972) + '\066', 0b1000), nzTpIcepk0o8('\060' + chr(0b1101111) + chr(0b110010) + chr(0b110011) + '\065', 40543 - 40535), nzTpIcepk0o8(chr(970 - 922) + chr(0b1101111) + '\x37' + '\066', 0b1000), nzTpIcepk0o8(chr(48) + chr(0b1101111) + '\x32' + chr(52) + '\065', 42290 - 42282), nzTpIcepk0o8(chr(48) + '\157' + '\x31' + chr(0b110100) + chr(53), ord("\x08")), nzTpIcepk0o8(chr(1769 - 1721) + chr(0b1001000 + 0o47) + '\x31' + chr(0b110111), 0o10), nzTpIcepk0o8(chr(48) + '\x6f' + chr(0b10001 + 0o42) + chr(49) + chr(54), 43196 - 43188), nzTpIcepk0o8('\060' + '\x6f' + chr(0b110010 + 0o2) + chr(0b11111 + 0o21), 0b1000), nzTpIcepk0o8('\060' + chr(111) + '\x31' + chr(1759 - 1711), 18630 - 18622), nzTpIcepk0o8('\x30' + '\157' + chr(0b110011) + chr(0b101001 + 0o14) + chr(55), 57819 - 57811), nzTpIcepk0o8('\x30' + chr(0b1101111) + chr(761 - 711) + chr(0b101111 + 0o2) + chr(0b110011), 0o10), nzTpIcepk0o8(chr(0b101111 + 0o1) + '\157' + chr(0b10011 + 0o40) + chr(710 - 662) + '\060', ord("\x08")), nzTpIcepk0o8(chr(1519 - 1471) + chr(0b1101111) + chr(0b10110 + 0o34) + chr(53), ord("\x08")), nzTpIcepk0o8('\x30' + chr(0b11001 + 0o126) + '\062' + chr(2319 - 2269) + chr(632 - 581), 0b1000), nzTpIcepk0o8(chr(48) + chr(0b110011 + 0o74) + chr(0b11110 + 0o25) + '\x34' + chr(50), 0o10), nzTpIcepk0o8('\x30' + '\157' + '\063' + chr(0b110001) + chr(50), 0o10), nzTpIcepk0o8(chr(0b11101 + 0o23) + chr(0b1100100 + 0o13) + '\x33' + chr(55) + chr(1898 - 1850), 0o10), nzTpIcepk0o8(chr(48) + chr(3869 - 3758) + chr(0b110001) + chr(0b110100) + chr(0b1001 + 0o51), ord("\x08")), nzTpIcepk0o8(chr(240 - 192) + '\157' + chr(2027 - 1976) + chr(1456 - 1408), 0b1000), nzTpIcepk0o8(chr(2124 - 2076) + '\x6f' + chr(0b101010 + 0o10) + chr(2651 - 2599) + '\x35', 8), nzTpIcepk0o8(chr(0b110000) + chr(3939 - 3828) + chr(0b110010) + chr(1439 - 1386) + chr(2068 - 2020), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(3969 - 3858) + '\062' + chr(0b110001) + chr(0b110010), 0b1000), nzTpIcepk0o8(chr(0b110 + 0o52) + chr(10167 - 10056) + '\065' + '\065', ord("\x08")), nzTpIcepk0o8(chr(928 - 880) + '\x6f' + '\x33' + chr(0b101000 + 0o17) + chr(0b10010 + 0o41), 0o10), nzTpIcepk0o8(chr(0b110000) + chr(9223 - 9112) + chr(1604 - 1555) + '\063' + '\062', 338 - 330), nzTpIcepk0o8(chr(0b110000) + chr(11631 - 11520) + chr(0b101001 + 0o11) + chr(52) + chr(1064 - 1015), ord("\x08")), nzTpIcepk0o8(chr(48) + chr(111) + '\x33' + chr(233 - 179) + chr(53), 0o10), nzTpIcepk0o8('\060' + chr(0b1101110 + 0o1) + chr(0b10000 + 0o43) + '\065' + '\x33', 4340 - 4332), nzTpIcepk0o8(chr(48) + chr(0b1011001 + 0o26) + chr(0b1110 + 0o43) + chr(0b110100) + '\x36', 0o10), nzTpIcepk0o8(chr(607 - 559) + '\x6f' + '\063' + chr(170 - 117) + chr(55), 8), nzTpIcepk0o8(chr(1783 - 1735) + chr(2555 - 2444) + '\063' + '\062' + '\067', ord("\x08")), nzTpIcepk0o8('\060' + chr(0b111111 + 0o60) + '\061' + chr(0b110001) + chr(2769 - 2714), 0o10), nzTpIcepk0o8(chr(541 - 493) + '\x6f' + '\062' + '\x36' + chr(0b110011), 0b1000), nzTpIcepk0o8('\x30' + '\x6f' + chr(51) + chr(54), 0o10), nzTpIcepk0o8('\x30' + chr(111) + '\066' + '\x37', 8), nzTpIcepk0o8(chr(2012 - 1964) + '\x6f' + chr(0b110001) + '\x35' + chr(0b110 + 0o53), 0o10)][ZlbFMSG8gCoF % nzTpIcepk0o8(chr(1487 - 1439) + chr(0b1101111) + chr(0b10001 + 0o44) + chr(580 - 532), 33622 - 33614)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'\x19'), chr(100) + '\x65' + '\x63' + '\x6f' + '\144' + chr(101))(chr(7703 - 7586) + chr(0b101010 + 0o112) + '\146' + chr(0b1011 + 0o42) + chr(948 - 892)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def oEndwNoxdAeb(hXMPsSrOQzbh, q33KG3foQ_CJ=roI3spqORKae(ES5oEprVxulp(b'T\x05`'), '\144' + '\x65' + chr(0b1100011) + chr(10650 - 10539) + '\x64' + chr(0b1100101))(chr(10794 - 10677) + chr(116) + chr(0b11 + 0o143) + '\x2d' + chr(0b1111 + 0o51)), **q5n0sHDDTy90):
_9ve2uheHd6a = hXMPsSrOQzbh.to_haplotypes()
tF75nqoNENFL = _9ve2uheHd6a.to_sparse(format=q33KG3foQ_CJ, **q5n0sHDDTy90)
return tF75nqoNENFL |
cggh/scikit-allel | allel/model/ndarray.py | GenotypeArray.from_sparse | def from_sparse(m, ploidy, order=None, out=None):
"""Construct a genotype array from a sparse matrix.
Parameters
----------
m : scipy.sparse.spmatrix
Sparse matrix
ploidy : int
The sample ploidy.
order : {'C', 'F'}, optional
Whether to store data in C (row-major) or Fortran (column-major)
order in memory.
out : ndarray, shape (n_variants, n_samples), optional
Use this array as the output buffer.
Returns
-------
g : GenotypeArray, shape (n_variants, n_samples, ploidy)
Genotype array.
Examples
--------
>>> import allel
>>> import numpy as np
>>> import scipy.sparse
>>> data = np.array([ 1, 1, 1, 1, -1, -1], dtype=np.int8)
>>> indices = np.array([1, 3, 0, 1, 2, 3], dtype=np.int32)
>>> indptr = np.array([0, 0, 2, 4, 6], dtype=np.int32)
>>> m = scipy.sparse.csr_matrix((data, indices, indptr))
>>> g = allel.GenotypeArray.from_sparse(m, ploidy=2)
>>> g
<GenotypeArray shape=(4, 2, 2) dtype=int8>
0/0 0/0
0/1 0/1
1/1 0/0
0/0 ./.
"""
h = HaplotypeArray.from_sparse(m, order=order, out=out)
g = h.to_genotypes(ploidy=ploidy)
return g | python | def from_sparse(m, ploidy, order=None, out=None):
"""Construct a genotype array from a sparse matrix.
Parameters
----------
m : scipy.sparse.spmatrix
Sparse matrix
ploidy : int
The sample ploidy.
order : {'C', 'F'}, optional
Whether to store data in C (row-major) or Fortran (column-major)
order in memory.
out : ndarray, shape (n_variants, n_samples), optional
Use this array as the output buffer.
Returns
-------
g : GenotypeArray, shape (n_variants, n_samples, ploidy)
Genotype array.
Examples
--------
>>> import allel
>>> import numpy as np
>>> import scipy.sparse
>>> data = np.array([ 1, 1, 1, 1, -1, -1], dtype=np.int8)
>>> indices = np.array([1, 3, 0, 1, 2, 3], dtype=np.int32)
>>> indptr = np.array([0, 0, 2, 4, 6], dtype=np.int32)
>>> m = scipy.sparse.csr_matrix((data, indices, indptr))
>>> g = allel.GenotypeArray.from_sparse(m, ploidy=2)
>>> g
<GenotypeArray shape=(4, 2, 2) dtype=int8>
0/0 0/0
0/1 0/1
1/1 0/0
0/0 ./.
"""
h = HaplotypeArray.from_sparse(m, order=order, out=out)
g = h.to_genotypes(ploidy=ploidy)
return g | [
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... | Construct a genotype array from a sparse matrix.
Parameters
----------
m : scipy.sparse.spmatrix
Sparse matrix
ploidy : int
The sample ploidy.
order : {'C', 'F'}, optional
Whether to store data in C (row-major) or Fortran (column-major)
order in memory.
out : ndarray, shape (n_variants, n_samples), optional
Use this array as the output buffer.
Returns
-------
g : GenotypeArray, shape (n_variants, n_samples, ploidy)
Genotype array.
Examples
--------
>>> import allel
>>> import numpy as np
>>> import scipy.sparse
>>> data = np.array([ 1, 1, 1, 1, -1, -1], dtype=np.int8)
>>> indices = np.array([1, 3, 0, 1, 2, 3], dtype=np.int32)
>>> indptr = np.array([0, 0, 2, 4, 6], dtype=np.int32)
>>> m = scipy.sparse.csr_matrix((data, indices, indptr))
>>> g = allel.GenotypeArray.from_sparse(m, ploidy=2)
>>> g
<GenotypeArray shape=(4, 2, 2) dtype=int8>
0/0 0/0
0/1 0/1
1/1 0/0
0/0 ./. | [
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"matrix",
"."
] | 3c979a57a100240ba959dd13f98839349530f215 | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/model/ndarray.py#L1691-L1733 | train | Construct a genotype array from a sparse matrix. | 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(0b100011 + 0o15) + chr(0b1101111) + chr(50) + chr(0b110111), ord("\x08")), nzTpIcepk0o8(chr(1360 - 1312) + chr(111) + chr(957 - 906) + chr(48) + '\067', 0o10), nzTpIcepk0o8(chr(0b110000) + chr(0b100011 + 0o114) + chr(2742 - 2689) + '\060', 0b1000), nzTpIcepk0o8(chr(1192 - 1144) + chr(0b1101111) + chr(0b110111), ord("\x08")), nzTpIcepk0o8('\060' + chr(11913 - 11802) + chr(0b110010) + chr(0b11100 + 0o25), 53560 - 53552), nzTpIcepk0o8('\x30' + '\157' + chr(0b110 + 0o54) + chr(55) + chr(0b110000), 0b1000), nzTpIcepk0o8('\060' + chr(11329 - 11218) + chr(0b110110) + '\062', ord("\x08")), nzTpIcepk0o8(chr(1846 - 1798) + chr(111) + chr(0b110010) + chr(2148 - 2100) + chr(52), 0b1000), nzTpIcepk0o8(chr(1237 - 1189) + chr(111) + chr(0b1111 + 0o43) + '\x37' + '\061', ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(7080 - 6969) + chr(51) + '\x33' + '\065', 60894 - 60886), nzTpIcepk0o8(chr(0b101010 + 0o6) + chr(0b1101111) + chr(49) + '\x31' + '\062', 36095 - 36087), nzTpIcepk0o8(chr(48) + chr(0b1101110 + 0o1) + chr(154 - 103) + chr(0b110 + 0o56) + chr(48), 0b1000), nzTpIcepk0o8(chr(2271 - 2223) + chr(10538 - 10427) + '\064' + '\061', 4575 - 4567), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b110010) + chr(0b1111 + 0o43) + '\063', ord("\x08")), nzTpIcepk0o8(chr(48) + chr(7779 - 7668) + '\063' + chr(0b110011) + chr(53), 8), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(1258 - 1209) + chr(1036 - 988) + chr(50), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\x6f' + chr(0b101101 + 0o5) + chr(0b101110 + 0o3) + '\066', 0b1000), nzTpIcepk0o8('\060' + chr(2157 - 2046) + chr(48), ord("\x08")), nzTpIcepk0o8(chr(1878 - 1830) + chr(111) + '\x33' + chr(48) + chr(0b110001 + 0o0), 35523 - 35515), nzTpIcepk0o8(chr(48) + '\x6f' + chr(563 - 509) + '\x36', 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(0b1101111) + '\062' + chr(0b110110) + '\061', 0o10), nzTpIcepk0o8(chr(0b1101 + 0o43) + chr(12039 - 11928) + '\x31' + '\x36' + chr(0b110101), 0b1000), nzTpIcepk0o8(chr(0b110000) + chr(111) + chr(51) + chr(55) + '\064', 0o10), nzTpIcepk0o8(chr(761 - 713) + chr(111) + chr(0b110001) + chr(2181 - 2132) + chr(788 - 736), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + chr(0b1011000 + 0o27) + chr(0b101101 + 0o4) + '\066' + chr(49), 10970 - 10962), nzTpIcepk0o8(chr(1309 - 1261) + chr(111) + chr(1076 - 1027) + '\067' + chr(0b11100 + 0o32), 0o10), nzTpIcepk0o8('\060' + chr(111) + chr(2021 - 1966) + '\061', 0b1000), nzTpIcepk0o8(chr(1250 - 1202) + chr(1705 - 1594) + '\x33' + chr(0b110101) + chr(51), 30933 - 30925), nzTpIcepk0o8(chr(2224 - 2176) + '\157' + chr(0b1011 + 0o46) + '\060' + chr(1448 - 1397), ord("\x08")), nzTpIcepk0o8('\060' + chr(0b1101111) + '\063' + '\067' + '\065', 0b1000), nzTpIcepk0o8(chr(0b1001 + 0o47) + chr(1505 - 1394) + '\061' + chr(2784 - 2730), 6198 - 6190), nzTpIcepk0o8(chr(0b1110 + 0o42) + '\x6f' + chr(54), ord("\x08")), nzTpIcepk0o8(chr(48) + '\x6f' + chr(51) + chr(0b110101) + '\x30', 2658 - 2650), nzTpIcepk0o8(chr(114 - 66) + chr(0b1101111) + '\x37', 8), nzTpIcepk0o8('\060' + '\x6f' + '\061' + '\063' + chr(306 - 252), 0b1000), nzTpIcepk0o8(chr(421 - 373) + chr(111) + '\x33' + chr(937 - 887) + chr(1207 - 1159), 1916 - 1908), nzTpIcepk0o8(chr(48) + chr(0b10101 + 0o132) + chr(0b110000 + 0o5) + chr(0b110001), ord("\x08")), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(49) + '\062' + chr(0b110 + 0o55), 59008 - 59000), nzTpIcepk0o8(chr(1870 - 1822) + chr(0b1011000 + 0o27) + chr(0b110010) + chr(176 - 128) + '\x31', 0b1000), nzTpIcepk0o8(chr(0b110000) + '\157' + chr(179 - 128) + '\060' + chr(52), 0b1000)][ZlbFMSG8gCoF % nzTpIcepk0o8('\x30' + '\x6f' + chr(681 - 628) + chr(0b110000), 8)] for (ZlbFMSG8gCoF, bI5jsQ9OkQtj) in _kV_Bomx8PZ4(R7ltlgvcKSD4)])
def rFFUeiYWzOhx(pOp6HxxfV61L, pXRQUD7VR93J):
try:
return zGgTE_CdZfvi(pOp6HxxfV61L + roI3spqORKae(ES5oEprVxulp(b'9'), '\144' + '\145' + chr(0b1100011) + chr(0b1101111) + chr(5994 - 5894) + '\145')('\165' + chr(884 - 768) + chr(0b1100110) + chr(0b11111 + 0o16) + chr(0b110010 + 0o6)) + pXRQUD7VR93J)
except fPFTJxVnGShv:
return zGgTE_CdZfvi(pOp6HxxfV61L)
def zbx_JfLeQeNv(tF75nqoNENFL, QEldLunXvDJ_, gwJk_IgdwKDy=None, VwOu8WkJ9cpc=None):
_9ve2uheHd6a = qbEQNEu82teb.from_sparse(tF75nqoNENFL, order=gwJk_IgdwKDy, out=VwOu8WkJ9cpc)
KQq7Z9J63zv1 = _9ve2uheHd6a.to_genotypes(ploidy=QEldLunXvDJ_)
return KQq7Z9J63zv1 |
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