<s> import os , sys , re , math , argparse , collections , tempfile <EOL> import dxpy <EOL> from . . utils . resolver import ResolutionError , resolve_existing_path <EOL> from . . utils . printing import fill <EOL> from . . compat import str <EOL> parser = argparse . ArgumentParser ( description = '<STR_LIT>' ) <EOL> parser . add_argument ( "<STR_LIT:path>" , help = "<STR_LIT>" ) <EOL> parser . add_argument ( '<STR_LIT>' , "<STR_LIT>" , help = '<STR_LIT>' ) <EOL> parser . add_argument ( "<STR_LIT>" , action = "<STR_LIT:store_true>" , help = "<STR_LIT>" ) <EOL> parser . add_argument ( "<STR_LIT>" , action = "<STR_LIT:store_true>" , help = "<STR_LIT>" ) <EOL> parser . add_argument ( "<STR_LIT>" , action = "<STR_LIT>" , help = "<STR_LIT>" ) <EOL> parser . add_argument ( "<STR_LIT>" , dest = "<STR_LIT>" , action = "<STR_LIT>" , help = "<STR_LIT>" ) <EOL> parser . add_argument ( "<STR_LIT>" , help = "<STR_LIT>" ) <EOL> def main ( ** kwargs ) : <EOL> if len ( kwargs ) == <NUM_LIT:0> : <EOL> kwargs = vars ( parser . parse_args ( sys . argv [ <NUM_LIT:1> : ] ) ) <EOL> try : <EOL> project , folderpath , entity_result = resolve_existing_path ( kwargs [ '<STR_LIT:path>' ] , expected = '<STR_LIT>' ) <EOL> except ResolutionError as details : <EOL> parser . exit ( <NUM_LIT:1> , fill ( str ( details ) ) + '<STR_LIT:\n>' ) <EOL> if entity_result is None : <EOL> parser . exit ( <NUM_LIT:1> , fill ( '<STR_LIT>' + kwargs [ '<STR_LIT:path>' ] + '<STR_LIT>' ) + '<STR_LIT:\n>' ) <EOL> filename = kwargs [ '<STR_LIT>' ] <EOL> if filename is None : <EOL> filename = entity_result [ '<STR_LIT>' ] [ '<STR_LIT:name>' ] . replace ( '<STR_LIT:/>' , '<STR_LIT>' ) + "<STR_LIT>" <EOL> if kwargs [ '<STR_LIT>' ] == '<STR_LIT:->' : <EOL> outputFile = sys . stdout <EOL> else : <EOL> outputFile = open ( filename , '<STR_LIT:w>' ) <EOL> exportRef = kwargs [ '<STR_LIT>' ] <EOL> exportNoCall = kwargs [ '<STR_LIT>' ] <EOL> variantsTable = dxpy . open_dxgtable ( entity_result [ '<STR_LIT:id>' ] ) <EOL> try : <EOL> originalContigSet = variantsTable . get_details ( ) [ '<STR_LIT>' ] <EOL> except : <EOL> raise dxpy . AppError ( "<STR_LIT>" ) <EOL> contigDetails = dxpy . DXRecord ( originalContigSet ) . get_details ( ) <EOL> if kwargs [ '<STR_LIT>' ] is not None : <EOL> refFileName = kwargs [ '<STR_LIT>' ] <EOL> if not os . path . isfile ( refFileName ) : <EOL> raise dxpy . AppError ( "<STR_LIT>" ) <EOL> else : <EOL> refFileName = tempfile . NamedTemporaryFile ( prefix = '<STR_LIT>' , suffix = '<STR_LIT>' , delete = False ) . name <EOL> dxpy . download_dxfile ( contigDetails [ '<STR_LIT>' ] [ '<STR_LIT>' ] , refFileName ) <EOL> if kwargs [ '<STR_LIT>' ] : <EOL> infos = variantsTable . get_details ( ) . get ( '<STR_LIT>' ) <EOL> formats = variantsTable . get_details ( ) . get ( '<STR_LIT>' ) <EOL> alts = variantsTable . get_details ( ) . get ( '<STR_LIT>' ) <EOL> filters = variantsTable . get_details ( ) . get ( '<STR_LIT>' ) <EOL> samples = variantsTable . get_details ( ) . get ( '<STR_LIT>' ) <EOL> outputFile . write ( "<STR_LIT>" ) <EOL> if infos is not None : <EOL> for k , v in collections . OrderedDict ( sorted ( infos . iteritems ( ) ) ) . iteritems ( ) : <EOL> outputFile . write ( "<STR_LIT>" + k + "<STR_LIT>" + v [ '<STR_LIT>' ] + "<STR_LIT>" + v [ '<STR_LIT:type>' ] + "<STR_LIT>" + v [ '<STR_LIT:description>' ] + "<STR_LIT>" ) <EOL> if len ( samples ) > <NUM_LIT:0> : <EOL> outputFile . write ( "<STR_LIT>" ) <EOL> outputFile . write ( "<STR_LIT>" ) <EOL> outputFile . write ( "<STR_LIT>" ) <EOL> if formats is not None : <EOL> for k , v in collections . OrderedDict ( sorted ( formats . iteritems ( ) ) ) . iteritems ( ) : <EOL> outputFile . write ( "<STR_LIT>" + k + "<STR_LIT>" + v [ '<STR_LIT>' ] + "<STR_LIT>" + v [ '<STR_LIT:type>' ] + "<STR_LIT>" + v [ '<STR_LIT:description>' ] + "<STR_LIT>" ) <EOL> if alts is not None : <EOL> for k , v in collections . OrderedDict ( sorted ( alts . iteritems ( ) ) ) . iteritems ( ) : <EOL> outputFile . write ( "<STR_LIT>" + k + "<STR_LIT>" + v [ '<STR_LIT:description>' ] + "<STR_LIT>" ) <EOL> if filters is not None : <EOL> for k , v in collections . OrderedDict ( sorted ( filters . iteritems ( ) ) ) . iteritems ( ) : <EOL> outputFile . write ( "<STR_LIT>" + k + "<STR_LIT>" + v + "<STR_LIT>" ) <EOL> for i in range ( len ( contigDetails [ '<STR_LIT>' ] [ '<STR_LIT>' ] ) ) : <EOL> outputFile . write ( "<STR_LIT>" + contigDetails [ '<STR_LIT>' ] [ '<STR_LIT>' ] [ i ] + "<STR_LIT>" + str ( contigDetails [ '<STR_LIT>' ] [ '<STR_LIT>' ] [ i ] ) + "<STR_LIT>" ) <EOL> outputFile . write ( "<STR_LIT>" ) <EOL> if len ( samples ) > <NUM_LIT:0> : <EOL> outputFile . write ( "<STR_LIT>" ) <EOL> for x in samples : <EOL> outputFile . write ( "<STR_LIT:\t>" + x ) <EOL> outputFile . write ( "<STR_LIT:\n>" ) <EOL> chromosomeOffsets = { } <EOL> for i in range ( len ( contigDetails [ '<STR_LIT>' ] [ '<STR_LIT>' ] ) ) : <EOL> chromosomeOffsets [ contigDetails [ '<STR_LIT>' ] [ '<STR_LIT>' ] [ i ] ] = contigDetails [ '<STR_LIT>' ] [ '<STR_LIT>' ] [ i ] <EOL> contigSequence = open ( refFileName , '<STR_LIT:r>' ) . read ( ) <EOL> col = { } <EOL> names = variantsTable . get_col_names ( ) <EOL> for i in range ( len ( names ) ) : <EOL> col [ names [ i ] ] = i + <NUM_LIT:1> <EOL> col = collections . OrderedDict ( sorted ( col . items ( ) ) ) <EOL> chromosomeList = contigDetails [ '<STR_LIT>' ] [ '<STR_LIT>' ] <EOL> if kwargs [ '<STR_LIT>' ] is not None : <EOL> intersection = [ ] <EOL> for x in chromosomeList : <EOL> if x in kwargs [ '<STR_LIT>' ] : <EOL> intersection . append ( x ) <EOL> chromosomeList = intersection [ : ] <EOL> for chromosome in chromosomeList : <EOL> buff = [ ] <EOL> lastPosition = - <NUM_LIT:1> <EOL> query = variantsTable . genomic_range_query ( chr = chromosome , lo = <NUM_LIT:0> , hi = sys . maxsize ) <EOL> for row in variantsTable . get_rows ( query = query , limit = <NUM_LIT:1> ) [ '<STR_LIT:data>' ] : <EOL> startRow = row [ <NUM_LIT:0> ] <EOL> for row in variantsTable . iterate_rows ( start = startRow ) : <EOL> if row [ <NUM_LIT:1> ] != chromosome : <EOL> break <EOL> if lastPosition < row [ col [ "<STR_LIT>" ] ] : <EOL> writeBuffer ( buff , col , outputFile , contigSequence , chromosomeOffsets , exportRef , exportNoCall ) <EOL> buff = [ ] <EOL> buff . append ( row ) <EOL> lastPosition = row [ col [ "<STR_LIT>" ] ] <EOL> writeBuffer ( buff , col , outputFile , contigSequence , chromosomeOffsets , exportRef , exportNoCall ) <EOL> buff = [ ] <EOL> def writeBuffer ( buff , col , outputFile , contigSequence , chromosomeOffsets , exportRef , exportNoCall ) : <EOL> for x in buff : <EOL> printPreceedingCharacter = False <EOL> altOptions = x [ col [ "<STR_LIT>" ] ] . split ( "<STR_LIT:U+002C>" ) <EOL> for y in altOptions : <EOL> if ( len ( x [ col [ "<STR_LIT>" ] ] ) != len ( y ) or len ( x [ col [ "<STR_LIT>" ] ] ) == <NUM_LIT:0> or len ( y ) == <NUM_LIT:0> ) and not re . search ( "<STR_LIT>" , y ) : <EOL> printPreceedingCharacter = True <EOL> break <EOL> if printPreceedingCharacter : <EOL> writeRowCheck ( x [ : ] , col , outputFile , contigSequence , chromosomeOffsets , exportRef , exportNoCall ) <EOL> for x in buff : <EOL> printPreceedingCharacter = False <EOL> altOptions = x [ col [ "<STR_LIT>" ] ] . split ( "<STR_LIT:U+002C>" ) <EOL> for y in altOptions : <EOL> if ( len ( x [ col [ "<STR_LIT>" ] ] ) != len ( y ) or len ( x [ col [ "<STR_LIT>" ] ] ) == <NUM_LIT:0> or len ( y ) == <NUM_LIT:0> ) and not re . search ( "<STR_LIT>" , y ) : <EOL> printPreceedingCharacter = True <EOL> break <EOL> if printPreceedingCharacter == False : <EOL> writeRowCheck ( x [ : ] , col , outputFile , contigSequence , chromosomeOffsets , exportRef , exportNoCall ) <EOL> def writeRowCheck ( row , col , outputFile , contigSequence , chromosomeOffsets , exportRef , exportNoCall ) : <EOL> if checkRowIsAllType ( row , col , "<STR_LIT>" ) : <EOL> if exportRef : <EOL> writeRow ( row , col , outputFile , contigSequence , chromosomeOffsets ) <EOL> elif checkRowIsAllType ( row , col , "<STR_LIT>" ) : <EOL> if exportNoCall : <EOL> writeRow ( row , col , outputFile , contigSequence , chromosomeOffsets ) <EOL> else : <EOL> writeRow ( row , col , outputFile , contigSequence , chromosomeOffsets ) <EOL> def parseRegions ( input ) : <EOL> result = [ ] <EOL> for x in input : <EOL> result . append ( re . findall ( "<STR_LIT>" , x ) ) <EOL> return result <EOL> def writeRow ( row , col , outputFile , contigSequence , chromosomeOffsets ) : <EOL> chr = str ( row [ col [ "<STR_LIT>" ] ] ) . strip ( ) <EOL> pos = row [ col [ "<STR_LIT>" ] ] + <NUM_LIT:1> <EOL> ref = row [ col [ "<STR_LIT>" ] ] . strip ( ) <EOL> alt = row [ col [ "<STR_LIT>" ] ] . strip ( ) <EOL> ids = '<STR_LIT:.>' <EOL> if col . get ( "<STR_LIT>" ) is not None : <EOL> if row [ col [ "<STR_LIT>" ] ] != '<STR_LIT>' : <EOL> ids = row [ col [ "<STR_LIT>" ] ] . strip ( ) <EOL> filt = '<STR_LIT:.>' <EOL> if col . get ( "<STR_LIT>" ) is not None : <EOL> if row [ col [ "<STR_LIT>" ] ] != '<STR_LIT>' : <EOL> filt = row [ col [ "<STR_LIT>" ] ] . strip ( ) <EOL> else : <EOL> filt = "<STR_LIT>" <EOL> qual = '<STR_LIT:.>' <EOL> if col . get ( "<STR_LIT>" ) is not None : <EOL> if row [ col [ "<STR_LIT>" ] ] != dxpy . NULL or row [ col [ "<STR_LIT>" ] ] == - <NUM_LIT> : <EOL> qual = row [ col [ "<STR_LIT>" ] ] <EOL> sample = <NUM_LIT:0> <EOL> printPreceedingCharacter = False <EOL> altOptions = row [ col [ "<STR_LIT>" ] ] . split ( "<STR_LIT:U+002C>" ) <EOL> if altOptions == [ '<STR_LIT>' ] : <EOL> printPreceedingCharacter = True <EOL> for x in altOptions : <EOL> if ( len ( ref ) != len ( x ) or len ( ref ) == <NUM_LIT:0> or len ( alt ) == <NUM_LIT:0> ) and not re . search ( "<STR_LIT>" , x ) : <EOL> printPreceedingCharacter = True <EOL> if printPreceedingCharacter : <EOL> ref = contigSequence [ chromosomeOffsets [ chr ] + int ( pos ) - <NUM_LIT:2> ] + ref <EOL> altOptions = row [ col [ "<STR_LIT>" ] ] . split ( "<STR_LIT:U+002C>" ) <EOL> alt = '<STR_LIT>' <EOL> for x in altOptions : <EOL> if re . search ( "<STR_LIT>" , x ) : <EOL> alt += x + "<STR_LIT:U+002C>" <EOL> else : <EOL> alt += contigSequence [ chromosomeOffsets [ chr ] + int ( pos ) - <NUM_LIT:2> ] + x + "<STR_LIT:U+002C>" <EOL> validAlt = False <EOL> alt = alt . rstrip ( "<STR_LIT:U+002C>" ) <EOL> pos -= <NUM_LIT:1> <EOL> outputFile . write ( chr + "<STR_LIT:\t>" + str ( pos ) . strip ( ) + "<STR_LIT:\t>" + str ( ids ) . strip ( ) + "<STR_LIT:\t>" + ref . upper ( ) . strip ( ) + "<STR_LIT:\t>" + alt . upper ( ) . strip ( ) + "<STR_LIT:\t>" + str ( qual ) . strip ( ) + "<STR_LIT:\t>" + str ( filt ) . strip ( ) ) <EOL> infos = '<STR_LIT>' <EOL> for x in col : <EOL> if "<STR_LIT>" in x : <EOL> if col . get ( x ) is not None : <EOL> if isinstance ( row [ col [ x ] ] , bool ) : <EOL> if row [ col [ x ] ] == True : <EOL> infos += x . lstrip ( "<STR_LIT>" ) + "<STR_LIT:;>" <EOL> elif isDefault ( row [ col [ x ] ] ) : <EOL> infos += x . lstrip ( "<STR_LIT>" ) + "<STR_LIT:=>" + str ( row [ col [ x ] ] ) + "<STR_LIT:;>" <EOL> if infos == '<STR_LIT>' : <EOL> infos = '<STR_LIT:.>' <EOL> outputFile . write ( "<STR_LIT:\t>" + infos . rstrip ( "<STR_LIT:;>" ) ) <EOL> sample = <NUM_LIT:0> <EOL> coverage = False <EOL> totalCoverage = False <EOL> while <NUM_LIT:1> : <EOL> if col . get ( "<STR_LIT>" + str ( sample ) ) is None : <EOL> break <EOL> if coverage == False : <EOL> coverage = col . get ( "<STR_LIT>" + str ( sample ) ) <EOL> if totalCoverage == False : <EOL> totalCoverage = col . get ( "<STR_LIT>" + str ( sample ) ) <EOL> sample += <NUM_LIT:1> <EOL> observedFormats = [ ] <EOL> for x in col : <EOL> if "<STR_LIT>" in x : <EOL> if col . get ( x ) is not None : <EOL> entrySplit = x . split ( "<STR_LIT:_>" ) [ <NUM_LIT:1> : ] <EOL> entrySplit . pop ( ) <EOL> tag = '<STR_LIT:_>' . join ( entrySplit ) <EOL> if tag not in observedFormats : <EOL> observedFormats . append ( tag ) <EOL> if col . get ( "<STR_LIT>" ) is not None : <EOL> outputFile . write ( "<STR_LIT:\t>" ) <EOL> formatOrdering = '<STR_LIT>' <EOL> if coverage : <EOL> formatOrdering += "<STR_LIT>" <EOL> if totalCoverage : <EOL> formatOrdering += "<STR_LIT>" <EOL> for x in observedFormats : <EOL> formatOrdering += x + "<STR_LIT::>" <EOL> outputFile . write ( formatOrdering . rstrip ( "<STR_LIT::>" ) ) <EOL> sample = <NUM_LIT:0> <EOL> while <NUM_LIT:1> : <EOL> if col . get ( "<STR_LIT>" + str ( sample ) ) is not None : <EOL> formats = row [ col [ "<STR_LIT>" + str ( sample ) ] ] + "<STR_LIT::>" <EOL> if coverage : <EOL> if col . get ( "<STR_LIT>" + str ( sample ) ) : <EOL> cov = row [ col . get ( "<STR_LIT>" + str ( sample ) ) ] <EOL> formats += cov + "<STR_LIT::>" <EOL> else : <EOL> cov += "<STR_LIT>" <EOL> if totalCoverage : <EOL> if col . get ( "<STR_LIT>" + str ( sample ) ) is not None : <EOL> tCov = row [ col . get ( "<STR_LIT>" + str ( sample ) ) ] <EOL> if tCov == dxpy . NULL or tCov == - <NUM_LIT> : <EOL> formats += "<STR_LIT>" <EOL> else : <EOL> formats += str ( tCov ) + "<STR_LIT::>" <EOL> else : <EOL> formats += "<STR_LIT>" <EOL> for x in observedFormats : <EOL> if col . get ( "<STR_LIT>" + x + "<STR_LIT:_>" + str ( sample ) ) is not None : <EOL> if isinstance ( row [ col [ "<STR_LIT>" + x + "<STR_LIT:_>" + str ( sample ) ] ] , bool ) : <EOL> if row [ col [ "<STR_LIT>" + x + "<STR_LIT:_>" + str ( sample ) ] ] : <EOL> formats += x <EOL> else : <EOL> formats += "<STR_LIT:.>" <EOL> elif row [ col [ "<STR_LIT>" + x + "<STR_LIT:_>" + str ( sample ) ] ] == dxpy . NULL or row [ col [ "<STR_LIT>" + x + "<STR_LIT:_>" + str ( sample ) ] ] == - <NUM_LIT> : <EOL> formats += "<STR_LIT:.>" <EOL> else : <EOL> formats += str ( row [ col [ "<STR_LIT>" + x + "<STR_LIT:_>" + str ( sample ) ] ] ) <EOL> else : <EOL> formats += "<STR_LIT:.>" <EOL> formats += "<STR_LIT::>" <EOL> outputFile . write ( "<STR_LIT:\t>" + formats . rstrip ( "<STR_LIT::>" ) ) <EOL> else : <EOL> break <EOL> sample += <NUM_LIT:1> <EOL> outputFile . write ( "<STR_LIT:\n>" ) <EOL> def isDefault ( entry ) : <EOL> if isinstance ( entry , float ) : <EOL> if entry == dxpy . NULL or entry == - <NUM_LIT> : <EOL> return False <EOL> if isinstance ( entry , bool ) : <EOL> if entry == False : <EOL> return False <EOL> if isinstance ( entry , int ) : <EOL> if entry == dxpy . NULL or entry == - <NUM_LIT> : <EOL> return False <EOL> if entry == '<STR_LIT>' : <EOL> return False <EOL> return True <EOL> def checkRowIsAllType ( row , col , typ ) : <EOL> sample = <NUM_LIT:0> <EOL> while <NUM_LIT:1> : <EOL> if col . get ( "<STR_LIT>" + str ( sample ) ) is None : <EOL> if sample > <NUM_LIT:0> : <EOL> return True <EOL> else : <EOL> return False <EOL> if row [ col [ "<STR_LIT>" + str ( sample ) ] ] != typ : <EOL> return False <EOL> sample += <NUM_LIT:1> <EOL> if __name__ == '<STR_LIT:__main__>' : <EOL> main ( ) </s>
