def main(): usage = ( 'usage: %prog --maf=file.maf --referenceGenome=A --comparisonGenome=B --chrNames=c0,c1,... --chrLengths=N1,N2,... --outDir=path/to/dir/\n\n' '%prog takes in a maf filename ( --maf ), a reference genome name as\n' 'it appears in the maf ( --referenceGenome ), a genome name to compare against\n' '( --comparisonGenome ), a paired list of chromosome names ( --chrNames comma\n' 'separated ) and chromosome lengths ( --chrLengths comma separated ) and a path\n' 'to a directory where the maf pickles will be written ( --outDir ), one pickle\n' 'per chromosome.') data = Data() parser = OptionParser(usage=usage) initOptions(parser) options, args = parser.parse_args() checkOptions(options, parser, data) readMaf(options, data) switchToPositiveStrandCoordinates(options, data) for c in data.chroms: data.mafBlocksByChrom[c].sort(key=lambda x: x.refStart, reverse=False) trimDups(options, data) if options.verify: verifyDistinct(options, data) convertDataToWiggle(options, data) recordCoverage(options, data) if options.verify: verifyStacks(options, data) verifyElements(options, data) verifyLengths(options, data) packData(data.mafWigDict, options.filename, options)
def main(): usage = ( 'usage: %prog --maf=file.maf --referenceGenome=A --comparisonGenome=B --chrNames=c0,c1,... --chrLengths=N1,N2,... --outDir=path/to/dir/\n\n' '%prog takes in a maf filename ( --maf ), a reference genome name as\n' 'it appears in the maf ( --referenceGenome ), a genome name to compare against\n' '( --comparisonGenome ), a paired list of chromosome names ( --chrNames comma\n' 'separated ) and chromosome lengths ( --chrLengths comma separated ) and a path\n' 'to a directory where the maf pickles will be written ( --outDir ), one pickle\n' 'per chromosome.') data = Data() parser = OptionParser( usage=usage ) initOptions( parser ) options, args = parser.parse_args() checkOptions( options, parser, data ) readMaf( options, data ) switchToPositiveStrandCoordinates( options, data ) for c in data.chroms: data.mafBlocksByChrom[ c ].sort( key = lambda x: x.refStart, reverse=False ) trimDups( options, data ) if options.verify: verifyDistinct( options, data ) convertDataToWiggle( options, data ) recordCoverage( options, data ) if options.verify: verifyStacks( options, data ) verifyElements( options, data ) verifyLengths( options, data ) packData( data.mafWigDict, options.filename, options )
def main(): usage = ( 'usage: %prog --gff=file.gff --outDir=path/to/dir/ --chrLengths=N1,N2,... --chrNames=A,B,...\n\n' '%prog takes in a gff file ( --gff ), an output directory ( --outDir ), and\n' 'pairs of chromosome names ( --chrNames comma separated ) and chromosome \n' 'lengths ( --chrLengths comma separated ) and returns one annotation wig\n' 'pickle per chromosome in the output directory.') data = Data() parser = OptionParser( usage=usage ) initOptions( parser ) options, args = parser.parse_args() checkOptions( options, parser, data ) readGff( options, data ) for c in data.chrNames: data.gffRecordsByChrom[ c ].sort( key = lambda x: x.start, reverse=False ) convertDataToWiggle( options, data ) packData( data.annotWigDict, options.filename, options )
def main(): usage = ( 'usage: %prog --gff=file.gff --outDir=path/to/dir/ --chrLengths=N1,N2,... --chrNames=A,B,...\n\n' '%prog takes in a gff file ( --gff ), an output directory ( --outDir ), and\n' 'pairs of chromosome names ( --chrNames comma separated ) and chromosome \n' 'lengths ( --chrLengths comma separated ) and returns one annotation wig\n' 'pickle per chromosome in the output directory.') data = Data() parser = OptionParser(usage=usage) initOptions(parser) options, args = parser.parse_args() checkOptions(options, parser, data) readGff(options, data) for c in data.chrNames: data.gffRecordsByChrom[c].sort(key=lambda x: x.start, reverse=False) convertDataToWiggle(options, data) packData(data.annotWigDict, options.filename, options)