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)
