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 [options]\n\n'
'%prog takes in a reference genome name ( --referenceGenome ),\n'
'optionally a directory where annotation wig pickles are stored ( --annotPickleDir [optional] ),\n'
'a directory where maf wig pickles are stored ( --mafPickleDir ), a paired set of chromosome names\n'
'( --chrNames comma separated ) and chromosome lengths ( --chrLengths comma separated ) and \n'
'then various other options specifed below to draw a figure.')
data = Data()
parser = OptionParser( usage=usage )
initOptions( parser )
las.initOptions( parser )
lpt.initOptions( parser )
options, args = parser.parse_args()
checkOptions( options, parser, data )
las.checkOptions( options, parser )
lpt.checkOptions( options, parser )
loadAnnots( options, data )
loadMafs( options, data )
normalizeData( options, data )
transformData( options, data )
figHeight = ( data.numberOfMafs + len( data.annotationOrder ) + 0.5 ) / 4.0
fig, pdf = lpt.initImage( 8.0, figHeight, options, data )
axDict = establishAxes( fig, options, data )
labelAxes( fig, axDict, options, data )
drawAnnotations( axDict, options, data )
drawMafs( axDict, options, data )
drawLegend( options, data )
setAxisLimits( axDict, options, data )
lpt.writeImage( fig, pdf, options )
def main():
usage = ('usage: %prog [options] --dir=path/to/dir/\n\n'
'%prog takes in a copy statistics file\n'
'and creates an image file.')
data = Data()
parser = OptionParser(usage=usage)
initOptions(parser)
las.initOptions(parser)
lpt.initOptions(parser)
options, args = parser.parse_args()
checkOptions(args, options, parser)
las.checkOptions(options, parser)
lpt.checkOptions(options, parser)
if not options.outputRanks:
fig, pdf = lpt.initImage(8.0, 10.0, options, data)
stats = readFiles(options)
sortedOrder = sorted(stats.values(),
key=lambda x: x.sumLower,
reverse=False)
if options.outputRanks:
rankings(sortedOrder, options, data)
return
axDict = establishAxes(fig, options, data)
drawData(axDict, sortedOrder, options, data)
drawLegend(options, data)
drawAxisLabels(axDict, stats, options, data)
setAxisLimits(axDict, options, data)
lpt.writeImage(fig, pdf, options)
def main():
usage = (
'usage: %prog --key=KEY file1.maf.pickle file2.maf.pickle ...\n\n'
'%prog takes a valid key ( --key ) and one or more maf wiggle pickle(s)\n'
'and then pulls out all the counts stored in the numpy array for the key.'
)
data = Data()
parser = OptionParser(usage=usage)
initOptions(parser)
options, args = parser.parse_args()
checkOptions(args, options, parser, data)
loadPickles(args, options, data)
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 = (
'%prog --dir=path/to/dir --mode=[scaffPaths|contigs|contigPaths|blocks|contamination] [options]\n\n'
'%prog takes an aggregate directory ( --dir ) and a mode \n'
'( --mode ) and then produces a pretty picture.')
data = Data()
parser = OptionParser(usage=usage)
initOptions(parser)
lpt.initOptions(parser)
options, args = parser.parse_args()
checkOptions(options, parser)
lpt.checkOptions(options, parser)
readFiles(options, data)
lpt.initImage(7.0, 8.0, options, data)
establishAxis(options, data)
drawPlots(options, data)
lpt.writeImage(options, data)
def main():
usage = (
'%prog --file=file.txt --mode=[scaffPaths|contigs|contigPaths|blocks|contamination] [options]\n\n'
'%prog takes an aggregate text file ( --file ) and a mode \n'
'( --mode ) and then produces a pretty picture.')
data = Data()
parser = OptionParser(usage=usage)
initOptions(parser)
lpt.initOptions(parser)
options, args = parser.parse_args()
checkOptions(options, parser)
lpt.checkOptions(options, parser)
fig, pdf = lpt.initImage(8.0, 10.0, options, data)
axDict = establishAxes(fig, options, data)
data.valuesDict = readFile(options.file, options)
data.xData = data.valuesDict['columnLength']
if options.mode != 'contamination':
data.valuesDict = normalizeDataNormalMode(data.valuesDict, options,
data)
else:
normalizeDataContaminationMode(options, data)
setAxisLimits(axDict['main'], axDict['crazy'], axDict['blowUp'],
data.xData, options, data)
drawData(axDict['main'], axDict['crazy'], axDict['blowUp'], data.xData,
data.valuesDict, options, data)
drawLegend(options, data)
drawAxisLabels(fig, options, data)
setAxisLimits(axDict['main'], axDict['crazy'], axDict['blowUp'],
data.xData, options, data)
establishTicks(axDict['main'], axDict['crazy'], axDict['blowUp'], options,
data)
lpt.writeImage(fig, pdf, options)
def main():
usage = ('usage: %prog [options] file1.xml\n\n'
'%prog takes in a copy number statistics file\n'
'and creates an image file.')
data = Data()
parser = OptionParser(usage=usage)
initOptions(parser)
lpt.initOptions(parser)
options, args = parser.parse_args()
checkOptions(args, options, parser)
lpt.checkOptions(options, parser)
fig, pdf = lpt.initImage(11.0, 3.25, options, data)
storedCategories = readFiles(options)
establishGlobalMinMax(storedCategories, options, data)
axDict = establishAxes(fig, storedCategories, options, data)
drawData(axDict, storedCategories, options, data)
drawLegend(options, data)
drawAxisLabels(axDict, storedCategories, options, data)
setAxisLimits(axDict, options, data)
lpt.writeImage(fig, pdf, options)
