def main():
usage = ( 'usage: %prog --statsScaffoldsContigPathDir=path/to/dir/ [options]\n\n'
'%prog takes a directory of contig path stats xml files\n'
'( --statsScaffoldsContigPathDir ) named as NAME.contigPathStats.xml and creates a plot.')
data = Data()
parser = OptionParser( usage=usage )
initOptions( parser )
las.initOptions( parser )
lpt.initOptions( parser )
options, args = parser.parse_args()
las.checkOptions( options, parser )
lpt.checkOptions( options, parser )
checkOptions( options, parser )
assembliesDict = readDir( options.statsScaffoldsContigPathDir, options )
assembliesList = assembliesDict.values()
if len(assembliesList) <= 20:
fig, pdf = lpt.initImage( 14.0, 8.0, options, data )
else:
fig, pdf = lpt.initImage( 14.0, 24.0, options, data )
axDict = establishAxis( len(assembliesList), fig, options, data )
assembliesList = createXYData( assembliesList, options )
assembliesList = normalizeDist( assembliesList, options )
assembliesList = sorted( assembliesList,
key=lambda x: max(x.yData['insertionErrorSizeDistribution']),
reverse=True )
drawData( assembliesList, axDict, options, data )
drawLegend( assembliesList, axDict, options, data )
lpt.writeImage( fig, pdf, 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 --subStatsDir=path/to/dir/ [options]\n\n'
'%prog takes in a directory of substitution stats files ( --subStatsDir )\n'
'with filenames as NAME.subStats.[upper|lower].xml and produces a plot showing\n'
'the difference in subs in hap1 versus hap2.\n')
data = Data()
parser = OptionParser(usage=usage)
initOptions(parser)
las.initOptions(parser)
lpt.initOptions(parser)
options, args = parser.parse_args()
checkOptions(options, parser)
las.checkOptions(options, parser)
lpt.checkOptions(options, parser)
fig, pdf = lpt.initImage(11., 8., options, data)
axDict = establishAxis(fig, options, data)
assembliesDict = {}
assembliesDict = cssp.readSubStatsDir(assembliesDict, options)
valuesList = createValsList(assembliesDict.values(), options)
valuesList = sorted(valuesList,
key=lambda x: float(x[1]) / x[2],
reverse=False)
drawData(valuesList, axDict, options, data)
lpt.writeImage(fig, pdf, options)
def main():
usage = ( 'usage: %prog --subStatsDir=path/to/dir/ [options]\n\n'
'%prog takes in a directory of substitution stats files ( --subStatsDir )\n'
'with filenames as NAME.subStats.[upper|lower].xml and produces a plot.')
data = Data()
parser = OptionParser( usage=usage )
initOptions( parser )
las.initOptions( parser )
lpt.initOptions( parser )
options, args = parser.parse_args()
checkOptions( options, parser )
las.checkOptions( options, parser )
lpt.checkOptions( options, parser )
if not options.outputRanks:
fig, pdf = lpt.initImage( 9., 11., options, data )
axDict = establishAxes( fig, options, data )
assembliesDict = {}
assembliesDict = readSubStatsDir( assembliesDict, options )
sumErrors( assembliesDict, options )
normalizeData( assembliesDict, options )
sortOrder = sorted( assembliesDict, key=lambda key: assembliesDict[ key ].allLo, reverse=False )
if options.outputRanks:
rankings( assembliesDict, sortOrder, options, data )
return
drawData( assembliesDict, sortOrder, axDict, options, data )
lpt.writeImage( fig, pdf, options )
def main():
usage = ( 'usage: %prog --subStatsDir=path/to/dir/ [options]\n\n'
'%prog takes in a directory of substitution stats files ( --subStatsDir )\n'
'with filenames as NAME.subStats.[upper|lower].xml and produces a plot showing\n'
'the difference in subs in hap1 versus hap2.\n')
data = Data()
parser = OptionParser( usage=usage )
initOptions( parser )
las.initOptions( parser )
lpt.initOptions( parser )
options, args = parser.parse_args()
checkOptions( options, parser )
las.checkOptions( options, parser )
lpt.checkOptions( options, parser )
fig, pdf = lpt.initImage( 11., 8., options, data )
axDict = establishAxis( fig, options, data )
assembliesDict = {}
assembliesDict = cssp.readSubStatsDir( assembliesDict, options )
valuesList = createValsList( assembliesDict.values(), options )
valuesList = sorted( valuesList, key = lambda x: float(x[1])/x[2], reverse=False)
drawData( valuesList, axDict, options, data )
lpt.writeImage( fig, pdf, options )
def main():
usage = ( 'usage: %prog [options] file1.xml file2.xml\n\n'
'%prog takes in contiguous path statistics file(s)\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( 11., 8.0, options, data ) # 8
axDict = establishAxes( fig, options, data )
data.statsList, data.xData = readFiles( options )
for i in xrange( 0, len( data.statsList )):
# ensure that the buckets are all in order by their midpoint.
data.statsList[i] = sorted( data.statsList[i], key=lambda x: x.mid, reverse=False )
if options.outputRanks:
ranks = rankFiles( options, data )
printRanks( ranks, options, data )
sys.exit(0)
drawData( axDict['main'], data.xData, data.statsList, options, data )
drawLegend( options, data )
drawAxisLabels( fig, options, data )
setAxisLimits( axDict['main'], data.xData, options, data )
establishTicks( axDict['main'], data.xData, options, data )
lpt.writeImage( fig, pdf, options )
def main():
usage = (
"usage: %prog --statsScaffoldsContigPathDir=path/to/dir/ [options]\n\n"
"%prog takes a directory of contig path stats xml files\n"
"( --statsScaffoldsContigPathDir ) named as NAME.contigPathStats.xml and creates a plot."
)
data = Data()
parser = OptionParser(usage=usage)
initOptions(parser)
las.initOptions(parser)
lpt.initOptions(parser)
options, args = parser.parse_args()
las.checkOptions(options, parser)
lpt.checkOptions(options, parser)
checkOptions(options, parser)
assembliesDict = readDir(options.statsScaffoldsContigPathDir, options)
assembliesList = assembliesDict.values()
if len(assembliesList) <= 20:
fig, pdf = lpt.initImage(14.0, 8.0, options, data)
else:
fig, pdf = lpt.initImage(14.0, 24.0, options, data)
axDict = establishAxis(len(assembliesList), fig, options, data)
assembliesList = createXYData(assembliesList, options)
assembliesList = normalizeDist(assembliesList, options)
assembliesList = sorted(assembliesList, key=lambda x: max(x.yData["insertionErrorSizeDistribution"]), reverse=True)
drawData(assembliesList, axDict, options, data)
drawLegend(assembliesList, 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 [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 --statsScaffoldsContigPathDir=path/to/dir/ '
'--statsContigssContigPathDir=path/to/dir/ [options]\n\n'
'%prog takes a directory of scaffold-alignment contig path stats xml files\n'
'( --statsScaffoldsContigPathDir ) named as NAME.pathStats.xml, contig-alignment '
'contig path stats xml files ( --statsContigsContigPathDir ) named as NAME.pathStats.xml,'
' and creates a plot.\n')
data = Data()
parser = OptionParser( usage=usage )
initOptions( parser )
cscp.initOptions( parser )
las.initOptions( parser )
lpt.initOptions( parser )
options, args = parser.parse_args()
cscp.checkOptions( options, parser )
las.checkOptions( options, parser )
lpt.checkOptions( options, parser )
checkOptions( options, parser )
assembliesList = readDirs( options )
assembliesList = sorted( assembliesList, key=lambda x: x.valuesDict[ options.sortOn ],
reverse=True )
maxesMax, minsMin = findMaxMin( assembliesList, options )
if options.outputRanks:
rankings( assembliesList, options )
return
fig, pdf = lpt.initImage( 10.0, 8.0, options, data )
axDict = establishAxis( fig, options, data )
drawData( assembliesList, maxesMax, minsMin, axDict, options )
lpt.writeImage( fig, pdf, options )
def main():
usage = ('usage: %prog')
parser = OptionParser(usage=usage)
initOptions(parser)
las.initOptions(parser)
options, args = parser.parse_args()
checkOptions(args, options, parser)
las.checkOptions(options, parser)
assembliesDict = processDirectory(options)
outputDict(assembliesDict, options)
def main():
usage = ('usage: %prog')
parser = OptionParser( usage = usage )
initOptions( parser )
las.initOptions( parser )
options, args = parser.parse_args()
checkOptions( args, options, parser )
las.checkOptions( options, parser )
assembliesDict = processDirectory(options)
outputDict(assembliesDict, options)
def main():
usage = ( 'usage: %prog [options] < summarizeRankings.out\n\n'
'%prog takes in the output of summarizeRankings.py and reports only the.\n'
'top assembly per team. Use --reRank to rerank the top assembly per team\n'
'the tops from all the other teams.')
parser = OptionParser( usage=usage )
initOptions( parser )
las.initOptions( parser )
options, args = parser.parse_args()
checkOptions( options, parser )
las.checkOptions( options, parser )
if not options.reRank:
simpleProcessStream( options )
else:
fullProcessStream( options )
def main():
usage = (
'usage: %prog --statsScaffoldsContigPathDir=path/to/dir/ --statsContigsContigPathDir=path/to/dir/ [options]\n\n'
'%prog takes in the contig path statistics directories from both the Scaffolds and Contigs alignments\n'
'( --statsScaffoldsContigPathDir --statsContigsContigPathDir ) and prints to STDOUT a latex formatted table.'
)
parser = OptionParser(usage=usage)
initOptions(parser)
las.initOptions(parser)
options, args = parser.parse_args()
checkOptions(args, options, parser)
las.checkOptions(options, parser)
assembliesList = readDirs(options)
calculateErrors(assembliesList, options)
assembliesList = performSort(assembliesList, options)
sortString = {
'totalErrors': 'the sum of the errors (\\(\\sum\\) err)',
'errorsPerMappedBase': 'errors per mapped base (ePmb)',
'totalScaffoldGaps+totalBleedingHeartScaffoldGaps':
'the sum of the total number of scaffold gaps and liberal scaffold gaps (scf)',
'scaffolds':
'the sum of the total number of scaffold gaps and liberal scaffold gaps (scf)',
'totalContigEnds+totalContigEndsWithNs':
'the sum of total contig ends and the total contigs ending with N\'s (ctgE+ctgN)',
'totalHomoToHeteroSwitches':
'the total homozygous to heterozygous switches (hom/het sw)',
'errorsPerContig': 'errors per contig (ePc)',
'totalContigEndsWithInsert': 'total contigs ending with insert (e-i)',
'totalErrorsHaplotypeToHaplotype':
'total haplotype to haplotype errors (h-h)',
'totalErrorsHaplotypeToInsert':
'total haplotype to insert errors (h-i)',
'totalErrorsHaplotypeToDeletion':
'total haplotype to deletion errors (h-d)',
'totalErrorsNonSpecific': 'total non--specific errors (nonSpec)'
}
caption = 'The table is sorted on %s. Column headers are total homozygous to heterozygous switches (hom/het sw), sum of the total scaffold gaps and liberal scaffold gaps (scf), the sum of total contig ends and the total contigs ending with N\'s (ctgE+ctgN), errors per contig (ePc), errors per mapped base (ePmb), total contigs ending with insert (e-i), total haplotype to haplotype errors (h-h), total haplotype to insert errors (h-i), total haplotype to deletion errors (h-d), total non--specific errors (nonSpec) and sum of the errors (\\(\\sum\\) err).' % sortString[
options.sortOn]
if options.outputRanks:
printRanks(assembliesList, options)
else:
printTable(assembliesList, '', options)
def main():
usage = (
'usage: %prog [options] < summarizeRankings.out\n\n'
'%prog takes in the output of summarizeRankings.py and reports only the.\n'
'top assembly per team. Use --reRank to rerank the top assembly per team\n'
'the tops from all the other teams.')
parser = OptionParser(usage=usage)
initOptions(parser)
las.initOptions(parser)
options, args = parser.parse_args()
checkOptions(options, parser)
las.checkOptions(options, parser)
if not options.reRank:
simpleProcessStream(options)
else:
fullProcessStream(options)
def main():
usage = ('usage: %prog --subsetFile=file [options] < table.tab\n\n')
parser = OptionParser( usage=usage )
las.initOptions( parser )
options, args = parser.parse_args()
las.checkOptions( options, parser )
for line in sys.stdin:
line = line.strip()
if line == '':
continue
if line.startswith('#'):
print line
continue
if line.split('\t')[0] not in options.assemblySubset:
continue
print line
def main():
usage = ('usage: %prog --subsetFile=file [options] < table.tab\n\n')
parser = OptionParser(usage=usage)
las.initOptions(parser)
options, args = parser.parse_args()
las.checkOptions(options, parser)
for line in sys.stdin:
line = line.strip()
if line == '':
continue
if line.startswith('#'):
print line
continue
if line.split('\t')[0] not in options.assemblySubset:
continue
print line
def main():
usage = (
'usage: %prog --statsScaffoldsContigPathDir=path/to/dir/ '
'--statsContigssContigPathDir=path/to/dir/ '
'--statsScaffoldsContigPathPhasingDir=path/to/dir/ [options]\n\n'
'%prog takes a directory of scaffold-alignment contig path stats xml files\n'
'( --statsScaffoldsContigPathDir ) named as NAME.pathStats.xml, contig-alignment '
'contig path stats xml files ( --statsContigsContigPathDir ) named as NAME.pathStats.xml,'
'scaffold-alignment contig path phasing stats xml files ( --statsScaffoldsContigPathPhasingDir )'
' named as NAME.hap%d.pathStats.xml and creates a plot.\n')
data = Data()
parser = OptionParser(usage=usage)
initOptions(parser)
cscp.initOptions(parser)
las.initOptions(parser)
lpt.initOptions(parser)
options, args = parser.parse_args()
cscp.checkOptions(options, parser)
las.checkOptions(options, parser)
lpt.checkOptions(options, parser)
checkOptions(options, parser)
assembliesList = readData(options)
assembliesList = sorted(assembliesList,
key=lambda x: x.valuesDict[options.sortOn],
reverse=True)
maxesMax, minsMin = findMaxMin(assembliesList, options)
if options.outputRanks:
rankings(assembliesList, options)
return
fig, pdf = lpt.initImage(10.0, 8.0, options, data)
axDict = establishAxis(fig, options, data)
drawData(assembliesList, maxesMax, minsMin, axDict, options)
lpt.writeImage(fig, pdf, options)
def main():
usage = (
'usage: %prog --subStatsDir=path/to/dir/ [options]\n\n'
'%prog takes in a directory of substitution stats files ( --subStatsDir )\n'
'with filenames as NAME.subStats.[upper|lower].xml and produces a plot.'
)
data = Data()
parser = OptionParser(usage=usage)
initOptions(parser)
las.initOptions(parser)
lpt.initOptions(parser)
options, args = parser.parse_args()
checkOptions(options, parser)
las.checkOptions(options, parser)
lpt.checkOptions(options, parser)
if not options.outputRanks:
fig, pdf = lpt.initImage(9., 11., options, data)
axDict = establishAxes(fig, options, data)
assembliesDict = {}
assembliesDict = readSubStatsDir(assembliesDict, options)
sumErrors(assembliesDict, options)
normalizeData(assembliesDict, options)
sortOrder = sorted(assembliesDict,
key=lambda key: assembliesDict[key].allLo,
reverse=False)
if options.outputRanks:
rankings(assembliesDict, sortOrder, options, data)
return
drawData(assembliesDict, sortOrder, axDict, options, data)
lpt.writeImage(fig, pdf, options)
def main():
usage = ( 'usage: %prog --statsScaffoldsContigPathDir=path/to/dir/ --statsContigsContigPathDir=path/to/dir/ [options]\n\n'
'%prog takes in the contig path statistics directories from both the Scaffolds and Contigs alignments\n'
'( --statsScaffoldsContigPathDir --statsContigsContigPathDir ) and prints to STDOUT a latex formatted table.' )
parser = OptionParser( usage=usage )
initOptions( parser )
las.initOptions( parser )
options, args = parser.parse_args()
checkOptions( args, options, parser )
las.checkOptions( options, parser )
assembliesList = readDirs( options )
calculateErrors( assembliesList, options )
assembliesList = performSort( assembliesList, options )
sortString = { 'totalErrors':'the sum of the errors (\\(\\sum\\) err)',
'errorsPerMappedBase':'errors per mapped base (ePmb)',
'totalScaffoldGaps+totalBleedingHeartScaffoldGaps':'the sum of the total number of scaffold gaps and liberal scaffold gaps (scf)',
'scaffolds':'the sum of the total number of scaffold gaps and liberal scaffold gaps (scf)',
'totalContigEnds+totalContigEndsWithNs':'the sum of total contig ends and the total contigs ending with N\'s (ctgE+ctgN)',
'totalHomoToHeteroSwitches':'the total homozygous to heterozygous switches (hom/het sw)',
'errorsPerContig':'errors per contig (ePc)',
'totalContigEndsWithInsert':'total contigs ending with insert (e-i)',
'totalErrorsHaplotypeToHaplotype':'total haplotype to haplotype errors (h-h)',
'totalErrorsHaplotypeToInsert':'total haplotype to insert errors (h-i)',
'totalErrorsHaplotypeToDeletion':'total haplotype to deletion errors (h-d)',
'totalErrorsNonSpecific':'total non--specific errors (nonSpec)'
}
caption = 'The table is sorted on %s. Column headers are total homozygous to heterozygous switches (hom/het sw), sum of the total scaffold gaps and liberal scaffold gaps (scf), the sum of total contig ends and the total contigs ending with N\'s (ctgE+ctgN), errors per contig (ePc), errors per mapped base (ePmb), total contigs ending with insert (e-i), total haplotype to haplotype errors (h-h), total haplotype to insert errors (h-i), total haplotype to deletion errors (h-d), total non--specific errors (nonSpec) and sum of the errors (\\(\\sum\\) err).' % sortString[ options.sortOn ]
if options.outputRanks:
printRanks( assembliesList, options )
else:
printTable( assembliesList, '', options )