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 --contigPathStatsDir=path/to/dir/ [options]\n\n'
'%prog takes the contig path stats directory\n'
'( --contigPathStatsDir ) with names as NAME.contigPathStats.xml and then\n'
'writes to STDOUT a latex formatted table.')
parser = OptionParser( usage=usage )
cnfsp.initOptions( parser )
options, args = parser.parse_args()
cnfsp.checkOptions( options, parser )
assembliesList = ccpst.readDirs( options )
ccpst.calculateErrors( assembliesList, options )
assembliesList = sorted( assembliesList, key=lambda x: x.valuesDict[ options.sortOn ], reverse=True )
maxesDict = calculateMaxesDict( assembliesList )
caption = 'Columns are the total number of contigs in the assembly, N50, N50 relative to the number of columns in the alignment (NA50) as defined in the main text section \\ref{sect:NA50}, the scaffold path 50 (SPA50), contig path (HPA50), block path 50 (BA50), and the sum of the sum of the total number of errors present in the assembly (\\(\\sum\\) Errors).'
printTable( assembliesList, caption, maxesDict, options )
def main():
usage = (
'usage: %prog --contigPathStatsDir=path/to/dir/ [options]\n\n'
'%prog takes the contig path stats directory\n'
'( --contigPathStatsDir ) with names as NAME.contigPathStats.xml and then\n'
'writes to STDOUT a latex formatted table.')
parser = OptionParser(usage=usage)
cnfsp.initOptions(parser)
options, args = parser.parse_args()
cnfsp.checkOptions(options, parser)
assembliesList = ccpst.readDirs(options)
ccpst.calculateErrors(assembliesList, options)
assembliesList = sorted(assembliesList,
key=lambda x: x.valuesDict[options.sortOn],
reverse=True)
maxesDict = calculateMaxesDict(assembliesList)
caption = 'Columns are the total number of contigs in the assembly, N50, N50 relative to the number of columns in the alignment (NA50) as defined in the main text section \\ref{sect:NA50}, the scaffold path 50 (SPA50), contig path (HPA50), block path 50 (BA50), and the sum of the sum of the total number of errors present in the assembly (\\(\\sum\\) Errors).'
printTable(assembliesList, caption, maxesDict, 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 readData(options):
aList = readDirs(options)
hap1List = readPhasingDir(1, options)
hap2List = readPhasingDir(2, options)
assembliesList = mergeLists(aList, hap1List, hap2List)
return assembliesList
def readData( options ): aList = readDirs( options ) hap1List = readPhasingDir( 1, options ) hap2List = readPhasingDir( 2, options ) assembliesList = mergeLists( aList, hap1List, hap2List ) return assembliesList
