def main():
usage = ('Usage: %prog [options] inputDirectory\n')
parser = OptionParser(usage = usage)
initOptions( parser )
#libplot.initOptions( parser )
iseqlib.initPlotOptions( parser )
options, args = parser.parse_args()
checkOptions( args, options, parser )
#libplot.checkOptions( options, parser )
iseqlib.checkPlotOptions( options, parser )
samples = readfiles( args[0], options.cumulative )
if options.group:
group2samples = readGroup2Samples(options.group)
samples = getAvrSamples(samples, group2samples, options.cumulative)
#drawCloneSizeDist( samples, options, True, False, False, options.cumulative )
#drawCloneSizeDist( samples, options, False, False, False, options.cumulative )
#drawCloneSizeDist( samples, options, True, False, True, options.cumulative )
#drawCloneSizeDist( samples, options, False, False, True, options.cumulative )
#drawCloneSizeDist( samples, options, True, True, False, options.cumulative )
#drawCloneSizeDist( samples, options, False, True, False, options.cumulative )
#drawCloneSizeDist( samples, options, options.isAbs, options.yaxisPcReads, options.yaxisPcClones, options.cumulative )
#if not options.group:
# drawCloneVsRead( samples, options, True )
# drawCloneVsRead( samples, options, False )
drawCombine( samples, options )
def main():
parser = immunoseqLib.initOptions()
initOptions( parser )
immunoseqLib.initPlotOptions( parser )
options, args = parser.parse_args()
checkOptions( args, options, parser )
immunoseqLib.checkPlotOptions( options, parser )
samples, stds = readfiles( options.indir, options.noheader )
type2intersectGenes = getIntersect(samples) #Get genes that are present in all samples
type2selectedGenes = getSelectedGenes(type2intersectGenes, options.vs, options.js) #Select only genes of interest that are present in all samples
group2samples = readGroup2samples(options.group2samples)
#Intersect VJ:
if options.ttest or options.vj or options.pca:
#intersectVJ(samples, type2intersectGenes, options.vjs) #added intersectVJusage, normIntersectVJusage
intersectVJ(samples, type2selectedGenes) #added intersectVJusage, normIntersectVJusage
#Pca:
if options.pca:
vPcaOut = os.path.join(options.outdir, "vPca")
getPcaTransformedMatrix(samples, group2samples, type2intersectGenes, options.vjs, 'v', options.abs, vPcaOut, options)
vjPcaOut = os.path.join(options.outdir, "vjPca")
getPcaTransformedMatrix(samples, group2samples, type2intersectGenes, options.vjs, 'vj', options.abs, vjPcaOut, options)
#return
#Student's t test:
if options.ttest:
outfile = os.path.join(options.outdir, "ttest.txt")
ttests(samples, group2samples, outfile, type2selectedGenes, options.vjs, options.ttestTargetGroup, options.abs, options.pval)
#HACK: Sort samples:
#sampleOrder = 'SBC1,SBC7,SBC3,SBC4,SBC5,SBC6,SBC2,SBC8,Patient-01-R,Patient-01-D,Patient-10,Patient-11,Patient-12,Patient-13,Patient-B-R,Patient-B-D,Patient-8-D,Patient-15-D'
if options.sampleOrder:
orders = options.sampleOrder
sortedSamples = []
for s in orders:
for sample in samples:
if sample.name == s:
sortedSamples.append(sample)
for s in samples:
if s not in sortedSamples:
sortedSamples.append(s)
else:
sortedSamples = samples
#checkSamples( samples )
if not options.noplot:
drawUsageDist( sortedSamples, stds, options, 'v', type2selectedGenes['v'] )
drawUsageDist( sortedSamples, stds, options, 'j', type2selectedGenes['j'] )
if options.vj:
minvj, maxvj = getMinMaxVJusage(samples, options.abs)
for sample in samples:
drawVJ( sample, type2selectedGenes['v'], type2selectedGenes['j'], options, minvj, maxvj )
def main():
parser = iseqlib.initOptions()
Stack.addJobTreeOptions( parser )
iseqlib.initPlotOptions( parser )
addOptions(parser)
options, args = parser.parse_args()
iseqlib.checkPlotOptions( options, parser )
mincount = options.mincount
#samples = readfiles(options.indir, mincount)
i = Stack( Setup(options) ).startJobTree(options)
if i:
raise RuntimeError("The jobtree contains %d failed jobs.\n" %i)
def main():
usage=('Usage: %prog [options] inputDir outputDir')
parser = OptionParser(usage=usage)
parser.add_option('-s', '--sampling', dest='sampling', action='store_true', default=False, help='If specified, will randomly sampling sequences from each file with sampling size equals to size of the smallest sample')
parser.add_option('--numSamplings', dest='numSamplings', type='int', default=100, help='Number of samplings. Default=%default')
iseqlib.initPlotOptions(parser)
options, args = parser.parse_args()
iseqlib.checkPlotOptions(options, parser)
indir = args[0]
outdir = args[1]
sample2freqs = readfiles(indir)
if options.sampling:
sample2data = samplingSamples(sample2freqs, options.numSamplings)
else:
sample2data = binDataSamples(sample2freqs)
drawClonesizeDist(outdir, options, sample2data)
def main():
parser = iseqlib.initOptions()
iseqlib.initPlotOptions(parser)
parser.add_option('-i', '--indir', dest='indir')
parser.add_option('-o', '--outdir', dest='outdir', default = '.')
parser.add_option('-m', '--mode', dest='mode', default='1,2', type='string', help='Specify how you would like to aggregate the data. Should be a comma seperated list of any of the valid choices: [1, 2]. Mode 1 is one statistics of interest across different cutoffs. Mode 2 is different statistics for 1 cutoff.')
parser.add_option('-s', '--stats_type', dest='stats_type', default='readAvr', help='Option for mode 1. Specify which overlapping statistics of interest to print out. Default = %default. Valid values are [clone1, clone2, cloneAvr, read1, read2, readAvr], where clone# is percentage of clones in sample # that passed each cutoff and are also in the other sample; cloneAvr is average of clone1 and clone2; read# is percentage of reads in clones of sample # that passed cutoff and also in the other sample; readAvr: average of read1 and read2')
parser.add_option('-c', '--cutoffs', dest='cutoffs', default='all', help='Option for mode 2. Comma separated list of cutoffs of interest. Default=%default' )
parser.add_option('-a', '--sampleOrder', dest='sampleOrder')
parser.add_option('-l', '--latex', dest='latex', action='store_true', default=False)
parser.add_option('-g', '--groupToSamples', dest='group2samples')
options, args = parser.parse_args()
iseqlib.checkPlotOptions( options, parser )
if options.sampleOrder:
options.sampleOrder = options.sampleOrder.split(',')
indir = options.indir
if not os.path.isdir(indir):
raise ValueError("Input directory %s is not a directory\n" %indir)
options.mode = options.mode.split(',')
options.cutoffs = options.cutoffs.split(',')
exps = []
for file in os.listdir(indir):
if os.path.isdir( os.path.join(indir, file) ):
continue
exp = readFile( os.path.join(indir, file) )
exps.append(exp)
if options.group2samples:
options.group2samples = readGroup2Samples(options.group2samples)
orfile = os.path.join(options.outdir, "overlapReads-%s.tex" %options.stats_type)
#getOverlapReadsTab(exps, orfile)
if '1' in options.mode:
getCutoffsLatexTab(exps, orfile, options.stats_type, options.sampleOrder)
#drawOverlapReads(exps, options)
if '2' in options.mode:
getAllStatsLatexTabs(exps, options.outdir, options.cutoffs, options.sampleOrder, options.latex)
def main():
parser = iseqlib.initOptions()
parser.add_option('-i', '--infile', dest='infile', default='-', help='Input file. Default is stdin')
parser.add_option('-o', '--outdir', dest='outdir', default='.', help='Output directory. Default is current directory')
parser.add_option('--noplot', dest='noplot', action='store_true', default=False, help='If specified, do not draw plot')
parser.add_option('-t', '--table', dest='table', action='store_true', default=False, help='If specified, make latex table')
#parser.add_option('-o', '--outfile', dest='outfile', default='-', help='Output file. Default is stdout')
iseqlib.initPlotOptions(parser)
options, args = parser.parse_args()
iseqlib.checkPlotOptions( options, parser )
rowname2row, index2colname = readfile(options.infile)
if not options.noplot:
drawPlots(options, options.outdir, rowname2row, index2colname)
if options.table:
outfile = os.path.join(options.outdir, "%s.tex" %( os.path.basename(options.infile).split('.')[0] ))
getLatexTab(outfile, rowname2row, index2colname)
def main():
parser = iseqlib.initOptions()
iseqlib.initPlotOptions( parser )
addOptions(parser)
options, args = parser.parse_args()
iseqlib.checkPlotOptions( options, parser )
samples = readfiles(options.indir, options.count, options.translate)
if options.drawdist:
drawDist(samples, options)
#printSharedSeqFreqAll( samples, minsam, "counts-atleast3sams" )
if options.fasta:
faoutdir = os.path.join(options.outdir, "fasta-atleast%dsams" %options.minsam)
system("mkdir -p %s" %faoutdir)
filterByNumSampleAll(samples, options.minsam, faoutdir, options.freq)
if options.clonematrix:
printCloneMatrixAll(options.outdir, samples, options.minsam, options.freqTransform)
