def run(self):
globalTempDir = self.getGlobalTempDir()
ext = "pickle"
files = iseqlib.getfiles(self.indir, ext)
samples = [file.split('.')[0] for file in files]
for sample in samples:
samplefile = os.path.join(self.indir, "%s.%s"%(sample, ext))
sampledir = os.path.join(globalTempDir, sample)
system("mkdir -p %s" %sampledir)
if self.options.sampling:
for i in xrange(self.options.numsam): #sampling a number of times
samplingdir = os.path.join(sampledir, "%d" %i)
system("mkdir -p %s" %samplingdir)
self.addChildTarget( Sampling(samplefile, samplingdir, self.options) )
else:
tempoutdir = os.path.join(sampledir, "0")
system("mkdir -p %s" %tempoutdir)
#filtering if selected Vs and/or selected Js were specified
if self.options.vs or self.options.js:
sampleObj = pickle.load( gzip.open(samplefile, "rb") )
subsample = iseqlib.filterSampleByGenes(sampleObj, self.options.vs, self.options.js)
system("rm %s" %samplefile)
pickle.dump( subsample, gzip.open(samplefile, "wb") )
self.addChildTarget( Analyses(samplefile, tempoutdir, self.options) )
#Calculate means & standard deviations of samplings
self.setFollowOnTarget( AverageResults(globalTempDir, self.options) )
def filterSamples(indir, vs, js):
if not vs and not js:
return
ext = 'pickle'
files = iseqlib.getfiles(indir, ext)
for file in files:
filepath = os.path.join(indir, file)
sample = pickle.load( gzip.open(filepath, "rb") )
subsample = iseqlib.filterSampleByGenes(sample, vs, js)
system("rm %s" %filepath)
pickle.dump(subsample, gzip.open(filepath, "wb"))
return
def run(self):
sample = pickle.load( gzip.open(self.samplefile, "rb") )
if self.options.uniq:
subsample = iseqlib.samplingSample_weightedUniq(sample, self.size)
#subsample = iseqlib.samplingSample_uniq(sample, self.size)
else:
subsample = iseqlib.samplingSample(sample, self.size)
#filtering if selected Vs and/or selected Js were specified
subsample = iseqlib.filterSampleByGenes(subsample, self.options.vs, self.options.js)
pickle.dump(subsample, gzip.open(self.outfile, "wb"))
def run(self):
globalTempDir = self.getGlobalTempDir()
#sampling
sample = pickle.load( gzip.open(self.samplefile, "rb") )
if self.options.uniq:
subsample = iseqlib.samplingSample_weightedUniq(sample, size)
else:
subsample = iseqlib.samplingSample(sample, self.size)
#filtering if selected Vs and/or selected Js were specified
subsample = iseqlib.filterSampleByGenes(subsample, self.options.vs, self.options.js)
picklefile = os.path.join(globalTempDir, "%s.pickle" %sample.name)
pickle.dump(subsample, gzip.open(picklefile, "wb"))
self.addChildTarget( Analyses(picklefile, self.outdir, self.options) )