def run(self):
name = os.path.basename(self.file).split('.')[0]
sample = iseqlib.Sample(name)
mode = 1 #seqs = {header: seq}
seqs, total = iseqlib.readFile( self.file, self.mincount, mode)
for s in seqs.values():
s.setFreq(total)
sample.seqs = seqs
sample.setTotal(total)
picklefile = os.path.join(self.outdir, "%s.pickle" %name)
pickle.dump( sample, gzip.open(picklefile, "wb") )
def run(self):
mode = 1 #seqs = { header: Seq() }
mincount = 1
seqs, total = iseqlib.readFile(self.infile, mincount, mode)
total = sum([seq.count for seq in seqs.values()])
for s in seqs.values():
s.setFreq(total)
sample = iseqlib.Sample(self.name)
sample.seqs = seqs
sample.setTotal(total)
pickleFile = os.path.join(self.outdir, "%s.pickle" %self.name)
pickle.dump( sample, gzip.open(pickleFile, "wb") )
