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") )