def action(args):
seqdict = {s.id: s for s in args.raw_reads}
if args.rlefile:
def rlemap(seq):
decoded = homodecode(seq.seq, from_ascii(args.rlefile[seq.id]))
return SeqLite(seq.id, seq.description, decoded)
groups = groupby(csv.reader(args.readmap), itemgetter(1))
for cons, group in groups:
if args.pattern and not re.search(r'' + args.pattern, cons):
continue
log.info(cons)
reads, _ = zip(*group)
seqs = [seqdict[name] for name in reads]
if len(seqs) > args.sample:
seqs = random.sample(seqs, args.sample)
if args.rlefile:
seqs = (rlemap(s) for s in seqs)
outfile = path.join(
args.outdir,
'{}.{}.fasta'.format(cons, args.name_suffix))
if args.align:
with fasta_tempfile(seqs) as f:
command = ['muscle', '-quiet', '-seqtype', 'dna',
'-in', f, '-out', outfile]
log.debug(' '.join(command))
subprocess.check_call(command)
else:
with open(outfile, 'w') as f:
f.write('\n'.join('>{}\n{}'.format(s.id, s.seq) for s in seqs))
def action(args):
seqdict = {s.id: s for s in args.raw_reads}
if args.rlefile:
def rlemap(seq):
decoded = homodecode(seq.seq, from_ascii(args.rlefile[seq.id]))
return SeqLite(seq.id, seq.description, decoded)
groups = groupby(csv.reader(args.readmap), itemgetter(1))
for cons, group in groups:
if args.pattern and not re.search(r'' + args.pattern, cons):
continue
log.info(cons)
reads, _ = zip(*group)
seqs = [seqdict[name] for name in reads]
if len(seqs) > args.sample:
seqs = random.sample(seqs, args.sample)
if args.rlefile:
seqs = (rlemap(s) for s in seqs)
outfile = path.join(
args.outdir,
'{}.{}.fasta'.format(cons, args.name_suffix))
if args.align:
with fasta_tempfile(seqs) as f:
command = [
'muscle', '-quiet', '-seqtype', 'dna', '-in', f,
'-out', outfile
]
log.debug(' '.join(command))
subprocess.check_call(command)
else:
with open(outfile, 'w') as f:
f.write('\n'.join('>{}\n{}'.format(s.id, s.seq)
for s in seqs))
def test02(self):
with sequtils.fasta_tempfile(self.seqs, dir=self.outdir) as f:
self.assertTrue(path.exists(f))
self.assertFalse(path.exists(f))
def test01(self):
with sequtils.fasta_tempfile(self.seqs) as f:
self.assertTrue(path.exists(f))
self.assertFalse(path.exists(f))
