def ichunker(seqs, rledict=None, min_clust_size=1, max_clust_size=sys.maxint):
"""Return iterator of (seqlist, rlelist) tuples. Clusters are broken
into chunks no larger than 0.5*max_clust_size. Returns an iterator
of (cluster_seqs, rle_info). If rle_info is not provided, rle_info
is None.
"""
for cluster in seqs:
cluster = list(cluster)
if len(cluster) < min_clust_size:
continue
elif len(cluster) > max_clust_size:
shuffle(cluster)
# combine trailing chunk with next to last if less than
# half the target chunk size
combine_last = max_clust_size * 0.5
for chunk in chunker(cluster, max_clust_size, combine_last):
rlelist = [from_ascii(rledict[s.id])
for s in chunk] if rledict else None
yield (chunk, rlelist)
else:
rlelist = [from_ascii(rledict[s.id])
for s in cluster] if rledict else None
yield (cluster, rlelist)
def decode(aligns):
aligns["t_seq"], aligns["q_seq"] = homodecodealignment(
aligns["t_seq"],
from_ascii(decoding[aligns["t_name"]]),
aligns["q_seq"],
from_ascii(decoding[aligns["q_name"]]),
)
return aligns
def action(args):
# Ignore SIGPIPE, for head support
utils.exit_on_sigpipe()
utils.exit_on_sigint()
rledict = {seqname: rle for seqname, rle in csv.reader(args.rle)}
seqs = ((s, from_ascii(rledict[s.id])) for s in args.seqs)
pool = Pool(processes=args.threads)
seqs = pool.imap(seq_and_homodecode, seqs, chunksize=140)
for seq, decoded in seqs:
args.outfile.write('>{}\n{}\n'.format(seq.description, decoded))
def action(args):
# Ignore SIGPIPE, for head support
utils.exit_on_sigpipe()
utils.exit_on_sigint()
rledict = {seqname: rle for seqname, rle in csv.reader(args.rle)}
seqs = ((s, from_ascii(rledict[s.id])) for s in args.seqs)
pool = Pool(processes=args.threads)
seqs = pool.imap(seq_and_homodecode, seqs, chunksize=140)
for seq, decoded in seqs:
args.outfile.write('>{}\n{}\n'.format(seq.description, decoded))
def ichunker(seqs, rledict=None, min_clust_size=1, max_clust_size=sys.maxint):
"""Return iterator of (seqlist, rlelist) tuples. Clusters are broken
into chunks no larger than 0.5*max_clust_size. Returns an iterator
of (cluster_seqs, rle_info). If rle_info is not provided, rle_info
is None.
"""
for cluster in seqs:
cluster = list(cluster)
if len(cluster) < min_clust_size:
continue
elif len(cluster) > max_clust_size:
shuffle(cluster)
# combine trailing chunk with next to last if less than
# half the target chunk size
combine_last = max_clust_size * 0.5
for chunk in chunker(cluster, max_clust_size, combine_last):
rlelist = [from_ascii(rledict[s.id]) for s in chunk] if rledict else None
yield (chunk, rlelist)
else:
rlelist = [from_ascii(rledict[s.id]) for s in cluster] if rledict else None
yield (cluster, rlelist)
def decode(aligns):
aligns['t_seq'], aligns['q_seq'] = homodecodealignment(
aligns['t_seq'], from_ascii(decoding[aligns['t_name']]),
aligns['q_seq'], from_ascii(decoding[aligns['q_name']]))
return aligns
def rlemap(seq):
decoded = homodecode(seq.seq, from_ascii(args.rlefile[seq.id]))
return SeqLite(seq.id, seq.description, decoded)
def decode(aligns):
aligns['t_seq'], aligns['q_seq'] = homodecodealignment(
aligns['t_seq'], from_ascii(decoding[aligns['t_name']]),
aligns['q_seq'], from_ascii(decoding[aligns['q_name']]))
return aligns
def test01(self):
v = range(79)
self.assertEqual(v, sequtils.from_ascii(sequtils.to_ascii(v)))
def rlemap(seq):
decoded = homodecode(seq.seq, from_ascii(args.rlefile[seq.id]))
return SeqLite(seq.id, seq.description, decoded)
