def align_and_consensus(chunk):
"""Wraps functions for alignment and consensus generation. Does not
perform alignment for clusters of length 1.
"""
i, (cluster, rlelist) = chunk
if len(cluster) == 1:
# no need to align...
seq = cluster[0]
rle = rlelist[0] if rlelist else None
cons = homodecode(seq, rle) if rle else seq.seq
else:
log.debug('aligning cluster {} len {}'.format(i, len(cluster)))
cons = consensus(run_muscle(cluster), rlelist)
return cluster, cons
def align_and_consensus(chunk):
"""Wraps functions for alignment and consensus generation. Does not
perform alignment for clusters of length 1.
"""
i, (cluster, rlelist) = chunk
if len(cluster) == 1:
# no need to align...
seq = cluster[0]
rle = rlelist[0] if rlelist else None
cons = homodecode(seq, rle) if rle else seq.seq
else:
log.debug('aligning cluster {} len {}'.format(i, len(cluster)))
cons = consensus(run_muscle(cluster), rlelist)
return cluster, cons
def seq_and_homodecode(seq_rle):
seq, rle = seq_rle
assert len(seq.seq) == len(rle)
return seq, homodecode(seq.seq, rle)
def rlemap(seq):
decoded = homodecode(seq.seq, from_ascii(args.rlefile[seq.id]))
return SeqLite(seq.id, seq.description, decoded)
def test01(self):
seq = 'TCTGGACCGTGTCTTTCAGTTCCAAAGTGTGACTGATCCATCCTCTCAGACC'
e, c = sequtils.homoencode(seq)
self.assertEquals(seq, sequtils.homodecode(e, c))
def rlemap(seq):
decoded = homodecode(seq.seq, from_ascii(args.rlefile[seq.id]))
return SeqLite(seq.id, seq.description, decoded)
def seq_and_homodecode(seq_rle):
seq, rle = seq_rle
assert len(seq.seq) == len(rle)
return seq, homodecode(seq.seq, rle)
