def action(args):
if args.seqname:
seqname = args.seqname
else:
seqname = 'consensus' if args.infile is sys.stdin \
else splitext(basename(args.infile.name))[0]
seqs = list(fastalite(args.infile, 'fasta'))
if args.rlefile:
rledict = json.load(args.rlefile)
rlelist = [rledict[s.id] for s in seqs]
cons = consensus(seqs, rlelist, degap=not args.gaps)
else:
cons = consensus(seqs, degap=not args.gaps)
args.outfile.write('>{}\n{}\n'.format(seqname, cons))
def action(args):
if args.seqname:
seqname = args.seqname
else:
seqname = 'consensus' if args.infile is sys.stdin \
else splitext(basename(args.infile.name))[0]
seqs = list(fastalite(args.infile, 'fasta'))
if args.rlefile:
rledict = json.load(args.rlefile)
rlelist = [rledict[s.id] for s in seqs]
cons = consensus(seqs, rlelist, degap=not args.gaps)
else:
cons = consensus(seqs, degap=not args.gaps)
args.outfile.write('>{}\n{}\n'.format(seqname, 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 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