def recursive_align(seqsA, seqsB, depth=0, max_seqs=1000):
#print depth, len(seqsA), len(seqsB)
if len(seqsA) > max_seqs:
print 'recursingA', len(seqsA), depth
seqsA = recursive_align(*split_seqs(seqsA),
depth=depth+1, max_seqs=max_seqs)
elif any(len(seqsA[0][1]) != len(s) for _, s in seqsA):
print 'aligningA', len(seqsA), depth
seqsA = call_muscle(seqsA)
else:
print 'FinishedA', depth
if len(seqsB) > max_seqs:
print 'recursingB', len(seqsB), depth
seqsB = recursive_align(*split_seqs(seqsB),
depth=depth+1, max_seqs=max_seqs)
elif any(len(seqsB[0][1]) != len(s) for _, s in seqsB):
print 'aligningB', len(seqsB), depth
seqsB = call_muscle(seqsB)
else:
print 'FinishedB', depth
if len(seqsA[0][1]) == len(seqsB[0][1]):
print 'Easy join', depth
return seqsA + seqsB
else:
print 'Hard join', depth
return call_muscle(seqsA + seqsB)
def align_seq_ser(seq_series):
nseqs = [(i, s) for i, s in zip(seq_series.index, seq_series.values)]
nseqs += [('hxb2', hxb2_ltr)]
daln = dict(call_muscle(nseqs))
aln = [daln[str(s)] for s, _ in nseqs]
aln_ser = Series(aln[:-1], seq_series.index)
return aln_ser
def get_wanted_seq_cols(seq_series):
nseqs = [('test', seq_series.values[0]),
('hxb2', hxb2_ltr)]
daln = dict(call_muscle(nseqs))
out = dict([(str(x), None) for x in wanted_seq_cols])
scols = set(wanted_seq_cols)
hxb2pos = 0
for hxb2_l, test_l in zip(daln['hxb2'], daln['test']):
if hxb2_l != '-':
hxb2pos += 1 #1-based!
if hxb2pos in scols:
out[str(hxb2pos)] = test_l
out_ser = Series(out)
return out_ser
def get_wanted_seq_cols(seq_series):
nseqs = [(i, s) for i, s in zip(seq_series.index, seq_series.values)]
nseqs += [('hxb2', hxb2_ltr)]
daln = dict(call_muscle(nseqs))
aln = [daln[str(s)] for s, _ in nseqs]
outs = [[] for _ in range(len(aln)-1)]
hxb2pos = 0
for tup in zip(*aln):
if tup[-1] != '-':
hxb2pos += 1 #1-based!
if hxb2pos in wanted_seq_cols:
for out, let in zip(outs, tup):
out.append(let)
out_ser = Series(outs, seq_series.index)
return out_ser
#from Bio import SeqIO
from Bio.SeqIO.AbiIO import AbiIterator
files = glob.glob('../Wigdahl Trace files/2:11:11/*.ab1')
seqs = []
for f in files:
rec = AbiIterator(open(f, mode = 'rb'), trim = True).next()
seqs.append( (rec.id, rec.seq.tostring()) )
# <codecell>
!/home/will/staden-2.0.0b9.x86_64/bin/convert_trace --help
# <codecell>
res = call_muscle(seqs)
with open('align_data.fasta', 'w') as handle:
fasta_writer(handle, res)
# <codecell>
from HIVTransTool import process_seqs
results = list(process_seqs(seqs[:50], extract_regions = True, known_names = 50))
# <codecell>
for row in results:
if row['RegionName'] == 'LTR5':
print row['Name'], row['QueryNuc']