def assemble(read1, read2, *extra_seqs):
tracks1 = ab1.read(read1)
tracks2 = ab1.read(read2)
ref = contig.contig(tracks1['sequence'], tracks1['confidences'],
tracks.revcomp(tracks2['sequence']),
tracks.revcomp(tracks2['confidences']))
t = tracks.TrackSet()
read1_offset, read1_sequence = ref['read1']
read2_offset, read2_sequence = ref['read2']
read1_confs = tracks.regap(read1_sequence, tracks1['confidences'])
read2_confs = tracks.regap(read2_sequence, tracks.revcomp(tracks2['confidences']))
read1_traces = tracks.regap(read1_sequence, tracks1['traces'])
read2_traces = tracks.regap(read2_sequence, tracks.revcomp(tracks2['traces']))
t.extend([
tracks.TrackEntry('read 1 traces', read1_offset, read1_traces),
tracks.TrackEntry('read 1 confidences', read1_offset, read1_confs),
tracks.TrackEntry('read 1 bases', read1_offset, read1_sequence),
tracks.TrackEntry('read 2 traces', read2_offset, read2_traces),
tracks.TrackEntry('read 2 confidences', read2_offset, read2_confs),
tracks.TrackEntry('read 2 bases', read2_offset, read2_sequence)])
if ref['reference'] != None:
reference_offset, reference_sequence = ref['reference']
t.append(tracks.TrackEntry('reference', reference_offset, reference_sequence))
for (name,s) in extra_seqs:
if ref['reference'] != None:
(roffset, _), (soffset, saligned) = fasta.fasta(reference_sequence, s)
t.append(tracks.TrackEntry(name, reference_offset + soffset - roffset,
tracks.sequence(saligned)))
else:
t.append(tracks.TrackEntry(name, 0, s))
# Now add an assembly of the lab sequence and reference sequence
if len(extra_seqs) == 1 and ref['reference'] != None:
labtrack = t[-1]
reftrack = t[-2]
offset = max(labtrack.offset, reftrack.offset)
loffset = offset - labtrack.offset
roffset = offset - reftrack.offset
assert loffset >= 0 and roffset >= 0 and (loffset == 0 or roffset == 0)
bases = tracks.sequence(''.join([a == b and ' ' or 'X' for a,b in
zip(labtrack.track[loffset:],
reftrack.track[roffset:])]))
if 'X' in bases:
t.append(tracks.TrackEntry('mismatches', offset, bases))
return (t, ref['strands'])
