def orient_subreads(self):
"""Find orientation of subreads with respect to consensus sequence.
:returns: `medaka.align.Alignment` s of subreads to consensus.
"""
# TODO: use a profile here
# TODO: refactor with align_to_template
self._orient = []
alignments = []
for sr in self.subreads:
rc_seq = medaka.common.reverse_complement(sr.seq)
result_fwd = parasail.sw_trace_striped_16(
sr.seq, self.consensus, 8, 4, parasail.dnafull)
result_rev = parasail.sw_trace_striped_16(
rc_seq, self.consensus, 8, 4, parasail.dnafull)
is_fwd = result_fwd.score > result_rev.score
self._orient.append(is_fwd)
result = result_fwd if is_fwd else result_rev
seq = sr.seq if is_fwd else rc_seq
if result.cigar.beg_ref >= result.end_ref or \
result.cigar.beg_query >= result.end_query:
# unsure why this can happen
continue
rstart, cigar = medaka.align.parasail_to_sam(result, seq)
flag = 0 if is_fwd else 16
aln = Alignment(
'consensus_{}'.format(self.name), sr.name,
flag, rstart, seq, cigar)
alignments.append(aln)
return alignments
def align_to_template(self, template, template_name):
"""Align subreads to a template sequence using Smith-Waterman.
:param template: sequence to which to align subreads.
:param template_name: name of template sequence.
:returns: `Alignment` tuples.
"""
self.initialize()
alignments = []
for orient, sr in zip(self._orient, self.subreads):
if orient:
seq = sr.seq
else:
seq = medaka.common.reverse_complement(sr.seq)
result = parasail.sw_trace_striped_16(
seq, template, 8, 4, parasail.dnafull)
if result.cigar.beg_ref >= result.end_ref or \
result.cigar.beg_query >= result.end_query:
# unsure why this can happen
continue
rstart, cigar = medaka.align.parasail_to_sam(result, seq)
flag = 0 if orient else 16
aln = Alignment(template_name, sr.name, flag, rstart, seq, cigar)
alignments.append(aln)
return alignments
