def _align(record):
records = (record, _rc(record)) if do_revcomp else (record, )
score, ref_, record = max(
(aln(ref.value.decode('utf-8'), record) for record in records),
key=itemgetter(0))
record_ = compute_cigar(ref_, record, ref_name)
return score, record_
def iterate(records):
for record in records:
if ('CIGAR' in record.annotations and
'position' in record.annotations):
yield record
else:
yield compute_cigar(reference, record, new_style)
def _align(record):
records = (record, _rc(record)) if do_revcomp else (record,)
score, ref_, record = max(
(aln(ref.value.decode('utf-8'), record) for record in records),
key=itemgetter(0)
)
record_ = compute_cigar(ref_, record, ref_name)
return score, record_
def _align(record, aln, ref, ref_name, do_revcomp):
records = (record, _rc(record)) if do_revcomp else (record,)
score, ref_, record = max(
(aln(ref, record) for record in records),
key=itemgetter(0)
)
record_ = compute_cigar(ref_, record, ref_name)
return score, record_
def iterate(records):
for record in records:
if ('CIGAR' in record.annotations and
'position' in record.annotations):
yield record
elif reference is not None and len(record) == len(reference):
yield compute_cigar(reference, record, new_style=new_style)
else:
msg = 'provide aligned SeqRecords with their reference or position- and CIGAR-annotated SeqRecords'
raise RuntimeError(msg)
def allseqs(records):
yield compute_cigar(reference, reference)
for record in records:
print(record)
yield record
def allseqs(records):
yield compute_cigar(reference, reference)
for record in records:
yield record