def cigar2reflen(cigar):
"""infer ref length from cigar struct or string
>>> cigar2reflen("10M")
10
>>> cigar2reflen("10M1S")
10
>>> cigar2reflen("1S10M")
10
>>> cigar2reflen("1S10M1S")
10
>>> cigar2reflen("1S5M1D5M1S")
11
>>> cigar2reflen("1S5M1I5M1S")
10
"""
cig = chimeras2.cigar_to_list(cigar)
rlen = 0
#ref_consuming = 'MDN=X'
for (op_len, op_type) in cig:
if op_type in Cigar.ref_consuming_ops:
rlen += op_len
return rlen
def cigar2reflen(cigar):
"""infer ref length from cigar struct or string
>>> cigar2reflen("10M")
10
>>> cigar2reflen("10M1S")
10
>>> cigar2reflen("1S10M")
10
>>> cigar2reflen("1S10M1S")
10
>>> cigar2reflen("1S5M1D5M1S")
11
>>> cigar2reflen("1S5M1I5M1S")
10
"""
cig = chimeras2.cigar_to_list(cigar)
rlen = 0
#ref_consuming = 'MDN=X'
for (op_len, op_type) in cig:
if op_type in Cigar.ref_consuming_ops:
rlen += op_len
return rlen
def cigar2querylen(cigar):
"""Determine length of query sequence from cigar string
"""
cig = chimeras2.cigar_to_list(cigar)
qlen = 0
for (op_len, op_type) in cig:
assert not isinstance(op_type, int), (
"Do not understand cigar {}. Might be from pysam?".format(op_type))
if op_type in ['M', 'I', '=', 'X']:
# FIXME check SAM spec for more
qlen += op_len
return qlen
def cigar2querylen(cigar):
"""Determine length of query sequence from cigar string
"""
cig = chimeras2.cigar_to_list(cigar)
qlen = 0
for (op_len, op_type) in cig:
assert not isinstance(op_type, int), (
"Do not understand cigar {}. Might be from pysam?".format(op_type))
if op_type in ['M', 'I', '=', 'X']:
# FIXME check SAM spec for more
qlen += op_len
return qlen
def query_aln_seq(queryseq, cigar):
"""Infer aligned bit of query sequence from cigar
>>> query_aln_seq("ACGTACGT", "8M")
'ACGTACGT'
>>> query_aln_seq("ACGTACGT", "1M7S")
'A'
>>> query_aln_seq("ACGTACGT", "6S2M")
'GT'
>>> query_aln_seq("ACGTACGT", "6S2M")
'GT'
>>> query_aln_seq("ACGTACGT", "2S4M2S")
'GTAC'
>>> query_aln_seq("ACGTACGT", "2S1M2I1M2S")
'GTAC'
"""
cig = chimeras2.cigar_to_list(cigar)
start = 0
for (op_len, op_type) in cig:
if op_type == 'S':
start += op_len
else:
break
end = len(queryseq)
for (op_len, op_type) in cig[::-1]:
if op_type == 'S':
end -= op_len
else:
break
assert end > 0 and start < end
assert cigar2querylen(cig) == end - start, ("{} != {}".format(
cigar2querylen(cig), end - start))
return queryseq[start:end]
def query_aln_seq(queryseq, cigar):
"""Infer aligned bit of query sequence from cigar
>>> query_aln_seq("ACGTACGT", "8M")
'ACGTACGT'
>>> query_aln_seq("ACGTACGT", "1M7S")
'A'
>>> query_aln_seq("ACGTACGT", "6S2M")
'GT'
>>> query_aln_seq("ACGTACGT", "6S2M")
'GT'
>>> query_aln_seq("ACGTACGT", "2S4M2S")
'GTAC'
>>> query_aln_seq("ACGTACGT", "2S1M2I1M2S")
'GTAC'
"""
cig = chimeras2.cigar_to_list(cigar)
start = 0
for (op_len, op_type) in cig:
if op_type == 'S':
start += op_len
else:
break
end = len(queryseq)
for (op_len, op_type) in cig[::-1]:
if op_type == 'S':
end -= op_len
else:
break
assert end > 0 and start < end
assert cigar2querylen(cig) == end-start, ("{} != {}".format(cigar2querylen(cig), end-start))
return queryseq[start:end]
