def testInsertionQualityJustEnough(self):
ins1 = {2: ('CCC', 'JJJ')}
ins2 = {10: ('GGG', 'JBJ')}
expected_merged = {2: 'CCC', 10: 'GGG'}
merged = merge_inserts(ins1, ins2, q_cutoff=32)
self.assertEqual(expected_merged, merged)
def testNone(self):
ins1 = None
ins2 = None
expected_merged = {}
merged = merge_inserts(ins1, ins2)
self.assertEqual(expected_merged, merged)
def testConflictingInsertionsTooCloseInQuality(self):
ins1 = {2: ('CCC', 'JJJ')}
ins2 = {2: ('CTC', 'JAJ')}
expected_merged = {2: 'CNC'}
merged = merge_inserts(ins1, ins2, minimum_q_delta=20)
self.assertEqual(expected_merged, merged)
def testInsertionQualityTooLowReverse(self):
ins1 = {2: ('CCC', 'JJJ')}
ins2 = {10: ('GGG', 'JAJ')}
expected_merged = {2: 'CCC'}
merged = merge_inserts(ins1, ins2, q_cutoff=32)
self.assertEqual(expected_merged, merged)
def testConflictingInsertions(self):
ins1 = {2: ('CCC', 'JJJ')}
ins2 = {2: ('CTC', 'JAJ')}
expected_merged = {2: 'CCC'}
merged = merge_inserts(ins1, ins2)
self.assertEqual(expected_merged, merged)
def testIdenticalInsertions(self):
ins1 = {2: ('CCC', 'JJJ')}
ins2 = {2: ('CCC', 'JJJ')}
expected_merged = {2: 'CCC'}
merged = merge_inserts(ins1, ins2)
self.assertEqual(expected_merged, merged)
def testSeparateInsertions(self):
ins1 = {2: ('CCC', 'JJJ')}
ins2 = {10: ('GGG', 'JJJ')}
expected_merged = {2: 'CCC', 10: 'GGG'}
merged = merge_inserts(ins1, ins2)
self.assertEqual(expected_merged, merged)
def merge_reads(quality_cutoff, read_pair):
""" Merge a pair of reads.
Also skip reads that don't meet certain criteria.
@param quality_cutoff: minimum quality score for a base to be counted
@param read_pair: a sequence of two sequences, each with fields from a
SAM file record
@return: (rname, mseq, merged_inserts, qual1, qual2) or None to skip the pair
"""
read1, read2 = read_pair
if read2 and read1[2] != read2[2]:
# region mismatch, ignore the read pair.
return None
filtered_reads = []
rname = None
for read in read_pair:
if not read:
continue
(_qname,
flag,
rname,
refpos_str,
_mapq,
cigar,
_rnext,
_pnext,
_tlen,
seq,
qual) = read[:11] # ignore optional fields
if is_unmapped_read(flag):
continue
filtered_reads.append(dict(rname=rname,
cigar=cigar,
seq=seq,
qual=qual,
pos=int(refpos_str)))
if not filtered_reads:
return None
seq1, qual1, ins1 = apply_cigar(filtered_reads[0]['cigar'],
filtered_reads[0]['seq'],
filtered_reads[0]['qual'],
filtered_reads[0]['pos']-1)
if len(filtered_reads) == 1:
seq2 = qual2 = ''
ins2 = None
else:
seq2, qual2, ins2 = apply_cigar(filtered_reads[1]['cigar'],
filtered_reads[1]['seq'],
filtered_reads[1]['qual'],
filtered_reads[1]['pos']-1)
mseq = merge_pairs(seq1, seq2, qual1, qual2, q_cutoff=quality_cutoff)
merged_inserts = merge_inserts(ins1, ins2, quality_cutoff)
return rname, mseq, merged_inserts, qual1, qual2
def merge_reads(quality_cutoff, read_pair):
""" Merge a pair of reads.
Also skip reads that don't meet certain criteria.
@param quality_cutoff: minimum quality score for a base to be counted
@param read_pair: a sequence of two sequences, each with fields from a
SAM file record
@return: (rname, mseq, merged_inserts, qual1, qual2) or None to skip the pair
"""
read1, read2 = read_pair
if read2 and read1[2] != read2[2]:
# region mismatch, ignore the read pair.
return None
filtered_reads = []
for read in read_pair:
if not read:
continue
(_qname,
flag,
rname,
refpos_str,
_mapq,
cigar,
_rnext,
_pnext,
_tlen,
seq,
qual) = read[:11] # ignore optional fields
if is_unmapped_read(flag):
continue
filtered_reads.append(dict(rname=rname,
cigar=cigar,
seq=seq,
qual=qual,
pos=int(refpos_str)))
if not filtered_reads:
return None
seq1, qual1, ins1 = apply_cigar(filtered_reads[0]['cigar'],
filtered_reads[0]['seq'],
filtered_reads[0]['qual'],
filtered_reads[0]['pos']-1)
if len(filtered_reads) == 1:
seq2 = qual2 = ''
ins2 = None
else:
seq2, qual2, ins2 = apply_cigar(filtered_reads[1]['cigar'],
filtered_reads[1]['seq'],
filtered_reads[1]['qual'],
filtered_reads[1]['pos']-1)
mseq = merge_pairs(seq1, seq2, qual1, qual2, q_cutoff=quality_cutoff)
merged_inserts = merge_inserts(ins1, ins2, quality_cutoff)
return rname, mseq, merged_inserts, qual1, qual2
