def test_read_pair_inversion_gap_in_query_coverage(self):
# seq AAATTTCCCGGGAATTCCGGATCGATCGAT
# r1 AAATTTCCCGGGAATTccggatcgatcgat +
# r2c aaatttcccgggaattccGGATCGATCGAT -
# i ----------------CC------------
# r2 ATCTATCGATCCggaattcccgggaaattt 100+12 = 111 - 3 = 108
seq = 'AAATTTCCCGGGAATTCCGGATCGATCGAT' # 30
r1 = MockRead(reference_id=0,
reference_name='1',
reference_start=0,
cigar=[(CIGAR.M, 16), (CIGAR.S, 14)],
query_sequence=seq,
is_reverse=False)
r2 = MockRead(reference_id=0,
reference_name='1',
reference_start=99,
cigar=[(CIGAR.M, 12), (CIGAR.S, 18)],
query_sequence=reverse_complement(seq),
is_reverse=True)
bpp = align.call_paired_read_event(r1, r2)
self.assertEqual(STRAND.POS, bpp.break1.strand)
self.assertEqual(STRAND.NEG, bpp.break2.strand)
self.assertEqual(ORIENT.LEFT, bpp.break1.orient)
self.assertEqual(ORIENT.LEFT, bpp.break2.orient)
self.assertEqual('CC', bpp.untemplated_seq)
self.assertEqual(16, bpp.break1.start)
self.assertEqual(111, bpp.break2.start)
self.assertEqual('AAATTTCCCGGGAATT', bpp.break1.seq)
self.assertEqual(reverse_complement('GGATCGATCGAT'), bpp.break2.seq)
def test_read_pair_deletion_overlapping_query_coverage(self):
# seq AAATTTCCCGGGAATTCCGGATCGATCGAT
# r1 AAATTTCCCGGGAATTCCGGAtcgatcgat
# r2 aaatttcccgggaattccGGATCGATCGAT
seq = 'AAATTTCCCGGGAATTCCGGATCGATCGAT' # 30
r1 = MockRead(reference_id=0,
reference_name='1',
reference_start=0,
cigar=[(CIGAR.M, 21), (CIGAR.S, 9)],
query_sequence=seq,
is_reverse=False)
r2 = MockRead(reference_id=0,
reference_name='1',
reference_start=99,
cigar=[(CIGAR.S, 18), (CIGAR.M, 12)],
query_sequence=seq,
is_reverse=False)
self.assertEqual(21, r1.reference_end)
bpp = align.call_paired_read_event(r1, r2)
self.assertEqual(STRAND.POS, bpp.break1.strand)
self.assertEqual(STRAND.POS, bpp.break2.strand)
self.assertEqual(ORIENT.LEFT, bpp.break1.orient)
self.assertEqual(ORIENT.RIGHT, bpp.break2.orient)
self.assertEqual('', bpp.untemplated_seq)
self.assertEqual(21, bpp.break1.start)
self.assertEqual(103, bpp.break2.start)
self.assertEqual('AAATTTCCCGGGAATTCCGGA', bpp.break1.seq)
self.assertEqual('TCGATCGAT', bpp.break2.seq)
def test_read_pair_large_inversion_overlapping_query_coverage(self):
s = 'CTGAGCATGAAAGCCCTGTAAACACAGAATTTGGATTCTTTCCTGTTTGGTTCCTGGTCGTGAGTGGCAGGTGCCATCATGTTTCATTCTGCCTGAGAGCAGTCTACCTAAATATATAGCTCTGCTCACAGTTTCCCTGCAATGCATAATTAAAATAGCACTATGCAGTTGCTTACACTTCAGATAATGGCTTCCTACATATTGTTGGTTATGAAATTTCAGGGTTTTCATTTCTGTATGTTAAT'
read1 = MockRead(reference_id=3,
reference_start=1114,
cigar=[(CIGAR.S, 125), (CIGAR.EQ, 120)],
query_sequence=s,
is_reverse=False)
read2 = MockRead(reference_id=3,
reference_start=2187,
cigar=[(CIGAR.S, 117), (CIGAR.EQ, 8), (CIGAR.D, 1),
(CIGAR.M, 120)],
query_sequence=reverse_complement(s),
is_reverse=True)
bpp = align.call_paired_read_event(read1, read2)
self.assertEqual(STRAND.POS, bpp.break1.strand)
self.assertEqual(STRAND.NEG, bpp.break2.strand)
self.assertEqual(ORIENT.RIGHT, bpp.break1.orient)
self.assertEqual(ORIENT.RIGHT, bpp.break2.orient)
self.assertEqual('', bpp.untemplated_seq)
self.assertEqual(1115, bpp.break1.start)
self.assertEqual(2188 + 3, bpp.break2.start)
print(bpp.break1.seq)
print(bpp.break2.seq)
self.assertEqual(
'TCACAGTTTCCCTGCAATGCATAATTAAAATAGCACTATGCAGTTGCTTACACTTCAGATAATGGCTTCCTACATATTGTTGGTTATGAAATTTCAG'
'GGTTTTCATTTCTGTATGTTAAT', bpp.break1.seq)
self.assertEqual(
'GCAGAGCTATATATTTAGGTAGACTGCTCTCAGGCAGAATGAAACATGATGGCACCTGCCACTCACGACCAGGAACCAAACAGGAAAGAATCCA'
'AATTCTGTGTTTACAGGGCTTTCATGCTCAG', bpp.break2.seq)
def test_read_pair_indel(self):
# seq AAATTTCCCGGGAATTCCGGATCGATCGAT 1-30 1-?
# r1 AAATTTCCCgggaattccggatcgatcgat 1-9 1-9
# r2 aaatttcccgggaattccggaTCGATCGAT 22-30 100-108
# i ---------GGGAATTCCGGA--------- 10-21 n/a
seq = 'AAATTTCCCGGGAATTCCGGATCGATCGAT' # 30
r1 = MockRead(reference_id=0,
reference_name='1',
reference_start=0,
cigar=[(CIGAR.M, 9), (CIGAR.S, 21)],
query_sequence=seq,
is_reverse=False)
r2 = MockRead(reference_id=0,
reference_name='1',
reference_start=99,
cigar=[(CIGAR.S, 21), (CIGAR.M, 9)],
query_sequence=seq,
is_reverse=False)
bpp = align.call_paired_read_event(r1, r2)
self.assertEqual(STRAND.POS, bpp.break1.strand)
self.assertEqual(STRAND.POS, bpp.break2.strand)
self.assertEqual(ORIENT.LEFT, bpp.break1.orient)
self.assertEqual(ORIENT.RIGHT, bpp.break2.orient)
self.assertEqual('GGGAATTCCGGA', bpp.untemplated_seq)
self.assertEqual(9, bpp.break1.start)
self.assertEqual(100, bpp.break2.start)
self.assertEqual('AAATTTCCC', bpp.break1.seq)
self.assertEqual('TCGATCGAT', bpp.break2.seq)
def test_read_pair_translocation(self):
# seq AAATTTCCCGGGAATTCCGGATCGATCGAT
# r1 AAATTTCCCGGGAATTCCGGAtcgatcgat
# r2 aaatttcccgggaattccggaTCGATCGAT
seq = 'AAATTTCCCGGGAATTCCGGATCGATCGAT' # 30
r1 = MockRead(reference_id=0,
reference_name='2',
reference_start=0,
cigar=[(CIGAR.M, 21), (CIGAR.S, 9)],
query_sequence=seq,
is_reverse=False)
r2 = MockRead(reference_id=0,
reference_name='1',
reference_start=99,
cigar=[(CIGAR.S, 21), (CIGAR.M, 9)],
query_sequence=seq,
is_reverse=False)
bpp = align.call_paired_read_event(r1, r2)
self.assertEqual(STRAND.POS, bpp.break1.strand)
self.assertEqual(STRAND.POS, bpp.break2.strand)
self.assertEqual(ORIENT.RIGHT, bpp.break1.orient)
self.assertEqual(ORIENT.LEFT, bpp.break2.orient)
self.assertEqual('1', bpp.break1.chr)
self.assertEqual('2', bpp.break2.chr)
self.assertEqual('', bpp.untemplated_seq)
def test_read_pair_large_inversion_overlapping_query_coverage(self):
s = 'CTGAGCATGAAAGCCCTGTAAACACAGAATTTGGATTCTTTCCTGTTTGGTTCCTGGTCGTGAGTGGCAGGTGCCATCATGTTTCATTCTGCCTGAGAGCAGTCTACCTAAATATATAGCTCTGCTCACAGTTTCCCTGCAATGCATAATTAAAATAGCACTATGCAGTTGCTTACACTTCAGATAATGGCTTCCTACATATTGTTGGTTATGAAATTTCAGGGTTTTCATTTCTGTATGTTAAT'
read1 = MockRead(
reference_id=3,
reference_start=1114,
cigar=[(CIGAR.S, 125), (CIGAR.EQ, 120)],
query_sequence=s,
is_reverse=False,
)
read2 = MockRead(
reference_id=3,
reference_start=2187,
cigar=[(CIGAR.S, 117), (CIGAR.EQ, 8), (CIGAR.D, 1), (CIGAR.M, 120)],
query_sequence=reverse_complement(s),
is_reverse=True,
)
bpp = align.call_paired_read_event(read1, read2, is_stranded=True)
assert bpp.break1.strand == STRAND.POS
assert bpp.break2.strand == STRAND.NEG
assert bpp.break1.orient == ORIENT.RIGHT
assert bpp.break2.orient == ORIENT.RIGHT
assert bpp.untemplated_seq == ''
assert bpp.break1.start == 1115
assert bpp.break2.start == 2188 + 3
print(bpp.break1.seq)
print(bpp.break2.seq)
assert (
bpp.break1.seq
== 'TCACAGTTTCCCTGCAATGCATAATTAAAATAGCACTATGCAGTTGCTTACACTTCAGATAATGGCTTCCTACATATTGTTGGTTATGAAATTTCAGGGTTTTCATTTCTGTATGTTAAT'
)
assert (
bpp.break2.seq
== 'GCAGAGCTATATATTTAGGTAGACTGCTCTCAGGCAGAATGAAACATGATGGCACCTGCCACTCACGACCAGGAACCAAACAGGAAAGAATCCAAATTCTGTGTTTACAGGGCTTTCATGCTCAG'
)
def test_read_pair_inversion_overlapping_query_coverage(self):
# seq AAATTTCCCGGGAATTCCGGATCGATCGAT
# r1 AAATTTCCCGGGAATTCCGGAtcgatcgat +
# r2c aaatttcccgggaattccGGATCGATCGAT -
# i ------------------GGA---------
# r2 ATCTATCGATCCggaattcccgggaaattt 100+12 = 111 - 3 = 108
seq = 'AAATTTCCCGGGAATTCCGGATCGATCGAT' # 30
r1 = MockRead(
reference_id=0,
reference_name='1',
reference_start=0,
cigar=[(CIGAR.M, 21), (CIGAR.S, 9)],
query_sequence=seq,
is_reverse=False,
)
r2 = MockRead(
reference_id=0,
reference_name='1',
reference_start=99,
cigar=[(CIGAR.M, 12), (CIGAR.S, 18)],
query_sequence=reverse_complement(seq),
is_reverse=True,
)
bpp = align.call_paired_read_event(r1, r2, is_stranded=True)
assert bpp.break1.strand == STRAND.POS
assert bpp.break2.strand == STRAND.NEG
assert bpp.break1.orient == ORIENT.LEFT
assert bpp.break2.orient == ORIENT.LEFT
assert bpp.untemplated_seq == ''
assert bpp.break1.start == 21
assert bpp.break2.start == 108
assert bpp.break1.seq == 'AAATTTCCCGGGAATTCCGGA'
assert bpp.break2.seq == reverse_complement('TCGATCGAT')
def test_read_pair_deletion_overlapping_query_coverage(self):
# seq AAATTTCCCGGGAATTCCGGATCGATCGAT
# r1 AAATTTCCCGGGAATTCCGGAtcgatcgat
# r2 aaatttcccgggaattccGGATCGATCGAT
seq = 'AAATTTCCCGGGAATTCCGGATCGATCGAT' # 30
r1 = MockRead(
reference_id=0,
reference_name='1',
reference_start=0,
cigar=[(CIGAR.M, 21), (CIGAR.S, 9)],
query_sequence=seq,
is_reverse=False,
)
r2 = MockRead(
reference_id=0,
reference_name='1',
reference_start=99,
cigar=[(CIGAR.S, 18), (CIGAR.M, 12)],
query_sequence=seq,
is_reverse=False,
)
assert r1.reference_end == 21
bpp = align.call_paired_read_event(r1, r2, is_stranded=True)
assert bpp.break1.strand == STRAND.POS
assert bpp.break2.strand == STRAND.POS
assert bpp.break1.orient == ORIENT.LEFT
assert bpp.break2.orient == ORIENT.RIGHT
assert bpp.untemplated_seq == ''
assert bpp.break1.start == 21
assert bpp.break2.start == 103
assert bpp.break1.seq == 'AAATTTCCCGGGAATTCCGGA'
assert bpp.break2.seq == 'TCGATCGAT'
def test_read_pair_translocation(self):
# seq AAATTTCCCGGGAATTCCGGATCGATCGAT
# r1 AAATTTCCCGGGAATTCCGGAtcgatcgat
# r2 aaatttcccgggaattccggaTCGATCGAT
seq = 'AAATTTCCCGGGAATTCCGGATCGATCGAT' # 30
r1 = MockRead(
reference_id=0,
reference_name='2',
reference_start=0,
cigar=[(CIGAR.M, 21), (CIGAR.S, 9)],
query_sequence=seq,
is_reverse=False,
)
r2 = MockRead(
reference_id=0,
reference_name='1',
reference_start=99,
cigar=[(CIGAR.S, 21), (CIGAR.M, 9)],
query_sequence=seq,
is_reverse=False,
)
bpp = align.call_paired_read_event(r1, r2, is_stranded=True)
assert bpp.break1.strand == STRAND.POS
assert bpp.break2.strand == STRAND.POS
assert bpp.break1.orient == ORIENT.RIGHT
assert bpp.break2.orient == ORIENT.LEFT
assert bpp.break1.chr == '1'
assert bpp.break2.chr == '2'
assert bpp.untemplated_seq == ''
def test_read_pair_indel(self):
# seq AAATTTCCCGGGAATTCCGGATCGATCGAT 1-30 1-?
# r1 AAATTTCCCgggaattccggatcgatcgat 1-9 1-9
# r2 aaatttcccgggaattccggaTCGATCGAT 22-30 100-108
# i ---------GGGAATTCCGGA--------- 10-21 n/a
seq = 'AAATTTCCCGGGAATTCCGGATCGATCGAT' # 30
r1 = MockRead(
reference_id=0,
reference_name='1',
reference_start=0,
cigar=[(CIGAR.M, 9), (CIGAR.S, 21)],
query_sequence=seq,
is_reverse=False,
)
r2 = MockRead(
reference_id=0,
reference_name='1',
reference_start=99,
cigar=[(CIGAR.S, 21), (CIGAR.M, 9)],
query_sequence=seq,
is_reverse=False,
)
bpp = align.call_paired_read_event(r1, r2, is_stranded=True)
assert bpp.break1.strand == STRAND.POS
assert bpp.break2.strand == STRAND.POS
assert bpp.break1.orient == ORIENT.LEFT
assert bpp.break2.orient == ORIENT.RIGHT
assert bpp.untemplated_seq == 'GGGAATTCCGGA'
assert bpp.break1.start == 9
assert bpp.break2.start == 100
assert bpp.break1.seq == 'AAATTTCCC'
assert bpp.break2.seq == 'TCGATCGAT'
