def test_single_duplication_with_trailing_untemp(self):
r = MockRead(query_sequence=(
'GGATGATTTACCTTGGGTAATGAAACTCA'
'GATTTTGCTGTTGTTTTTGTTC'
'GATTTTGCTGTTGTTTTTGTTC'
'GTCAA'
'CAAAGTGTTTTATACTGATAAAGCAACCCCGGTTTAGCATTGCCATTGGTAA'),
query_name='duplication_with_untemp',
reference_id=2,
reference_name='reference3',
reference_start=1497,
cigar=[(CIGAR.EQ, 51), (CIGAR.I, 27), (CIGAR.EQ, 52)],
is_reverse=False)
# repeat: GATTTTGCTGTTGTTTTTGTTC
print(r)
print(REFERENCE_GENOME['reference3'][1497:1497 + 51])
print(REFERENCE_GENOME['reference3'][1548 - 21:1548 + 1])
bpp = align.call_read_events(r)[0]
print(bpp)
bpp = align.convert_to_duplication(bpp, REFERENCE_GENOME)
print(bpp)
self.assertEqual('GTCAA', bpp.untemplated_seq)
self.assertEqual(ORIENT.RIGHT, bpp.break1.orient)
self.assertEqual(ORIENT.LEFT, bpp.break2.orient)
self.assertEqual(bpp.break2.start, 1548)
self.assertEqual(bpp.break1.start, 1527)
def test_ins_and_del(self):
r = MockRead(
reference_id=0,
reference_name='1',
reference_start=0,
cigar=[(CIGAR.M, 10), (CIGAR.I, 3), (CIGAR.M, 5), (CIGAR.D, 7),
(CIGAR.M, 5)],
query_sequence='ACTGAATCGTGGGTAGCTGCTAG',
)
# only report the major del event for now
bpps = align.call_read_events(r)
self.assertEqual(2, len(bpps))
bpp = bpps[0]
self.assertEqual(False, bpp.opposing_strands)
self.assertEqual(10, bpp.break1.start)
self.assertEqual(10, bpp.break1.end)
self.assertEqual(11, bpp.break2.start)
self.assertEqual(11, bpp.break2.end)
self.assertEqual('GGG', bpp.untemplated_seq)
bpp = bpps[1]
self.assertEqual(False, bpp.opposing_strands)
self.assertEqual(15, bpp.break1.start)
self.assertEqual(15, bpp.break1.end)
self.assertEqual(23, bpp.break2.start)
self.assertEqual(23, bpp.break2.end)
def test_read_with_exons(self):
contig = MockRead(
query_sequence='CTTGAAGGAAACTGAATTCAAAAAGATCAAAGTGCTGGGCTCCGGTGCGTTCGGCACGGTGTATAAGGGACTCTGGATCCCAGAAGGTGAGAAAGTTAAAATTCCCGTCGCTATCAAGACATCTCCGAAAGCCAACAAGGAAATCCTCGATGAAGCCTACGTGATGGCCAGCGTGGACAACCCCCACGTGTGCCGCCTGCTGGGCATCTGCCTCACCTCCACCGTGCAGCTCATCATGCAGCTCATGCCCTTCGGCTGCCTCCTGGACTATGTCCGGGAACACAAAGACAATATTGGCTCCCAGTACCTGCTCAACTGGTGTGTGCAGATCGCAAAGGGCATGAACTACTTGGAGGACCGTCGCTTGGTGCACCGCGACCTGGCAGCCAGGAACGTACTGGTGAAAACACCGCAGCATGTCAAGATCACAGATTTTGGGCTGGCCAAACTGCTGGGTGCGGAAGAGAAAGAATACCATGCAGAAGGAGGCAAAGTGCCTATCAAGTGGATGGCATTGGAATCAATTTTACACAGAATCTATACCCACCAGAGTGATGTCTGGAGCTACGGGGTGACCGTTTGGGAGTTGATGACCTTTGGATCCAA',
cigar=_cigar.convert_string_to_cigar('68M678D50M15D34M6472D185M10240D158M891D74M8I5883D29M'),
reference_name='7',
reference_id=6,
reference_start=55241669
)
self.assertEqual(6, len(align.call_read_events(contig)))
def test_single_insertion(self):
r = MockRead(reference_id=0,
reference_name='1',
reference_start=0,
cigar=[(CIGAR.M, 10), (CIGAR.I, 8), (CIGAR.M, 5)],
query_sequence='ACTGAATCGTGGGTAGCTGCTAG')
bpp = align.call_read_events(r)[0]
self.assertEqual(False, bpp.opposing_strands)
self.assertEqual(10, bpp.break1.start)
self.assertEqual(10, bpp.break1.end)
self.assertEqual(11, bpp.break2.start)
self.assertEqual(11, bpp.break2.end)
self.assertEqual('GGGTAGCT', bpp.untemplated_seq)
def test_single_duplication(self):
r = MockRead(
name='seq1',
reference_name='gene3',
reference_start=27155,
cigar=[(CIGAR.M, 65), (CIGAR.I, 6), (CIGAR.D, 95), (CIGAR.M, 21), (CIGAR.S, 17)],
query_sequence='TAGTTGGATCTCTGTGCTGACTGACTGACAGACAGACTTTAGTGTCTGTGTGCTGACTGACAGACAGACTTTAGTGTCTGTGTGCTGACT'
'GACAGACTCTAGTAGTGTC'
)
bpp = align.call_read_events(r)[0]
self.assertEqual(27220, bpp.break1.start)
self.assertEqual(27316, bpp.break2.start)
self.assertEqual('AGACTT', bpp.untemplated_seq)
def test_hardclipping(self):
read = SamRead(reference_name='15')
read.reference_start = 71491944
read.cigar = _cigar.convert_string_to_cigar('12=1D25=113H')
read.query_sequence = 'GTGTGTGGTGTGGGGTGTGTGGTGTGTGTGGTGTGTG'
read.is_reverse = True
expected_bpp = BreakpointPair(
Breakpoint('15', 71491956, orient='L', strand='-'),
Breakpoint('15', 71491958, orient='R', strand='-'),
untemplated_seq='')
events = align.call_read_events(read, is_stranded=True)
self.assertEqual(1, len(events))
self.assertEqual(expected_bpp.break1, events[0].break1)
self.assertEqual(expected_bpp.break2, events[0].break2)
def test_single_insertion(self):
r = MockRead(
reference_id=0,
reference_name='1',
reference_start=0,
cigar=[(CIGAR.M, 10), (CIGAR.I, 8), (CIGAR.M, 5)],
query_sequence='ACTGAATCGTGGGTAGCTGCTAG',
)
bpp = align.call_read_events(r)[0]
assert bpp.opposing_strands is False
assert bpp.break1.start == 10
assert bpp.break1.end == 10
assert bpp.break2.start == 11
assert bpp.break2.end == 11
assert bpp.untemplated_seq == 'GGGTAGCT'
def test_single_one_event(self):
r = MockRead(reference_id=0,
reference_name='1',
reference_start=0,
cigar=[(CIGAR.M, 10), (CIGAR.I, 3), (CIGAR.D, 7),
(CIGAR.M, 10)],
query_sequence='ACTGAATCGTGGGTAGCTGCTAG')
bpps = align.call_read_events(r)
self.assertEqual(1, len(bpps))
bpp = bpps[0]
self.assertEqual(False, bpp.opposing_strands)
self.assertEqual(10, bpp.break1.start)
self.assertEqual(10, bpp.break1.end)
self.assertEqual(18, bpp.break2.start)
self.assertEqual(18, bpp.break2.end)
self.assertEqual('GGG', bpp.untemplated_seq)
def test_single_duplication_with_leading_untemp(self):
r = MockRead(
query_sequence=(
'CTCCCACCAGGAGCTCGTCCTCACCACGTCCTGCACCAGCACCTCCAGCTCCCGCAGCAGCGCCTCGCCCCCACGGTGCGCGCTCCGCGCCGGTTCC'
'ATGGGCTCCGTAGGTTCCATGGGCTCCGTAGGTTCCATGGGCTCCGTAGGTTCCATGGGCTCCGTAGGTTCCATCGGCTCCGTGGGTTCCATGGACT'
'CTGTGGGCTCGGGCCCGACGCGCACGGAGGACTGGAGGACTGGGGCGTGTGTCTGCGGTGCAGGCGAGGCGGGGCGGGC'),
query_name='duplication_with_untemp',
reference_id=16,
reference_name='reference17',
reference_start=1882,
cigar=[(CIGAR.EQ, 126), (CIGAR.I, 54), (CIGAR.EQ, 93)],
is_reverse=False)
bpp = align.call_read_events(r)[0]
self.assertEqual('AGGTTCCATGGGCTCCGTAGGTTCCATGGGCTCCGTAGGTTCCATCGGCTCCGT', bpp.untemplated_seq)
self.assertEqual(ORIENT.LEFT, bpp.break1.orient)
self.assertEqual(ORIENT.RIGHT, bpp.break2.orient)
def test_single_one_event(self):
r = MockRead(
reference_id=0,
reference_name='1',
reference_start=0,
cigar=[(CIGAR.M, 10), (CIGAR.I, 3), (CIGAR.D, 7), (CIGAR.M, 10)],
query_sequence='ACTGAATCGTGGGTAGCTGCTAG',
)
bpps = align.call_read_events(r)
assert len(bpps) == 1
bpp = bpps[0]
assert bpp.opposing_strands is False
assert bpp.break1.start == 10
assert bpp.break1.end == 10
assert bpp.break2.start == 18
assert bpp.break2.end == 18
assert bpp.untemplated_seq == 'GGG'
def test_single_duplication_with_no_untemp(self):
r = MockRead(query_sequence=(
'GGATGATTTACCTTGGGTAATGAAACTCAGATTTTGCTGTTGTTTTTGTTCGATTTTGCTGTTGTTTTTGTTCCAAAGTGTTTTATACTGATAAAGCAACC'
'CCGGTTTAGCATTGCCATTGGTAA'),
query_name='duplication_with_untemp',
reference_id=2,
reference_name='reference3',
reference_start=1497,
cigar=[(CIGAR.EQ, 51), (CIGAR.I, 22), (CIGAR.EQ, 52)],
is_reverse=False)
# repeat: GATTTTGCTGTTGTTTTTGTTC
bpp = align.convert_to_duplication(
align.call_read_events(r)[0], REFERENCE_GENOME)
self.assertEqual('', bpp.untemplated_seq)
self.assertEqual(ORIENT.RIGHT, bpp.break1.orient)
self.assertEqual(ORIENT.LEFT, bpp.break2.orient)
self.assertEqual(bpp.break2.start, 1548)
self.assertEqual(bpp.break1.start, 1527)
def test_ins_and_del(self):
r = MockRead(
reference_id=0,
reference_name='1',
reference_start=0,
cigar=[(CIGAR.M, 10), (CIGAR.I, 3), (CIGAR.M, 5), (CIGAR.D, 7), (CIGAR.M, 5)],
query_sequence='ACTGAATCGTGGGTAGCTGCTAG',
)
# only report the major del event for now
bpps = align.call_read_events(r)
assert len(bpps) == 2
bpp = bpps[0]
assert bpp.opposing_strands is False
assert bpp.break1.start == 10
assert bpp.break1.end == 10
assert bpp.break2.start == 11
assert bpp.break2.end == 11
assert bpp.untemplated_seq == 'GGG'
bpp = bpps[1]
assert bpp.opposing_strands is False
assert bpp.break1.start == 15
assert bpp.break1.end == 15
assert bpp.break2.start == 23
assert bpp.break2.end == 23
