def test_complex_alignment(self):
cigar = [
(CIGAR.M, 137),
(CIGAR.D, 14823),
(CIGAR.M, 19),
(CIGAR.D, 1),
(CIGAR.M, 5),
(CIGAR.I, 18),
(CIGAR.D, 18),
(CIGAR.M, 16),
(CIGAR.I, 1),
(CIGAR.D, 120),
(CIGAR.M, 22),
(CIGAR.S, 147),
]
read = Mock(cigar=cigar, query_sequence='A' * 365, reference_start=88217410)
with pytest.raises(NotImplementedError):
_read.convert_events_to_softclipping(read, ORIENT.LEFT, 50, 50)
read.cigar = [(CIGAR.EQ if x == CIGAR.M else x, y) for x, y in read.cigar]
converted = _read.convert_events_to_softclipping(read, ORIENT.LEFT, 50, 50)
assert converted.cigar == [(CIGAR.EQ, 137), (CIGAR.S, 365 - 137)]
converted = _read.convert_events_to_softclipping(read, ORIENT.RIGHT, 50, 100)
assert converted.cigar == read.cigar
def test_left_combined_small_events(self):
read = Mock(cigar=[(CIGAR.EQ, 10), (CIGAR.D, 6), (CIGAR.I, 5),
(CIGAR.EQ, 35)],
query_sequence='A' * 50)
converted = _read.convert_events_to_softclipping(
read, ORIENT.LEFT, 10, 10)
self.assertEqual([(CIGAR.EQ, 10), (CIGAR.S, 40)], converted.cigar)
def test_left_anchor_after_event(self):
read = Mock(
cigar=[(CIGAR.EQ, 4), (CIGAR.D, 10), (CIGAR.EQ, 40), (CIGAR.D, 10), (CIGAR.EQ, 6)],
query_sequence='A' * 50,
)
converted = _read.convert_events_to_softclipping(read, ORIENT.LEFT, 5, 5)
assert converted.cigar == [(CIGAR.EQ, 4), (CIGAR.D, 10), (CIGAR.EQ, 40), (CIGAR.S, 6)]
def test_right_large_deletion(self):
read = Mock(cigar=[(CIGAR.EQ, 10), (CIGAR.D, 10), (CIGAR.EQ, 40)],
query_sequence='A' * 50,
reference_start=100)
converted = _read.convert_events_to_softclipping(
read, ORIENT.RIGHT, 5, 5)
self.assertEqual([(CIGAR.S, 10), (CIGAR.EQ, 40)], converted.cigar)
self.assertEqual(read.reference_start + 20, converted.reference_start)
def test_right_anchor_after_event(self):
read = Mock(
cigar=[(CIGAR.EQ, 6), (CIGAR.D, 10), (CIGAR.EQ, 40), (CIGAR.D, 10), (CIGAR.EQ, 4)],
query_sequence='A' * 50,
reference_start=100,
)
converted = _read.convert_events_to_softclipping(read, ORIENT.RIGHT, 5, 5)
assert converted.cigar == [(CIGAR.S, 6), (CIGAR.EQ, 40), (CIGAR.D, 10), (CIGAR.EQ, 4)]
assert converted.reference_start == read.reference_start + 16
def test_multiple_events(self):
cigar = [(CIGAR.EQ, 18), (CIGAR.X, 1), (CIGAR.EQ, 30), (CIGAR.D, 8146),
(CIGAR.EQ, 10), (CIGAR.D, 62799), (CIGAR.EQ, 28),
(CIGAR.D, 2), (CIGAR.EQ, 27), (CIGAR.S, 77)]
qlen = sum([v for c, v in cigar if c in _cigar.QUERY_ALIGNED_STATES])
read = Mock(cigar=cigar,
query_sequence=('N' * qlen),
reference_start=1000)
converted = _read.convert_events_to_softclipping(
read, ORIENT.RIGHT, 50, 50)
exp = [(CIGAR.S, 59), (CIGAR.EQ, 28), (CIGAR.D, 2), (CIGAR.EQ, 27),
(CIGAR.S, 77)]
self.assertEqual(exp, converted.cigar)
def test_multiple_left_with_ins(self):
cigar = [(4, 94), (7, 1), (8, 1), (7, 10), (8, 1), (7, 4), (1, 2),
(7, 40), (1, 1), (2, 714), (7, 7), (1, 38), (7, 1), (8, 1),
(7, 17), (2, 1), (7, 1), (8, 1), (7, 26), (2, 17), (7, 10),
(4, 4)]
exp = [(4, 94), (7, 1), (8, 1), (7, 10), (8, 1), (7, 4), (1, 2),
(7, 40), (4, 38 + 8 + 20 + 1 + 26 + 10 + 4)]
qlen = sum([v for c, v in cigar if c in _cigar.QUERY_ALIGNED_STATES])
read = Mock(cigar=cigar,
query_sequence=('N' * qlen),
reference_start=1000)
converted = _read.convert_events_to_softclipping(
read, ORIENT.LEFT, 50, 50)
self.assertEqual(exp, converted.cigar)
def test_left_all_mismatch_error(self):
read = Mock(cigar=[(CIGAR.X, 10), (CIGAR.D, 10), (CIGAR.X, 40)],
query_sequence='A' * 50)
converted = _read.convert_events_to_softclipping(
read, ORIENT.LEFT, 5, 5)
self.assertEqual(read, converted)
def test_left_large_deletion(self):
read = Mock(cigar=[(CIGAR.EQ, 10), (CIGAR.D, 10), (CIGAR.EQ, 40)],
query_sequence='A' * 50)
converted = _read.convert_events_to_softclipping(
read, ORIENT.LEFT, 5, 5)
self.assertEqual([(CIGAR.EQ, 10), (CIGAR.S, 40)], converted.cigar)
