class TestEvidenceGathering(unittest.TestCase):
def setUp(self):
# test loading of evidence for event found on reference3 1114 2187
self.ev1 = GenomeEvidence(Breakpoint('reference3',
1114,
orient=ORIENT.RIGHT),
Breakpoint('reference3',
2187,
orient=ORIENT.RIGHT),
BAM_CACHE,
REFERENCE_GENOME,
opposing_strands=True,
read_length=125,
stdev_fragment_size=100,
median_fragment_size=380,
stdev_count_abnormal=3,
min_flanking_pairs_resolution=3,
assembly_min_edge_trim_weight=3)
def test_collect_split_read(self):
ev1_sr = MockRead(
query_name='HISEQX1_11:3:1105:15351:25130:split',
reference_id=1,
cigar=[(4, 68), (7, 82)],
reference_start=1114,
reference_end=1154,
query_alignment_start=110,
query_sequence=
'TCGTGAGTGGCAGGTGCCATCGTGTTTCATTCTGCCTGAGAGCAGTCTACCTAAATATATAGCTCTGCTCACAGTTTCCCTGCAATGCATAATTAAAATAGCACTATGCAGTTGCTTACACTTCAGATAATGGCTTCCTACATATTGTTG',
query_alignment_end=150,
flag=113,
next_reference_id=1,
next_reference_start=2341)
self.ev1.collect_split_read(ev1_sr, True)
self.assertEqual(ev1_sr, list(self.ev1.split_reads[0])[0])
def test_collect_split_read_failure(self):
# wrong cigar string
ev1_sr = MockRead(
query_name='HISEQX1_11:4:1203:3062:55280:split',
reference_id=1,
cigar=[(7, 110), (7, 40)],
reference_start=1114,
reference_end=1154,
query_alignment_start=110,
query_sequence=
'CTGTAAACACAGAATTTGGATTCTTTCCTGTTTGGTTCCTGGTCGTGAGTGGCAGGTGCCATCGTGTTTCATTCTGCCTGAGAGCAGTCTACCTAAATATATAGCTCTGCTCACAGTTTCCCTGCAATGCATAATTAAAATAGCACTATG',
query_alignment_end=150,
flag=371,
next_reference_id=1,
next_reference_start=2550)
self.assertFalse(self.ev1.collect_split_read(ev1_sr, True))
def test_collect_flanking_pair(self):
self.ev1.collect_flanking_pair(
MockRead(reference_id=1,
reference_start=2214,
reference_end=2364,
is_reverse=True,
next_reference_id=1,
next_reference_start=1120,
mate_is_reverse=True),
MockRead(reference_id=1,
reference_start=1120,
reference_end=2364,
is_reverse=True,
next_reference_id=1,
next_reference_start=1120,
mate_is_reverse=True,
is_read1=False))
self.assertEqual(1, len(self.ev1.flanking_pairs))
def test_collect_flanking_pair_not_overlapping_evidence_window(self):
# first read in pair does not overlap the first evidence window
# therefore this should return False and not add to the flanking_pairs
pair = mock_read_pair(
MockRead(reference_id=1,
reference_start=1903,
reference_end=2053,
is_reverse=True),
MockRead(reference_id=1,
reference_start=2052,
reference_end=2053,
is_reverse=True))
self.assertFalse(self.ev1.collect_flanking_pair(*pair))
self.assertEqual(0, len(self.ev1.flanking_pairs))
# @unittest.skip("demonstrating skipping")
def test_load_evidence(self):
print(self.ev1)
self.ev1.load_evidence()
print(self.ev1.spanning_reads)
self.assertEqual(
2,
len([
r for r in self.ev1.split_reads[0]
if not r.has_tag(PYSAM_READ_FLAGS.TARGETED_ALIGNMENT)
]))
self.assertEqual(7, len(self.ev1.flanking_pairs))
self.assertEqual(
2,
len([
r for r in self.ev1.split_reads[1]
if not r.has_tag(PYSAM_READ_FLAGS.TARGETED_ALIGNMENT)
]))
# @unittest.skip("demonstrating skipping")
def test_assemble_split_reads(self):
sr1 = MockRead(
query_name='HISEQX1_11:3:1105:15351:25130:split',
query_sequence=
'TCGTGAGTGGCAGGTGCCATCGTGTTTCATTCTGCCTGAGAGCAGTCTACCTAAATATATAGCTCTGCTCACAGTTTCCCTGCAATGCATAATTAAAATAGCACTATGCAGTTGCTTACACTTCAGATAATGGCTTCCTACATATTGTTG',
flag=113)
sr2 = MockRead(
query_sequence=
'GTCGTGAGTGGCAGGTGCCATCGTGTTTCATTCTGCCTGAGAGCAGTCTACCTAAATATATAGCTCTGCTCACAGTTTCCCTGCAATGCATAATTAAAATAGCACTATGCAGTTGCTTACACTTCAGATAATGGCTTCCTACATATTGTT',
flag=121)
sr3 = MockRead(
query_sequence=
'TCGTGAGTGGCAGGTGCCATCGTGTTTCATTCTGCCTGAGAGCAGTCTACCTAAATATATAGCTCTGCTCACAGTTTCCCTGCAATGCATAATTAAAATAGCACTATGCAGTTGCTTACACTTCAGATAATGGCTTCCTACATATTGTTG',
flag=113)
sr7 = MockRead(
query_sequence=
'TGAAAGCCCTGTAAACACAGAATTTGGATTCTTTCCTGTTTGGTTCCTGGTCGTGAGTGGCAGGTGCCATCATGTTTCATTCTGCCTGAGAGCAGTCTACCTAAATATATAGCTCTGCTCACAGTTTCCCTGCAATGCATAATTAAAATA',
flag=113)
sr9 = MockRead(
query_sequence=
'TGTAAACACAGAATTTGGATTCTTTCCTGTTTGGTTCCTGGTCGTGAGTGGCAGGTGCCATCATGTTTCATTCTGCCTGAGAGCAGTCTACCTAAATATATAGCTCTGCTCACAGTTTCCCTGCAATGCATAATTAAAATAGCACTATGC',
flag=113)
sr12 = MockRead(
query_sequence=
'GATTCTTTCCTGTTTGGTTCCTGGTCGTGAGTGGCAGGTGCCATCATGTTTCATTCTGCCTGAGAGCAGTCTACCTAAATATATAGCTCTGCTCACAGTTTCCCTGCAATGCATAATTAAAATAGCACTATGCAGTTGCTTACACTTCAG',
flag=113)
sr15 = MockRead(
query_sequence=
'GTTCCTGGTCGTGAGTGGCAGGTGCCATCATGTTTCATTCTGCCTGAGAGCAGTCTACCTAAATATATAGCTCTGCTCACAGTTTCCCTGCAATGCATAATTAAAATAGCACTATGCAGTTGCTTACACTTCAGATAATGGCTTCCTACA',
flag=113)
sr19 = MockRead(
query_sequence=
'TGCCATCATGTTTCATTCTGCCTGAGAGCAGTCTACCTAAATATATAGCTCTGCTCACAGTTTCCCTGCAATGCATAATTAAAATAGCACTATGCAGTTGCTTACACTTCAGATAATGGCTTCCTACATATTGTTGGTTATGAAATTTCA',
flag=113)
sr24 = MockRead(
query_sequence=
'CTGAGAGCAGTCTACCTAAATATATAGCTCTGCTCACAGTTTCCCTGCAATGCATAATTAAAATAGCACTATGCAGTTGCTTACACTTCAGATAATGGCTTCCTACATATTGTTGGTTATGAAATTTCAGGGTTTTCATTTCTGTATGTT',
flag=113)
self.ev1.split_reads = ({sr1},
{sr1, sr3, sr7, sr9, sr12, sr15, sr19,
sr24}) # subset needed to make a contig
# self.ev1.split_reads=([],[sr1,sr3,sr5,sr6,sr7,sr8,sr9,sr10,sr11,sr12,sr13,sr14,sr15,sr16,sr17,sr18,sr19,sr20,sr21,sr22,sr23,sr24]) #full set of reads produces different contig from subset.
# full contig with more read support should be
# CTGAGCATGAAAGCCCTGTAAACACAGAATTTGGATTCTTTCCTGTTTGGTTCCTGGTCGTGAGTGGCAGGTGCCATCATGTTTCATTCTGCCTGAGAGCAGTCTACCTAAATATATAGCTCTGCTCACAGTTTCCCTGCAATGCATAATTAAAATAGCACTATGCAGTTGCTTACACTTCAGATAATGGCTTCCTACATATTGTTGGTTATGAAATTTCAGGGTTTTCATTTCTGTATGTTAAT
self.ev1.half_mapped = (set(), {sr2})
self.ev1.assemble_contig()
print(self.ev1.contigs)
exp = 'CAACAATATGTAGGAAGCCATTATCTGAAGTGTAAGCAACTGCATAGTGCTATTTTAATTATGCATTGCAGGGAAACTGTGAGCAGAGCTATATATTTAGGTAGACTGCTCTCAGGCAGAATGAAACATGATGGCACCTGCCACTCACGACCAGGAACCAAACAGGAAAGAATC'
self.assertEqual(exp, self.ev1.contigs[0].seq)
class TestGenomeEvidenceAddReads(unittest.TestCase):
def setUp(self):
self.ge = GenomeEvidence(
Breakpoint('1', 1500, orient=ORIENT.LEFT),
Breakpoint('1', 6001, orient=ORIENT.RIGHT),
BamCache(MockBamFileHandle({'1': 0})),
None, # reference_genome
opposing_strands=False,
read_length=150,
stdev_fragment_size=500,
median_fragment_size=100,
call_error=0,
stdev_count_abnormal=1,
)
# outer windows (901, 1649) (5852, 6600)
# inner windows (1351, 1649) (5852, 6150)
def test_collect_flanking_pair_error_unmapped_read(self):
read, mate = mock_read_pair(
MockRead('test', 0, 900, 1000, is_reverse=False),
MockRead('test', 0, 6000, 6099, is_reverse=True),
)
read.is_unmapped = True
with self.assertRaises(ValueError):
self.ge.collect_flanking_pair(read, mate)
def test_collect_flanking_pair_error_mate_unmapped(self):
read, mate = mock_read_pair(
MockRead('test', 0, 900, 1000, is_reverse=False),
MockRead('test', 0, 6000, 6099, is_reverse=True),
)
mate.is_unmapped = True
with self.assertRaises(ValueError):
self.ge.collect_flanking_pair(read, mate)
def test_collect_flanking_pair_error_query_names_dont_match(self):
read, mate = mock_read_pair(
MockRead('test1', 0, 900, 1000, is_reverse=False),
MockRead('test', 0, 6000, 6099, is_reverse=True),
)
with self.assertRaises(ValueError):
self.ge.collect_flanking_pair(read, mate)
def test_collect_flanking_pair_error_template_lengths_dont_match(self):
read, mate = mock_read_pair(
MockRead('test',
0,
900,
1000,
is_reverse=False,
template_length=50),
MockRead('test', 0, 6000, 6099, is_reverse=True),
)
mate.template_length = 55
with self.assertRaises(ValueError):
self.ge.collect_flanking_pair(read, mate)
def test_collect_flanking_pair_read_low_mq(self):
read, mate = mock_read_pair(
MockRead('test', 0, 900, 1000, is_reverse=False),
MockRead('test', 0, 6000, 6099, is_reverse=True),
)
read.mapping_quality = 0
self.assertFalse(self.ge.collect_flanking_pair(read, mate))
def test_collect_flanking_pair_mate_low_mq(self):
read, mate = mock_read_pair(
MockRead('test', 0, 900, 1000, is_reverse=False),
MockRead('test', 0, 6000, 6099, is_reverse=True),
)
mate.mapping_quality = 0
self.assertFalse(self.ge.collect_flanking_pair(read, mate))
def test_collect_flanking_pair_interchromosomal(self):
read, mate = mock_read_pair(
MockRead('test', 1, 900, 1000, is_reverse=False),
MockRead('test', 0, 6000, 6099, is_reverse=True),
)
self.assertFalse(self.ge.collect_flanking_pair(read, mate))
