def test_blat_contigs_deletion(self):
ev = GenomeEvidence(
Breakpoint('fake', 1714, orient=ORIENT.LEFT),
Breakpoint('fake', 2968, orient=ORIENT.RIGHT),
opposing_strands=False,
bam_cache=BAM_CACHE,
reference_genome=REFERENCE_GENOME,
read_length=40,
stdev_fragment_size=25,
median_fragment_size=100
)
ev.contigs = [
Contig(
'GGTATATATTTCTCAGATAAAAGATATTTTCCCTTTTATCTTTCCCTAAGCTCACACTACATATATTGCATTTATCTTATATCTGCTTTAAAACCTATTTAT'
'TATGTCATTTAAATATCTAGAAAAGTTATGACTTCACCAGGTATGAAAAATATAAAAAGAACTCTGTCAAGAAT', 0)
]
seq = align.align_sequences({'seq': ev.contigs[0].seq}, BAM_CACHE, REFERENCE_GENOME, aligner_reference=get_data('mock_reference_genome.2bit'), aligner='blat')
for query, reads in seq.items():
print('>>>', query)
for read in reads:
print(repr(read))
align.select_contig_alignments(ev, seq)
alignments = list(ev.contigs[0].alignments)
print('alignments:')
for aln in alignments:
print(aln, repr(aln.read1), repr(aln.read2))
self.assertEqual(1, len(alignments))
alignment = alignments[0]
self.assertTrue(alignment.read2 is None)
self.assertEqual(0, alignment.read1.reference_id)
self.assertTrue(not alignment.read1.is_reverse)
self.assertEqual(Interval(0, 175), align.query_coverage_interval(alignment.read1))
self.assertEqual(1612, alignment.read1.reference_start)
self.assertEqual([(CIGAR.EQ, 102), (CIGAR.D, 1253), (CIGAR.EQ, 74)], alignment.read1.cigar)
def setUp(self):
b1 = Breakpoint('1', 1051, 1051, 'L')
b2 = Breakpoint('1', 1551, 1551, 'R')
self.read_length = 50
self.trans_ev = TranscriptomeEvidence(
{}, # fake the annotations
b1,
b2,
None,
None, # bam_cache and reference_genome
opposing_strands=False,
read_length=self.read_length,
stdev_fragment_size=100,
median_fragment_size=100,
stdev_count_abnormal=1,
)
self.genomic_ev = GenomeEvidence(
b1,
b2,
None,
None, # bam_cache and reference_genome
opposing_strands=False,
read_length=self.read_length,
stdev_fragment_size=100,
median_fragment_size=100,
stdev_count_abnormal=1,
)
def test_blat_contigs(self):
ev = GenomeEvidence(
Breakpoint('reference3', 1114, orient=ORIENT.RIGHT),
Breakpoint('reference3', 2187, orient=ORIENT.RIGHT),
opposing_strands=True,
bam_cache=BAM_CACHE,
reference_genome=REFERENCE_GENOME,
read_length=40,
stdev_fragment_size=25,
median_fragment_size=100,
stdev_count_abnormal=2,
min_splits_reads_resolution=1,
min_flanking_pairs_resolution=1
)
ev.contigs = [
Contig(
'CTGAGCATGAAAGCCCTGTAAACACAGAATTTGGATTCTTTCCTGTTTGGTTCCTGGTCGTGAGTGGCAGGTGCCATCATGTTTCATTCTGCCTGAGAGCAG'
'TCTACCTAAATATATAGCTCTGCTCACAGTTTCCCTGCAATGCATAATTAAAATAGCACTATGCAGTTGCTTACACTTCAGATAATGGCTTCCTACATATTG'
'TTGGTTATGAAATTTCAGGGTTTTCATTTCTGTATGTTAAT', 0)
]
print(ev.contigs[0].seq)
seq = align.align_sequences({'seq': ev.contigs[0].seq}, BAM_CACHE, REFERENCE_GENOME, aligner_reference=get_data('mock_reference_genome.2bit'), aligner='blat')
print(seq)
align.select_contig_alignments(ev, seq)
print(ev.contigs[0].alignments)
alignment = list(ev.contigs[0].alignments)[0]
self.assertEqual(1, alignment.read1.reference_id)
self.assertEqual(1, alignment.read2.reference_id)
self.assertEqual(Interval(125, 244), align.query_coverage_interval(alignment.read1))
self.assertEqual(Interval(117, 244), align.query_coverage_interval(alignment.read2))
self.assertEqual(1114, alignment.read1.reference_start)
self.assertEqual(2187, alignment.read2.reference_start)
self.assertEqual([(CIGAR.S, 125), (CIGAR.EQ, 120)], alignment.read1.cigar)
self.assertEqual([(CIGAR.S, 117), (CIGAR.EQ, 128)], alignment.read2.cigar)
def test_blat_contigs_deletion_revcomp(self):
ev = GenomeEvidence(Breakpoint('fake', 1714, orient=ORIENT.LEFT),
Breakpoint('fake', 2968, orient=ORIENT.RIGHT),
opposing_strands=False,
bam_cache=BAM_CACHE,
reference_genome=REFERENCE_GENOME,
read_length=40,
stdev_fragment_size=25,
median_fragment_size=100)
seq = 'GGTATATATTTCTCAGATAAAAGATATTTTCCCTTTTATCTTTCCCTAAGCTCACACTACATATATTGCATTTATCTTATATCTGCTTTAAAACCTATTTAT' \
'TATGTCATTTAAATATCTAGAAAAGTTATGACTTCACCAGGTATGAAAAATATAAAAAGAACTCTGTCAAGAAT'
ev.contigs = [Contig(reverse_complement(seq), 0)]
align.select_contig_alignments(
ev,
align.align_sequences({'seq': ev.contigs[0].seq},
BAM_CACHE,
REFERENCE_GENOME,
aligner_reference=REFERENCE_GENOME_FILE_2BIT,
aligner='blat'))
print('alignments:', ev.contigs[0].alignments)
alignment = list(ev.contigs[0].alignments)[0]
print(alignment)
self.assertTrue(alignment.read2 is None)
self.assertEqual(0, alignment.read1.reference_id)
self.assertTrue(alignment.read1.is_reverse)
self.assertEqual(seq, alignment.read1.query_sequence)
self.assertEqual(Interval(0, 175),
align.query_coverage_interval(alignment.read1))
self.assertEqual(1612, alignment.read1.reference_start)
self.assertEqual([(CIGAR.EQ, 102), (CIGAR.D, 1253), (CIGAR.EQ, 74)],
alignment.read1.cigar)
class TestComputeFragmentSizes(unittest.TestCase):
def setUp(self):
b1 = Breakpoint('1', 1051, 1051, 'L')
b2 = Breakpoint('1', 1551, 1551, 'R')
self.read_length = 50
self.trans_ev = TranscriptomeEvidence(
{}, # fake the annotations
b1,
b2,
None,
None, # bam_cache and reference_genome
opposing_strands=False,
read_length=self.read_length,
stdev_fragment_size=100,
median_fragment_size=100,
stdev_count_abnormal=1,
)
self.genomic_ev = GenomeEvidence(
b1,
b2,
None,
None, # bam_cache and reference_genome
opposing_strands=False,
read_length=self.read_length,
stdev_fragment_size=100,
median_fragment_size=100,
stdev_count_abnormal=1)
def test_genomic_vs_trans_no_annotations(self):
# should be identical
read, mate = mock_read_pair(
MockRead('name',
'1',
1051 - self.read_length + 1,
1051,
is_reverse=False),
MockRead('name',
'1',
2300,
2300 + self.read_length - 1,
is_reverse=True))
self.assertEqual(self.trans_ev.compute_fragment_size(read, mate),
self.genomic_ev.compute_fragment_size(read, mate))
def test_reverse_reads(self):
read, mate = mock_read_pair(
MockRead('name', '1', 1001, 1100, is_reverse=False),
MockRead('name', '1', 2201, 2301, is_reverse=True))
self.assertEqual(Interval(1300),
self.genomic_ev.compute_fragment_size(read, mate))
self.assertEqual(Interval(1300),
self.genomic_ev.compute_fragment_size(mate, read))
self.assertEqual(Interval(1300),
self.trans_ev.compute_fragment_size(read, mate))
self.assertEqual(Interval(1300),
self.trans_ev.compute_fragment_size(mate, read))
def test_before_start(self, trans_window_setup):
b = Breakpoint(chr='1', start=100, orient=ORIENT.RIGHT)
assert transcriptome_window(
trans_window_setup.trans_evidence, b
) == GenomeEvidence.generate_window(trans_window_setup.genome_evidence, b)
b = Breakpoint(chr='1', start=500, orient=ORIENT.RIGHT)
assert transcriptome_window(
trans_window_setup.trans_evidence, b
) == GenomeEvidence.generate_window(trans_window_setup.genome_evidence, b)
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)
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_bwa_contigs(self):
ev = GenomeEvidence(
Breakpoint('reference3', 1114, orient=ORIENT.RIGHT),
Breakpoint('reference3', 2187, orient=ORIENT.RIGHT),
opposing_strands=True,
bam_cache=BAM_CACHE,
reference_genome=REFERENCE_GENOME,
read_length=40,
stdev_fragment_size=25,
median_fragment_size=100,
config={
'validate.stdev_count_abnormal': 2,
'validate.min_splits_reads_resolution': 1,
'validate.min_flanking_pairs_resolution': 1,
},
)
ev.contigs = [
Contig(
'CTGAGCATGAAAGCCCTGTAAACACAGAATTTGGATTCTTTCCTGTTTGGTTCCTGGTCGTGAGTGGCAGGTGCCATCATGTTTCATTCTGCCTGAGAGCAG'
'TCTACCTAAATATATAGCTCTGCTCACAGTTTCCCTGCAATGCATAATTAAAATAGCACTATGCAGTTGCTTACACTTCAGATAATGGCTTCCTACATATTG'
'TTGGTTATGAAATTTCAGGGTTTTCATTTCTGTATGTTAAT',
0,
)
]
print(ev.contigs[0].seq)
seq = align.align_sequences(
{'seq': ev.contigs[0].seq},
BAM_CACHE,
REFERENCE_GENOME,
aligner_reference=get_data('mock_reference_genome.fa'),
aligner='bwa mem',
aligner_output_file='mem.out',
aligner_fa_input_file='mem.in.fa',
)
align.select_contig_alignments(ev, seq)
print(ev.contigs[0].alignments)
alignment = list(ev.contigs[0].alignments)[0]
assert alignment.read2.query_sequence == reverse_complement(alignment.read1.query_sequence)
assert alignment.read1.reference_name == 'reference3'
assert alignment.read2.reference_name == 'reference3'
assert alignment.read1.reference_id == 1
assert alignment.read2.reference_id == 1
assert align.query_coverage_interval(alignment.read1) == Interval(125, 244)
assert align.query_coverage_interval(alignment.read2) == Interval(117, 244)
assert alignment.read1.reference_start == 1114
assert alignment.read2.reference_start == 2187
assert alignment.read1.cigar == [(CIGAR.S, 125), (CIGAR.EQ, 120)]
assert alignment.read2.cigar == [(CIGAR.S, 117), (CIGAR.EQ, 128)]
def test_orient_right(self):
bpp = Breakpoint(chr='1', start=1000, end=1000, orient=ORIENT.RIGHT)
window = GenomeEvidence.generate_window(
MockObject(read_length=100,
call_error=11,
max_expected_fragment_size=550), bpp)
self.assertEqual(890, window.start)
self.assertEqual(1560, window.end)
self.assertEqual(671, len(window))
def genomic_evidence(read_length):
return GenomeEvidence(
Breakpoint('1', 1051, 1051, 'L'),
Breakpoint('1', 1551, 1551, 'R'),
None,
None, # bam_cache and reference_genome
opposing_strands=False,
read_length=read_length,
stdev_fragment_size=100,
median_fragment_size=100,
config={'validate.stdev_count_abnormal': 1},
)
def flanking_ge(read_length):
return 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,
config={'validate.stdev_count_abnormal': 1, 'validate.call_error': 0},
)
def test_orient_right(self):
bpp = Breakpoint(chr='1', start=1000, end=1000, orient=ORIENT.RIGHT)
window = GenomeEvidence.generate_window(
MockObject(
read_length=100,
max_expected_fragment_size=550,
config={**DEFAULTS, 'validate.call_error': 11},
),
bpp,
)
assert window.start == 890
assert window.end == 1560
assert len(window) == 671
def test_blat_contigs_deletion_revcomp(self):
ev = GenomeEvidence(
Breakpoint('fake', 1714, orient=ORIENT.LEFT),
Breakpoint('fake', 2968, orient=ORIENT.RIGHT),
opposing_strands=False,
bam_cache=BAM_CACHE,
reference_genome=REFERENCE_GENOME,
read_length=40,
stdev_fragment_size=25,
median_fragment_size=100,
)
seq = (
'GGTATATATTTCTCAGATAAAAGATATTTTCCCTTTTATCTTTCCCTAAGCTCACACTACATATATTGCATTTATCTTATATCTGCTTTAAAACCTATTTAT'
'TATGTCATTTAAATATCTAGAAAAGTTATGACTTCACCAGGTATGAAAAATATAAAAAGAACTCTGTCAAGAAT'
)
ev.contigs = [Contig(reverse_complement(seq), 0)]
align.select_contig_alignments(
ev,
align.align_sequences(
{'seq': ev.contigs[0].seq},
BAM_CACHE,
REFERENCE_GENOME,
aligner_reference=get_data('mock_reference_genome.2bit'),
aligner='blat',
),
)
print('alignments:', ev.contigs[0].alignments)
alignment = list(ev.contigs[0].alignments)[0]
print(alignment)
assert alignment.read2 is None
assert alignment.read1.reference_id == 0
assert alignment.read1.is_reverse
assert alignment.read1.query_sequence == seq
assert align.query_coverage_interval(alignment.read1) == Interval(0, 175)
assert alignment.read1.reference_start == 1612
assert alignment.read1.cigar == [(CIGAR.EQ, 102), (CIGAR.D, 1253), (CIGAR.EQ, 74)]
def ev_gathering_setup():
return 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,
config={
'validate.stdev_count_abnormal': 3,
'validate.min_flanking_pairs_resolution': 3,
'validate.assembly_min_edge_trim_weight': 3,
},
)
def genome_evidence(self, break1, break2, opposing_strands):
ge = GenomeEvidence(
break1, break2, FULL_BAM_CACHE, REFERENCE_GENOME,
opposing_strands=opposing_strands,
read_length=125,
stdev_fragment_size=100,
median_fragment_size=380,
stdev_count_abnormal=3,
min_flanking_pairs_resolution=3,
max_sc_preceeding_anchor=3,
outer_window_min_event_size=0,
min_mapping_quality=20
)
print(ge.min_expected_fragment_size, ge.max_expected_fragment_size)
print(ge.break1.chr, ge.outer_window1)
print(ge.break1.chr, ge.inner_window1)
print(ge.break2.chr, ge.outer_window2)
print(ge.break2.chr, ge.inner_window2)
return ge
def test_window_accessors(self):
ge = GenomeEvidence(
Breakpoint('1', 1500, orient=ORIENT.LEFT),
Breakpoint('1', 6001, orient=ORIENT.RIGHT),
None,
None, # bam_cache and reference_genome
opposing_strands=False,
read_length=150,
stdev_fragment_size=500,
median_fragment_size=100,
config={'validate.stdev_count_abnormal': 1, 'validate.call_error': 0},
)
assert ge.outer_window1.start == 901
assert ge.outer_window1.end == 1649
assert ge.outer_window2.end == 6600
assert ge.outer_window2.start == 5852
assert ge.inner_window1.start == 1351
assert ge.inner_window1.end == 1649
assert ge.inner_window2.end == 6150
assert ge.inner_window2.start == 5852
def test_window_accessors(self):
ge = GenomeEvidence(
Breakpoint('1', 1500, orient=ORIENT.LEFT),
Breakpoint('1', 6001, orient=ORIENT.RIGHT),
None,
None, # bam_cache and reference_genome
opposing_strands=False,
read_length=150,
stdev_fragment_size=500,
median_fragment_size=100,
call_error=0,
stdev_count_abnormal=1)
self.assertEqual(901, ge.outer_window1.start)
self.assertEqual(1649, ge.outer_window1.end)
self.assertEqual(6600, ge.outer_window2.end)
self.assertEqual(5852, ge.outer_window2.start)
self.assertEqual(1351, ge.inner_window1.start)
self.assertEqual(1649, ge.inner_window1.end)
self.assertEqual(6150, ge.inner_window2.end)
self.assertEqual(5852, ge.inner_window2.start)
def test_left_after_transcript(self, tranverse_trans_rev_setup):
gpos = tranverse_trans_rev_setup.trans_evidence.traverse(2200, 100, ORIENT.LEFT)
assert GenomeEvidence.traverse(2200, 100, ORIENT.LEFT) == gpos
assert gpos == Interval(2100)
def test_left_after_transcript(self):
gpos = self.trans_evidence.traverse(2200, 100, ORIENT.LEFT)
self.assertEqual(gpos, GenomeEvidence.traverse(2200, 100, ORIENT.LEFT))
self.assertEqual(Interval(2100), gpos)
def test_intronic_long_exon(self, trans_window_setup):
b = Breakpoint(chr='1', start=2970, orient=ORIENT.RIGHT)
assert transcriptome_window(
trans_window_setup.trans_evidence, b
) == GenomeEvidence.generate_window(trans_window_setup.genome_evidence, b)
def genome_window(self, breakpoint):
return GenomeEvidence.generate_window(self.genome_evidence, breakpoint)
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))
def test_left_before_transcript(self, tranverse_trans_rev_setup):
gpos = tranverse_trans_rev_setup.trans_evidence.traverse(900, 500 - 1, ORIENT.LEFT)
assert gpos == Interval(401)
assert GenomeEvidence.traverse(900, 500 - 1, ORIENT.LEFT) == gpos
def test_left_before_transcript(self):
gpos = self.trans_evidence.traverse(900, 500 - 1, ORIENT.LEFT)
self.assertEqual(Interval(401), gpos)
self.assertEqual(gpos,
GenomeEvidence.traverse(900, 500 - 1, ORIENT.LEFT))
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)