def setUp(self):
self.contig = Contig(' ' * 60, None)
self.contig.add_mapped_sequence(
MockObject(reference_start=0, reference_end=10))
self.contig.add_mapped_sequence(
MockObject(reference_start=0, reference_end=20))
self.contig.add_mapped_sequence(
MockObject(reference_start=50, reference_end=60))
def test_drop_similar_different_lengths(self):
c1 = Contig(
'atcgatcgatcgatcgatatcgatcgatcgatcgatatcgatcgatcgatcgatatcgatcgatcgatcgatcgatcgatatgggcatcagc',
2)
c2 = Contig(
'atcgatcgatcgatcgatatcgatcgatcgatcgatatcgatcgatcgatcgatatcgatcgatcgatcgatcgatcgatagggcatcagc',
1)
result = filter_contigs([c2, c1], 0.10)
self.assertEqual(1, len(result))
self.assertEqual(c1.seq, result[0].seq)
def test_drop_similar_different_lengths(self):
c1 = Contig(
'atcgatcgatcgatcgatatcgatcgatcgatcgatatcgatcgatcgatcgatatcgatcgatcgatcgatcgatcgatatgggcatcagc',
2,
)
c2 = Contig(
'atcgatcgatcgatcgatatcgatcgatcgatcgatatcgatcgatcgatcgatatcgatcgatcgatcgatcgatcgatagggcatcagc',
1,
)
result = filter_contigs([c2, c1], 0.10)
assert len(result) == 1
assert result[0].seq == c1.seq
class TestBreakpointContigRemappedDepth(unittest.TestCase):
def setUp(self):
self.contig = Contig(' ' * 60, None)
self.contig.add_mapped_sequence(MockObject(reference_start=0, reference_end=10))
self.contig.add_mapped_sequence(MockObject(reference_start=0, reference_end=20))
self.contig.add_mapped_sequence(MockObject(reference_start=50, reference_end=60))
def test_break_left_deletion(self):
b = Breakpoint('10', 1030, 1030, orient=ORIENT.LEFT)
read = MockRead(
cigar=_cigar.convert_string_to_cigar('35M10D5I20M'),
reference_start=999,
reference_name='10'
)
align.SplitAlignment.breakpoint_contig_remapped_depth(b, self.contig, read)
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)
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(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 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_break_left_deletion(self):
contig = Contig(' ' * 60, None)
contig.add_mapped_sequence(MockObject(reference_start=0, reference_end=10))
contig.add_mapped_sequence(MockObject(reference_start=0, reference_end=20))
contig.add_mapped_sequence(MockObject(reference_start=50, reference_end=60))
b = Breakpoint('10', 1030, 1030, orient=ORIENT.LEFT)
read = MockRead(
cigar=_cigar.convert_string_to_cigar('35M10D5I20M'),
reference_start=999,
reference_name='10',
)
align.SplitAlignment.breakpoint_contig_remapped_depth(b, contig, read)
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 test_retain_disimilar_different_lengths(self):
c1 = Contig('atcgatcgatcgatcgatcgatcgatatagggcatcagc', 2)
c2 = Contig('atcgatcgatcgatcgatcgatcccgtgatatagggcatcagc', 1)
result = filter_contigs([c2, c1], 0.10)
self.assertEqual(2, len(result))
def test_retain_disimilar(self):
c1 = Contig('atcgatcgatcgatcgatcgatcgatatagggcatcagc', 2)
c2 = Contig('atcgadatcgatcgatcgatctgtdstcgatatagggca', 1)
result = filter_contigs([c2, c1], 0.10)
self.assertEqual(2, len(result))
def test_drop_alt_allele_by_score(self):
c1 = Contig('atcgatcgatcgatcgatcgatcgatatagggcatcagc', 2)
c2 = Contig('atcgatcgatcgatcgatctatcgatatagggcatcagc', 1)
result = filter_contigs([c2, c1], 0.10)
self.assertEqual(1, len(result))
self.assertEqual(c1.seq, result[0].seq)
def test_drop_reverse_complement(self):
c1 = Contig('atcgatcgatcgatcgatcgatcgatatagggcatcagc', 1)
c2 = Contig('gctgatgccctatatcgatcgatcgatcgatcgatcgat', 1)
result = filter_contigs([c2, c1], 0.10)
self.assertEqual(1, len(result))
self.assertEqual(c1.seq, result[0].seq)
def test_drop_alt_allele_by_score(self):
c1 = Contig('atcgatcgatcgatcgatcgatcgatatagggcatcagc', 2)
c2 = Contig('atcgatcgatcgatcgatctatcgatatagggcatcagc', 1)
result = filter_contigs([c2, c1], 0.10)
assert len(result) == 1
assert result[0].seq == c1.seq
def test_drop_reverse_complement(self):
c1 = Contig('atcgatcgatcgatcgatcgatcgatatagggcatcagc', 1)
c2 = Contig('gctgatgccctatatcgatcgatcgatcgatcgatcgat', 1)
result = filter_contigs([c2, c1], 0.10)
assert len(result) == 1
assert result[0].seq == c1.seq