def test_read_pair_inversion_overlapping_query_coverage(self):
# seq AAATTTCCCGGGAATTCCGGATCGATCGAT
# r1 AAATTTCCCGGGAATTCCGGAtcgatcgat +
# r2c aaatttcccgggaattccGGATCGATCGAT -
# i ------------------GGA---------
# r2 ATCTATCGATCCggaattcccgggaaattt 100+12 = 111 - 3 = 108
seq = 'AAATTTCCCGGGAATTCCGGATCGATCGAT' # 30
r1 = MockRead(
reference_id=0,
reference_name='1',
reference_start=0,
cigar=[(CIGAR.M, 21), (CIGAR.S, 9)],
query_sequence=seq,
is_reverse=False,
)
r2 = MockRead(
reference_id=0,
reference_name='1',
reference_start=99,
cigar=[(CIGAR.M, 12), (CIGAR.S, 18)],
query_sequence=reverse_complement(seq),
is_reverse=True,
)
bpp = align.call_paired_read_event(r1, r2, is_stranded=True)
assert bpp.break1.strand == STRAND.POS
assert bpp.break2.strand == STRAND.NEG
assert bpp.break1.orient == ORIENT.LEFT
assert bpp.break2.orient == ORIENT.LEFT
assert bpp.untemplated_seq == ''
assert bpp.break1.start == 21
assert bpp.break2.start == 108
assert bpp.break1.seq == 'AAATTTCCCGGGAATTCCGGA'
assert bpp.break2.seq == reverse_complement('TCGATCGAT')
def test_read_pair_inversion_gap_in_query_coverage(self):
# seq AAATTTCCCGGGAATTCCGGATCGATCGAT
# r1 AAATTTCCCGGGAATTccggatcgatcgat +
# r2c aaatttcccgggaattccGGATCGATCGAT -
# i ----------------CC------------
# r2 ATCTATCGATCCggaattcccgggaaattt 100+12 = 111 - 3 = 108
seq = 'AAATTTCCCGGGAATTCCGGATCGATCGAT' # 30
r1 = MockRead(reference_id=0,
reference_name='1',
reference_start=0,
cigar=[(CIGAR.M, 16), (CIGAR.S, 14)],
query_sequence=seq,
is_reverse=False)
r2 = MockRead(reference_id=0,
reference_name='1',
reference_start=99,
cigar=[(CIGAR.M, 12), (CIGAR.S, 18)],
query_sequence=reverse_complement(seq),
is_reverse=True)
bpp = align.call_paired_read_event(r1, r2)
self.assertEqual(STRAND.POS, bpp.break1.strand)
self.assertEqual(STRAND.NEG, bpp.break2.strand)
self.assertEqual(ORIENT.LEFT, bpp.break1.orient)
self.assertEqual(ORIENT.LEFT, bpp.break2.orient)
self.assertEqual('CC', bpp.untemplated_seq)
self.assertEqual(16, bpp.break1.start)
self.assertEqual(111, bpp.break2.start)
self.assertEqual('AAATTTCCCGGGAATT', bpp.break1.seq)
self.assertEqual(reverse_complement('GGATCGATCGAT'), bpp.break2.seq)
def test_read_pair_large_inversion_overlapping_query_coverage(self):
s = 'CTGAGCATGAAAGCCCTGTAAACACAGAATTTGGATTCTTTCCTGTTTGGTTCCTGGTCGTGAGTGGCAGGTGCCATCATGTTTCATTCTGCCTGAGAGCAGTCTACCTAAATATATAGCTCTGCTCACAGTTTCCCTGCAATGCATAATTAAAATAGCACTATGCAGTTGCTTACACTTCAGATAATGGCTTCCTACATATTGTTGGTTATGAAATTTCAGGGTTTTCATTTCTGTATGTTAAT'
read1 = MockRead(reference_id=3,
reference_start=1114,
cigar=[(CIGAR.S, 125), (CIGAR.EQ, 120)],
query_sequence=s,
is_reverse=False)
read2 = MockRead(reference_id=3,
reference_start=2187,
cigar=[(CIGAR.S, 117), (CIGAR.EQ, 8), (CIGAR.D, 1),
(CIGAR.M, 120)],
query_sequence=reverse_complement(s),
is_reverse=True)
bpp = align.call_paired_read_event(read1, read2)
self.assertEqual(STRAND.POS, bpp.break1.strand)
self.assertEqual(STRAND.NEG, bpp.break2.strand)
self.assertEqual(ORIENT.RIGHT, bpp.break1.orient)
self.assertEqual(ORIENT.RIGHT, bpp.break2.orient)
self.assertEqual('', bpp.untemplated_seq)
self.assertEqual(1115, bpp.break1.start)
self.assertEqual(2188 + 3, bpp.break2.start)
print(bpp.break1.seq)
print(bpp.break2.seq)
self.assertEqual(
'TCACAGTTTCCCTGCAATGCATAATTAAAATAGCACTATGCAGTTGCTTACACTTCAGATAATGGCTTCCTACATATTGTTGGTTATGAAATTTCAG'
'GGTTTTCATTTCTGTATGTTAAT', bpp.break1.seq)
self.assertEqual(
'GCAGAGCTATATATTTAGGTAGACTGCTCTCAGGCAGAATGAAACATGATGGCACCTGCCACTCACGACCAGGAACCAAACAGGAAAGAATCCA'
'AATTCTGTGTTTACAGGGCTTTCATGCTCAG', bpp.break2.seq)
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_inversion_and_deletion(self):
s = 'CTGAGCATGAAAGCCCTGTAAACACAGAATTTGGATTCTTTCCTGTTTGGTTCCTGGTCGTGAGTGGCAGGTGCCATCATGTTTCATTCTGCCTGAGAGCAGTCTACCTAAATATATAGCTCTGCTCACAGTTTCCCTGCAATGCATAATTAAAATAGCACTATGCAGTTGCTTACACTTCAGATAATGGCTTCCTACATATTGTTGGTTATGAAATTTCAGGGTTTTCATTTCTGTATGTTAAT'
evidence = MockObject(
interchromosomal=False,
opposing_strands=True,
break1=MockObject(orient=ORIENT.RIGHT, chr='3'),
break2=MockObject(orient=ORIENT.RIGHT, chr='3'),
contigs=[MockObject(seq=s, alignments=set())],
standardize_read=lambda x: x,
contig_aln_max_event_size=DEFAULTS.contig_aln_max_event_size,
contig_aln_merge_inner_anchor=5,
contig_aln_merge_outer_anchor=DEFAULTS.contig_aln_merge_outer_anchor,
contig_aln_min_query_consumption=0.9,
contig_aln_min_extend_overlap=DEFAULTS.contig_aln_min_extend_overlap,
contig_aln_min_anchor_size=DEFAULTS.contig_aln_min_anchor_size,
contig_aln_min_score=DEFAULTS.contig_aln_min_score,
outer_window1=Interval(1000, 1200),
outer_window2=Interval(2000, 2200),
reference_genome=None,
bam_cache=mock.Mock(stranded=False)
)
read1 = SamRead(
reference_id=3, reference_start=1114, cigar=[(CIGAR.S, 125), (CIGAR.EQ, 120)], query_sequence=s,
is_reverse=False, reference_name='3', alignment_rank=0
)
read2 = SamRead(
reference_id=3, reference_start=2187, cigar=[(CIGAR.S, 117), (CIGAR.EQ, 8), (CIGAR.D, 1), (CIGAR.EQ, 120)],
query_sequence=reverse_complement(s), is_reverse=True, reference_name='3', alignment_rank=1
)
raw_alignments = {s: [read1, read2]}
align.select_contig_alignments(evidence, raw_alignments)
alignments = list(evidence.contigs[0].alignments)
self.assertEqual(2, len(alignments))
def test_gimap4_reverse(self):
gimap4 = EXAMPLE_GENES['GIMAP4']
gimap4_seq = reverse_complement(gimap4.seq)
donors = predict_splice_sites(gimap4_seq, True)
for d in donors:
assert gimap4_seq[d.start - 1:d.end] == d.seq
assert len(donors) == 5
def test_read_pair_large_inversion_overlapping_query_coverage(self):
s = 'CTGAGCATGAAAGCCCTGTAAACACAGAATTTGGATTCTTTCCTGTTTGGTTCCTGGTCGTGAGTGGCAGGTGCCATCATGTTTCATTCTGCCTGAGAGCAGTCTACCTAAATATATAGCTCTGCTCACAGTTTCCCTGCAATGCATAATTAAAATAGCACTATGCAGTTGCTTACACTTCAGATAATGGCTTCCTACATATTGTTGGTTATGAAATTTCAGGGTTTTCATTTCTGTATGTTAAT'
read1 = MockRead(
reference_id=3,
reference_start=1114,
cigar=[(CIGAR.S, 125), (CIGAR.EQ, 120)],
query_sequence=s,
is_reverse=False,
)
read2 = MockRead(
reference_id=3,
reference_start=2187,
cigar=[(CIGAR.S, 117), (CIGAR.EQ, 8), (CIGAR.D, 1), (CIGAR.M, 120)],
query_sequence=reverse_complement(s),
is_reverse=True,
)
bpp = align.call_paired_read_event(read1, read2, is_stranded=True)
assert bpp.break1.strand == STRAND.POS
assert bpp.break2.strand == STRAND.NEG
assert bpp.break1.orient == ORIENT.RIGHT
assert bpp.break2.orient == ORIENT.RIGHT
assert bpp.untemplated_seq == ''
assert bpp.break1.start == 1115
assert bpp.break2.start == 2188 + 3
print(bpp.break1.seq)
print(bpp.break2.seq)
assert (
bpp.break1.seq
== 'TCACAGTTTCCCTGCAATGCATAATTAAAATAGCACTATGCAGTTGCTTACACTTCAGATAATGGCTTCCTACATATTGTTGGTTATGAAATTTCAGGGTTTTCATTTCTGTATGTTAAT'
)
assert (
bpp.break2.seq
== 'GCAGAGCTATATATTTAGGTAGACTGCTCTCAGGCAGAATGAAACATGATGGCACCTGCCACTCACGACCAGGAACCAAACAGGAAAGAATCCAAATTCTGTGTTTACAGGGCTTTCATGCTCAG'
)
def test_gimap4_reverse(self):
gimap4 = EXAMPLE_GENES['GIMAP4']
gimap4_seq = reverse_complement(gimap4.seq)
donors = predict_splice_sites(gimap4_seq, True)
for d in donors:
self.assertEqual(d.seq, gimap4_seq[d.start - 1:d.end])
self.assertEqual(5, len(donors))
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,
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.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]
self.assertEqual(reverse_complement(alignment.read1.query_sequence),
alignment.read2.query_sequence)
self.assertEqual('reference3', alignment.read1.reference_name)
self.assertEqual('reference3', alignment.read2.reference_name)
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_simple(self):
row = {
'match': 142,
'mismatch': 0,
'repmatch': 0,
'ncount': 0,
'qgap_count': 0,
'qgap_bases': 0,
'tgap_count': 0,
'tgap_bases': 0,
'strand': '-',
'qname': 'seq1',
'qsize': 204,
'qstart': 0,
'qend': 142,
'tname': '17',
'tsize': 81195210,
'tstart': 32673408,
'tend': 32673550,
'block_count': 1,
'block_sizes': [142],
'qstarts': [62],
'tstarts': [32673408],
'_index': 880,
'score': 142,
'percent_ident': 100.0,
'qseq_full': (
'ACATGTGCACAACGTGCAGGTTTGTTACATATGTATACATGTGCCATGTTGGTTTGCTGCACCCATTAACTCGTCCTAGTTTATTACTAGTCTTCAGACATC'
'CAGAAAATAGAGTAAGATACTAGGTAGACATAACACCTAGATACATCCGTAAGGCATTTGTTTCCTATCACATGGCCCATTCTAGCTTAACACCCACCAACT'
)}
refseq = {'17': Mock(seq=MockLongString(
'ACTAGGTGTTATGTCTACCTAGTATCTTACTCTATTTTCTGGATGTCTGAAGACTAGTAATAAACTAGGACGAGTTAATGGGTGCAGCAAACCAACATGGCACATG'
'TATACATATGTAACAAACCTGCACGTTGTGCACATGTACCCTAAAACTTAAAGTATAAAAAAAAATTTCACTGAGCATAAGACTTCAGACACAAAAGAGTGCATGC'
'CATATAATTCCATTTATGTGAATTTCAAGAACAATCAGTGATGACAGAAGTCAAAGTAGTGGTCACCTCTGGAAGGTGGGACATTGACC',
32673407))}
cache = Mock(reference_id=MockFunction(16))
read = Blat.pslx_row_to_pysam(row, cache, refseq)
self.assertEqual(16, read.reference_id)
self.assertEqual('17', read.reference_name)
self.assertEqual(row['qseq_full'], reverse_complement(read.query_sequence))
self.assertEqual([(CIGAR.S, 62), (CIGAR.EQ, 142)], read.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=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_pslx_row_to_pysam_inversion(self):
s = 'CTGAGCATGAAAGCCCTGTAAACACAGAATTTGGATTCTTTCCTGTTTGGTTCCTGGTCGTGAGTGGCAGGTGCCATCATGTTTCATTCTGCCTGAGAGCAGTCTACCTAAATATATAGCTCTGCTCACAGTTTCCCTGCAATGCATAATTAAAATAGCACTATGCAGTTGCTTACACTTCAGATAATGGCTTCCTACATATTGTTGGTTATGAAATTTCAGGGTTTTCATTTCTGTATGTTAAT'
# first part of the inversion
pslx_row = {
'block_count':
1,
'tstarts': [1114],
'block_sizes': [120],
'qname':
'seq1',
'tname':
'reference3',
'qstarts': [125],
'strand':
'+',
'qseq_full':
s,
'score':
1,
'qseqs': [
'TCACAGTTTCCCTGCAATGCATAATTAAAATAGCACTATGCAGTTGCTTACACTTCAGATAATGGCTTCCTACATATTGTTGGTTATGAAATTTCAGGG'
'TTTTCATTTCTGTATGTTAAT'
],
'tseqs': [
'TCACAGTTTCCCTGCAATGCATAATTAAAATAGCACTATGCAGTTGCTTACACTTCAGATAATGGCTTCCTACATATTGTTGGTTATGAAATTTCAGGG'
'TTTTCATTTCTGTATGTTAAT'
],
}
read1 = Blat.pslx_row_to_pysam(pslx_row, self.cache, REFERENCE_GENOME)
self.assertEqual(3, read1.reference_id)
self.assertEqual(Interval(125, 244), query_coverage_interval(read1))
self.assertEqual(1114, read1.reference_start)
self.assertEqual([(CIGAR.S, 125), (CIGAR.EQ, 120)], read1.cigar)
# second part of the inversion
pslx_row = {
'block_count':
1,
'tstarts': [2187],
'block_sizes': [128],
'qname':
'seq1',
'tname':
'reference3',
'qstarts': [117],
'strand':
'-',
'qseq_full':
s,
'score':
1,
'qseqs': [
'TGAGCAGAGCTATATATTTAGGTAGACTGCTCTCAGGCAGAATGAAACATGATGGCACCTGCCACTCACGACCAGGAACCAAACAGGAAAGAATCCAAAT'
'TCTGTGTTTACAGGGCTTTCATGCTCAG'
],
'tseqs': [
'TGAGCAGAGCTATATATTTAGGTAGACTGCTCTCAGGCAGAATGAAACATGATGGCACCTGCCACTCACGACCAGGAACCAAACAGGAAAGAATCCAAAT'
'TCTGTGTTTACAGGGCTTTCATGCTCAG'
],
}
read2 = Blat.pslx_row_to_pysam(pslx_row, self.cache, REFERENCE_GENOME)
self.assertEqual(3, read2.reference_id)
self.assertEqual(2187, read2.reference_start)
self.assertEqual([(CIGAR.S, 117), (CIGAR.EQ, 128)], read2.cigar)
self.assertEqual(Interval(117, 244), query_coverage_interval(read2))
self.assertEqual(read1.query_sequence,
reverse_complement(read2.query_sequence))
def test_reverse_complement(self):
assert reverse_complement('CGAT') == 'ATCG'
assert reverse_complement('') == ''
def test_reverse_complement(self):
self.assertEqual('ATCG', reverse_complement('CGAT'))
self.assertEqual('', reverse_complement(''))
