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_deletion_repeat(self):
qseq = (
'GAGT'
'GAGACTCTGT'
'GAA'
'AAAGAAAAAAAAAA'
'A'
'ATATATATATATATAAATATA'
'C'
'ATATTATGTATCAAATATATAT'
'TATGTGTAATATACATCATGTATCAAATATATATTATGTATAATATACATCATATATCAAATATATATTATGTG'
)
# deleted reference: TATGTGTAATATACATCATGTATCAAA
print(qseq[:76], qseq[76:])
read = MockRead('name',
reference_name='11_86018001-86018500',
reference_start=28,
cigar=[(CIGAR.S, 4), (CIGAR.EQ, 10), (CIGAR.X, 3),
(CIGAR.EQ, 14), (CIGAR.X, 1), (CIGAR.EQ, 21),
(CIGAR.X, 1), (CIGAR.EQ, 22), (CIGAR.D, 27),
(CIGAR.EQ, 74)],
query_sequence=qseq)
expected_cigar = [(CIGAR.S, 4), (CIGAR.EQ, 10), (CIGAR.X, 3),
(CIGAR.EQ, 14), (CIGAR.X, 1), (CIGAR.EQ, 21),
(CIGAR.X, 1), (CIGAR.EQ, 22 + 30), (CIGAR.D, 27),
(CIGAR.EQ, 74 - 30)]
std_cigar = hgvs_standardize_cigar(
read, REFERENCE_GENOME[read.reference_name].seq)
print(SamRead.deletion_sequences(read, REFERENCE_GENOME))
read.cigar = std_cigar
print(SamRead.deletion_sequences(read, REFERENCE_GENOME))
self.assertEqual(expected_cigar, std_cigar)
def test_bubble_sort_indel_sections_drop_mismatch_with_hardclipping(self):
ref = 'ATAGGC' 'ATCT' 'ACGA' 'ACGA' 'ACGA' 'GATCGCTACG'
# original
# ATAGGCATCTACG AA CGAACGAGATCGCTACG
# ATCTC TTT TTCGAACG
# expected
# ATAGGCATCT ACGAACGAACGAGATCGCTACG
# ATCTCTTTTT CGAACG
read = MockRead(
'name',
1,
6,
reference_name='1',
query_sequence='ATCTCTTTTTCGAACG',
cigar=[
(CIGAR.H, 10),
(CIGAR.EQ, 4),
(CIGAR.X, 1),
(CIGAR.D, 2),
(CIGAR.I, 3),
(CIGAR.D, 2),
(CIGAR.I, 2),
(CIGAR.EQ, 6),
],
)
print(SamRead.deletion_sequences(read, {'1': MockObject(seq=ref)}))
print(SamRead.insertion_sequences(read))
print(read.query_sequence, len(read.query_sequence))
self.assertEqual(
[(CIGAR.H, 10), (CIGAR.EQ, 4), (CIGAR.I, 6), (CIGAR.D, 5),
(CIGAR.EQ, 6)],
hgvs_standardize_cigar(read, ref),
)
def test_shift_overaligned(self):
# qwertyuiopas---kkkkk------dfghjklzxcvbnm
# .......... ................
gene = Gene('1', 1, 1000, strand='+')
transcript = PreTranscript(exons=[(1, 12), (20, 28)], gene=gene, strand='+')
for spl_patt in transcript.generate_splicing_patterns():
transcript.transcripts.append(Transcript(transcript, spl_patt))
gene.transcripts.append(transcript)
read = SamRead(
reference_name='1',
reference_start=0,
cigar=_cigar.convert_string_to_cigar('14=7D12='),
query_sequence='qwertyuiopasdfghjklzxcvbnm',
)
evidence = TranscriptomeEvidence(
annotations={},
reference_genome={'1': MockObject(seq='qwertyuiopasdfkkkkkdfghjklzxcvbnm')},
bam_cache=MockObject(get_read_reference_name=lambda r: r.reference_name),
break1=Breakpoint('1', 1, orient='L', strand='+'),
break2=Breakpoint('1', 10, orient='R', strand='+'),
read_length=75,
stdev_fragment_size=75,
median_fragment_size=220,
)
evidence.overlapping_transcripts.add(transcript)
new_read = evidence.standardize_read(read)
assert new_read.cigar == _cigar.convert_string_to_cigar('12=7N14=')
def test_insertions(self):
exp = ['kkk', 'kkkk']
read = MockRead(reference_start=0,
reference_name='1',
query_sequence='abcdekkkfghijklmnopqkkkkrstuvwxyz',
cigar=convert_string_to_cigar('5=3I12=4I9='))
self.assertEqual(exp, SamRead.insertion_sequences(read))
def test_deletions(self):
exp = ['cde', 'nopq']
read = MockRead(
reference_start=0, reference_name='1', query_sequence='',
cigar=convert_string_to_cigar('2=3D8=4D9=')
)
self.assertEqual(exp, SamRead.deletion_sequences(read, self.reference_genome))
def test_odd_deletion_in_repeat(self):
rseq = 'AAAGAAAAAAAAAAAAT' 'ATATATATATA' 'TAAATATACATATTATGTATCAAATATATATTATGTGTAATATACATCATGTATC'
qseq = 'TTTTAAAAAAAAAAAAT' 'ATATATATATA' 'ATATACATATTATGTATCAAATATATATTATGTGTAATATACATCATGTATC'
print(len(qseq) - 28)
read = MockRead('name',
reference_name='1',
reference_start=4,
cigar=convert_string_to_cigar('4S13=3D63='),
query_sequence=qseq)
reference_genome = {'1': MockObject(seq=rseq)}
exp = convert_string_to_cigar('4S24=3D52=')
new_cigar = hgvs_standardize_cigar(read, rseq)
print(SamRead.deletion_sequences(read, reference_genome))
read.cigar = new_cigar
print(SamRead.deletion_sequences(read, reference_genome))
self.assertEqual(exp, new_cigar)
def test_complex(self):
qseq = (
'TATTTGGAAATATTTGTAAGATAGATGTCTCTG' 'C'
'CTCCTTCTGTTTCTGTCTCTGTCTCTTGCACTCTCTCTCTCCCTCTCTT'
'TCTCTCTCTCTCTCTCTCTCTCTCTC'
'TCTATATATATATATATA'
'T' 'A' 'T' 'C' 'T'
'ACACACACACACACACAC')
rseq = (
'TATTTGGAAATATTTGTAAGATAGATGTCTCTG' 'T'
'CTCCTTCTGTTTCTGTCTCTGTCTCTTGCACTCTCTCTCTCCCTCTCTT'
'TCTATATATATATATATA'
'C' 'A' 'C'
'ACACACACACACACACAC')
read = MockRead(
'name', reference_name='mock', reference_start=0, query_sequence=qseq,
cigar=[
(CIGAR.EQ, 33), (CIGAR.X, 1), (CIGAR.EQ, 49), (CIGAR.I, 26),
(CIGAR.EQ, 18), (CIGAR.X, 1), (CIGAR.EQ, 1), (CIGAR.I, 1),
(CIGAR.EQ, 1), (CIGAR.I, 1), (CIGAR.EQ, 18)]
)
print(rseq)
print(read.query_sequence[:83], read.query_sequence[83 + 26: 83 + 26 + 20], read.query_sequence[83 + 26 + 22:])
print(read.query_sequence)
print(SamRead.insertion_sequences(read))
new_cigar = [
(CIGAR.EQ, 33), (CIGAR.X, 1), (CIGAR.EQ, 52), (CIGAR.I, 26),
(CIGAR.EQ, 15), (CIGAR.X, 1), (CIGAR.EQ, 1), (CIGAR.I, 1),
(CIGAR.EQ, 1), (CIGAR.I, 1), (CIGAR.EQ, 18)]
std_cigar = hgvs_standardize_cigar(read, rseq)
print(new_cigar)
print(std_cigar)
self.assertEqual(new_cigar, std_cigar)
def test_bwa_mem(self):
# SamRead(1:224646710-224646924, 183=12D19=, TCAGCTCTCT...) TCAGCTCTCTTAGGGCACACCCTCCAAGGTGCCTAAATGCCATCCCAGGATTGGTTCCAGTGTCTATTATCTGTTTGACTCCAAATGGCCAAACACCTGACTTCCTCTCTGGTAGCCTGGCTTTTATCTTCTAGGACATCCAGGGCCCCTCTCTTTGCCTTCCCCTCTTTCTTCCTTCTACTGCTTCAGCAGACATCATGTG
# std SamRead(1:224646710-224646924, 183=12D19=, TCAGCTCTCT...) TCAGCTCTCTTAGGGCACACCCTCCAAGGTGCCTAAATGCCATCCCAGGATTGGTTCCAGTGTCTATTATCTGTTTGACTCCAAATGGCCAAACACCTGACTTCCTCTCTGGTAGCCTGGCTTTTATCTTCTAGGACATCCAGGGCCCCTCTCTTTGCCTTCCCCTCTTTCTTCCTTCTACTGCTTCAGCAGACATCATGTG
# > BPP(Breakpoint(1:224646893L-), Breakpoint(1:224646906R-), opposing=False, seq='')
read = SamRead(reference_name='1')
read.query_sequence = 'TCAGCTCTCTTAGGGCACACCCTCCAAGGTGCCTAAATGCCATCCCAGGATTGGTTCCAGTGTCTATTATCTGTTTGACTCCAAATGGCCAAACACCTGACTTCCTCTCTGGTAGCCTGGCTTTTATCTTCTAGGACATCCAGGGCCCCTCTCTTTGCCTTCCCCTCTTTCTTCCTTCTACTGCTTCAGCAGACATCATGTG'
read.reference_start = 224646710
read.reference_id = 0
print(_cigar.convert_string_to_cigar('183=12D19='))
read.cigar = _cigar.join(_cigar.convert_string_to_cigar('183=12D19='))
read.query_name = 'name'
read.mapping_quality = NA_MAPPING_QUALITY
std_read = Evidence.standardize_read(self.mock_evidence, read)
print(SamRead.__repr__(read))
print(SamRead.__repr__(std_read))
self.assertEqual(_cigar.convert_string_to_cigar('186=12D16='), std_read.cigar)
self.assertEqual(read.reference_start, std_read.reference_start)
def test_deletions(self):
exp = ['cde', 'nopq']
read = MockRead(
reference_start=0,
reference_name='1',
query_sequence='',
cigar=convert_string_to_cigar('2=3D8=4D9='),
)
assert (SamRead.deletion_sequences(
read, {'1': MockObject(seq='abcdefghijklmnopqrstuvwxyz')}) == exp)
def test_even_deletion_in_repeat(self):
rseq = ('AAAGAAAAAAAAAAAAT'
'ATATATATATA'
'TAAATATACATATTATGTATCAAATATATATTATGTGTAATATACATCATGTATC')
qseq = ('TTTTAAAAAAAAAAAAT'
'ATATATATATA'
'AATATACATATTATGTATCAAATATATATTATGTGTAATATACATCATGTATC')
print(len(qseq) - 28)
read = MockRead(
'name',
reference_name='1',
reference_start=4,
cigar=convert_string_to_cigar('4S13=2D64='),
query_sequence=qseq,
)
reference_genome = {'1': MockObject(seq=rseq)}
exp = convert_string_to_cigar('4S24=2D53=')
new_cigar = hgvs_standardize_cigar(read, rseq)
print(SamRead.deletion_sequences(read, reference_genome))
read.cigar = new_cigar
print(SamRead.deletion_sequences(read, reference_genome))
assert new_cigar == exp
def test_shift_no_transcripts(self):
read = SamRead(reference_name='1',
reference_start=0,
cigar=_cigar.convert_string_to_cigar('14=7D18='),
query_sequence='qwertyuiopasdfdfghjklzxcvbnm')
evidence = TranscriptomeEvidence(
annotations={},
reference_genome={
'1': MockObject(seq='qwertyuiopasdfkkkkkdfghjklzxcvbnm')
},
bam_cache=None,
break1=Breakpoint('1', 1, orient='L', strand='+'),
break2=Breakpoint('1', 10, orient='R', strand='+'),
read_length=75,
stdev_fragment_size=75,
median_fragment_size=220)
new_cigar = evidence.exon_boundary_shift_cigar(read)
self.assertEqual(_cigar.convert_string_to_cigar('14=7D18='), new_cigar)
def test_bwa_mem(self):
mock_evidence = MockObject(
reference_genome={
'1': MockObject(
seq=MockLongString(
'TGGGTATCAGACACACTGGGTAGCTGAGTGCTCAGAGGAAGATGCGAGGTATTCAGGGAAAGTGTCAGTGGGGTCTCCCAGTGCCTGTTTGGTCCACAGTTAGGAGA'
'GGCCCTGCTTGCACTTCTAATACAGTCCCGGAAAGACGGGGCCAGAACTTAGGAGGGGAGCGCTTTGCAGCAACTTTTCAAGAAAAGGGGAAAATTTAAGCACCATA'
'CTGTTATGTGGTCCTTGTACCCAGAGGCCCTGTTCAGCTCCAGTGATCAGCTCTCTTAGGGCACACCCTCCAAGGTGCCTAAATGCCATCCCAGGATTGGTTCCAGT'
'GTCTATTATCTGTTTGACTCCAAATGGCCAAACACCTGACTTCCTCTCTGGTAGCCTGGCTTTTATCTTCTAGGACATCCAGGGCCCCTCTCTTTGCCTTCCCCTCT'
'TTCTTCCTTCTACTGCTTAGATCAAGTCTTCAGCAGACATCATGTGACCTTGAGGATGGATGTCACATGCTGGAGGAAACAGAAGGCCGAAACCCTGATGACTTCAC'
'AGAGCTGCCAAAACAGTTCCTGACTGTTTATTCCGGGTCTTTAACAAAGTGATGAAAAGAAATCCTTGCAGTATGAAAACAACTTTTCTATTCCATGGAGCCAAACC'
'TCATTATAACAGATAACGTGACCCTCAGCGATATCCCAAGTATTTTCCTGTTCTCATCTATACTATGGCAAAGGGGCAAATACCTCTCAGTAAAGAAAGAAATAACA'
'ACTTCTATCTTGGGCGAGGCATTTCTTCTGTTAGAACTTTGTACACGGAATAAAATAGATCTGTTTGTGCTTATCTTTCTCCTTAGAATTATTGAATTTGAAGTCTT'
'TCCCAGGGTGGGGGTGGAGTGAAGCTGGGGTTTCATAAGCACATAGATAGTAGTG',
offset=224646450,
)
)
},
bam_cache=MockObject(get_read_reference_name=lambda x: x.reference_name),
config={
'validate.contig_aln_merge_inner_anchor': 10,
'validate.contig_aln_merge_outer_anchor': 20,
**DEFAULTS,
},
)
# SamRead(1:224646710-224646924, 183=12D19=, TCAGCTCTCT...) TCAGCTCTCTTAGGGCACACCCTCCAAGGTGCCTAAATGCCATCCCAGGATTGGTTCCAGTGTCTATTATCTGTTTGACTCCAAATGGCCAAACACCTGACTTCCTCTCTGGTAGCCTGGCTTTTATCTTCTAGGACATCCAGGGCCCCTCTCTTTGCCTTCCCCTCTTTCTTCCTTCTACTGCTTCAGCAGACATCATGTG
# std SamRead(1:224646710-224646924, 183=12D19=, TCAGCTCTCT...) TCAGCTCTCTTAGGGCACACCCTCCAAGGTGCCTAAATGCCATCCCAGGATTGGTTCCAGTGTCTATTATCTGTTTGACTCCAAATGGCCAAACACCTGACTTCCTCTCTGGTAGCCTGGCTTTTATCTTCTAGGACATCCAGGGCCCCTCTCTTTGCCTTCCCCTCTTTCTTCCTTCTACTGCTTCAGCAGACATCATGTG
# > BPP(Breakpoint(1:224646893L-), Breakpoint(1:224646906R-), opposing=False, seq='')
read = SamRead(reference_name='1')
read.query_sequence = 'TCAGCTCTCTTAGGGCACACCCTCCAAGGTGCCTAAATGCCATCCCAGGATTGGTTCCAGTGTCTATTATCTGTTTGACTCCAAATGGCCAAACACCTGACTTCCTCTCTGGTAGCCTGGCTTTTATCTTCTAGGACATCCAGGGCCCCTCTCTTTGCCTTCCCCTCTTTCTTCCTTCTACTGCTTCAGCAGACATCATGTG'
read.reference_start = 224646710
read.reference_id = 0
print(_cigar.convert_string_to_cigar('183=12D19='))
read.cigar = _cigar.join(_cigar.convert_string_to_cigar('183=12D19='))
read.query_name = 'name'
read.mapping_quality = NA_MAPPING_QUALITY
std_read = Evidence.standardize_read(mock_evidence, read)
assert std_read.cigar == _cigar.convert_string_to_cigar('186=12D16=')
assert std_read.reference_start == read.reference_start
def test_hardclipping(self):
read = SamRead(reference_name='15')
read.reference_start = 71491944
read.cigar = _cigar.convert_string_to_cigar('12=1D25=113H')
read.query_sequence = 'GTGTGTGGTGTGGGGTGTGTGGTGTGTGTGGTGTGTG'
read.is_reverse = True
expected_bpp = BreakpointPair(
Breakpoint('15', 71491956, orient='L', strand='-'),
Breakpoint('15', 71491958, orient='R', strand='-'),
untemplated_seq='')
events = align.call_read_events(read, is_stranded=True)
self.assertEqual(1, len(events))
self.assertEqual(expected_bpp.break1, events[0].break1)
self.assertEqual(expected_bpp.break2, events[0].break2)