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_deletion_partial_repeat(self):
qseq = ('ATCTTAGCCAGGT' 'AGTTACATACATATC')
rseq = ('ATCTTAGCCAGGT' 'AGCTAT' 'AGTTACATACATATC')
read = MockRead(
'name', reference_name='mock', reference_start=0, query_sequence=qseq,
cigar=convert_string_to_cigar('13=6D15=')
)
self.assertEqual(convert_string_to_cigar('15=6D13='), hgvs_standardize_cigar(read, rseq))
def test_unecessary_indel_end_match2(self):
rseq = 'GGGTGCAGTGGCTTACACCT' 'GTAATCCAAACACCTTGGGAGCCGCCCCCTGAG' 'CCTCCAGGCCCGGGACAGA'
qseq = 'GGGTGCAGTGGCTTACACCT' 'CCAGG' 'CCTCCAGGCCCGGGACAGA'
read = MockRead('name',
reference_name='1',
reference_start=0,
cigar=convert_string_to_cigar('20=5I33D19='),
query_sequence=qseq)
reference_genome = {'1': MockObject(seq=rseq)}
exp = convert_string_to_cigar('20=4I32D20=')
new_cigar = hgvs_standardize_cigar(read, rseq)
self.assertEqual(exp, new_cigar)
def test_unecessary_indel_end_match(self):
rseq = 'qwertyuiopasdfghjklzxcvbnm'
qseq = 'qwertyuiopasdfkmkghjklzxcvbnm'
read = MockRead('name',
reference_name='1',
reference_start=0,
cigar=convert_string_to_cigar('14=5I2D10='),
query_sequence=qseq)
reference_genome = {'1': MockObject(seq=rseq)}
exp = convert_string_to_cigar('14=3I12=')
new_cigar = hgvs_standardize_cigar(read, rseq)
self.assertEqual(exp, new_cigar)
def test_unecessary_indel_end_match(self):
rseq = 'qwertyuiopasdfghjklzxcvbnm'
qseq = 'qwertyuiopasdfkmkghjklzxcvbnm'
read = MockRead(
'name',
reference_name='1',
reference_start=0,
cigar=convert_string_to_cigar('14=5I2D10='),
query_sequence=qseq,
)
exp = convert_string_to_cigar('14=3I12=')
new_cigar = hgvs_standardize_cigar(read, rseq)
assert new_cigar == exp
def test_even_insertion_in_repeat(self):
rseq = 'AAAGAAAAAAAAAAAAT' 'ATATATATATATA' 'AATATACATATTATGTATCAAATATATATTATGTGTAATATACATCATGTATC'
qseq = 'TTTTAAAAAAAAAAAAT' 'ATATATATATATA' 'TAAATATACATATTATGTATCAAATATATATTATGTGTAATATACATCATGTATC'
print(len(qseq) - 13 - 4)
read = MockRead('name',
reference_name='1',
reference_start=4,
cigar=convert_string_to_cigar('4S13=2I66='),
query_sequence=qseq)
reference_genome = {'1': MockObject(seq=rseq)}
exp = convert_string_to_cigar('4S26=2I53=')
new_cigar = hgvs_standardize_cigar(read, rseq)
read.cigar = new_cigar
self.assertEqual(exp, new_cigar)
def test_indel_repeat(self):
qseq = 'ATCTTAGCCAGGT' 'C' 'AGTTACATACATATC'
rseq = 'ATCTTAGCCAGGT' 'AGCTAT' 'AGTTACATACATATC'
print(qseq)
print(rseq)
read = MockRead(
'name',
reference_name='mock',
reference_start=0,
query_sequence=qseq,
cigar=convert_string_to_cigar('13=1I6D15='),
)
self.assertEqual(convert_string_to_cigar('13=1I6D15='),
hgvs_standardize_cigar(read, rseq))
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_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_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_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_shift_complex_indel(self):
refseq = 'ATATATCTATTTTTTTCTTTCTTTTTTTTACTTTCATTAAGTGCCACTAAAAAATTAGGTTCAATTAAACTTTATTAATCTCTTCTGAGTTTTGATTGAGTATATATATATATATACCCAGTTTCAAGCAGGTATCTGCCTTTAAAGATAAGAGACCTCCTAAATGCTTTCTTTTATTAGTTGCCCTGTTTCAGATTCAGCTTTGTATCTATATCACCTGTTAATATGTGTGGACTCACAGAAATGATCATTGAGGGAATGCACCCTGTTTGGGTGTAAGTAGCTCAGGGAAAAAATCCTAG'
read = MockRead(
'name',
reference_name='18',
reference_start=40237946 - 40237890,
query_sequence=
'AGGTTCAATTAAACTTTATTAATCTCTTCTGAGTTTTGATTGAGTGTATATATATATATATATATATATATATATATACCCAGTTTCAAGCAGGTATCTGCCTTTAAAGATAAGAGACCTCCTAAGTGCTTTCTTTTATTAGTGGCCCTG',
cigar=convert_string_to_cigar('44M18I88M'),
)
print(_read.convert_cigar_to_string(read.cigar))
read.cigar = recompute_cigar_mismatch(read, refseq)
assert read.cigar == convert_string_to_cigar('44=18I63=1X17=1X6=')
print(_read.convert_cigar_to_string(read.cigar))
read.cigar = hgvs_standardize_cigar(read, refseq)
print(_read.convert_cigar_to_string(read.cigar))
assert read.cigar == convert_string_to_cigar('45=18I62=1X17=1X6=')
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_small_exact_match(self):
cigar = convert_string_to_cigar(
'283M17506D5M21275D596M17506D5M21275D313M')
# [(0, 283), (2, 17506), (0, 5), (2, 21275), (0, 596), (2, 17506), (0, 5), (2, 21275), (0, 313)]
new_cigar = merge_internal_events(cigar, 20, 15)
exp = [(CIGAR.M, 283), (CIGAR.I, 5), (CIGAR.D, 17506 + 21275 + 5),
(CIGAR.M, 596), (CIGAR.I, 5), (CIGAR.D, 17506 + 21275 + 5),
(CIGAR.M, 313)]
self.assertEqual(exp, new_cigar)
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_read_with_exons(self):
contig = MockRead(
query_sequence='CTTGAAGGAAACTGAATTCAAAAAGATCAAAGTGCTGGGCTCCGGTGCGTTCGGCACGGTGTATAAGGGACTCTGGATCCCAGAAGGTGAGAAAGTTAAAATTCCCGTCGCTATCAAGACATCTCCGAAAGCCAACAAGGAAATCCTCGATGAAGCCTACGTGATGGCCAGCGTGGACAACCCCCACGTGTGCCGCCTGCTGGGCATCTGCCTCACCTCCACCGTGCAGCTCATCATGCAGCTCATGCCCTTCGGCTGCCTCCTGGACTATGTCCGGGAACACAAAGACAATATTGGCTCCCAGTACCTGCTCAACTGGTGTGTGCAGATCGCAAAGGGCATGAACTACTTGGAGGACCGTCGCTTGGTGCACCGCGACCTGGCAGCCAGGAACGTACTGGTGAAAACACCGCAGCATGTCAAGATCACAGATTTTGGGCTGGCCAAACTGCTGGGTGCGGAAGAGAAAGAATACCATGCAGAAGGAGGCAAAGTGCCTATCAAGTGGATGGCATTGGAATCAATTTTACACAGAATCTATACCCACCAGAGTGATGTCTGGAGCTACGGGGTGACCGTTTGGGAGTTGATGACCTTTGGATCCAA',
cigar=_cigar.convert_string_to_cigar('68M678D50M15D34M6472D185M10240D158M891D74M8I5883D29M'),
reference_name='7',
reference_id=6,
reference_start=55241669
)
self.assertEqual(6, len(align.call_read_events(contig)))
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_insertion_in_repeat(self):
rseq = ('AAAGAAAAAAAAAAAAT'
'ATATATATATATA'
'AATATACATATTATGTATCAAATATATATTATGTGTAATATACATCATGTATC')
qseq = ('TTTTAAAAAAAAAAAAT'
'ATATATATATATA'
'TAAATATACATATTATGTATCAAATATATATTATGTGTAATATACATCATGTATC')
print(len(qseq) - 13 - 4)
read = MockRead(
'name',
reference_name='1',
reference_start=4,
cigar=convert_string_to_cigar('4S13=2I66='),
query_sequence=qseq,
)
exp = convert_string_to_cigar('4S26=2I53=')
new_cigar = hgvs_standardize_cigar(read, rseq)
read.cigar = new_cigar
assert new_cigar == 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_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_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(self):
string = '283M' '17506D' '5M' '21275D' '596M' '17506D' '5M' '21275D' '313M'
exp = [
(CIGAR.M, 283),
(CIGAR.D, 17506),
(CIGAR.M, 5),
(CIGAR.D, 21275),
(CIGAR.M, 596),
(CIGAR.D, 17506),
(CIGAR.M, 5),
(CIGAR.D, 21275),
(CIGAR.M, 313),
]
self.assertEqual(exp, convert_string_to_cigar(string))
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)
def setUp(self):
self.contig_read = MockRead(
cigar=_cigar.convert_string_to_cigar('275M18I12041D278M'),
reference_start=89700025,
reference_name='10',
)
def test_softclipped_right(self):
c = convert_string_to_cigar(
'70=2X1=8X4=1X1=4X1=6X1=4X1=4X2=5X3=3X1=4X1=3X1=14X1=1X2=1S')
cnew, prefix = extend_softclipping(c, 6)
assert prefix == 0
assert cnew == convert_string_to_cigar('70=80S')
def test_softclipped_right(self):
c = convert_string_to_cigar(
'70=2X1=8X4=1X1=4X1=6X1=4X1=4X2=5X3=3X1=4X1=3X1=14X1=1X2=1S')
cnew, prefix = extend_softclipping(c, 6)
self.assertEqual(0, prefix)
self.assertEqual(convert_string_to_cigar('70=80S'), cnew)
def contig_read():
return MockRead(
cigar=_cigar.convert_string_to_cigar('275M18I12041D278M'),
reference_start=89700025,
reference_name='10',
)
def test_mismatch_only(self):
exp = _cigar.convert_string_to_cigar('39=1X16=1X71=22S')
assert _cigar.merge_internal_events(exp, 20, 15) == exp
