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 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_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