def test_homopolymer_even_odd(self):
ref = 'ATCGAGAT' + 'A' * 15 + 'TCGAGAT'
read = MockRead(
'name',
1,
1,
query_sequence='ATCGAGATA' + 'A' * 12 + 'TCGAGAT',
cigar=[(CIGAR.EQ, 8), (CIGAR.D, 2), (CIGAR.EQ, 20)],
)
self.assertEqual([(CIGAR.EQ, 9 + 12), (CIGAR.D, 2), (CIGAR.EQ, 7)],
hgvs_standardize_cigar(read, ref))
ref = (
'CCCCGGCTCATGTCTGGTTTTGTTTTCCGGGGGCGGGGGGGCTCCCTGGGGATGATGGTGATTTTTTTTTTTTTTTAATCCTCAACTAGGAGAGAAAA'
'TGAGGCAGAGACAATGTGGGGAGCGAGAGAGGGGAAAAGGACGGGGGAGG')
read = MockRead(
'name',
'1',
0,
149,
query_sequence=
('CCCCGGCTCATGTCTGGTTTTGTTTTCCGGGGGCGGGGGGGCTCCCTGGGGATGATGGTGATTTTTTTTTTTTTTTTTAATCCTCAACTAGGAGAGAAAA'
'TGAGGCAGAGACAATGTGGGGAGCGAGAGAGGGGAAAAGGACGGGGGAGG'),
cigar=[(CIGAR.EQ, 61), (CIGAR.I, 2), (CIGAR.EQ, 87)],
)
self.assertEqual(
[(CIGAR.EQ, 61 + 15), (CIGAR.I, 2), (CIGAR.EQ, 87 - 15)],
hgvs_standardize_cigar(read, ref),
)
ref = (
'CCTCCTCGGTCGGGCAGATCTTTCAGAAGCAGGAGCCCAGGATCATGTCTGGTTTTGTTTTCCGAGGGCGAGGGGGCTCCCTGAGGATGATGGTGATTT'
'TTTTTTTTTTTTAATCCTCAACTAGGAGAGAAAATGAGGCAGAGACA')
read = MockRead(
'name',
'1',
0,
149,
query_sequence=
('CCCCTCCTCGGTCGGGCAGATCTTTCAGAAGCAGGAGCCCAGGATCATGTCTGGTTTTGTTTTCCGAGGGCGAGGGGGCTCCCTGAGGATGATGGTGATTTT'
'TTTTTTTTTTTTTAATCCTCAACTAGGAGAGAAAATGAGGCAGAGACA'),
cigar=[(CIGAR.S, 2), (CIGAR.EQ, 96), (CIGAR.I, 2), (CIGAR.EQ, 50)],
)
self.assertEqual(
[(CIGAR.S, 2), (CIGAR.EQ, 96 + 15), (CIGAR.I, 2),
(CIGAR.EQ, 50 - 15)],
hgvs_standardize_cigar(read, ref),
)
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_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_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 no_change_aligned(self):
ref = 'AAATTTGGGCCCAATT'
read = MockRead('name',
'1',
1,
cigar=[(CIGAR.M, 10)],
query_sequence='AAATTTGGGC')
self.assertEqual([(CIGAR.M, 10)], hgvs_standardize_cigar(read, ref))
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_deletion_in_repeat(self):
ref = 'ATAGGC' 'ATCT' 'ACGA' 'ACGA' 'ACGA' 'GATCGCTACG'
read = MockRead(
'name',
1,
6,
query_sequence='ATCT' 'ACGA' 'ACGA' 'GATC',
cigar=[(CIGAR.EQ, 4), (CIGAR.D, 4), (CIGAR.EQ, 12)]
)
self.assertEqual([(CIGAR.EQ, 12), (CIGAR.D, 4), (CIGAR.EQ, 4)], hgvs_standardize_cigar(read, ref))
def test_bubble_sort_indel_sections(self):
rseq = 'ATAGGC' 'ATCT' 'GG' 'GA' 'GCGA' 'GATCGCTACG'
qseq = 'ATCT' 'TTT' 'TT' 'GCGA' 'GATC'
read = MockRead('name',
1,
6,
query_sequence=qseq,
cigar=[(CIGAR.EQ, 4), (CIGAR.D, 2), (CIGAR.I, 3),
(CIGAR.D, 2), (CIGAR.I, 2), (CIGAR.EQ, 8)])
self.assertEqual([(CIGAR.EQ, 4), (CIGAR.I, 5), (CIGAR.D, 4),
(CIGAR.EQ, 8)], hgvs_standardize_cigar(read, rseq))
def no_change_proper_indel(self):
ref = 'ATAGGC' 'ATCTACGAG' 'ATCGCTACG'
read = MockRead(
'name',
1,
6,
query_sequence='ATCTAC' 'CCC' 'ATCG',
cigar=[(CIGAR.EQ, 6), (CIGAR.I, 3), (CIGAR.D, 3), (CIGAR.EQ, 4)]
)
self.assertEqual(
[(CIGAR.EQ, 6), (CIGAR.I, 3), (CIGAR.D, 3), (CIGAR.EQ, 4)], hgvs_standardize_cigar(read, ref))
def ins_after_deletion(self):
ref = 'ATAGGC' 'ATCTACGAG' 'ATCGCTACG'
read = MockRead(
'name',
1,
6,
query_sequence='ATCTAC' 'CCC' 'ATCG',
cigar=[(CIGAR.EQ, 6), (CIGAR.D, 3), (CIGAR.I, 3), (CIGAR.EQ, 4)]
)
self.assertEqual(
[(CIGAR.EQ, 6), (CIGAR.I, 3), (CIGAR.D, 3), (CIGAR.EQ, 4)], hgvs_standardize_cigar(read, ref))
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_bubble_sort_indel_sections_drop_mismatch(self):
rseq = 'ATAGGC' 'ATCT' 'A' 'CGA' 'AGCAT' 'ACGA' 'GATCGCTACG'
# ATCT CTTTT TACGA
qseq = 'ATCT' 'C' 'TT' 'TTT' 'ACGA' 'GATC'
read = MockRead('name',
1,
6,
query_sequence=qseq,
cigar=[(CIGAR.EQ, 4), (CIGAR.X, 1), (CIGAR.D, 3),
(CIGAR.I, 2), (CIGAR.D, 5), (CIGAR.I, 3),
(CIGAR.EQ, 8)])
self.assertEqual([(CIGAR.EQ, 4), (CIGAR.I, 5), (CIGAR.D, 8),
(CIGAR.EQ, 9)], hgvs_standardize_cigar(read, rseq))
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_insertion_in_repeat(self):
ref = 'ATAGGC' 'ATCT' 'ACGA' 'GATCGCTACG'
read = MockRead(
'name',
1,
6,
query_sequence='ATCT'
'ACGA'
'ACGA'
'GATC',
cigar=[(CIGAR.EQ, 4), (CIGAR.I, 4), (CIGAR.EQ, 8)],
)
assert [(CIGAR.EQ, 8), (CIGAR.I, 4),
(CIGAR.EQ, 4)] == hgvs_standardize_cigar(read, ref)
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_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_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_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