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_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_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_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
