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_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)