def test_decompose_single_alterations(self):
ref_seq = "CAGGTCCAGATGAAGCTCCCAGAATGCCAGAGGCTGCTCCCCCCGTGGCCCCTGCACCAGC"
ref_path = kmerize(ref_seq, 18)
alt_seq = "CAGGTCCAGATGAAGCTCCCXGAATGCCAGAGGCTGCTCCCCCCGTGGCCCCTGCACCAGC"
alt_path = kmerize(alt_seq, 18)
decomposed_alt = list(
decompose_multiple_alterations(ref_path, alt_path, 18))
for alt_seq, at_path in decomposed_alt:
print ref_seq, alt_seq
self.assertEqual(len(decomposed_alt), 1)
def test_decompose_multiple_alterations_with_end_insertions(self):
ref_seq = "CAGGTCCAGATGAAGCTCCCAGAATGCCAGAGGCTGCTCCCCCCGTGGCCCCTGCACCAGC"
ref_path = kmerize(ref_seq, 18)
alt_seq = "CAGGTCCAGATGAAGCTCCXXXXXCAGAATGCCAGAGGCTGCTCCCCCCGTGGCCCCTGCACCAGCXXXXX"
alt_path = kmerize(alt_seq, 18)
decomposed_alt = list(
decompose_multiple_alterations(ref_path, alt_path, 18))
for alt_seq, at_path in decomposed_alt:
print ref_seq, alt_seq
self.assertEqual(len([x for x in alt_seq if x == "X"]),
5) #at most 5 alt
self.assertEqual(len(decomposed_alt), 2)
def test_decompose_single_alterations_with_end_insertions(self):
ref_seq = "AAAA"
ref_path = kmerize(ref_seq, 18)
alt_seq = "XXXXXAAXXXXXAAXXXXX"
alt_path = kmerize(alt_seq, 18)
decomposed_alt = list(
decompose_multiple_alterations(ref_path, alt_path, 18))
for alt_seq, at_path in decomposed_alt:
print ref_seq, alt_seq
self.assertEqual(len([x for x in alt_seq if x == "X"]),
5) #at most 5 alt
self.assertEqual(len(decomposed_alt), 3)
def test_decompose_multiple_mismatches(self):
ref_seq = "CAGGTCCAGATGAAGCTCCCAGAATGCCAGAGGCTGCTCCCCCCGTGGCCCCTGCACCAGC"
ref_path = kmerize(ref_seq, 18)
alt_seq = "CAGGTCCAGATGAAGCTCXXAGAATGCCAGXGGCTGCTCCCCXCGTGGCCCCTGCACCAGC"
alt_path = kmerize(alt_seq, 18)
decomposed_alt = list(
decompose_multiple_alterations(ref_path, alt_path, 18))
for alt_seq, at_path in decomposed_alt:
print ref_seq, alt_seq
self.assertEqual(len([x for x in alt_seq if x == "X"]),
1) # at most 1 alt
self.assertEqual(len(ref_seq), len(alt_seq)) # at most 1 alt
self.assertEqual(len(decomposed_alt), 4)