def test_needleman_wunsch_score_BLOSUMXX(self):
test_cases = [
("BLOSUM45", 513),
("BLOSUM62", 426),
("BLOSUM80", 452)
]
for x, output in test_cases:
with self.subTest(name=x):
sa = SequenceAlignment(self.ab_collection_1[0], self.ab_collection_2, 'needleman_wunsch', x)
sa.align_sequences()
self.assertEqual(sa.score[self.ab_collection_2.names[0]], output)
def test_alignment_indel_sign(self):
# if indel is positive the user receives a warning and indel will be set to -indel
sa = SequenceAlignment(self.ab_collection_1[0], self.ab_collection_2, 'needleman_wunsch', 'BLOSUM62')
sa.align_sequences(indel=-10)
sa_score_1 = sa.score
sa = SequenceAlignment(self.ab_collection_1[0], self.ab_collection_2, 'needleman_wunsch', 'BLOSUM62')
sa.align_sequences(indel=10)
sa_score_2 = sa.score
# since the second indel is positive it will be set to
# its negative, which runs the algorithms
# with the same params again and will get the same scores
self.assertEqual(sa_score_1, sa_score_2)
def test_alignment_print_string(self):
sa = SequenceAlignment(self.ab_collection_1[0], self.ab_collection_2, 'needleman_wunsch', 'BLOSUM62')
sa.align_sequences()
self.assertEqual(len(sa._aligned_sequences_string()), 3)
def test_alignment_exception_3(self):
# catch error when user tries to print alignment before calling .align_sequences()
sa = SequenceAlignment(self.ab_collection_1[0], self.ab_collection_2, 'foo', 'BLOSUM62')
self.assertRaises(ValueError, sa.print_aligned_sequences)
def test_alignment_exception_2(self):
# catch exception when algorithm is not known
sa = SequenceAlignment(self.ab_collection_1[0], self.ab_collection_2, 'foo', 'BLOSUM62')
self.assertRaises(ValueError, sa.align_sequences)
def test_needleman_wunsch_aligned_sequences(self):
sa = SequenceAlignment(self.ab_collection_1[0], self.ab_collection_2, 'needleman_wunsch', 'BLOSUM62')
sa.align_sequences()
self.assertEqual(sa.aligned_sequences[self.ab_collection_2.names[0]], self.seq2_aligned)
def test_needleman_wunsch_score_BLOSUM45(self):
sa = SequenceAlignment(self.ab_collection_1[0], self.ab_collection_2, 'needleman_wunsch', 'BLOSUM45')
sa.align_sequences()
self.assertEqual(sa.score[self.ab_collection_2.names[0]], 513)
def test_sequence_alignment_target(self):
sa = SequenceAlignment(self.ab_collection_1[0], self.ab_collection_2, 'needleman_wunsch', 'BLOSUM62')
self.assertEqual(sa.target_sequence, self.ab_collection_1[0].sequence)