def test_should_remove_gap(self):
# setup
problem = MSA(score_list=[])
problem.identifiers = ['seq1', 'seq2', 'seq3']
problem.number_of_variables = 3
msa = MSASolution(problem,
msa=[('seq1', 'AC---TGAC'), ('seq2', 'AC---TGAC'),
('seq3', 'AC---TGAC')])
msa.remove_gap_from_sequence(0, 2)
msa.remove_gap_from_sequence(1, 2)
msa.remove_gap_from_sequence(2, 2)
# check
self.assertEqual(['AC--TGAC', 'AC--TGAC', 'AC--TGAC'],
msa.decode_alignment_as_list_of_sequences())
def test_should_remove_gap_case_b(self):
# setup
problem = MSA(score_list=[])
problem.identifiers = ['seq1', 'seq2']
problem.number_of_variables = 2
msa = MSASolution(problem,
msa=[('seq1', 'AB--CD-E'), ('seq2', 'AB--CDE-')])
msa.remove_gap_from_sequence(0, 3)
self.assertEqual(['AB-CD-E', 'AB--CDE-'],
msa.decode_alignment_as_list_of_sequences())
msa.remove_gap_from_sequence(0, 2)
self.assertEqual(['ABCD-E', 'AB--CDE-'],
msa.decode_alignment_as_list_of_sequences())
msa.remove_gap_from_sequence(1, 3)
self.assertEqual(['ABCD-E', 'AB-CDE-'],
msa.decode_alignment_as_list_of_sequences())
msa.remove_gap_from_sequence(1, 2)
self.assertEqual(['ABCD-E', 'ABCDE-'],
msa.decode_alignment_as_list_of_sequences())
