def test_same_as_using_StripedSmithWaterman_object(self): query_sequence = 'ATGGAAGCTATAAGCGCGGGTGAG' target_sequence = 'AACTTATATAATAAAAATTATATATTCGTTGGGTTCTTTTGATATAAATC' query = StripedSmithWaterman(query_sequence) align1 = query(target_sequence) align2 = align_striped_smith_waterman(query_sequence, target_sequence) self._check_alignment(align2, align1)
def test_kwargs_are_usable(self): kwargs = {} kwargs['zero_index'] = False kwargs['match'] = 5 query_sequence = 'AGGGTAATTAGGCGTGTTCACCTA' target_sequence = 'TACTTATAAGATGTCTCAACGGCATGCGCAACTTGTGAAGTG' query = StripedSmithWaterman(query_sequence, **kwargs) align1 = query(target_sequence) align2 = align_striped_smith_waterman(query_sequence, target_sequence, **kwargs) self._check_alignment(align2, align1)