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_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)
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)
