Python align_striped_smith_waterman Examples

Example #1

 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)

Example #2

File: test_ssw.py Project: charudatta-navare/scikit-bio

 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)

Example #3

 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)

Example #4

File: test_ssw.py Project: charudatta-navare/scikit-bio

 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)