Python local_pairwise_align_ssw Examples

Example #1

File: test_ssw.py Project: jairideout/scikit-bio

    def test_constructor(self):
        query_sequence = 'AGGGTAATTAGGCGTGTTCACCTA'
        target_sequence = 'TACTTATAAGATGTCTCAACGGCATGCGCAACTTGTGAAGTG'

        align1 = local_pairwise_align_ssw(query_sequence, target_sequence)
        align2 = local_pairwise_align_ssw(query_sequence, target_sequence,
                                          constructor=DNA)

        self.assertEqual(type(align1[0]), Sequence)
        self.assertEqual(type(align2[0]), DNA)

Example #2

    def test_constructor(self):
        query_sequence = 'AGGGTAATTAGGCGTGTTCACCTA'
        target_sequence = 'TACTTATAAGATGTCTCAACGGCATGCGCAACTTGTGAAGTG'

        align1 = local_pairwise_align_ssw(query_sequence, target_sequence)
        align2 = local_pairwise_align_ssw(query_sequence, target_sequence,
                                          constructor=DNA)

        self.assertEqual(type(align1[0]), Sequence)
        self.assertEqual(type(align2[0]), DNA)

Example #3

File: test_ssw.py Project: gblanchard4/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 = local_pairwise_align_ssw(query_sequence, target_sequence)
     self._check_Alignment_to_AlignmentStructure(align2, align1)

Example #4

File: test_ssw.py Project: Kleptobismol/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 = local_pairwise_align_ssw(query_sequence,
                                       target_sequence)
     self._check_Alignment_to_AlignmentStructure(align2, align1)

Example #5

File: test_ssw.py Project: Kleptobismol/scikit-bio

 def test_kwargs_are_usable(self):
     kwargs = {}
     kwargs['mismatch_score'] = -2
     kwargs['match_score'] = 5
     query_sequence = 'AGGGTAATTAGGCGTGTTCACCTA'
     target_sequence = 'TACTTATAAGATGTCTCAACGGCATGCGCAACTTGTGAAGTG'
     query = StripedSmithWaterman(query_sequence, **kwargs)
     align1 = query(target_sequence)
     align2 = local_pairwise_align_ssw(query_sequence,
                                       target_sequence, **kwargs)
     self._check_Alignment_to_AlignmentStructure(align2, align1)

Example #6

 def test_kwargs_are_usable(self):
     kwargs = {}
     kwargs['mismatch_score'] = -2
     kwargs['match_score'] = 5
     query_sequence = 'AGGGTAATTAGGCGTGTTCACCTA'
     target_sequence = 'TACTTATAAGATGTCTCAACGGCATGCGCAACTTGTGAAGTG'
     query = StripedSmithWaterman(query_sequence, **kwargs)
     align1 = query(target_sequence)
     align2 = local_pairwise_align_ssw(query_sequence,
                                       target_sequence, **kwargs)
     self._check_Alignment_to_AlignmentStructure(align2, align1)

Example #7

 def test_same_as_using_StripedSmithWaterman_object_Protein(self):
     query_sequence = 'HEAGAWGHEE'
     target_sequence = 'PAWHEAE'
     query = StripedSmithWaterman(query_sequence,
                                  protein=True,
                                  substitution_matrix=blosum50)
     align1 = query(target_sequence)
     align2 = local_pairwise_align_ssw(Protein(query_sequence),
                                       Protein(target_sequence),
                                       substitution_matrix=blosum50)
     self._check_TabularMSA_to_AlignmentStructure(align2, align1, Protein)

Example #8

 def test_type_mismatch(self):
     with self.assertRaisesRegex(TypeError, r"same type: 'DNA' != 'RNA'"):
         local_pairwise_align_ssw(DNA('ACGT'), RNA('ACGU'))

Example #9

    def test_invalid_type(self):
        with self.assertRaisesRegex(TypeError, r"not type 'Sequence'"):
            local_pairwise_align_ssw(DNA('ACGT'), Sequence('ACGT'))

        with self.assertRaisesRegex(TypeError, r"not type 'str'"):
            local_pairwise_align_ssw('ACGU', RNA('ACGU'))