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