def test_nucleotide_aligners_use_substitution_matrices(self): alt_sub = _make_nt_substitution_matrix(10, -10) # alternate substitution matrix yields different alignment (the # aligned sequences and the scores are different) with local alignment with warnings.catch_warnings(): warnings.simplefilter("ignore") actual_no_sub = local_pairwise_align_nucleotide( "GACCTTGACCAGGTACC", "GAACTTTGACGTAAC", gap_open_penalty=10., gap_extend_penalty=5., match_score=5, mismatch_score=-4) actual_alt_sub = local_pairwise_align_nucleotide( "GACCTTGACCAGGTACC", "GAACTTTGACGTAAC", gap_open_penalty=10., gap_extend_penalty=5., match_score=5, mismatch_score=-4, substitution_matrix=alt_sub) self.assertNotEqual(str(actual_no_sub[0]), str(actual_alt_sub[0])) self.assertNotEqual(str(actual_no_sub[1]), str(actual_alt_sub[1])) self.assertNotEqual(actual_no_sub.score(), actual_alt_sub.score()) # alternate substitution matrix yields different alignment (the # aligned sequences and the scores are different) with global alignment with warnings.catch_warnings(): warnings.simplefilter("ignore") actual_no_sub = local_pairwise_align_nucleotide( "GACCTTGACCAGGTACC", "GAACTTTGACGTAAC", gap_open_penalty=10., gap_extend_penalty=5., match_score=5, mismatch_score=-4) actual_alt_sub = global_pairwise_align_nucleotide( "GACCTTGACCAGGTACC", "GAACTTTGACGTAAC", gap_open_penalty=10., gap_extend_penalty=5., match_score=5, mismatch_score=-4, substitution_matrix=alt_sub) self.assertNotEqual(str(actual_no_sub[0]), str(actual_alt_sub[0])) self.assertNotEqual(str(actual_no_sub[1]), str(actual_alt_sub[1])) self.assertNotEqual(actual_no_sub.score(), actual_alt_sub.score())
def test_local_pairwise_align_nucleotide(self): m = _make_nt_substitution_matrix(5, -4) expected = ("ACCTTGACCAGGTACC", "ACTTTGAC---GTAAC", 41.0, 1, 2) with warnings.catch_warnings(): warnings.simplefilter("ignore") actual = local_pairwise_align_nucleotide( "GACCTTGACCAGGTACC", "GAACTTTGACGTAAC", gap_open_penalty=5., gap_extend_penalty=0.5, match_score=5, mismatch_score=-4) self.assertEqual(str(actual[0]), expected[0]) self.assertEqual(str(actual[1]), expected[1]) self.assertEqual(actual.score(), expected[2]) self.assertEqual(actual.start_end_positions(), [(1, 16), (2, 14)]) self.assertEqual(actual.ids(), list('01')) expected = ("ACCTTGAC", "ACTTTGAC", 31.0, 1, 2) with warnings.catch_warnings(): warnings.simplefilter("ignore") actual = local_pairwise_align_nucleotide( "GACCTTGACCAGGTACC", "GAACTTTGACGTAAC", gap_open_penalty=10., gap_extend_penalty=5., match_score=5, mismatch_score=-4) self.assertEqual(str(actual[0]), expected[0]) self.assertEqual(str(actual[1]), expected[1]) self.assertEqual(actual.score(), expected[2]) self.assertEqual(actual.start_end_positions(), [(1, 8), (2, 9)]) self.assertEqual(actual.ids(), list('01')) # DNA (rather than str) as input expected = ("ACCTTGAC", "ACTTTGAC", 31.0, 1, 2) with warnings.catch_warnings(): warnings.simplefilter("ignore") actual = local_pairwise_align_nucleotide( DNA("GACCTTGACCAGGTACC", "s1"), DNA("GAACTTTGACGTAAC", "s2"), gap_open_penalty=10., gap_extend_penalty=5., match_score=5, mismatch_score=-4) self.assertEqual(str(actual[0]), expected[0]) self.assertEqual(str(actual[1]), expected[1]) self.assertEqual(actual.score(), expected[2]) self.assertEqual(actual.start_end_positions(), [(1, 8), (2, 9)]) self.assertEqual(actual.ids(), ["s1", "s2"]) # ids are provided if they're not passed in with warnings.catch_warnings(): warnings.simplefilter("ignore") actual = local_pairwise_align_nucleotide( DNA("GACCTTGACCAGGTACC"), DNA("GAACTTTGACGTAAC"), gap_open_penalty=10., gap_extend_penalty=5., match_score=5, mismatch_score=-4) self.assertEqual(actual.ids(), list('01'))