def test_pairwise_returns_score(self):
"""exercise pairwise local/global returns alignment score"""
S = make_dna_scoring_dict(10, -1, -8)
aln, score = local_pairwise(seq1, seq2, S, 10, 2, return_score=True)
self.assertTrue(score > 100)
aln, score = global_pairwise(seq1, seq2, S, 10, 2, return_score=True)
self.assertTrue(score > 100)
def test_local_tiebreak(self):
"""Should pick the first best-equal hit rather than the last one"""
# so that the Pyrex and Python versions give the same result.
score_matrix = make_dna_scoring_dict(match=1,
transition=-1,
transversion=-1)
pattern = DNA.make_seq("cwc", name="pattern")
two_hit = DNA.make_seq("cactc", name="target")
aln = local_pairwise(pattern, two_hit, score_matrix, 5, 2)
hit = aln.named_seqs["target"]
self.assertEqual(str(hit).lower(), "cac")