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")
def test(r=1, **kw):
S = make_dna_scoring_dict(10, -1, -8)
seq2 = DNA.make_seq("AAAATGCTTA" * r)
seq1 = DNA.make_seq("AATTTTGCTG" * r)
t0 = time.clock()
try:
# return_alignment is False in order to emphasise the quadratic part of
# the work.
aln = classic_align_pairwise(seq1,
seq2,
S,
10,
2,
local=False,
return_alignment=False,
**kw)
except ArithmeticError:
return "*"
else:
t = time.clock() - t0
return int((len(seq1) * len(seq2)) / t / 1000)
def _aligned_both_ways(self, seq1, seq2, **kw):
S = make_dna_scoring_dict(10, -1, -8)
a1 = classic_align_pairwise(seq1, seq2, S, 10, 2, **kw)
a2 = classic_align_pairwise(seq2, seq1, S, 10, 2, **kw)
return [a1, a2]
