def test_pwise_protein(self):
"""works for pairwise protein alignment"""
from cogent3 import PROTEIN
S = make_generic_scoring_dict(1, PROTEIN)
seq1 = PROTEIN.make_seq("MAYPFQLGLQD", "seq1")
seq2 = PROTEIN.make_seq("MAYPFGLQD", "seq2")
a1 = classic_align_pairwise(seq1, seq2, S, 10, 2, local=False)
self.assertEqual(a1.to_dict(),
dict(seq1="MAYPFQLGLQD", seq2="MAYPF--GLQD"))
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]