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]