def test_global_pairwise_align_nucleotide_penalize_terminal_gaps(self):
# in these tests one sequence is about 3x the length of the other.
# we toggle penalize_terminal_gaps to confirm that it results in
# different alignments and alignment scores.
seq1 = "ACCGTGGACCGTTAGGATTGGACCCAAGGTTG"
seq2 = "T"*25 + "ACCGTGGACCGTAGGATTGGACCAAGGTTA" + "A"*25
aln1 = ("-------------------------ACCGTGGACCGTTAGGA"
"TTGGACCCAAGGTTG-------------------------")
aln2 = ("TTTTTTTTTTTTTTTTTTTTTTTTTACCGTGGACCGT-AGGA"
"TTGGACC-AAGGTTAAAAAAAAAAAAAAAAAAAAAAAAAA")
expected = (aln1, aln2, 131.0)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
actual = global_pairwise_align_nucleotide(
seq1, seq2, gap_open_penalty=5., gap_extend_penalty=0.5,
match_score=5, mismatch_score=-4, penalize_terminal_gaps=False)
self.assertEqual(str(actual[0]), expected[0])
self.assertEqual(str(actual[1]), expected[1])
self.assertEqual(actual.score(), expected[2])
aln1 = ("-------------------------ACCGTGGACCGTTAGGA"
"TTGGACCCAAGGTT-------------------------G")
aln2 = ("TTTTTTTTTTTTTTTTTTTTTTTTTACCGTGGACCGT-AGGA"
"TTGGACC-AAGGTTAAAAAAAAAAAAAAAAAAAAAAAAAA")
expected = (aln1, aln2, 97.0)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
actual = global_pairwise_align_nucleotide(
seq1, seq2, gap_open_penalty=5., gap_extend_penalty=0.5,
match_score=5, mismatch_score=-4, penalize_terminal_gaps=True)
self.assertEqual(str(actual[0]), expected[0])
self.assertEqual(str(actual[1]), expected[1])
self.assertEqual(actual.score(), expected[2])
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_global_pairwise_align_nucleotide(self):
expected = ("G-ACCTTGACCAGGTACC", "GAACTTTGAC---GTAAC", 41.0, 0, 0)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
actual = global_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(), [(0, 16), (0, 14)])
self.assertEqual(actual.ids(), list('01'))
expected = ("-GACCTTGACCAGGTACC", "GAACTTTGAC---GTAAC", 32.0, 0, 0)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
actual = global_pairwise_align_nucleotide(
"GACCTTGACCAGGTACC", "GAACTTTGACGTAAC", gap_open_penalty=10.,
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(), [(0, 16), (0, 14)])
self.assertEqual(actual.ids(), list('01'))
# DNA (rather than str) as input
expected = ("-GACCTTGACCAGGTACC", "GAACTTTGAC---GTAAC", 32.0, 0, 0)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
actual = global_pairwise_align_nucleotide(
DNA("GACCTTGACCAGGTACC", "s1"), DNA("GAACTTTGACGTAAC", "s2"),
gap_open_penalty=10., 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(), [(0, 16), (0, 14)])
self.assertEqual(actual.ids(), ["s1", "s2"])
# ids are provided if they're not passed in
with warnings.catch_warnings():
warnings.simplefilter("ignore")
actual = global_pairwise_align_nucleotide(
DNA("GACCTTGACCAGGTACC"), DNA("GAACTTTGACGTAAC"),
gap_open_penalty=10., gap_extend_penalty=0.5, match_score=5,
mismatch_score=-4)
self.assertEqual(actual.ids(), list('01'))
