def test_nucleotide_aligners_use_substitution_matrices(self):
alt_sub = make_identity_substitution_matrix(10, -10)
# alternate substitution matrix yields different alignment (the
# aligned sequences and the scores are different) with local alignment
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
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_nucleotide_aligners_use_substitution_matrices(self):
alt_sub = make_identity_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_local_pairwise_align_nucleotide(self):
expected = ("ACCTTGACCAGGTACC", "ACTTTGAC---GTAAC", 41.0, 1, 2)
actual = local_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(), [(1, 16), (2, 14)])
self.assertEqual(actual.ids(), list('01'))
expected = ("ACCTTGAC", "ACTTTGAC", 31.0, 1, 2)
actual = local_pairwise_align_nucleotide(
"GACCTTGACCAGGTACC", "GAACTTTGACGTAAC", gap_open_penalty=10.,
gap_extend_penalty=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(), [(1, 8), (2, 9)])
self.assertEqual(actual.ids(), list('01'))
# DNA (rather than str) as input
expected = ("ACCTTGAC", "ACTTTGAC", 31.0, 1, 2)
actual = local_pairwise_align_nucleotide(
DNA("GACCTTGACCAGGTACC", "s1"), DNA("GAACTTTGACGTAAC", "s2"),
gap_open_penalty=10., gap_extend_penalty=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(), [(1, 8), (2, 9)])
self.assertEqual(actual.ids(), ["s1", "s2"])
# Fails when either input is passed as an Alignment
self.assertRaises(TypeError, local_pairwise_align_nucleotide,
Alignment([DNA("GACCTTGACCAGGTACC", "s1")]),
DNA("GAACTTTGACGTAAC", "s2"),
gap_open_penalty=10., gap_extend_penalty=5.,
match_score=5, mismatch_score=-4)
self.assertRaises(TypeError, local_pairwise_align_nucleotide,
DNA("GACCTTGACCAGGTACC", "s1"),
Alignment([DNA("GAACTTTGACGTAAC", "s2")]),
gap_open_penalty=10., gap_extend_penalty=5.,
match_score=5, mismatch_score=-4)
# ids are provided if they're not passed in
actual = local_pairwise_align_nucleotide(
DNA("GACCTTGACCAGGTACC"), DNA("GAACTTTGACGTAAC"),
gap_open_penalty=10., gap_extend_penalty=5., match_score=5,
mismatch_score=-4)
self.assertEqual(actual.ids(), list('01'))
# TypeError on invalid input
self.assertRaises(TypeError, local_pairwise_align_nucleotide,
42, "HEAGAWGHEE")
self.assertRaises(TypeError, local_pairwise_align_nucleotide,
"HEAGAWGHEE", 42)
def test_local_pairwise_align_nucleotide(self):
obs_msa, obs_score, obs_start_end = local_pairwise_align_nucleotide(
DNA("GACCTTGACCAGGTACC"), DNA("GAACTTTGACGTAAC"),
gap_open_penalty=5., gap_extend_penalty=0.5, match_score=5,
mismatch_score=-4)
self.assertEqual(obs_msa, TabularMSA([DNA("ACCTTGACCAGGTACC"),
DNA("ACTTTGAC---GTAAC")]))
self.assertEqual(obs_score, 41.0)
self.assertEqual(obs_start_end, [(1, 16), (2, 14)])
obs_msa, obs_score, obs_start_end = local_pairwise_align_nucleotide(
DNA("GACCTTGACCAGGTACC"), DNA("GAACTTTGACGTAAC"),
gap_open_penalty=10., gap_extend_penalty=5., match_score=5,
mismatch_score=-4)
self.assertEqual(obs_msa, TabularMSA([DNA("ACCTTGAC"),
DNA("ACTTTGAC")]))
self.assertEqual(obs_score, 31.0)
self.assertEqual(obs_start_end, [(1, 8), (2, 9)])
# DNA sequences with metadata
obs_msa, obs_score, obs_start_end = local_pairwise_align_nucleotide(
DNA("GACCTTGACCAGGTACC", metadata={'id': "s1"}),
DNA("GAACTTTGACGTAAC", metadata={'id': "s2"}),
gap_open_penalty=10., gap_extend_penalty=5., match_score=5,
mismatch_score=-4)
self.assertEqual(
obs_msa,
TabularMSA([DNA("ACCTTGAC", metadata={'id': "s1"}),
DNA("ACTTTGAC", metadata={'id': "s2"})]))
self.assertEqual(obs_score, 31.0)
self.assertEqual(obs_start_end, [(1, 8), (2, 9)])
# Fails when either input is passed as a TabularMSA
self.assertRaises(TypeError, local_pairwise_align_nucleotide,
TabularMSA([DNA("GACCTTGACCAGGTACC",
metadata={'id': "s1"})]),
DNA("GAACTTTGACGTAAC", metadata={'id': "s2"}),
gap_open_penalty=10., gap_extend_penalty=5.,
match_score=5, mismatch_score=-4)
self.assertRaises(TypeError, local_pairwise_align_nucleotide,
DNA("GACCTTGACCAGGTACC", metadata={'id': "s1"}),
TabularMSA([DNA("GAACTTTGACGTAAC",
metadata={'id': "s2"})]),
gap_open_penalty=10., gap_extend_penalty=5.,
match_score=5, mismatch_score=-4)
# TypeError on invalid input
self.assertRaises(TypeError, local_pairwise_align_nucleotide,
42, DNA("ACGT"))
self.assertRaises(TypeError, local_pairwise_align_nucleotide,
DNA("ACGT"), 42)
def test_nucleotide_aligners_use_substitution_matrices(self):
alt_sub = make_identity_substitution_matrix(10, -10)
# alternate substitution matrix yields different alignment (the
# aligned sequences and the scores are different) with local alignment
msa_no_sub, score_no_sub, start_end_no_sub = \
local_pairwise_align_nucleotide(
DNA("GACCTTGACCAGGTACC"), DNA("GAACTTTGACGTAAC"),
gap_open_penalty=10., gap_extend_penalty=5., match_score=5,
mismatch_score=-4)
msa_alt_sub, score_alt_sub, start_end_alt_sub = \
local_pairwise_align_nucleotide(
DNA("GACCTTGACCAGGTACC"), DNA("GAACTTTGACGTAAC"),
gap_open_penalty=10., gap_extend_penalty=5., match_score=5,
mismatch_score=-4, substitution_matrix=alt_sub)
self.assertNotEqual(msa_no_sub, msa_alt_sub)
self.assertNotEqual(score_no_sub, score_alt_sub)
self.assertNotEqual(start_end_no_sub, start_end_alt_sub)
# alternate substitution matrix yields different alignment (the
# aligned sequences and the scores are different) with global alignment
msa_no_sub, score_no_sub, start_end_no_sub = \
global_pairwise_align_nucleotide(
DNA("GACCTTGACCAGGTACC"), DNA("GAACTTTGACGTAAC"),
gap_open_penalty=10., gap_extend_penalty=5., match_score=5,
mismatch_score=-4)
msa_alt_sub, score_alt_sub, start_end_alt_sub = \
global_pairwise_align_nucleotide(
DNA("GACCTTGACCAGGTACC"), DNA("GAACTTTGACGTAAC"),
gap_open_penalty=10., gap_extend_penalty=5., match_score=5,
mismatch_score=-4, substitution_matrix=alt_sub)
self.assertNotEqual(msa_no_sub, msa_alt_sub)
self.assertNotEqual(score_no_sub, score_alt_sub)
self.assertEqual(start_end_no_sub, start_end_alt_sub)
def dnaAlign(seq1, seq2, gap_open_penalty, gap_extend_penalty, local=False):
seq1 = seq1.upper()
seq2 = seq2.upper()
if local:
aln, score, _ = local_pairwise_align_nucleotide(
DNA(seq1), DNA(seq2), gap_open_penalty, gap_extend_penalty)
else:
aln, score, _ = global_pairwise_align_nucleotide(
DNA(seq1), DNA(seq2), gap_open_penalty, gap_extend_penalty)
response = {
'aln1':
str(aln[0]),
'aln2':
str(aln[1]),
'score':
score,
'similarity':
float('{:.2f}'.format(aln[0].match_frequency(aln[1], relative=True) *
100))
}
return response
def test_local_pairwise_align_nucleotide(self):
expected = ("ACCTTGACCAGGTACC", "ACTTTGAC---GTAAC", 41.0, 1, 2)
actual = local_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(), [(1, 16), (2, 14)])
self.assertEqual(actual.ids(), list('01'))
expected = ("ACCTTGAC", "ACTTTGAC", 31.0, 1, 2)
actual = local_pairwise_align_nucleotide("GACCTTGACCAGGTACC",
"GAACTTTGACGTAAC",
gap_open_penalty=10.,
gap_extend_penalty=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(), [(1, 8), (2, 9)])
self.assertEqual(actual.ids(), list('01'))
# DNA (rather than str) as input
expected = ("ACCTTGAC", "ACTTTGAC", 31.0, 1, 2)
actual = local_pairwise_align_nucleotide(DNA("GACCTTGACCAGGTACC",
"s1"),
DNA("GAACTTTGACGTAAC", "s2"),
gap_open_penalty=10.,
gap_extend_penalty=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(), [(1, 8), (2, 9)])
self.assertEqual(actual.ids(), ["s1", "s2"])
# Fails when either input is passed as an Alignment
self.assertRaises(TypeError,
local_pairwise_align_nucleotide,
Alignment([DNA("GACCTTGACCAGGTACC", "s1")]),
DNA("GAACTTTGACGTAAC", "s2"),
gap_open_penalty=10.,
gap_extend_penalty=5.,
match_score=5,
mismatch_score=-4)
self.assertRaises(TypeError,
local_pairwise_align_nucleotide,
DNA("GACCTTGACCAGGTACC", "s1"),
Alignment([DNA("GAACTTTGACGTAAC", "s2")]),
gap_open_penalty=10.,
gap_extend_penalty=5.,
match_score=5,
mismatch_score=-4)
# ids are provided if they're not passed in
actual = local_pairwise_align_nucleotide(DNA("GACCTTGACCAGGTACC"),
DNA("GAACTTTGACGTAAC"),
gap_open_penalty=10.,
gap_extend_penalty=5.,
match_score=5,
mismatch_score=-4)
self.assertEqual(actual.ids(), list('01'))
# TypeError on invalid input
self.assertRaises(TypeError, local_pairwise_align_nucleotide, 42,
"HEAGAWGHEE")
self.assertRaises(TypeError, local_pairwise_align_nucleotide,
"HEAGAWGHEE", 42)