def test_global_pairwise_align_protein_penalize_terminal_gaps(self):
obs_msa, obs_score, obs_start_end = global_pairwise_align_protein(
Protein("HEAGAWGHEE"), Protein("PAWHEAE"), gap_open_penalty=10.,
gap_extend_penalty=5., penalize_terminal_gaps=True)
self.assertEqual(obs_msa, TabularMSA([Protein("HEAGAWGHEE"),
Protein("---PAWHEAE")]))
self.assertEqual(obs_score, 1.0)
self.assertEqual(obs_start_end, [(0, 9), (0, 6)])
def test_global_pairwise_align_protein_penalize_terminal_gaps(self):
expected = ("HEAGAWGHEE", "---PAWHEAE", 1.0)
actual = global_pairwise_align_protein(
"HEAGAWGHEE", "PAWHEAE", gap_open_penalty=10.,
gap_extend_penalty=5., penalize_terminal_gaps=True)
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, 9), (0, 6)])
self.assertEqual(actual.ids(), list('01'))
def test_global_pairwise_align_protein_penalize_terminal_gaps(self):
expected = ("HEAGAWGHEE", "---PAWHEAE", 1.0)
actual = global_pairwise_align_protein("HEAGAWGHEE",
"PAWHEAE",
gap_open_penalty=10.,
gap_extend_penalty=5.,
penalize_terminal_gaps=True)
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, 9), (0, 6)])
self.assertEqual(actual.ids(), list('01'))
def test_global_pairwise_align_protein_invalid_dtype(self):
with self.assertRaisesRegex(TypeError,
"TabularMSA with Protein dtype.*dtype "
"'DNA'"):
global_pairwise_align_protein(TabularMSA([Protein('PAW')]),
TabularMSA([DNA('ACGT')]))
def test_global_pairwise_align_protein(self):
obs_msa, obs_score, obs_start_end = global_pairwise_align_protein(
Protein("HEAGAWGHEE"), Protein("PAWHEAE"), gap_open_penalty=10.,
gap_extend_penalty=5.)
self.assertEqual(obs_msa, TabularMSA([Protein("HEAGAWGHEE-"),
Protein("---PAW-HEAE")]))
self.assertEqual(obs_score, 23.0)
self.assertEqual(obs_start_end, [(0, 9), (0, 6)])
# EMBOSS result: P---AW-HEAE
obs_msa, obs_score, obs_start_end = global_pairwise_align_protein(
Protein("HEAGAWGHEE"), Protein("PAWHEAE"), gap_open_penalty=5.,
gap_extend_penalty=0.5)
self.assertEqual(obs_msa, TabularMSA([Protein("HEAGAWGHE-E"),
Protein("---PAW-HEAE")]))
self.assertEqual(obs_score, 30.0)
self.assertEqual(obs_start_end, [(0, 9), (0, 6)])
# Protein sequences with metadata
obs_msa, obs_score, obs_start_end = global_pairwise_align_protein(
Protein("HEAGAWGHEE", metadata={'id': "s1"}),
Protein("PAWHEAE", metadata={'id': "s2"}),
gap_open_penalty=10., gap_extend_penalty=5.)
self.assertEqual(
obs_msa,
TabularMSA([Protein("HEAGAWGHEE-", metadata={'id': "s1"}),
Protein("---PAW-HEAE", metadata={'id': "s2"})]))
self.assertEqual(obs_score, 23.0)
self.assertEqual(obs_start_end, [(0, 9), (0, 6)])
# One TabularMSA and one Protein as input
obs_msa, obs_score, obs_start_end = global_pairwise_align_protein(
TabularMSA([Protein("HEAGAWGHEE", metadata={'id': "s1"})]),
Protein("PAWHEAE", metadata={'id': "s2"}),
gap_open_penalty=10., gap_extend_penalty=5.)
self.assertEqual(
obs_msa,
TabularMSA([Protein("HEAGAWGHEE-", metadata={'id': "s1"}),
Protein("---PAW-HEAE", metadata={'id': "s2"})]))
self.assertEqual(obs_score, 23.0)
self.assertEqual(obs_start_end, [(0, 9), (0, 6)])
# One single-sequence alignment as input and one double-sequence
# alignment as input. Score confirmed manually.
obs_msa, obs_score, obs_start_end = global_pairwise_align_protein(
TabularMSA([Protein("HEAGAWGHEE", metadata={'id': "s1"}),
Protein("HDAGAWGHDE", metadata={'id': "s2"})]),
TabularMSA([Protein("PAWHEAE", metadata={'id': "s3"})]),
gap_open_penalty=10., gap_extend_penalty=5.)
self.assertEqual(
obs_msa,
TabularMSA([Protein("HEAGAWGHEE-", metadata={'id': "s1"}),
Protein("HDAGAWGHDE-", metadata={'id': "s2"}),
Protein("---PAW-HEAE", metadata={'id': "s3"})]))
self.assertEqual(obs_score, 21.0)
self.assertEqual(obs_start_end, [(0, 9), (0, 6)])
# TypeError on invalid input
self.assertRaises(TypeError, global_pairwise_align_protein,
42, Protein("HEAGAWGHEE"))
self.assertRaises(TypeError, global_pairwise_align_protein,
Protein("HEAGAWGHEE"), 42)
def test_global_pairwise_align_protein(self):
expected = ("HEAGAWGHEE-", "---PAW-HEAE", 23.0)
actual = global_pairwise_align_protein("HEAGAWGHEE",
"PAWHEAE",
gap_open_penalty=10.,
gap_extend_penalty=5.)
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, 9), (0, 6)])
self.assertEqual(actual.ids(), list('01'))
expected = ("HEAGAWGHE-E", "---PAW-HEAE", 30.0)
# EMBOSS result: P---AW-HEAE
actual = global_pairwise_align_protein("HEAGAWGHEE",
"PAWHEAE",
gap_open_penalty=5.,
gap_extend_penalty=0.5)
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, 9), (0, 6)])
self.assertEqual(actual.ids(), list('01'))
# Protein (rather than str) as input
expected = ("HEAGAWGHEE-", "---PAW-HEAE", 23.0)
actual = global_pairwise_align_protein(Protein("HEAGAWGHEE", "s1"),
Protein("PAWHEAE", "s2"),
gap_open_penalty=10.,
gap_extend_penalty=5.)
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, 9), (0, 6)])
self.assertEqual(actual.ids(), ["s1", "s2"])
# One Alignment and one Protein as input
expected = ("HEAGAWGHEE-", "---PAW-HEAE", 23.0)
actual = global_pairwise_align_protein(Alignment(
[Protein("HEAGAWGHEE", "s1")]),
Protein("PAWHEAE", "s2"),
gap_open_penalty=10.,
gap_extend_penalty=5.)
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, 9), (0, 6)])
self.assertEqual(actual.ids(), ["s1", "s2"])
# One single-sequence alignment as input and one double-sequence
# alignment as input. Score confirmed manually.
expected = ("HEAGAWGHEE-", "HDAGAWGHDE-", "---PAW-HEAE", 21.0)
actual = global_pairwise_align_protein(Alignment(
[Protein("HEAGAWGHEE", "s1"),
Protein("HDAGAWGHDE", "s2")]),
Alignment(
[Protein("PAWHEAE", "s3")]),
gap_open_penalty=10.,
gap_extend_penalty=5.)
self.assertEqual(str(actual[0]), expected[0])
self.assertEqual(str(actual[1]), expected[1])
self.assertEqual(str(actual[2]), expected[2])
self.assertEqual(actual.score(), expected[3])
self.assertEqual(actual.start_end_positions(), [(0, 9), (0, 6)])
self.assertEqual(actual.ids(), ["s1", "s2", "s3"])
# ids are provided if they're not passed in
actual = global_pairwise_align_protein(Protein("HEAGAWGHEE"),
Protein("PAWHEAE"),
gap_open_penalty=10.,
gap_extend_penalty=5.)
self.assertEqual(actual.ids(), list('01'))
# TypeError on invalid input
self.assertRaises(TypeError, global_pairwise_align_protein, 42,
"HEAGAWGHEE")
self.assertRaises(TypeError, global_pairwise_align_protein,
"HEAGAWGHEE", 42)
def test_global_pairwise_align_protein(self):
expected = ("HEAGAWGHEE-", "---PAW-HEAE", 23.0)
actual = global_pairwise_align_protein(
"HEAGAWGHEE", "PAWHEAE", gap_open_penalty=10.,
gap_extend_penalty=5.)
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, 9), (0, 6)])
self.assertEqual(actual.ids(), list('01'))
expected = ("HEAGAWGHE-E", "---PAW-HEAE", 30.0)
# EMBOSS result: P---AW-HEAE
actual = global_pairwise_align_protein(
"HEAGAWGHEE", "PAWHEAE", gap_open_penalty=5.,
gap_extend_penalty=0.5)
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, 9), (0, 6)])
self.assertEqual(actual.ids(), list('01'))
# Protein (rather than str) as input
expected = ("HEAGAWGHEE-", "---PAW-HEAE", 23.0)
actual = global_pairwise_align_protein(
Protein("HEAGAWGHEE", metadata={'id': "s1"}),
Protein("PAWHEAE", metadata={'id': "s2"}),
gap_open_penalty=10., gap_extend_penalty=5.)
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, 9), (0, 6)])
self.assertEqual(actual.ids(), ["s1", "s2"])
# One Alignment and one Protein as input
expected = ("HEAGAWGHEE-", "---PAW-HEAE", 23.0)
actual = global_pairwise_align_protein(
Alignment([Protein("HEAGAWGHEE", metadata={'id': "s1"})]),
Protein("PAWHEAE", metadata={'id': "s2"}),
gap_open_penalty=10., gap_extend_penalty=5.)
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, 9), (0, 6)])
self.assertEqual(actual.ids(), ["s1", "s2"])
# One single-sequence alignment as input and one double-sequence
# alignment as input. Score confirmed manually.
expected = ("HEAGAWGHEE-", "HDAGAWGHDE-", "---PAW-HEAE", 21.0)
actual = global_pairwise_align_protein(
Alignment([Protein("HEAGAWGHEE", metadata={'id': "s1"}),
Protein("HDAGAWGHDE", metadata={'id': "s2"})]),
Alignment([Protein("PAWHEAE", metadata={'id': "s3"})]),
gap_open_penalty=10., gap_extend_penalty=5.)
self.assertEqual(str(actual[0]), expected[0])
self.assertEqual(str(actual[1]), expected[1])
self.assertEqual(str(actual[2]), expected[2])
self.assertEqual(actual.score(), expected[3])
self.assertEqual(actual.start_end_positions(), [(0, 9), (0, 6)])
self.assertEqual(actual.ids(), ["s1", "s2", "s3"])
# ids are provided if they're not passed in
actual = global_pairwise_align_protein(
Protein("HEAGAWGHEE"),
Protein("PAWHEAE"),
gap_open_penalty=10., gap_extend_penalty=5.)
self.assertEqual(actual.ids(), list('01'))
# TypeError on invalid input
self.assertRaises(TypeError, global_pairwise_align_protein,
42, "HEAGAWGHEE")
self.assertRaises(TypeError, global_pairwise_align_protein,
"HEAGAWGHEE", 42)
