def test_global_pairwise_align_protein(self):
expected = ("HEAGAWGHEE-", "---PAW-HEAE", 23.0)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
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
with warnings.catch_warnings():
warnings.simplefilter("ignore")
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)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
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"])
# ids are provided if they're not passed in
with warnings.catch_warnings():
warnings.simplefilter("ignore")
actual = global_pairwise_align_protein(
Protein("HEAGAWGHEE"), Protein("PAWHEAE"),
gap_open_penalty=10., gap_extend_penalty=5.)
self.assertEqual(actual.ids(), list('01'))
def test_global_pairwise_align_protein_penalize_terminal_gaps(self):
expected = ("HEAGAWGHEE", "---PAWHEAE", 1.0)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
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'))
