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# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# ----------------------------------------------------------------------------
import unittest
import numpy as np
import numpy.testing as npt
from skbio import Protein
class TestProtein(unittest.TestCase):
def test_alphabet(self):
expected = set("ACDEFGHIKLMNPQRSTVWYBZX-.*")
self.assertIs(type(Protein.alphabet), set)
self.assertEqual(Protein.alphabet, expected)
Protein.alphabet.add("JO")
self.assertEqual(Protein.alphabet, expected)
self.assertEqual(Protein('').alphabet, expected)
with self.assertRaises(AttributeError):
Protein('').alphabet = set("ABCD")
# TODO: duplicate of test_definite_chars, remove when nondegenerate_chars,
# is removed
def test_nondegenerate_chars(self):
exp = set("ACDEFGHIKLMNPQRSTVWY")
self.assertEqual(Protein("").nondegenerate_chars, exp)
self.assertEqual(Protein.nondegenerate_chars, exp)
def test_definite_chars(self):
exp = set("ACDEFGHIKLMNPQRSTVWY")
self.assertEqual(Protein("").definite_chars, exp)
self.assertEqual(Protein.definite_chars, exp)
def test_degenerate_map(self):
exp = {
'B': set(['D', 'N']), 'Z': set(['E', 'Q']),
'X': set(['A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M',
'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y'])
}
self.assertEqual(Protein("").degenerate_map, exp)
self.assertEqual(Protein.degenerate_map, exp)
def test_stop_chars(self):
expected = set('*')
self.assertIs(type(Protein.stop_chars), set)
self.assertEqual(Protein.stop_chars, expected)
Protein.stop_chars.add("JO")
self.assertEqual(Protein.stop_chars, expected)
self.assertEqual(Protein('').stop_chars, expected)
with self.assertRaises(AttributeError):
Protein('').stop_chars = set("^&")
def test_stops(self):
npt.assert_array_equal(Protein('').stops(), np.array([]))
npt.assert_array_equal(Protein('P').stops(), np.array([False]))
npt.assert_array_equal(Protein('PAW').stops(),
np.array([False, False, False]))
npt.assert_array_equal(Protein('PAW*').stops(),
np.array([False, False, False, True]))
npt.assert_array_equal(Protein('P*W*').stops(),
np.array([False, True, False, True]))
npt.assert_array_equal(Protein('****').stops(),
np.array([True, True, True, True]))
npt.assert_array_equal(Protein('XZB-.').stops(),
np.array([False, False, False, False, False]))
def test_has_stops(self):
self.assertFalse(Protein('').has_stops())
self.assertFalse(Protein('P').has_stops())
self.assertFalse(Protein('PAW').has_stops())
self.assertTrue(Protein('PAW*').has_stops())
self.assertTrue(Protein('P*W*').has_stops())
self.assertTrue(Protein('****').has_stops())
self.assertFalse(Protein('XZB-.').has_stops())
def test_motif_n_glycosylation(self):
seq = Protein("ACDFFACGNPSL")
self.assertEqual(list(seq.find_motifs("N-glycosylation")), [])
seq = Protein("ACDFNFTACGNPSL")
self.assertEqual(list(seq.find_motifs("N-glycosylation")),
[slice(4, 8)])
seq = Protein("AC-DFN-FTACGNPSL")
self.assertEqual(list(seq.find_motifs("N-glycosylation",
ignore=seq.gaps())),
[slice(5, 10)])
def test_repr(self):
# basic sanity checks for custom repr stats. more extensive testing is
# performed on Sequence.__repr__
obs = repr(Protein(''))
# obtained from super()
self.assertIn('has gaps: False', obs)
# custom to Protein
self.assertIn('has stops: False', obs)
obs = repr(Protein('PAW'))
self.assertIn('has gaps: False', obs)
self.assertIn('has stops: False', obs)
obs = repr(Protein('PA*W-'))
self.assertIn('has gaps: True', obs)
self.assertIn('has stops: True', obs)
obs = repr(Protein('*****'))
self.assertIn('has gaps: False', obs)
self.assertIn('has stops: True', obs)
def test_cannot_subclass(self):
with self.assertRaisesRegex(TypeError, "Subclassing disabled"):
class CustomSequence(Protein):
pass
if __name__ == "__main__":
unittest.main()
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