def test_dot_plot(self):
s1 = BioSeq("ATAT", "DNA")
s2 = BioSeq("ATAT", "DNA")
m = s1.dot_plot(s2)
self.assertEqual(m.sum(), 8)
s3 = BioSeq("XXXT", "DNA")
m = s1.dot_plot(s3)
self.assertEqual(m.sum(), 2)
def test_eq(self):
s1 = BioSeq("ATATAT", "DNA")
s2 = BioSeq("ATATAT", "DNA")
self.assertTrue(s1 == s2)
self.assertFalse(s1 != s2)
s3 = BioSeq("ATATATX", "DNA")
s4 = BioSeq("ATATAT", "PROTEIN")
self.assertFalse(s1 == s3)
def test_global_align(self):
# example from page 39 from slides
s1 = BioSeq("PHSWG", "PROTEIN")
s2 = BioSeq("HGWAG", "PROTEIN")
sm = read_substitution_matrix_file("test/blosum62.mat")
s, t = s1.global_align_multiple_solutions(s2, sm, -8)
self.assertListEqual([-40, -24, -10, 3, 11, 9], s[-1])
recover = list(s1.recover_global_align_multiple_solutions(s2, t))
self.assertListEqual([('PHSW_G', '_HGWAG')], recover)
def test_save_load(self):
filename = "test_save_load.tmp"
s = BioSeq("ATATACAGATGAT", "DNA")
s.save(filename)
s2 = BioSeq("", "RNA")
s2.load(filename)
self.assertEqual(s.seq_type, s2.seq_type)
self.assertEqual(s.sequence, s2.sequence)
os.remove(filename)
def test_hamming_distance(self):
s1 = BioSeq("ATATACAGATGAT", "DNA")
s2 = BioSeq("ATATACAGATGAT", "DNA")
self.assertEqual(0, s1.hamming_distance(s2))
self.assertEqual(0, s2.hamming_distance(s1))
s3 = BioSeq("ATATACAGATGAX", "DNA")
self.assertEqual(1, s1.hamming_distance(s3))
self.assertEqual(1, s3.hamming_distance(s1))
s4 = BioSeq("AAA", "DNA")
self.assertRaises(Exception, s1.hamming_distance, s4)
def test_global_align2(self):
# example from page 46 from slides
s1 = BioSeq("PHSWG", "PROTEIN")
s2 = BioSeq("HGWAG", "PROTEIN")
sm = read_substitution_matrix_file("test/blosum62.mat")
s, t = s1.local_align_multiple_solutions(s2, sm, -8)
self.assertListEqual([0, 0, 6, 11, 19, 17], s[-1])
recover = list(s1.recover_local_align_multiple_solutions(s2, t, s))
self.assertListEqual([('HSW', 'HGW'), ('HSWG', 'HGWA')], recover)
self.assertEqual(
len(BioSeq.compare_pairwise_global_align([s1, s2], sm, -8)), 2)
self.assertEqual(
len(BioSeq.compare_pairwise_local_align([s1, s2], sm, -8)), 2)
def test_gc_content(self):
s = BioSeq("AACCCCCTGG", "DNA")
self.assertEqual(0.70, s.gc_content())
s.sequence = "AA"
self.assertEqual(0.0, s.gc_content())
s.sequence = "GC"
self.assertEqual(1.0, s.gc_content())
def test_frequency(self):
s = BioSeq("AACCCCCTGG", "DNA")
self.assertDictEqual({
"A": 0.2,
"C": 0.5,
"T": 0.1,
"G": 0.2
}, s.frequency())
def test_getslice(self):
s = BioSeq("ATATAT", "DNA")
self.assertEqual("A", s[0:1])
self.assertEqual("T", s[-1:])
self.assertEqual("AT", s[0:2])
self.assertEqual("A", s[0:1:1])
self.assertEqual("T", s[-1::1])
self.assertEqual("AAA", s[0::2])
# explicit invocation of function
self.assertEqual("A", s.__getslice__(0, 1))
self.assertEqual("T", s.__getslice__(-1, len(s)))
self.assertEqual("AT", s.__getslice__(0, 2))
self.assertEqual("A", s.__getslice__(0, 1, 1))
self.assertEqual("T", s.__getslice__(-1, len(s), 1))
self.assertEqual("AAA", s.__getslice__(0, len(s), 2))
def test_add_gap(self):
s = BioSeq("ATGC", "DNA")
self.assertEqual("ATGC", str(s))
s.add_gap(2)
self.assertEqual("AT_GC", str(s))
def test_pretty_print(self):
s = BioSeq("ATATACAGATGAT", "DNA")
self._test_pretty_print(s)
def test_constructor(self):
s = BioSeq("ATATat", "DNa")
self.assertIsInstance(s, BioSeq)
self.assertEqual("ATATAT", s.sequence)
self.assertEqual("DNA", s.seq_type)
self.assertRaises(Exception, BioSeq, "ATAT", "smth")
def test_len(self):
s = BioSeq("ATATAT", "DNA")
self.assertEqual(6, len(s))
def test_getitem(self):
s = BioSeq("ATATAT", "DNA")
self.assertEqual("A", s[0])
self.assertEqual("T", s[-1])
def test_repr(self):
s = [BioSeq("ATATAT", "DNA")]
self.assertEqual("[ATATAT]", str(s))
def test_str(self):
s = BioSeq("ATATAT", "DNA")
self.assertEqual("ATATAT", str(s))
def test_score_seq(self):
sm = substitution_matrix("ATCG", 2, -3)
s1 = BioSeq("ATAT", "DNA")
s2 = BioSeq("ATAG", "DNA")
self.assertEqual(3, s1.score_seq(s2, sm, 3))
def test_score_affine_gap(self):
sm = read_substitution_matrix_file("test/blosum62.mat")
s1 = BioSeq("LGPSSGCASRIWTKSA", "PROTEIN")
s2 = BioSeq("TGPS_G__S_IWSKSG", "PROTEIN")
self.assertEqual(33, s1.score_affine_gap(s2, sm, -8, -2))
def test_assert_seq_type(self):
s = BioSeq("ATATAT", "DNA")
s = BioSeq("ATATAT", "RNA")
s = BioSeq("ATATAT", "PROTEIN")
self.assertRaises(Exception, BioSeq, "ATATA", "asd")