def test_nondefault_k(self):
seq1 = Sequence('GCTTATGGAGAGAGA')
seq2 = Sequence('CTCGAACTCCAGCCA')
obs = kmer_distance(seq1, seq2, 2)
exp = 0.7333333333333333
self.assertAlmostEqual(obs, exp)
seq1 = Sequence('EADDECAEECDEACD')
seq2 = Sequence('DCBCBADADABCCDA')
obs = kmer_distance(seq1, seq2, 1)
exp = 0.4
self.assertAlmostEqual(obs, exp)
def test_nondefault_k(self):
seq1 = Sequence('GCTTATGGAGAGAGA')
seq2 = Sequence('CTCGAACTCCAGCCA')
obs = kmer_distance(seq1, seq2, 2)
exp = 0.7333333333333333
self.assertAlmostEqual(obs, exp)
seq1 = Sequence('EADDECAEECDEACD')
seq2 = Sequence('DCBCBADADABCCDA')
obs = kmer_distance(seq1, seq2, 1)
exp = 0.4
self.assertAlmostEqual(obs, exp)
def test_with_metadata_sanity(self):
seq1 = Sequence('AACCTAGCAATGGAT',
metadata={'Name': 'Kestrel Gorlick'},
positional_metadata={'seq': list('ACTCAAGCTACGAAG')})
seq2 = Sequence('CAGGCAGTTCTCACC')
obs = kmer_distance(seq1, seq2, 3)
exp = 0.9130434782608695
self.assertAlmostEqual(obs, exp)
def test_with_metadata_sanity(self):
seq1 = Sequence('AACCTAGCAATGGAT',
metadata={'Name': 'Kestrel Gorlick'},
positional_metadata={'seq': list('ACTCAAGCTACGAAG')})
seq2 = Sequence('CAGGCAGTTCTCACC')
obs = kmer_distance(seq1, seq2, 3)
exp = 0.9130434782608695
self.assertAlmostEqual(obs, exp)
def test_type_mismatch_error(self):
seq1 = Sequence('ABC')
seq2 = DNA('ATC')
with self.assertRaisesRegex(TypeError, r"Type 'Sequence'.*type 'DNA'"):
kmer_distance(seq1, seq2, 3)
def test_no_kmers_found(self):
seq1 = Sequence('ATCG')
seq2 = Sequence('ACGT')
obs = kmer_distance(seq1, seq2, 5)
npt.assert_equal(obs, np.nan)
def test_empty_sequences(self):
seq1 = Sequence('')
seq2 = Sequence('')
obs = kmer_distance(seq1, seq2, 3)
npt.assert_equal(obs, np.nan)
def test_differing_length_seqs(self):
seq1 = Sequence('AGAAATCTGAGCAAGGATCA')
seq2 = Sequence('TTAGTGCGTAATCCG')
obs = kmer_distance(seq1, seq2, 3)
exp = 0.9285714285714286
self.assertAlmostEqual(obs, exp)
def test_entirely_different_sequences(self):
seq1 = Sequence('CCGTGGTCGTATAAG')
seq2 = Sequence('CGCCTTCCACATCAG')
obs = kmer_distance(seq1, seq2, 3)
exp = 1.0
self.assertEqual(obs, exp)
def test_return_type(self):
seq1 = Sequence('ATCG')
seq2 = Sequence('ATCG')
obs = kmer_distance(seq1, seq2, 3)
self.assertIsInstance(obs, float)
self.assertEqual(obs, 0.0)
def test_with_sequence_subclass(self):
seq1 = DNA('GATGGTACTGTAGGT')
seq2 = DNA('AGGGTGAAGGTATCA')
obs = kmer_distance(seq1, seq2, 3)
exp = 0.8421052631578947
self.assertAlmostEqual(obs, exp)
def test_differing_length_seqs(self):
seq1 = Sequence('AGAAATCTGAGCAAGGATCA')
seq2 = Sequence('TTAGTGCGTAATCCG')
obs = kmer_distance(seq1, seq2, 3)
exp = 0.9285714285714286
self.assertAlmostEqual(obs, exp)
def test_same_sequence(self):
seq1 = Sequence('CTGCGACAGTTGGTA')
seq2 = Sequence('CTGCGACAGTTGGTA')
obs = kmer_distance(seq1, seq2, 3)
exp = 0.0
self.assertEqual(obs, exp)
def test_entirely_different_sequences(self):
seq1 = Sequence('CCGTGGTCGTATAAG')
seq2 = Sequence('CGCCTTCCACATCAG')
obs = kmer_distance(seq1, seq2, 3)
exp = 1.0
self.assertEqual(obs, exp)
def test_overlap_false(self):
seq1 = Sequence('CGTTATGTCTGTGAT')
seq2 = Sequence('CTGAATCGGTAGTGT')
obs = kmer_distance(seq1, seq2, 3, overlap=False)
exp = 0.8888888888888888
self.assertAlmostEqual(obs, exp)
def test_empty_sequences(self):
seq1 = Sequence('')
seq2 = Sequence('')
obs = kmer_distance(seq1, seq2, 3)
npt.assert_equal(obs, np.nan)
def test_overlap_false(self):
seq1 = Sequence('CGTTATGTCTGTGAT')
seq2 = Sequence('CTGAATCGGTAGTGT')
obs = kmer_distance(seq1, seq2, 3, overlap=False)
exp = 0.8888888888888888
self.assertAlmostEqual(obs, exp)
def test_one_empty_sequence(self):
seq1 = Sequence('')
seq2 = Sequence('CGGGCAGCTCCTACCTGCTA')
obs = kmer_distance(seq1, seq2, 3)
exp = 1.0
self.assertAlmostEqual(obs, exp)
def test_same_sequence(self):
seq1 = Sequence('CTGCGACAGTTGGTA')
seq2 = Sequence('CTGCGACAGTTGGTA')
obs = kmer_distance(seq1, seq2, 3)
exp = 0.0
self.assertEqual(obs, exp)
def test_no_kmers_found(self):
seq1 = Sequence('ATCG')
seq2 = Sequence('ACGT')
obs = kmer_distance(seq1, seq2, 5)
npt.assert_equal(obs, np.nan)
def test_with_sequence_subclass(self):
seq1 = DNA('GATGGTACTGTAGGT')
seq2 = DNA('AGGGTGAAGGTATCA')
obs = kmer_distance(seq1, seq2, 3)
exp = 0.8421052631578947
self.assertAlmostEqual(obs, exp)
def test_k_less_than_one_error(self):
seq1 = Sequence('ATCG')
seq2 = Sequence('ACTG')
with self.assertRaisesRegex(ValueError, 'k must be greater than 0.'):
kmer_distance(seq1, seq2, 0)
def test_return_type(self):
seq1 = Sequence('ATCG')
seq2 = Sequence('ATCG')
obs = kmer_distance(seq1, seq2, 3)
self.assertIsInstance(obs, float)
self.assertEqual(obs, 0.0)
def test_type_mismatch_error(self):
seq1 = Sequence('ABC')
seq2 = DNA('ATC')
with self.assertRaisesRegex(TypeError, "Type 'Sequence'.*type 'DNA'"):
kmer_distance(seq1, seq2, 3)
def test_one_empty_sequence(self):
seq1 = Sequence('')
seq2 = Sequence('CGGGCAGCTCCTACCTGCTA')
obs = kmer_distance(seq1, seq2, 3)
exp = 1.0
self.assertAlmostEqual(obs, exp)
def test_non_sequence_error(self):
seq1 = Sequence('ATCG')
seq2 = 'ATCG'
with self.assertRaisesRegex(TypeError, "not 'str'"):
kmer_distance(seq1, seq2, 3)
def test_k_less_than_one_error(self):
seq1 = Sequence('ATCG')
seq2 = Sequence('ACTG')
with self.assertRaisesRegex(ValueError, r'k must be greater than 0.'):
kmer_distance(seq1, seq2, 0)
def test_default_kwargs(self):
seq1 = Sequence('AACCTAGCAATGGAT')
seq2 = Sequence('CAGGCAGTTCTCACC')
obs = kmer_distance(seq1, seq2, 3)
exp = 0.9130434782608695
self.assertAlmostEqual(obs, exp)
def test_non_sequence_error(self):
seq1 = Sequence('ATCG')
seq2 = 'ATCG'
with self.assertRaisesRegex(TypeError, r"not 'str'"):
kmer_distance(seq1, seq2, 3)
def test_default_kwargs(self):
seq1 = Sequence('AACCTAGCAATGGAT')
seq2 = Sequence('CAGGCAGTTCTCACC')
obs = kmer_distance(seq1, seq2, 3)
exp = 0.9130434782608695
self.assertAlmostEqual(obs, exp)