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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 itertools
import unittest
import numpy as np
import numpy.testing as npt
from skbio import Sequence, DNA
from skbio.sequence.distance import hamming, kmer_distance
class TestHamming(unittest.TestCase):
def test_non_sequence(self):
seq1 = Sequence('abc')
seq2 = 'abc'
with self.assertRaisesRegex(TypeError, 'seq1.*seq2.*Sequence.*str'):
hamming(seq1, seq2)
with self.assertRaisesRegex(TypeError, 'seq1.*seq2.*Sequence.*str'):
hamming(seq2, seq1)
def test_type_mismatch(self):
seq1 = Sequence('ABC')
seq2 = DNA('ACG')
with self.assertRaisesRegex(TypeError,
'Sequence.*does not match.*DNA'):
hamming(seq1, seq2)
def test_length_mismatch(self):
seq1 = Sequence('ABC')
seq2 = Sequence('ABCD')
with self.assertRaisesRegex(ValueError, 'equal length.*3 != 4'):
hamming(seq1, seq2)
def test_return_type(self):
seq1 = Sequence('ABC')
seq2 = Sequence('ABC')
distance = hamming(seq1, seq2)
self.assertIsInstance(distance, float)
self.assertEqual(distance, 0.0)
def test_minimum_distance(self):
seq1 = Sequence('ABC')
seq2 = Sequence('ABC')
distance = hamming(seq1, seq2)
self.assertEqual(distance, 0.0)
def test_mid_range_distance(self):
seq1 = Sequence("abcdefgh")
seq2 = Sequence("1b23ef45")
distance = hamming(seq1, seq2)
self.assertEqual(distance, 5.0/8.0)
def test_maximum_distance(self):
seq1 = Sequence('ABC')
seq2 = Sequence('CAB')
distance = hamming(seq1, seq2)
self.assertEqual(distance, 1.0)
def test_empty_sequences(self):
seq1 = Sequence('')
seq2 = Sequence('')
distance = hamming(seq1, seq2)
npt.assert_equal(distance, np.nan)
def test_single_character_sequences(self):
seq1 = Sequence('a')
seq2 = Sequence('b')
self.assertEqual(hamming(seq1, seq1), 0.0)
self.assertEqual(hamming(seq1, seq2), 1.0)
def test_sequence_subclass(self):
seq1 = DNA('ACG-T')
seq2 = DNA('ACCTT')
distance = hamming(seq1, seq2)
self.assertEqual(distance, 2.0/5.0)
def test_sequences_with_metadata(self):
# test for #1254
seqs1 = [
Sequence("ACGT"),
Sequence("ACGT", metadata={'id': 'abc'}),
Sequence("ACGT", positional_metadata={'qual': range(4)})
]
seqs2 = [
Sequence("AAAA"),
Sequence("AAAA", metadata={'id': 'def'}),
Sequence("AAAA", positional_metadata={'qual': range(4, 8)})
]
for seqs in seqs1, seqs2:
for seq1, seq2 in itertools.product(seqs, repeat=2):
distance = hamming(seq1, seq2)
self.assertEqual(distance, 0.0)
for seq1, seq2 in itertools.product(seqs1, seqs2):
distance = hamming(seq1, seq2)
self.assertEqual(distance, 0.75)
class TestKmerDistance(unittest.TestCase):
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_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_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_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_same_sequence(self):
seq1 = Sequence('CTGCGACAGTTGGTA')
seq2 = Sequence('CTGCGACAGTTGGTA')
obs = kmer_distance(seq1, seq2, 3)
exp = 0.0
self.assertEqual(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_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_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_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_empty_sequences(self):
seq1 = Sequence('')
seq2 = Sequence('')
obs = kmer_distance(seq1, seq2, 3)
npt.assert_equal(obs, np.nan)
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_no_kmers_found(self):
seq1 = Sequence('ATCG')
seq2 = Sequence('ACGT')
obs = kmer_distance(seq1, seq2, 5)
npt.assert_equal(obs, np.nan)
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_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_non_sequence_error(self):
seq1 = Sequence('ATCG')
seq2 = 'ATCG'
with self.assertRaisesRegex(TypeError, "not 'str'"):
kmer_distance(seq1, seq2, 3)
if __name__ == "__main__":
unittest.main()
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