class SequenceCollectionTests(TestCase):
def setUp(self):
self.d1 = DNA('GATTACA', metadata={'id': "d1"})
self.d2 = DNA('TTG', metadata={'id': "d2"})
self.d3 = DNA('GTATACA', metadata={'id': "d3"})
self.r1 = RNA('GAUUACA', metadata={'id': "r1"})
self.r2 = RNA('UUG', metadata={'id': "r2"})
self.r3 = RNA('U-----UGCC--', metadata={'id': "r3"})
self.seqs1 = [self.d1, self.d2]
self.seqs2 = [self.r1, self.r2, self.r3]
self.seqs3 = self.seqs1 + self.seqs2
self.seqs4 = [self.d1, self.d3]
self.s1 = SequenceCollection(self.seqs1)
self.s2 = SequenceCollection(self.seqs2)
self.s3 = SequenceCollection(self.seqs3)
self.s4 = SequenceCollection(self.seqs4)
self.empty = SequenceCollection([])
def test_init(self):
SequenceCollection(self.seqs1)
SequenceCollection(self.seqs2)
SequenceCollection(self.seqs3)
SequenceCollection([])
def test_init_fail(self):
# sequences with overlapping ids
s1 = [self.d1, self.d1]
self.assertRaises(SequenceCollectionError, SequenceCollection, s1)
def test_init_fail_no_id(self):
seq = Sequence('ACGTACGT')
with six.assertRaisesRegex(self, SequenceCollectionError,
"'id' must be included in the sequence "
"metadata"):
SequenceCollection([seq])
def test_contains(self):
self.assertTrue('d1' in self.s1)
self.assertTrue('r2' in self.s2)
self.assertFalse('r2' in self.s1)
def test_eq(self):
self.assertTrue(self.s1 == self.s1)
self.assertFalse(self.s1 == self.s2)
# different objects can be equal
self.assertTrue(self.s1 == SequenceCollection([self.d1, self.d2]))
self.assertTrue(SequenceCollection([self.d1, self.d2]) == self.s1)
# SequenceCollections with different number of sequences are not equal
self.assertFalse(self.s1 == SequenceCollection([self.d1]))
class FakeSequenceCollection(SequenceCollection):
pass
# SequenceCollections of different types are not equal
self.assertFalse(self.s4 == FakeSequenceCollection([self.d1, self.d3]))
self.assertFalse(self.s4 == Alignment([self.d1, self.d3]))
# SequenceCollections with different sequences are not equal
self.assertFalse(self.s1 == SequenceCollection([self.d1, self.r1]))
def test_getitem(self):
self.assertEqual(self.s1[0], self.d1)
self.assertEqual(self.s1[1], self.d2)
self.assertEqual(self.s2[0], self.r1)
self.assertEqual(self.s2[1], self.r2)
self.assertRaises(IndexError, self.empty.__getitem__, 0)
self.assertRaises(KeyError, self.empty.__getitem__, '0')
def test_iter(self):
s1_iter = iter(self.s1)
count = 0
for actual, expected in zip(s1_iter, self.seqs1):
count += 1
self.assertEqual(actual, expected)
self.assertEqual(count, len(self.seqs1))
self.assertRaises(StopIteration, lambda: next(s1_iter))
def test_len(self):
self.assertEqual(len(self.s1), 2)
self.assertEqual(len(self.s2), 3)
self.assertEqual(len(self.s3), 5)
self.assertEqual(len(self.empty), 0)
def test_ne(self):
self.assertFalse(self.s1 != self.s1)
self.assertTrue(self.s1 != self.s2)
# SequenceCollections with different number of sequences are not equal
self.assertTrue(self.s1 != SequenceCollection([self.d1]))
class FakeSequenceCollection(SequenceCollection):
pass
# SequenceCollections of different types are not equal
self.assertTrue(self.s4 != FakeSequenceCollection([self.d1, self.d3]))
self.assertTrue(self.s4 != Alignment([self.d1, self.d3]))
# SequenceCollections with different sequences are not equal
self.assertTrue(self.s1 !=
SequenceCollection([self.d1, self.r1]))
def test_repr(self):
self.assertEqual(repr(self.s1),
"<SequenceCollection: n=2; "
"mean +/- std length=5.00 +/- 2.00>")
self.assertEqual(repr(self.s2),
"<SequenceCollection: n=3; "
"mean +/- std length=7.33 +/- 3.68>")
self.assertEqual(repr(self.s3),
"<SequenceCollection: n=5; "
"mean +/- std length=6.40 +/- 3.32>")
self.assertEqual(repr(self.empty),
"<SequenceCollection: n=0; "
"mean +/- std length=0.00 +/- 0.00>")
def test_reversed(self):
s1_iter = reversed(self.s1)
count = 0
for actual, expected in zip(s1_iter, self.seqs1[::-1]):
count += 1
self.assertEqual(actual, expected)
self.assertEqual(count, len(self.seqs1))
self.assertRaises(StopIteration, lambda: next(s1_iter))
def test_kmer_frequencies(self):
expected1 = Counter({'GAT': 1, 'TAC': 1})
expected2 = Counter({'TTG': 1})
self.assertEqual(
self.s1.kmer_frequencies(k=3, overlap=False, relative=False),
[expected1, expected2])
expected1 = defaultdict(float)
expected1['A'] = 3 / 7.
expected1['C'] = 1 / 7.
expected1['G'] = 1 / 7.
expected1['T'] = 2 / 7.
expected2 = defaultdict(float)
expected2['G'] = 1 / 3.
expected2['T'] = 2 / 3.
self.assertEqual(self.s1.kmer_frequencies(k=1, relative=True),
[expected1, expected2])
expected1 = defaultdict(float)
expected1['GAT'] = 1 / 2.
expected1['TAC'] = 1 / 2.
expected2 = defaultdict(float)
expected2['TTG'] = 1 / 1.
self.assertEqual(
self.s1.kmer_frequencies(k=3, overlap=False, relative=True),
[expected1, expected2])
self.assertEqual(self.empty.kmer_frequencies(k=1, relative=True), [])
# Test to ensure floating point precision bug isn't present. See the
# tests for Sequence.kmer_frequencies for more details.
sc = SequenceCollection([RNA('C' * 10, metadata={'id': 's1'}),
RNA('G' * 10, metadata={'id': 's2'})])
self.assertEqual(sc.kmer_frequencies(1, relative=True),
[defaultdict(float, {'C': 1.0}),
defaultdict(float, {'G': 1.0})])
def test_str(self):
exp1 = ">d1\nGATTACA\n>d2\nTTG\n"
self.assertEqual(str(self.s1), exp1)
exp2 = ">r1\nGAUUACA\n>r2\nUUG\n>r3\nU-----UGCC--\n"
self.assertEqual(str(self.s2), exp2)
exp4 = ""
self.assertEqual(str(self.empty), exp4)
def test_distances(self):
s1 = SequenceCollection([DNA("ACGT", metadata={'id': "d1"}),
DNA("ACGG", metadata={'id': "d2"})])
expected = [[0, 0.25],
[0.25, 0]]
expected = DistanceMatrix(expected, ['d1', 'd2'])
def h(s1, s2):
return hamming(s1.values, s2.values)
actual = s1.distances(h)
self.assertEqual(actual, expected)
# alt distance function provided
def dumb_distance(s1, s2):
return 42.
expected = [[0, 42.],
[42., 0]]
expected = DistanceMatrix(expected, ['d1', 'd2'])
actual = s1.distances(dumb_distance)
self.assertEqual(actual, expected)
def test_distribution_stats(self):
actual1 = self.s1.distribution_stats()
self.assertEqual(actual1[0], 2)
self.assertAlmostEqual(actual1[1], 5.0, 3)
self.assertAlmostEqual(actual1[2], 2.0, 3)
actual2 = self.s2.distribution_stats()
self.assertEqual(actual2[0], 3)
self.assertAlmostEqual(actual2[1], 7.333, 3)
self.assertAlmostEqual(actual2[2], 3.682, 3)
actual3 = self.s3.distribution_stats()
self.assertEqual(actual3[0], 5)
self.assertAlmostEqual(actual3[1], 6.400, 3)
self.assertAlmostEqual(actual3[2], 3.323, 3)
actual4 = self.empty.distribution_stats()
self.assertEqual(actual4[0], 0)
self.assertEqual(actual4[1], 0.0)
self.assertEqual(actual4[2], 0.0)
def test_degap(self):
expected = SequenceCollection([
RNA('GAUUACA', metadata={'id': "r1"}),
RNA('UUG', metadata={'id': "r2"}),
RNA('UUGCC', metadata={'id': "r3"})])
actual = self.s2.degap()
self.assertEqual(actual, expected)
def test_get_seq(self):
self.assertEqual(self.s1.get_seq('d1'), self.d1)
self.assertEqual(self.s1.get_seq('d2'), self.d2)
def test_ids(self):
self.assertEqual(self.s1.ids(), ['d1', 'd2'])
self.assertEqual(self.s2.ids(), ['r1', 'r2', 'r3'])
self.assertEqual(self.s3.ids(),
['d1', 'd2', 'r1', 'r2', 'r3'])
self.assertEqual(self.empty.ids(), [])
def test_update_ids_default_behavior(self):
# 3 seqs
exp_sc = SequenceCollection([
RNA('GAUUACA', metadata={'id': "1"}),
RNA('UUG', metadata={'id': "2"}),
RNA('U-----UGCC--', metadata={'id': "3"})
])
exp_id_map = {'1': 'r1', '2': 'r2', '3': 'r3'}
obs_sc, obs_id_map = self.s2.update_ids()
self.assertEqual(obs_sc, exp_sc)
self.assertEqual(obs_id_map, exp_id_map)
# empty
obs_sc, obs_id_map = self.empty.update_ids()
self.assertEqual(obs_sc, self.empty)
self.assertEqual(obs_id_map, {})
def test_update_ids_prefix(self):
# 3 seqs
exp_sc = SequenceCollection([
RNA('GAUUACA', metadata={'id': "abc1"}),
RNA('UUG', metadata={'id': "abc2"}),
RNA('U-----UGCC--', metadata={'id': "abc3"})
])
exp_id_map = {'abc1': 'r1', 'abc2': 'r2', 'abc3': 'r3'}
obs_sc, obs_id_map = self.s2.update_ids(prefix='abc')
self.assertEqual(obs_sc, exp_sc)
self.assertEqual(obs_id_map, exp_id_map)
# empty
obs_sc, obs_id_map = self.empty.update_ids(prefix='abc')
self.assertEqual(obs_sc, self.empty)
self.assertEqual(obs_id_map, {})
def test_update_ids_func_parameter(self):
def append_42(ids):
return [id_ + '-42' for id_ in ids]
# 3 seqs
exp_sc = SequenceCollection([
RNA('GAUUACA', metadata={'id': "r1-42"}),
RNA('UUG', metadata={'id': "r2-42"}),
RNA('U-----UGCC--', metadata={'id': "r3-42"})
])
exp_id_map = {'r1-42': 'r1', 'r2-42': 'r2', 'r3-42': 'r3'}
obs_sc, obs_id_map = self.s2.update_ids(func=append_42)
self.assertEqual(obs_sc, exp_sc)
self.assertEqual(obs_id_map, exp_id_map)
# empty
obs_sc, obs_id_map = self.empty.update_ids(func=append_42)
self.assertEqual(obs_sc, self.empty)
self.assertEqual(obs_id_map, {})
def test_update_ids_ids_parameter(self):
# 3 seqs
exp_sc = SequenceCollection([
RNA('GAUUACA', metadata={'id': "abc"}),
RNA('UUG', metadata={'id': "def"}),
RNA('U-----UGCC--', metadata={'id': "ghi"})
])
exp_id_map = {'abc': 'r1', 'def': 'r2', 'ghi': 'r3'}
obs_sc, obs_id_map = self.s2.update_ids(ids=('abc', 'def', 'ghi'))
self.assertEqual(obs_sc, exp_sc)
self.assertEqual(obs_id_map, exp_id_map)
# empty
obs_sc, obs_id_map = self.empty.update_ids(ids=[])
self.assertEqual(obs_sc, self.empty)
self.assertEqual(obs_id_map, {})
def test_update_ids_sequence_attributes_propagated(self):
# 1 seq
exp_sc = Alignment([
DNA('ACGT', metadata={'id': "abc", 'description': 'desc'},
positional_metadata={'quality': range(4)})
])
exp_id_map = {'abc': 'seq1'}
obj = Alignment([
DNA('ACGT', metadata={'id': "seq1", 'description': 'desc'},
positional_metadata={'quality': range(4)})
])
obs_sc, obs_id_map = obj.update_ids(ids=('abc',))
self.assertEqual(obs_sc, exp_sc)
self.assertEqual(obs_id_map, exp_id_map)
# 2 seqs
exp_sc = Alignment([
DNA('ACGT', metadata={'id': "abc", 'description': 'desc1'},
positional_metadata={'quality': range(4)}),
DNA('TGCA', metadata={'id': "def", 'description': 'desc2'},
positional_metadata={'quality': range(4)[::-1]})
])
exp_id_map = {'abc': 'seq1', 'def': 'seq2'}
obj = Alignment([
DNA('ACGT', metadata={'id': "seq1", 'description': 'desc1'},
positional_metadata={'quality': (0, 1, 2, 3)}),
DNA('TGCA', metadata={'id': "seq2", 'description': 'desc2'},
positional_metadata={'quality': (3, 2, 1, 0)})
])
obs_sc, obs_id_map = obj.update_ids(ids=('abc', 'def'))
self.assertEqual(obs_sc, exp_sc)
self.assertEqual(obs_id_map, exp_id_map)
def test_update_ids_invalid_parameter_combos(self):
with six.assertRaisesRegex(self, SequenceCollectionError,
'ids and func'):
self.s1.update_ids(func=lambda e: e, ids=['foo', 'bar'])
with six.assertRaisesRegex(self, SequenceCollectionError, 'prefix'):
self.s1.update_ids(ids=['foo', 'bar'], prefix='abc')
with six.assertRaisesRegex(self, SequenceCollectionError, 'prefix'):
self.s1.update_ids(func=lambda e: e, prefix='abc')
def test_update_ids_invalid_ids(self):
# incorrect number of new ids
with six.assertRaisesRegex(self, SequenceCollectionError, '3 != 2'):
self.s1.update_ids(ids=['foo', 'bar', 'baz'])
with six.assertRaisesRegex(self, SequenceCollectionError, '4 != 2'):
self.s1.update_ids(func=lambda e: ['foo', 'bar', 'baz', 'abc'])
# duplicates
with six.assertRaisesRegex(self, SequenceCollectionError, 'foo'):
self.s2.update_ids(ids=['foo', 'bar', 'foo'])
with six.assertRaisesRegex(self, SequenceCollectionError, 'bar'):
self.s2.update_ids(func=lambda e: ['foo', 'bar', 'bar'])
def test_is_empty(self):
self.assertFalse(self.s1.is_empty())
self.assertFalse(self.s2.is_empty())
self.assertFalse(self.s3.is_empty())
self.assertTrue(self.empty.is_empty())
def test_iteritems(self):
self.assertEqual(list(self.s1.iteritems()),
[(s.metadata['id'], s) for s in self.s1])
def test_sequence_count(self):
self.assertEqual(self.s1.sequence_count(), 2)
self.assertEqual(self.s2.sequence_count(), 3)
self.assertEqual(self.s3.sequence_count(), 5)
self.assertEqual(self.empty.sequence_count(), 0)
def test_sequence_lengths(self):
self.assertEqual(self.s1.sequence_lengths(), [7, 3])
self.assertEqual(self.s2.sequence_lengths(), [7, 3, 12])
self.assertEqual(self.s3.sequence_lengths(), [7, 3, 7, 3, 12])
self.assertEqual(self.empty.sequence_lengths(), [])
class SequenceCollectionTests(TestCase):
def setUp(self):
self.d1 = DNASequence('GATTACA', id="d1")
self.d2 = DNASequence('TTG', id="d2")
self.d3 = DNASequence('GTATACA', id="d3")
self.d1_lower = DNASequence('gattaca', id="d1")
self.d2_lower = DNASequence('ttg', id="d2")
self.d3_lower = DNASequence('gtataca', id="d3")
self.r1 = RNASequence('GAUUACA', id="r1")
self.r2 = RNASequence('UUG', id="r2")
self.r3 = RNASequence('U-----UGCC--', id="r3")
self.i1 = DNASequence('GATXACA', id="i1")
self.seqs1 = [self.d1, self.d2]
self.seqs1_lower = [self.d1_lower, self.d2_lower]
self.seqs2 = [self.r1, self.r2, self.r3]
self.seqs3 = self.seqs1 + self.seqs2
self.seqs4 = [self.d1, self.d3]
self.seqs1_t = [('d1', 'GATTACA'), ('d2', 'TTG')]
self.seqs2_t = [('r1', 'GAUUACA'), ('r2', 'UUG'),
('r3', 'U-----UGCC--')]
self.seqs3_t = self.seqs1_t + self.seqs2_t
self.s1 = SequenceCollection(self.seqs1)
self.s1_lower = SequenceCollection(self.seqs1_lower)
self.s2 = SequenceCollection(self.seqs2)
self.s3 = SequenceCollection(self.seqs3)
self.s4 = SequenceCollection(self.seqs4)
self.empty = SequenceCollection([])
self.invalid_s1 = SequenceCollection([self.i1])
def test_init(self):
SequenceCollection(self.seqs1)
SequenceCollection(self.seqs2)
SequenceCollection(self.seqs3)
SequenceCollection([])
def test_init_fail(self):
# sequences with overlapping ids
s1 = [self.d1, self.d1]
self.assertRaises(SequenceCollectionError, SequenceCollection, s1)
def test_init_validate(self):
SequenceCollection(self.seqs1, validate=True)
SequenceCollection(self.seqs1, validate=True)
# can't validate self.seqs2 as a DNASequence
self.assertRaises(SequenceCollectionError, SequenceCollection,
self.invalid_s1, validate=True)
def test_contains(self):
self.assertTrue('d1' in self.s1)
self.assertTrue('r2' in self.s2)
self.assertFalse('r2' in self.s1)
def test_eq(self):
self.assertTrue(self.s1 == self.s1)
self.assertFalse(self.s1 == self.s2)
# different objects can be equal
self.assertTrue(self.s1 == SequenceCollection([self.d1, self.d2]))
self.assertTrue(SequenceCollection([self.d1, self.d2]) == self.s1)
# SequenceCollections with different number of sequences are not equal
self.assertFalse(self.s1 == SequenceCollection([self.d1]))
class FakeSequenceCollection(SequenceCollection):
pass
# SequenceCollections of different types are not equal
self.assertFalse(self.s4 == FakeSequenceCollection([self.d1, self.d3]))
self.assertFalse(self.s4 == Alignment([self.d1, self.d3]))
# SequenceCollections with different sequences are not equal
self.assertFalse(self.s1 == SequenceCollection([self.d1, self.r1]))
def test_getitem(self):
self.assertEqual(self.s1[0], self.d1)
self.assertEqual(self.s1[1], self.d2)
self.assertEqual(self.s2[0], self.r1)
self.assertEqual(self.s2[1], self.r2)
self.assertRaises(IndexError, self.empty.__getitem__, 0)
self.assertRaises(KeyError, self.empty.__getitem__, '0')
def test_iter(self):
s1_iter = iter(self.s1)
count = 0
for actual, expected in zip(s1_iter, self.seqs1):
count += 1
self.assertEqual(actual, expected)
self.assertEqual(count, len(self.seqs1))
self.assertRaises(StopIteration, lambda: next(s1_iter))
def test_len(self):
self.assertEqual(len(self.s1), 2)
self.assertEqual(len(self.s2), 3)
self.assertEqual(len(self.s3), 5)
self.assertEqual(len(self.empty), 0)
def test_ne(self):
self.assertFalse(self.s1 != self.s1)
self.assertTrue(self.s1 != self.s2)
# SequenceCollections with different number of sequences are not equal
self.assertTrue(self.s1 != SequenceCollection([self.d1]))
class FakeSequenceCollection(SequenceCollection):
pass
# SequenceCollections of different types are not equal
self.assertTrue(self.s4 != FakeSequenceCollection([self.d1, self.d3]))
self.assertTrue(self.s4 != Alignment([self.d1, self.d3]))
# SequenceCollections with different sequences are not equal
self.assertTrue(self.s1 !=
SequenceCollection([self.d1, self.r1]))
def test_repr(self):
self.assertEqual(repr(self.s1),
"<SequenceCollection: n=2; "
"mean +/- std length=5.00 +/- 2.00>")
self.assertEqual(repr(self.s2),
"<SequenceCollection: n=3; "
"mean +/- std length=7.33 +/- 3.68>")
self.assertEqual(repr(self.s3),
"<SequenceCollection: n=5; "
"mean +/- std length=6.40 +/- 3.32>")
self.assertEqual(repr(self.empty),
"<SequenceCollection: n=0; "
"mean +/- std length=0.00 +/- 0.00>")
def test_reversed(self):
s1_iter = reversed(self.s1)
count = 0
for actual, expected in zip(s1_iter, self.seqs1[::-1]):
count += 1
self.assertEqual(actual, expected)
self.assertEqual(count, len(self.seqs1))
self.assertRaises(StopIteration, lambda: next(s1_iter))
def test_k_word_frequencies(self):
expected1 = defaultdict(float)
expected1['A'] = 3 / 7.
expected1['C'] = 1 / 7.
expected1['G'] = 1 / 7.
expected1['T'] = 2 / 7.
expected2 = defaultdict(float)
expected2['G'] = 1 / 3.
expected2['T'] = 2 / 3.
self.assertEqual(self.s1.k_word_frequencies(k=1),
[expected1, expected2])
expected1 = defaultdict(float)
expected1['GAT'] = 1 / 2.
expected1['TAC'] = 1 / 2.
expected2 = defaultdict(float)
expected2['TTG'] = 1 / 1.
self.assertEqual(self.s1.k_word_frequencies(k=3, overlapping=False),
[expected1, expected2])
self.assertEqual(self.empty.k_word_frequencies(k=1), [])
# Test to ensure floating point precision bug isn't present. See the
# tests for BiologicalSequence.k_word_frequencies for more details.
sc = SequenceCollection([RNA('C' * 10, id='s1'),
RNA('G' * 10, id='s2')])
self.assertEqual(sc.k_word_frequencies(1),
[defaultdict(float, {'C': 1.0}),
defaultdict(float, {'G': 1.0})])
def test_str(self):
exp1 = ">d1\nGATTACA\n>d2\nTTG\n"
self.assertEqual(str(self.s1), exp1)
exp2 = ">r1\nGAUUACA\n>r2\nUUG\n>r3\nU-----UGCC--\n"
self.assertEqual(str(self.s2), exp2)
exp4 = ""
self.assertEqual(str(self.empty), exp4)
def test_distances(self):
s1 = SequenceCollection([DNA("ACGT", "d1"), DNA("ACGG", "d2")])
expected = [[0, 0.25],
[0.25, 0]]
expected = DistanceMatrix(expected, ['d1', 'd2'])
actual = s1.distances(hamming)
self.assertEqual(actual, expected)
# alt distance function provided
def dumb_distance(s1, s2):
return 42.
expected = [[0, 42.],
[42., 0]]
expected = DistanceMatrix(expected, ['d1', 'd2'])
actual = s1.distances(dumb_distance)
self.assertEqual(actual, expected)
def test_distribution_stats(self):
actual1 = self.s1.distribution_stats()
self.assertEqual(actual1[0], 2)
self.assertAlmostEqual(actual1[1], 5.0, 3)
self.assertAlmostEqual(actual1[2], 2.0, 3)
actual2 = self.s2.distribution_stats()
self.assertEqual(actual2[0], 3)
self.assertAlmostEqual(actual2[1], 7.333, 3)
self.assertAlmostEqual(actual2[2], 3.682, 3)
actual3 = self.s3.distribution_stats()
self.assertEqual(actual3[0], 5)
self.assertAlmostEqual(actual3[1], 6.400, 3)
self.assertAlmostEqual(actual3[2], 3.323, 3)
actual4 = self.empty.distribution_stats()
self.assertEqual(actual4[0], 0)
self.assertEqual(actual4[1], 0.0)
self.assertEqual(actual4[2], 0.0)
def test_degap(self):
expected = SequenceCollection([
RNASequence('GAUUACA', id="r1"),
RNASequence('UUG', id="r2"),
RNASequence('UUGCC', id="r3")])
actual = self.s2.degap()
self.assertEqual(actual, expected)
def test_get_seq(self):
self.assertEqual(self.s1.get_seq('d1'), self.d1)
self.assertEqual(self.s1.get_seq('d2'), self.d2)
def test_ids(self):
self.assertEqual(self.s1.ids(), ['d1', 'd2'])
self.assertEqual(self.s2.ids(), ['r1', 'r2', 'r3'])
self.assertEqual(self.s3.ids(),
['d1', 'd2', 'r1', 'r2', 'r3'])
self.assertEqual(self.empty.ids(), [])
def _assert_sequence_collections_equal(self, observed, expected):
"""Compare SequenceCollections strictly."""
# TODO remove this custom equality testing code when SequenceCollection
# has an equals method (part of #656). We need this method to include
# IDs in the comparison (not part of SequenceCollection.__eq__).
self.assertEqual(observed, expected)
for obs_seq, exp_seq in zip(observed, expected):
self.assertTrue(obs_seq.equals(exp_seq))
def test_update_ids_default_behavior(self):
# 3 seqs
exp_sc = SequenceCollection([
RNA('GAUUACA', id="1"),
RNA('UUG', id="2"),
RNA('U-----UGCC--', id="3")
])
exp_id_map = {'1': 'r1', '2': 'r2', '3': 'r3'}
obs_sc, obs_id_map = self.s2.update_ids()
self._assert_sequence_collections_equal(obs_sc, exp_sc)
self.assertEqual(obs_id_map, exp_id_map)
# empty
obs_sc, obs_id_map = self.empty.update_ids()
self._assert_sequence_collections_equal(obs_sc, self.empty)
self.assertEqual(obs_id_map, {})
def test_update_ids_prefix(self):
# 3 seqs
exp_sc = SequenceCollection([
RNA('GAUUACA', id="abc1"),
RNA('UUG', id="abc2"),
RNA('U-----UGCC--', id="abc3")
])
exp_id_map = {'abc1': 'r1', 'abc2': 'r2', 'abc3': 'r3'}
obs_sc, obs_id_map = self.s2.update_ids(prefix='abc')
self._assert_sequence_collections_equal(obs_sc, exp_sc)
self.assertEqual(obs_id_map, exp_id_map)
# empty
obs_sc, obs_id_map = self.empty.update_ids(prefix='abc')
self._assert_sequence_collections_equal(obs_sc, self.empty)
self.assertEqual(obs_id_map, {})
def test_update_ids_fn_parameter(self):
def append_42(ids):
return [id_ + '-42' for id_ in ids]
# 3 seqs
exp_sc = SequenceCollection([
RNA('GAUUACA', id="r1-42"),
RNA('UUG', id="r2-42"),
RNA('U-----UGCC--', id="r3-42")
])
exp_id_map = {'r1-42': 'r1', 'r2-42': 'r2', 'r3-42': 'r3'}
obs_sc, obs_id_map = self.s2.update_ids(fn=append_42)
self._assert_sequence_collections_equal(obs_sc, exp_sc)
self.assertEqual(obs_id_map, exp_id_map)
# empty
obs_sc, obs_id_map = self.empty.update_ids(fn=append_42)
self._assert_sequence_collections_equal(obs_sc, self.empty)
self.assertEqual(obs_id_map, {})
def test_update_ids_ids_parameter(self):
# 3 seqs
exp_sc = SequenceCollection([
RNA('GAUUACA', id="abc"),
RNA('UUG', id="def"),
RNA('U-----UGCC--', id="ghi")
])
exp_id_map = {'abc': 'r1', 'def': 'r2', 'ghi': 'r3'}
obs_sc, obs_id_map = self.s2.update_ids(ids=('abc', 'def', 'ghi'))
self._assert_sequence_collections_equal(obs_sc, exp_sc)
self.assertEqual(obs_id_map, exp_id_map)
# empty
obs_sc, obs_id_map = self.empty.update_ids(ids=[])
self._assert_sequence_collections_equal(obs_sc, self.empty)
self.assertEqual(obs_id_map, {})
def test_update_ids_sequence_attributes_propagated(self):
# 1 seq
exp_sc = Alignment([
DNA('ACGT', id="abc", description='desc', quality=range(4))
])
exp_id_map = {'abc': 'seq1'}
obj = Alignment([
DNA('ACGT', id="seq1", description='desc', quality=range(4))
])
obs_sc, obs_id_map = obj.update_ids(ids=('abc',))
self._assert_sequence_collections_equal(obs_sc, exp_sc)
self.assertEqual(obs_id_map, exp_id_map)
# 2 seqs
exp_sc = Alignment([
DNA('ACGT', id="abc", description='desc1', quality=range(4)),
DNA('TGCA', id="def", description='desc2', quality=range(4)[::-1])
])
exp_id_map = {'abc': 'seq1', 'def': 'seq2'}
obj = Alignment([
DNA('ACGT', id="seq1", description='desc1', quality=(0, 1, 2, 3)),
DNA('TGCA', id="seq2", description='desc2', quality=(3, 2, 1, 0))
])
obs_sc, obs_id_map = obj.update_ids(ids=('abc', 'def'))
self._assert_sequence_collections_equal(obs_sc, exp_sc)
self.assertEqual(obs_id_map, exp_id_map)
def test_update_ids_invalid_parameter_combos(self):
with self.assertRaisesRegexp(SequenceCollectionError, 'ids and fn'):
self.s1.update_ids(fn=lambda e: e, ids=['foo', 'bar'])
with self.assertRaisesRegexp(SequenceCollectionError, 'prefix'):
self.s1.update_ids(ids=['foo', 'bar'], prefix='abc')
with self.assertRaisesRegexp(SequenceCollectionError, 'prefix'):
self.s1.update_ids(fn=lambda e: e, prefix='abc')
def test_update_ids_invalid_ids(self):
# incorrect number of new ids
with self.assertRaisesRegexp(SequenceCollectionError, '3 != 2'):
self.s1.update_ids(ids=['foo', 'bar', 'baz'])
with self.assertRaisesRegexp(SequenceCollectionError, '4 != 2'):
self.s1.update_ids(fn=lambda e: ['foo', 'bar', 'baz', 'abc'])
# duplicates
with self.assertRaisesRegexp(SequenceCollectionError, 'foo'):
self.s2.update_ids(ids=['foo', 'bar', 'foo'])
with self.assertRaisesRegexp(SequenceCollectionError, 'bar'):
self.s2.update_ids(fn=lambda e: ['foo', 'bar', 'bar'])
def test_is_empty(self):
self.assertFalse(self.s1.is_empty())
self.assertFalse(self.s2.is_empty())
self.assertFalse(self.s3.is_empty())
self.assertTrue(self.empty.is_empty())
def test_is_valid(self):
self.assertTrue(self.s1.is_valid())
self.assertTrue(self.s2.is_valid())
self.assertTrue(self.s3.is_valid())
self.assertTrue(self.empty.is_valid())
self.assertFalse(self.invalid_s1.is_valid())
def test_iteritems(self):
self.assertEqual(list(self.s1.iteritems()),
[(s.id, s) for s in self.s1])
def test_lower(self):
self.assertEqual(self.s1.lower(), self.s1_lower)
def test_sequence_count(self):
self.assertEqual(self.s1.sequence_count(), 2)
self.assertEqual(self.s2.sequence_count(), 3)
self.assertEqual(self.s3.sequence_count(), 5)
self.assertEqual(self.empty.sequence_count(), 0)
def test_sequence_lengths(self):
self.assertEqual(self.s1.sequence_lengths(), [7, 3])
self.assertEqual(self.s2.sequence_lengths(), [7, 3, 12])
self.assertEqual(self.s3.sequence_lengths(), [7, 3, 7, 3, 12])
self.assertEqual(self.empty.sequence_lengths(), [])
def test_upper(self):
self.assertEqual(self.s1_lower.upper(), self.s1)
class SequenceCollectionTests(TestCase):
"""Tests of the SequenceCollection class """
def setUp(self):
"""Initialize values to be used in tests
"""
self.d1 = DNASequence('GATTACA', id="d1")
self.d2 = DNASequence('TTG', id="d2")
self.d1_lower = DNASequence('gattaca', id="d1")
self.d2_lower = DNASequence('ttg', id="d2")
self.r1 = RNASequence('GAUUACA', id="r1")
self.r2 = RNASequence('UUG', id="r2")
self.r3 = RNASequence('U-----UGCC--', id="r3")
self.i1 = DNASequence('GATXACA', id="i1")
self.seqs1 = [self.d1, self.d2]
self.seqs1_lower = [self.d1_lower, self.d2_lower]
self.seqs2 = [self.r1, self.r2, self.r3]
self.seqs3 = self.seqs1 + self.seqs2
self.seqs1_t = [('d1', 'GATTACA'), ('d2', 'TTG')]
self.seqs2_t = [('r1', 'GAUUACA'), ('r2', 'UUG'),
('r3', 'U-----UGCC--')]
self.seqs3_t = self.seqs1_t + self.seqs2_t
self.s1 = SequenceCollection(self.seqs1)
self.s1_lower = SequenceCollection(self.seqs1_lower)
self.s2 = SequenceCollection(self.seqs2)
self.s3 = SequenceCollection(self.seqs3)
self.empty = SequenceCollection([])
self.invalid_s1 = SequenceCollection([self.i1])
def test_init(self):
"""Initialization functions as expected with varied input types
"""
SequenceCollection(self.seqs1)
SequenceCollection(self.seqs2)
SequenceCollection(self.seqs3)
SequenceCollection([])
def test_init_fail(self):
"""initialization with sequences with overlapping ids fails
"""
s1 = [self.d1, self.d1]
self.assertRaises(SequenceCollectionError, SequenceCollection, s1)
def test_init_validate(self):
"""initialization with validation functions as expected
"""
SequenceCollection(self.seqs1, validate=True)
SequenceCollection(self.seqs1, validate=True)
# can't validate self.seqs2 as a DNASequence
self.assertRaises(SequenceCollectionError, SequenceCollection,
self.invalid_s1, validate=True)
def test_from_fasta_records(self):
"""Initialization from list of tuples functions as expected
"""
SequenceCollection.from_fasta_records(self.seqs1_t, DNASequence)
SequenceCollection.from_fasta_records(self.seqs2_t, RNASequence)
SequenceCollection.from_fasta_records(self.seqs3_t, NucleotideSequence)
def test_contains(self):
"""in operator functions as expected
"""
self.assertTrue('d1' in self.s1)
self.assertTrue('r2' in self.s2)
self.assertFalse('r2' in self.s1)
def test_eq(self):
"""equality operator functions as expected
"""
self.assertTrue(self.s1 == self.s1)
self.assertFalse(self.s1 == self.s2)
# different objects can be equal
self.assertTrue(self.s1 == SequenceCollection([self.d1, self.d2]))
self.assertTrue(SequenceCollection([self.d1, self.d2]) == self.s1)
# SequenceCollections with different number of sequences are not equal
self.assertFalse(self.s1 == SequenceCollection([self.d1]))
class FakeSequenceCollection(SequenceCollection):
pass
# SequenceCollections of different types are not equal
self.assertFalse(self.s1 == FakeSequenceCollection([self.d1, self.d2]))
self.assertFalse(self.s1 == Alignment([self.d1, self.d2]))
# SequenceCollections with different sequences are not equal
self.assertFalse(self.s1 == SequenceCollection([self.d1, self.r1]))
def test_getitem(self):
"""getitem functions as expected
"""
self.assertEqual(self.s1[0], self.d1)
self.assertEqual(self.s1[1], self.d2)
self.assertEqual(self.s2[0], self.r1)
self.assertEqual(self.s2[1], self.r2)
self.assertRaises(IndexError, self.empty.__getitem__, 0)
self.assertRaises(KeyError, self.empty.__getitem__, '0')
def test_iter(self):
"""iter functions as expected
"""
s1_iter = iter(self.s1)
count = 0
for actual, expected in zip(s1_iter, self.seqs1):
count += 1
self.assertEqual(actual, expected)
self.assertEqual(count, len(self.seqs1))
self.assertRaises(StopIteration, lambda: next(s1_iter))
def test_len(self):
"""len functions as expected
"""
self.assertEqual(len(self.s1), 2)
self.assertEqual(len(self.s2), 3)
self.assertEqual(len(self.s3), 5)
self.assertEqual(len(self.empty), 0)
def test_ne(self):
"""inequality operator functions as expected
"""
self.assertFalse(self.s1 != self.s1)
self.assertTrue(self.s1 != self.s2)
# SequenceCollections with different number of sequences are not equal
self.assertTrue(self.s1 != SequenceCollection([self.d1]))
class FakeSequenceCollection(SequenceCollection):
pass
# SequenceCollections of different types are not equal
self.assertTrue(self.s1 != FakeSequenceCollection([self.d1, self.d2]))
self.assertTrue(self.s1 != Alignment([self.d1, self.d2]))
# SequenceCollections with different sequences are not equal
self.assertTrue(self.s1 !=
SequenceCollection([self.d1, self.r1]))
def test_repr(self):
"""repr functions as expected
"""
self.assertEqual(repr(self.s1),
"<SequenceCollection: n=2; "
"mean +/- std length=5.00 +/- 2.00>")
self.assertEqual(repr(self.s2),
"<SequenceCollection: n=3; "
"mean +/- std length=7.33 +/- 3.68>")
self.assertEqual(repr(self.s3),
"<SequenceCollection: n=5; "
"mean +/- std length=6.40 +/- 3.32>")
self.assertEqual(repr(self.empty),
"<SequenceCollection: n=0; "
"mean +/- std length=0.00 +/- 0.00>")
def test_reversed(self):
"""reversed functions as expected
"""
s1_iter = reversed(self.s1)
count = 0
for actual, expected in zip(s1_iter, self.seqs1[::-1]):
count += 1
self.assertEqual(actual, expected)
self.assertEqual(count, len(self.seqs1))
self.assertRaises(StopIteration, lambda: next(s1_iter))
def test_k_word_frequencies(self):
"""k_word_frequencies functions as expected
"""
expected1 = defaultdict(int)
expected1['A'] = 3 / 7.
expected1['C'] = 1 / 7.
expected1['G'] = 1 / 7.
expected1['T'] = 2 / 7.
expected2 = defaultdict(int)
expected2['G'] = 1 / 3.
expected2['T'] = 2 / 3.
self.assertEqual(self.s1.k_word_frequencies(k=1),
[expected1, expected2])
expected1 = defaultdict(int)
expected1['GAT'] = 1 / 2.
expected1['TAC'] = 1 / 2.
expected2 = defaultdict(int)
expected2['TTG'] = 1 / 1.
self.assertEqual(self.s1.k_word_frequencies(k=3, overlapping=False),
[expected1, expected2])
self.assertEqual(self.empty.k_word_frequencies(k=1), [])
def test_str(self):
"""str functions as expected
"""
exp1 = ">d1\nGATTACA\n>d2\nTTG\n"
self.assertEqual(str(self.s1), exp1)
exp2 = ">r1\nGAUUACA\n>r2\nUUG\n>r3\nU-----UGCC--\n"
self.assertEqual(str(self.s2), exp2)
exp4 = ""
self.assertEqual(str(self.empty), exp4)
def test_distances(self):
"""distances functions as expected
"""
s1 = SequenceCollection([DNA("ACGT", "d1"), DNA("ACGG", "d2")])
expected = [[0, 0.25],
[0.25, 0]]
expected = DistanceMatrix(expected, ['d1', 'd2'])
actual = s1.distances(hamming)
self.assertEqual(actual, expected)
# alt distance function provided
def dumb_distance(s1, s2):
return 42.
expected = [[0, 42.],
[42., 0]]
expected = DistanceMatrix(expected, ['d1', 'd2'])
actual = s1.distances(dumb_distance)
self.assertEqual(actual, expected)
def test_distribution_stats(self):
"""distribution_stats functions as expected
"""
actual1 = self.s1.distribution_stats()
self.assertEqual(actual1[0], 2)
self.assertAlmostEqual(actual1[1], 5.0, 3)
self.assertAlmostEqual(actual1[2], 2.0, 3)
actual2 = self.s2.distribution_stats()
self.assertEqual(actual2[0], 3)
self.assertAlmostEqual(actual2[1], 7.333, 3)
self.assertAlmostEqual(actual2[2], 3.682, 3)
actual3 = self.s3.distribution_stats()
self.assertEqual(actual3[0], 5)
self.assertAlmostEqual(actual3[1], 6.400, 3)
self.assertAlmostEqual(actual3[2], 3.323, 3)
actual4 = self.empty.distribution_stats()
self.assertEqual(actual4[0], 0)
self.assertEqual(actual4[1], 0.0)
self.assertEqual(actual4[2], 0.0)
def test_degap(self):
"""degap functions as expected
"""
expected = [(id_, seq.replace('.', '').replace('-', ''))
for id_, seq in self.seqs2_t]
expected = SequenceCollection.from_fasta_records(expected, RNASequence)
actual = self.s2.degap()
self.assertEqual(actual, expected)
def test_get_seq(self):
"""getseq functions asexpected
"""
self.assertEqual(self.s1.get_seq('d1'), self.d1)
self.assertEqual(self.s1.get_seq('d2'), self.d2)
def test_ids(self):
"""ids functions as expected
"""
self.assertEqual(self.s1.ids(), ['d1', 'd2'])
self.assertEqual(self.s2.ids(), ['r1', 'r2', 'r3'])
self.assertEqual(self.s3.ids(),
['d1', 'd2', 'r1', 'r2', 'r3'])
self.assertEqual(self.empty.ids(), [])
def test_int_map(self):
"""int_map functions as expected
"""
expected1 = {"1": self.d1, "2": self.d2}
expected2 = {"1": "d1", "2": "d2"}
self.assertEqual(self.s1.int_map(), (expected1, expected2))
expected1 = {"h-1": self.d1, "h-2": self.d2}
expected2 = {"h-1": "d1", "h-2": "d2"}
self.assertEqual(self.s1.int_map(prefix='h-'), (expected1, expected2))
def test_is_empty(self):
"""is_empty functions as expected
"""
self.assertFalse(self.s1.is_empty())
self.assertFalse(self.s2.is_empty())
self.assertFalse(self.s3.is_empty())
self.assertTrue(self.empty.is_empty())
def test_is_valid(self):
"""is_valid functions as expected
"""
self.assertTrue(self.s1.is_valid())
self.assertTrue(self.s2.is_valid())
self.assertTrue(self.s3.is_valid())
self.assertTrue(self.empty.is_valid())
self.assertFalse(self.invalid_s1.is_valid())
def test_iteritems(self):
"""iteritems functions as expected
"""
self.assertEqual(list(self.s1.iteritems()),
[(s.id, s) for s in self.s1])
def test_lower(self):
"""lower functions as expected
"""
self.assertEqual(self.s1.lower(), self.s1_lower)
def test_sequence_count(self):
"""num_seqs functions as expected
"""
self.assertEqual(self.s1.sequence_count(), 2)
self.assertEqual(self.s2.sequence_count(), 3)
self.assertEqual(self.s3.sequence_count(), 5)
self.assertEqual(self.empty.sequence_count(), 0)
def test_sequence_lengths(self):
"""sequence_lengths functions as expected
"""
self.assertEqual(self.s1.sequence_lengths(), [7, 3])
self.assertEqual(self.s2.sequence_lengths(), [7, 3, 12])
self.assertEqual(self.s3.sequence_lengths(), [7, 3, 7, 3, 12])
self.assertEqual(self.empty.sequence_lengths(), [])
def test_to_fasta(self):
"""to_fasta functions as expected
"""
exp1 = ">d1\nGATTACA\n>d2\nTTG\n"
self.assertEqual(self.s1.to_fasta(), exp1)
exp2 = ">r1\nGAUUACA\n>r2\nUUG\n>r3\nU-----UGCC--\n"
self.assertEqual(self.s2.to_fasta(), exp2)
def test_toFasta(self):
with warnings.catch_warnings():
warnings.simplefilter("ignore")
exp = ">d1\nGATTACA\n>d2\nTTG\n"
self.assertEqual(self.s1.toFasta(), exp)
def test_upper(self):
"""upper functions as expected
"""
self.assertEqual(self.s1_lower.upper(), self.s1)
class SequenceCollectionTests(TestCase):
"""Tests of the SequenceCollection class """
def setUp(self):
"""Initialize values to be used in tests
"""
self.d1 = DNASequence('GATTACA', id="d1")
self.d2 = DNASequence('TTG', id="d2")
self.d1_lower = DNASequence('gattaca', id="d1")
self.d2_lower = DNASequence('ttg', id="d2")
self.r1 = RNASequence('GAUUACA', id="r1")
self.r2 = RNASequence('UUG', id="r2")
self.r3 = RNASequence('U-----UGCC--', id="r3")
self.i1 = DNASequence('GATXACA', id="i1")
self.seqs1 = [self.d1, self.d2]
self.seqs1_lower = [self.d1_lower, self.d2_lower]
self.seqs2 = [self.r1, self.r2, self.r3]
self.seqs3 = self.seqs1 + self.seqs2
self.seqs1_t = [('d1', 'GATTACA'), ('d2', 'TTG')]
self.seqs2_t = [('r1', 'GAUUACA'), ('r2', 'UUG'),
('r3', 'U-----UGCC--')]
self.seqs3_t = self.seqs1_t + self.seqs2_t
self.s1 = SequenceCollection(self.seqs1)
self.s1_lower = SequenceCollection(self.seqs1_lower)
self.s2 = SequenceCollection(self.seqs2)
self.s3 = SequenceCollection(self.seqs3)
self.empty = SequenceCollection([])
self.invalid_s1 = SequenceCollection([self.i1])
def test_init(self):
"""Initialization functions as expected with varied input types
"""
SequenceCollection(self.seqs1)
SequenceCollection(self.seqs2)
SequenceCollection(self.seqs3)
SequenceCollection([])
def test_init_fail(self):
"""initialization with sequences with overlapping ids fails
"""
s1 = [self.d1, self.d1]
self.assertRaises(SequenceCollectionError, SequenceCollection, s1)
def test_init_validate(self):
"""initialization with validation functions as expected
"""
SequenceCollection(self.seqs1, validate=True)
SequenceCollection(self.seqs1, validate=True)
# can't validate self.seqs2 as a DNASequence
self.assertRaises(SequenceCollectionError, SequenceCollection,
self.invalid_s1, validate=True)
def test_from_fasta_records(self):
"""Initialization from list of tuples functions as expected
"""
SequenceCollection.from_fasta_records(self.seqs1_t, DNASequence)
SequenceCollection.from_fasta_records(self.seqs2_t, RNASequence)
SequenceCollection.from_fasta_records(self.seqs3_t, NucleotideSequence)
def test_contains(self):
"""in operator functions as expected
"""
self.assertTrue('d1' in self.s1)
self.assertTrue('r2' in self.s2)
self.assertFalse('r2' in self.s1)
def test_eq(self):
"""equality operator functions as expected
"""
self.assertTrue(self.s1 == self.s1)
self.assertFalse(self.s1 == self.s2)
# different objects can be equal
self.assertTrue(self.s1 == SequenceCollection([self.d1, self.d2]))
self.assertTrue(SequenceCollection([self.d1, self.d2]) == self.s1)
# SequenceCollections with different number of sequences are not equal
self.assertFalse(self.s1 == SequenceCollection([self.d1]))
class FakeSequenceCollection(SequenceCollection):
pass
# SequenceCollections of different types are not equal
self.assertFalse(self.s1 == FakeSequenceCollection([self.d1, self.d2]))
self.assertFalse(self.s1 == Alignment([self.d1, self.d2]))
# SequenceCollections with different sequences are not equal
self.assertFalse(self.s1 == SequenceCollection([self.d1, self.r1]))
def test_getitem(self):
"""getitem functions as expected
"""
self.assertEqual(self.s1[0], self.d1)
self.assertEqual(self.s1[1], self.d2)
self.assertEqual(self.s2[0], self.r1)
self.assertEqual(self.s2[1], self.r2)
self.assertRaises(IndexError, self.empty.__getitem__, 0)
self.assertRaises(KeyError, self.empty.__getitem__, '0')
def test_iter(self):
"""iter functions as expected
"""
s1_iter = iter(self.s1)
count = 0
for actual, expected in zip(s1_iter, self.seqs1):
count += 1
self.assertEqual(actual, expected)
self.assertEqual(count, len(self.seqs1))
self.assertRaises(StopIteration, lambda: next(s1_iter))
def test_len(self):
"""len functions as expected
"""
self.assertEqual(len(self.s1), 2)
self.assertEqual(len(self.s2), 3)
self.assertEqual(len(self.s3), 5)
self.assertEqual(len(self.empty), 0)
def test_ne(self):
"""inequality operator functions as expected
"""
self.assertFalse(self.s1 != self.s1)
self.assertTrue(self.s1 != self.s2)
# SequenceCollections with different number of sequences are not equal
self.assertTrue(self.s1 != SequenceCollection([self.d1]))
class FakeSequenceCollection(SequenceCollection):
pass
# SequenceCollections of different types are not equal
self.assertTrue(self.s1 != FakeSequenceCollection([self.d1, self.d2]))
self.assertTrue(self.s1 != Alignment([self.d1, self.d2]))
# SequenceCollections with different sequences are not equal
self.assertTrue(self.s1 !=
SequenceCollection([self.d1, self.r1]))
def test_repr(self):
"""repr functions as expected
"""
self.assertEqual(repr(self.s1),
"<SequenceCollection: n=2; "
"mean +/- std length=5.00 +/- 2.00>")
self.assertEqual(repr(self.s2),
"<SequenceCollection: n=3; "
"mean +/- std length=7.33 +/- 3.68>")
self.assertEqual(repr(self.s3),
"<SequenceCollection: n=5; "
"mean +/- std length=6.40 +/- 3.32>")
self.assertEqual(repr(self.empty),
"<SequenceCollection: n=0; "
"mean +/- std length=0.00 +/- 0.00>")
def test_reversed(self):
"""reversed functions as expected
"""
s1_iter = reversed(self.s1)
count = 0
for actual, expected in zip(s1_iter, self.seqs1[::-1]):
count += 1
self.assertEqual(actual, expected)
self.assertEqual(count, len(self.seqs1))
self.assertRaises(StopIteration, lambda: next(s1_iter))
def test_k_word_frequencies(self):
"""k_word_frequencies functions as expected
"""
expected1 = defaultdict(int)
expected1['A'] = 3 / 7.
expected1['C'] = 1 / 7.
expected1['G'] = 1 / 7.
expected1['T'] = 2 / 7.
expected2 = defaultdict(int)
expected2['G'] = 1 / 3.
expected2['T'] = 2 / 3.
self.assertEqual(self.s1.k_word_frequencies(k=1),
[expected1, expected2])
expected1 = defaultdict(int)
expected1['GAT'] = 1 / 2.
expected1['TAC'] = 1 / 2.
expected2 = defaultdict(int)
expected2['TTG'] = 1 / 1.
self.assertEqual(self.s1.k_word_frequencies(k=3, overlapping=False),
[expected1, expected2])
self.assertEqual(self.empty.k_word_frequencies(k=1), [])
def test_str(self):
"""str functions as expected
"""
exp1 = ">d1\nGATTACA\n>d2\nTTG\n"
self.assertEqual(str(self.s1), exp1)
exp2 = ">r1\nGAUUACA\n>r2\nUUG\n>r3\nU-----UGCC--\n"
self.assertEqual(str(self.s2), exp2)
exp4 = ""
self.assertEqual(str(self.empty), exp4)
def test_distances(self):
"""distances functions as expected
"""
s1 = SequenceCollection([DNA("ACGT", "d1"), DNA("ACGG", "d2")])
expected = [[0, 0.25],
[0.25, 0]]
expected = DistanceMatrix(expected, ['d1', 'd2'])
actual = s1.distances(hamming)
self.assertEqual(actual, expected)
# alt distance function provided
def dumb_distance(s1, s2):
return 42.
expected = [[0, 42.],
[42., 0]]
expected = DistanceMatrix(expected, ['d1', 'd2'])
actual = s1.distances(dumb_distance)
self.assertEqual(actual, expected)
def test_distribution_stats(self):
"""distribution_stats functions as expected
"""
actual1 = self.s1.distribution_stats()
self.assertEqual(actual1[0], 2)
self.assertAlmostEqual(actual1[1], 5.0, 3)
self.assertAlmostEqual(actual1[2], 2.0, 3)
actual2 = self.s2.distribution_stats()
self.assertEqual(actual2[0], 3)
self.assertAlmostEqual(actual2[1], 7.333, 3)
self.assertAlmostEqual(actual2[2], 3.682, 3)
actual3 = self.s3.distribution_stats()
self.assertEqual(actual3[0], 5)
self.assertAlmostEqual(actual3[1], 6.400, 3)
self.assertAlmostEqual(actual3[2], 3.323, 3)
actual4 = self.empty.distribution_stats()
self.assertEqual(actual4[0], 0)
self.assertEqual(actual4[1], 0.0)
self.assertEqual(actual4[2], 0.0)
def test_degap(self):
"""degap functions as expected
"""
expected = [(id_, seq.replace('.', '').replace('-', ''))
for id_, seq in self.seqs2_t]
expected = SequenceCollection.from_fasta_records(expected, RNASequence)
actual = self.s2.degap()
self.assertEqual(actual, expected)
def test_get_seq(self):
"""getseq functions asexpected
"""
self.assertEqual(self.s1.get_seq('d1'), self.d1)
self.assertEqual(self.s1.get_seq('d2'), self.d2)
def test_ids(self):
"""ids functions as expected
"""
self.assertEqual(self.s1.ids(), ['d1', 'd2'])
self.assertEqual(self.s2.ids(), ['r1', 'r2', 'r3'])
self.assertEqual(self.s3.ids(),
['d1', 'd2', 'r1', 'r2', 'r3'])
self.assertEqual(self.empty.ids(), [])
def _assert_sequence_collections_equal(self, observed, expected):
"""Compare SequenceCollections strictly."""
# TODO remove this custom equality testing code when SequenceCollection
# has an equals method (part of #656). We need this method to include
# IDs in the comparison (not part of SequenceCollection.__eq__).
self.assertEqual(observed, expected)
for obs_seq, exp_seq in zip(observed, expected):
self.assertTrue(obs_seq.equals(exp_seq))
def test_update_ids_default_behavior(self):
# 3 seqs
exp_sc = SequenceCollection([
RNA('GAUUACA', id="1"),
RNA('UUG', id="2"),
RNA('U-----UGCC--', id="3")
])
exp_id_map = {'1': 'r1', '2': 'r2', '3': 'r3'}
obs_sc, obs_id_map = self.s2.update_ids()
self._assert_sequence_collections_equal(obs_sc, exp_sc)
self.assertEqual(obs_id_map, exp_id_map)
# empty
obs_sc, obs_id_map = self.empty.update_ids()
self._assert_sequence_collections_equal(obs_sc, self.empty)
self.assertEqual(obs_id_map, {})
def test_update_ids_prefix(self):
# 3 seqs
exp_sc = SequenceCollection([
RNA('GAUUACA', id="abc1"),
RNA('UUG', id="abc2"),
RNA('U-----UGCC--', id="abc3")
])
exp_id_map = {'abc1': 'r1', 'abc2': 'r2', 'abc3': 'r3'}
obs_sc, obs_id_map = self.s2.update_ids(prefix='abc')
self._assert_sequence_collections_equal(obs_sc, exp_sc)
self.assertEqual(obs_id_map, exp_id_map)
# empty
obs_sc, obs_id_map = self.empty.update_ids(prefix='abc')
self._assert_sequence_collections_equal(obs_sc, self.empty)
self.assertEqual(obs_id_map, {})
def test_update_ids_fn_parameter(self):
def append_42(ids):
return [id_ + '-42' for id_ in ids]
# 3 seqs
exp_sc = SequenceCollection([
RNA('GAUUACA', id="r1-42"),
RNA('UUG', id="r2-42"),
RNA('U-----UGCC--', id="r3-42")
])
exp_id_map = {'r1-42': 'r1', 'r2-42': 'r2', 'r3-42': 'r3'}
obs_sc, obs_id_map = self.s2.update_ids(fn=append_42)
self._assert_sequence_collections_equal(obs_sc, exp_sc)
self.assertEqual(obs_id_map, exp_id_map)
# empty
obs_sc, obs_id_map = self.empty.update_ids(fn=append_42)
self._assert_sequence_collections_equal(obs_sc, self.empty)
self.assertEqual(obs_id_map, {})
def test_update_ids_ids_parameter(self):
# 3 seqs
exp_sc = SequenceCollection([
RNA('GAUUACA', id="abc"),
RNA('UUG', id="def"),
RNA('U-----UGCC--', id="ghi")
])
exp_id_map = {'abc': 'r1', 'def': 'r2', 'ghi': 'r3'}
obs_sc, obs_id_map = self.s2.update_ids(ids=('abc', 'def', 'ghi'))
self._assert_sequence_collections_equal(obs_sc, exp_sc)
self.assertEqual(obs_id_map, exp_id_map)
# empty
obs_sc, obs_id_map = self.empty.update_ids(ids=[])
self._assert_sequence_collections_equal(obs_sc, self.empty)
self.assertEqual(obs_id_map, {})
def test_update_ids_sequence_attributes_propagated(self):
# 1 seq
exp_sc = Alignment([
DNA('ACGT', id="abc", description='desc', quality=range(4))
])
exp_id_map = {'abc': 'seq1'}
obj = Alignment([
DNA('ACGT', id="seq1", description='desc', quality=range(4))
])
obs_sc, obs_id_map = obj.update_ids(ids=('abc',))
self._assert_sequence_collections_equal(obs_sc, exp_sc)
self.assertEqual(obs_id_map, exp_id_map)
# 2 seqs
exp_sc = Alignment([
DNA('ACGT', id="abc", description='desc1', quality=range(4)),
DNA('TGCA', id="def", description='desc2', quality=range(4)[::-1])
])
exp_id_map = {'abc': 'seq1', 'def': 'seq2'}
obj = Alignment([
DNA('ACGT', id="seq1", description='desc1', quality=(0, 1, 2, 3)),
DNA('TGCA', id="seq2", description='desc2', quality=(3, 2, 1, 0))
])
obs_sc, obs_id_map = obj.update_ids(ids=('abc', 'def'))
self._assert_sequence_collections_equal(obs_sc, exp_sc)
self.assertEqual(obs_id_map, exp_id_map)
def test_update_ids_invalid_parameter_combos(self):
with self.assertRaisesRegexp(SequenceCollectionError, 'ids and fn'):
self.s1.update_ids(fn=lambda e: e, ids=['foo', 'bar'])
with self.assertRaisesRegexp(SequenceCollectionError, 'prefix'):
self.s1.update_ids(ids=['foo', 'bar'], prefix='abc')
with self.assertRaisesRegexp(SequenceCollectionError, 'prefix'):
self.s1.update_ids(fn=lambda e: e, prefix='abc')
def test_update_ids_invalid_ids(self):
# incorrect number of new ids
with self.assertRaisesRegexp(SequenceCollectionError, '3 != 2'):
self.s1.update_ids(ids=['foo', 'bar', 'baz'])
with self.assertRaisesRegexp(SequenceCollectionError, '4 != 2'):
self.s1.update_ids(fn=lambda e: ['foo', 'bar', 'baz', 'abc'])
# duplicates
with self.assertRaisesRegexp(SequenceCollectionError, 'foo'):
self.s2.update_ids(ids=['foo', 'bar', 'foo'])
with self.assertRaisesRegexp(SequenceCollectionError, 'bar'):
self.s2.update_ids(fn=lambda e: ['foo', 'bar', 'bar'])
def test_int_map(self):
expected1 = {"1": self.d1, "2": self.d2}
expected2 = {"1": "d1", "2": "d2"}
obs = npt.assert_warns(UserWarning, self.s1.int_map)
self.assertEqual(obs, (expected1, expected2))
expected1 = {"h-1": self.d1, "h-2": self.d2}
expected2 = {"h-1": "d1", "h-2": "d2"}
obs = npt.assert_warns(UserWarning, self.s1.int_map, prefix='h-')
self.assertEqual(obs, (expected1, expected2))
def test_is_empty(self):
"""is_empty functions as expected
"""
self.assertFalse(self.s1.is_empty())
self.assertFalse(self.s2.is_empty())
self.assertFalse(self.s3.is_empty())
self.assertTrue(self.empty.is_empty())
def test_is_valid(self):
"""is_valid functions as expected
"""
self.assertTrue(self.s1.is_valid())
self.assertTrue(self.s2.is_valid())
self.assertTrue(self.s3.is_valid())
self.assertTrue(self.empty.is_valid())
self.assertFalse(self.invalid_s1.is_valid())
def test_iteritems(self):
"""iteritems functions as expected
"""
self.assertEqual(list(self.s1.iteritems()),
[(s.id, s) for s in self.s1])
def test_lower(self):
"""lower functions as expected
"""
self.assertEqual(self.s1.lower(), self.s1_lower)
def test_sequence_count(self):
"""num_seqs functions as expected
"""
self.assertEqual(self.s1.sequence_count(), 2)
self.assertEqual(self.s2.sequence_count(), 3)
self.assertEqual(self.s3.sequence_count(), 5)
self.assertEqual(self.empty.sequence_count(), 0)
def test_sequence_lengths(self):
"""sequence_lengths functions as expected
"""
self.assertEqual(self.s1.sequence_lengths(), [7, 3])
self.assertEqual(self.s2.sequence_lengths(), [7, 3, 12])
self.assertEqual(self.s3.sequence_lengths(), [7, 3, 7, 3, 12])
self.assertEqual(self.empty.sequence_lengths(), [])
def test_to_fasta(self):
"""to_fasta functions as expected
"""
exp1 = ">d1\nGATTACA\n>d2\nTTG\n"
self.assertEqual(self.s1.to_fasta(), exp1)
exp2 = ">r1\nGAUUACA\n>r2\nUUG\n>r3\nU-----UGCC--\n"
self.assertEqual(self.s2.to_fasta(), exp2)
def test_toFasta(self):
exp = ">d1\nGATTACA\n>d2\nTTG\n"
obs = npt.assert_warns(UserWarning, self.s1.toFasta)
self.assertEqual(obs, exp)
def test_upper(self):
"""upper functions as expected
"""
self.assertEqual(self.s1_lower.upper(), self.s1)
class SequenceCollectionTests(TestCase):
def setUp(self):
self.d1 = DNA('GATTACA', metadata={'id': "d1"})
self.d2 = DNA('TTG', metadata={'id': "d2"})
self.d3 = DNA('GTATACA', metadata={'id': "d3"})
self.r1 = RNA('GAUUACA', metadata={'id': "r1"})
self.r2 = RNA('UUG', metadata={'id': "r2"})
self.r3 = RNA('U-----UGCC--', metadata={'id': "r3"})
self.seqs1 = [self.d1, self.d2]
self.seqs2 = [self.r1, self.r2, self.r3]
self.seqs3 = self.seqs1 + self.seqs2
self.seqs4 = [self.d1, self.d3]
self.s1 = SequenceCollection(self.seqs1)
self.s2 = SequenceCollection(self.seqs2)
self.s3 = SequenceCollection(self.seqs3)
self.s4 = SequenceCollection(self.seqs4)
self.empty = SequenceCollection([])
def test_init(self):
SequenceCollection(self.seqs1)
SequenceCollection(self.seqs2)
SequenceCollection(self.seqs3)
SequenceCollection([])
def test_init_fail(self):
# sequences with overlapping ids
s1 = [self.d1, self.d1]
self.assertRaises(SequenceCollectionError, SequenceCollection, s1)
def test_init_fail_no_id(self):
seq = Sequence('ACGTACGT')
with six.assertRaisesRegex(
self, SequenceCollectionError,
"'id' must be included in the sequence "
"metadata"):
SequenceCollection([seq])
def test_contains(self):
self.assertTrue('d1' in self.s1)
self.assertTrue('r2' in self.s2)
self.assertFalse('r2' in self.s1)
def test_eq(self):
self.assertTrue(self.s1 == self.s1)
self.assertFalse(self.s1 == self.s2)
# different objects can be equal
self.assertTrue(self.s1 == SequenceCollection([self.d1, self.d2]))
self.assertTrue(SequenceCollection([self.d1, self.d2]) == self.s1)
# SequenceCollections with different number of sequences are not equal
self.assertFalse(self.s1 == SequenceCollection([self.d1]))
class FakeSequenceCollection(SequenceCollection):
pass
# SequenceCollections of different types are not equal
self.assertFalse(self.s4 == FakeSequenceCollection([self.d1, self.d3]))
self.assertFalse(self.s4 == Alignment([self.d1, self.d3]))
# SequenceCollections with different sequences are not equal
self.assertFalse(self.s1 == SequenceCollection([self.d1, self.r1]))
def test_getitem(self):
self.assertEqual(self.s1[0], self.d1)
self.assertEqual(self.s1[1], self.d2)
self.assertEqual(self.s2[0], self.r1)
self.assertEqual(self.s2[1], self.r2)
self.assertRaises(IndexError, self.empty.__getitem__, 0)
self.assertRaises(KeyError, self.empty.__getitem__, '0')
def test_iter(self):
s1_iter = iter(self.s1)
count = 0
for actual, expected in zip(s1_iter, self.seqs1):
count += 1
self.assertEqual(actual, expected)
self.assertEqual(count, len(self.seqs1))
self.assertRaises(StopIteration, lambda: next(s1_iter))
def test_len(self):
self.assertEqual(len(self.s1), 2)
self.assertEqual(len(self.s2), 3)
self.assertEqual(len(self.s3), 5)
self.assertEqual(len(self.empty), 0)
def test_ne(self):
self.assertFalse(self.s1 != self.s1)
self.assertTrue(self.s1 != self.s2)
# SequenceCollections with different number of sequences are not equal
self.assertTrue(self.s1 != SequenceCollection([self.d1]))
class FakeSequenceCollection(SequenceCollection):
pass
# SequenceCollections of different types are not equal
self.assertTrue(self.s4 != FakeSequenceCollection([self.d1, self.d3]))
self.assertTrue(self.s4 != Alignment([self.d1, self.d3]))
# SequenceCollections with different sequences are not equal
self.assertTrue(self.s1 != SequenceCollection([self.d1, self.r1]))
def test_repr(self):
self.assertEqual(
repr(self.s1), "<SequenceCollection: n=2; "
"mean +/- std length=5.00 +/- 2.00>")
self.assertEqual(
repr(self.s2), "<SequenceCollection: n=3; "
"mean +/- std length=7.33 +/- 3.68>")
self.assertEqual(
repr(self.s3), "<SequenceCollection: n=5; "
"mean +/- std length=6.40 +/- 3.32>")
self.assertEqual(
repr(self.empty), "<SequenceCollection: n=0; "
"mean +/- std length=0.00 +/- 0.00>")
def test_reversed(self):
s1_iter = reversed(self.s1)
count = 0
for actual, expected in zip(s1_iter, self.seqs1[::-1]):
count += 1
self.assertEqual(actual, expected)
self.assertEqual(count, len(self.seqs1))
self.assertRaises(StopIteration, lambda: next(s1_iter))
def test_kmer_frequencies(self):
expected1 = Counter({'GAT': 1, 'TAC': 1})
expected2 = Counter({'TTG': 1})
self.assertEqual(
self.s1.kmer_frequencies(k=3, overlap=False, relative=False),
[expected1, expected2])
expected1 = defaultdict(float)
expected1['A'] = 3 / 7.
expected1['C'] = 1 / 7.
expected1['G'] = 1 / 7.
expected1['T'] = 2 / 7.
expected2 = defaultdict(float)
expected2['G'] = 1 / 3.
expected2['T'] = 2 / 3.
self.assertEqual(self.s1.kmer_frequencies(k=1, relative=True),
[expected1, expected2])
expected1 = defaultdict(float)
expected1['GAT'] = 1 / 2.
expected1['TAC'] = 1 / 2.
expected2 = defaultdict(float)
expected2['TTG'] = 1 / 1.
self.assertEqual(
self.s1.kmer_frequencies(k=3, overlap=False, relative=True),
[expected1, expected2])
self.assertEqual(self.empty.kmer_frequencies(k=1, relative=True), [])
# Test to ensure floating point precision bug isn't present. See the
# tests for Sequence.kmer_frequencies for more details.
sc = SequenceCollection([
RNA('C' * 10, metadata={'id': 's1'}),
RNA('G' * 10, metadata={'id': 's2'})
])
self.assertEqual(
sc.kmer_frequencies(1, relative=True),
[defaultdict(float, {'C': 1.0}),
defaultdict(float, {'G': 1.0})])
def test_str(self):
exp1 = ">d1\nGATTACA\n>d2\nTTG\n"
self.assertEqual(str(self.s1), exp1)
exp2 = ">r1\nGAUUACA\n>r2\nUUG\n>r3\nU-----UGCC--\n"
self.assertEqual(str(self.s2), exp2)
exp4 = ""
self.assertEqual(str(self.empty), exp4)
def test_distances(self):
s1 = SequenceCollection([
DNA("ACGT", metadata={'id': "d1"}),
DNA("ACGG", metadata={'id': "d2"})
])
expected = [[0, 0.25], [0.25, 0]]
expected = DistanceMatrix(expected, ['d1', 'd2'])
def h(s1, s2):
return hamming(s1.values, s2.values)
actual = s1.distances(h)
self.assertEqual(actual, expected)
# alt distance function provided
def dumb_distance(s1, s2):
return 42.
expected = [[0, 42.], [42., 0]]
expected = DistanceMatrix(expected, ['d1', 'd2'])
actual = s1.distances(dumb_distance)
self.assertEqual(actual, expected)
def test_distribution_stats(self):
actual1 = self.s1.distribution_stats()
self.assertEqual(actual1[0], 2)
self.assertAlmostEqual(actual1[1], 5.0, 3)
self.assertAlmostEqual(actual1[2], 2.0, 3)
actual2 = self.s2.distribution_stats()
self.assertEqual(actual2[0], 3)
self.assertAlmostEqual(actual2[1], 7.333, 3)
self.assertAlmostEqual(actual2[2], 3.682, 3)
actual3 = self.s3.distribution_stats()
self.assertEqual(actual3[0], 5)
self.assertAlmostEqual(actual3[1], 6.400, 3)
self.assertAlmostEqual(actual3[2], 3.323, 3)
actual4 = self.empty.distribution_stats()
self.assertEqual(actual4[0], 0)
self.assertEqual(actual4[1], 0.0)
self.assertEqual(actual4[2], 0.0)
def test_degap(self):
expected = SequenceCollection([
RNA('GAUUACA', metadata={'id': "r1"}),
RNA('UUG', metadata={'id': "r2"}),
RNA('UUGCC', metadata={'id': "r3"})
])
actual = self.s2.degap()
self.assertEqual(actual, expected)
def test_get_seq(self):
self.assertEqual(self.s1.get_seq('d1'), self.d1)
self.assertEqual(self.s1.get_seq('d2'), self.d2)
def test_ids(self):
self.assertEqual(self.s1.ids(), ['d1', 'd2'])
self.assertEqual(self.s2.ids(), ['r1', 'r2', 'r3'])
self.assertEqual(self.s3.ids(), ['d1', 'd2', 'r1', 'r2', 'r3'])
self.assertEqual(self.empty.ids(), [])
def test_update_ids_default_behavior(self):
# 3 seqs
exp_sc = SequenceCollection([
RNA('GAUUACA', metadata={'id': "1"}),
RNA('UUG', metadata={'id': "2"}),
RNA('U-----UGCC--', metadata={'id': "3"})
])
exp_id_map = {'1': 'r1', '2': 'r2', '3': 'r3'}
obs_sc, obs_id_map = self.s2.update_ids()
self.assertEqual(obs_sc, exp_sc)
self.assertEqual(obs_id_map, exp_id_map)
# empty
obs_sc, obs_id_map = self.empty.update_ids()
self.assertEqual(obs_sc, self.empty)
self.assertEqual(obs_id_map, {})
def test_update_ids_prefix(self):
# 3 seqs
exp_sc = SequenceCollection([
RNA('GAUUACA', metadata={'id': "abc1"}),
RNA('UUG', metadata={'id': "abc2"}),
RNA('U-----UGCC--', metadata={'id': "abc3"})
])
exp_id_map = {'abc1': 'r1', 'abc2': 'r2', 'abc3': 'r3'}
obs_sc, obs_id_map = self.s2.update_ids(prefix='abc')
self.assertEqual(obs_sc, exp_sc)
self.assertEqual(obs_id_map, exp_id_map)
# empty
obs_sc, obs_id_map = self.empty.update_ids(prefix='abc')
self.assertEqual(obs_sc, self.empty)
self.assertEqual(obs_id_map, {})
def test_update_ids_func_parameter(self):
def append_42(ids):
return [id_ + '-42' for id_ in ids]
# 3 seqs
exp_sc = SequenceCollection([
RNA('GAUUACA', metadata={'id': "r1-42"}),
RNA('UUG', metadata={'id': "r2-42"}),
RNA('U-----UGCC--', metadata={'id': "r3-42"})
])
exp_id_map = {'r1-42': 'r1', 'r2-42': 'r2', 'r3-42': 'r3'}
obs_sc, obs_id_map = self.s2.update_ids(func=append_42)
self.assertEqual(obs_sc, exp_sc)
self.assertEqual(obs_id_map, exp_id_map)
# empty
obs_sc, obs_id_map = self.empty.update_ids(func=append_42)
self.assertEqual(obs_sc, self.empty)
self.assertEqual(obs_id_map, {})
def test_update_ids_ids_parameter(self):
# 3 seqs
exp_sc = SequenceCollection([
RNA('GAUUACA', metadata={'id': "abc"}),
RNA('UUG', metadata={'id': "def"}),
RNA('U-----UGCC--', metadata={'id': "ghi"})
])
exp_id_map = {'abc': 'r1', 'def': 'r2', 'ghi': 'r3'}
obs_sc, obs_id_map = self.s2.update_ids(ids=('abc', 'def', 'ghi'))
self.assertEqual(obs_sc, exp_sc)
self.assertEqual(obs_id_map, exp_id_map)
# empty
obs_sc, obs_id_map = self.empty.update_ids(ids=[])
self.assertEqual(obs_sc, self.empty)
self.assertEqual(obs_id_map, {})
def test_update_ids_sequence_attributes_propagated(self):
# 1 seq
exp_sc = Alignment([
DNA('ACGT',
metadata={
'id': "abc",
'description': 'desc'
},
positional_metadata={'quality': range(4)})
])
exp_id_map = {'abc': 'seq1'}
obj = Alignment([
DNA('ACGT',
metadata={
'id': "seq1",
'description': 'desc'
},
positional_metadata={'quality': range(4)})
])
obs_sc, obs_id_map = obj.update_ids(ids=('abc', ))
self.assertEqual(obs_sc, exp_sc)
self.assertEqual(obs_id_map, exp_id_map)
# 2 seqs
exp_sc = Alignment([
DNA('ACGT',
metadata={
'id': "abc",
'description': 'desc1'
},
positional_metadata={'quality': range(4)}),
DNA('TGCA',
metadata={
'id': "def",
'description': 'desc2'
},
positional_metadata={'quality': range(4)[::-1]})
])
exp_id_map = {'abc': 'seq1', 'def': 'seq2'}
obj = Alignment([
DNA('ACGT',
metadata={
'id': "seq1",
'description': 'desc1'
},
positional_metadata={'quality': (0, 1, 2, 3)}),
DNA('TGCA',
metadata={
'id': "seq2",
'description': 'desc2'
},
positional_metadata={'quality': (3, 2, 1, 0)})
])
obs_sc, obs_id_map = obj.update_ids(ids=('abc', 'def'))
self.assertEqual(obs_sc, exp_sc)
self.assertEqual(obs_id_map, exp_id_map)
def test_update_ids_invalid_parameter_combos(self):
with six.assertRaisesRegex(self, SequenceCollectionError,
'ids and func'):
self.s1.update_ids(func=lambda e: e, ids=['foo', 'bar'])
with six.assertRaisesRegex(self, SequenceCollectionError, 'prefix'):
self.s1.update_ids(ids=['foo', 'bar'], prefix='abc')
with six.assertRaisesRegex(self, SequenceCollectionError, 'prefix'):
self.s1.update_ids(func=lambda e: e, prefix='abc')
def test_update_ids_invalid_ids(self):
# incorrect number of new ids
with six.assertRaisesRegex(self, SequenceCollectionError, '3 != 2'):
self.s1.update_ids(ids=['foo', 'bar', 'baz'])
with six.assertRaisesRegex(self, SequenceCollectionError, '4 != 2'):
self.s1.update_ids(func=lambda e: ['foo', 'bar', 'baz', 'abc'])
# duplicates
with six.assertRaisesRegex(self, SequenceCollectionError, 'foo'):
self.s2.update_ids(ids=['foo', 'bar', 'foo'])
with six.assertRaisesRegex(self, SequenceCollectionError, 'bar'):
self.s2.update_ids(func=lambda e: ['foo', 'bar', 'bar'])
def test_is_empty(self):
self.assertFalse(self.s1.is_empty())
self.assertFalse(self.s2.is_empty())
self.assertFalse(self.s3.is_empty())
self.assertTrue(self.empty.is_empty())
def test_iteritems(self):
self.assertEqual(list(self.s1.iteritems()),
[(s.metadata['id'], s) for s in self.s1])
def test_sequence_count(self):
self.assertEqual(self.s1.sequence_count(), 2)
self.assertEqual(self.s2.sequence_count(), 3)
self.assertEqual(self.s3.sequence_count(), 5)
self.assertEqual(self.empty.sequence_count(), 0)
def test_sequence_lengths(self):
self.assertEqual(self.s1.sequence_lengths(), [7, 3])
self.assertEqual(self.s2.sequence_lengths(), [7, 3, 12])
self.assertEqual(self.s3.sequence_lengths(), [7, 3, 7, 3, 12])
self.assertEqual(self.empty.sequence_lengths(), [])
class SequenceCollectionTests(TestCase):
"""Tests of the SequenceCollection class """
def setUp(self):
"""Initialize values to be used in tests
"""
self.d1 = DNASequence('GATTACA', id="d1")
self.d2 = DNASequence('TTG', id="d2")
self.d1_lower = DNASequence('gattaca', id="d1")
self.d2_lower = DNASequence('ttg', id="d2")
self.r1 = RNASequence('GAUUACA', id="r1")
self.r2 = RNASequence('UUG', id="r2")
self.r3 = RNASequence('U-----UGCC--', id="r3")
self.i1 = DNASequence('GATXACA', id="i1")
self.seqs1 = [self.d1, self.d2]
self.seqs1_lower = [self.d1_lower, self.d2_lower]
self.seqs2 = [self.r1, self.r2, self.r3]
self.seqs3 = self.seqs1 + self.seqs2
self.seqs1_t = [('d1', 'GATTACA'), ('d2', 'TTG')]
self.seqs2_t = [('r1', 'GAUUACA'), ('r2', 'UUG'),
('r3', 'U-----UGCC--')]
self.seqs3_t = self.seqs1_t + self.seqs2_t
self.s1 = SequenceCollection(self.seqs1)
self.s1_lower = SequenceCollection(self.seqs1_lower)
self.s2 = SequenceCollection(self.seqs2)
self.s3 = SequenceCollection(self.seqs3)
self.empty = SequenceCollection([])
self.invalid_s1 = SequenceCollection([self.i1])
def test_init(self):
"""Initialization functions as expected with varied input types
"""
SequenceCollection(self.seqs1)
SequenceCollection(self.seqs2)
SequenceCollection(self.seqs3)
SequenceCollection([])
def test_init_fail(self):
"""initialization with sequences with overlapping ids fails
"""
s1 = [self.d1, self.d1]
self.assertRaises(SequenceCollectionError, SequenceCollection, s1)
def test_init_validate(self):
"""initialization with validation functions as expected
"""
SequenceCollection(self.seqs1, validate=True)
SequenceCollection(self.seqs1, validate=True)
# can't validate self.seqs2 as a DNASequence
self.assertRaises(SequenceCollectionError,
SequenceCollection,
self.invalid_s1,
validate=True)
def test_from_fasta_records(self):
"""Initialization from list of tuples functions as expected
"""
SequenceCollection.from_fasta_records(self.seqs1_t, DNASequence)
SequenceCollection.from_fasta_records(self.seqs2_t, RNASequence)
SequenceCollection.from_fasta_records(self.seqs3_t, NucleotideSequence)
def test_contains(self):
"""in operator functions as expected
"""
self.assertTrue('d1' in self.s1)
self.assertTrue('r2' in self.s2)
self.assertFalse('r2' in self.s1)
def test_eq(self):
"""equality operator functions as expected
"""
self.assertTrue(self.s1 == self.s1)
self.assertFalse(self.s1 == self.s2)
# different objects can be equal
self.assertTrue(self.s1 == SequenceCollection([self.d1, self.d2]))
self.assertTrue(SequenceCollection([self.d1, self.d2]) == self.s1)
# SequenceCollections with different number of sequences are not equal
self.assertFalse(self.s1 == SequenceCollection([self.d1]))
class FakeSequenceCollection(SequenceCollection):
pass
# SequenceCollections of different types are not equal
self.assertFalse(self.s1 == FakeSequenceCollection([self.d1, self.d2]))
self.assertFalse(self.s1 == Alignment([self.d1, self.d2]))
# SequenceCollections with different sequences are not equal
self.assertFalse(self.s1 == SequenceCollection([self.d1, self.r1]))
def test_getitem(self):
"""getitem functions as expected
"""
self.assertEqual(self.s1[0], self.d1)
self.assertEqual(self.s1[1], self.d2)
self.assertEqual(self.s2[0], self.r1)
self.assertEqual(self.s2[1], self.r2)
self.assertRaises(IndexError, self.empty.__getitem__, 0)
self.assertRaises(KeyError, self.empty.__getitem__, '0')
def test_iter(self):
"""iter functions as expected
"""
s1_iter = iter(self.s1)
count = 0
for actual, expected in zip(s1_iter, self.seqs1):
count += 1
self.assertEqual(actual, expected)
self.assertEqual(count, len(self.seqs1))
self.assertRaises(StopIteration, lambda: next(s1_iter))
def test_len(self):
"""len functions as expected
"""
self.assertEqual(len(self.s1), 2)
self.assertEqual(len(self.s2), 3)
self.assertEqual(len(self.s3), 5)
self.assertEqual(len(self.empty), 0)
def test_ne(self):
"""inequality operator functions as expected
"""
self.assertFalse(self.s1 != self.s1)
self.assertTrue(self.s1 != self.s2)
# SequenceCollections with different number of sequences are not equal
self.assertTrue(self.s1 != SequenceCollection([self.d1]))
class FakeSequenceCollection(SequenceCollection):
pass
# SequenceCollections of different types are not equal
self.assertTrue(self.s1 != FakeSequenceCollection([self.d1, self.d2]))
self.assertTrue(self.s1 != Alignment([self.d1, self.d2]))
# SequenceCollections with different sequences are not equal
self.assertTrue(self.s1 != SequenceCollection([self.d1, self.r1]))
def test_repr(self):
"""repr functions as expected
"""
self.assertEqual(
repr(self.s1), "<SequenceCollection: n=2; "
"mean +/- std length=5.00 +/- 2.00>")
self.assertEqual(
repr(self.s2), "<SequenceCollection: n=3; "
"mean +/- std length=7.33 +/- 3.68>")
self.assertEqual(
repr(self.s3), "<SequenceCollection: n=5; "
"mean +/- std length=6.40 +/- 3.32>")
self.assertEqual(
repr(self.empty), "<SequenceCollection: n=0; "
"mean +/- std length=0.00 +/- 0.00>")
def test_reversed(self):
"""reversed functions as expected
"""
s1_iter = reversed(self.s1)
count = 0
for actual, expected in zip(s1_iter, self.seqs1[::-1]):
count += 1
self.assertEqual(actual, expected)
self.assertEqual(count, len(self.seqs1))
self.assertRaises(StopIteration, lambda: next(s1_iter))
def test_k_word_frequencies(self):
"""k_word_frequencies functions as expected
"""
expected1 = defaultdict(int)
expected1['A'] = 3 / 7.
expected1['C'] = 1 / 7.
expected1['G'] = 1 / 7.
expected1['T'] = 2 / 7.
expected2 = defaultdict(int)
expected2['G'] = 1 / 3.
expected2['T'] = 2 / 3.
self.assertEqual(self.s1.k_word_frequencies(k=1),
[expected1, expected2])
expected1 = defaultdict(int)
expected1['GAT'] = 1 / 2.
expected1['TAC'] = 1 / 2.
expected2 = defaultdict(int)
expected2['TTG'] = 1 / 1.
self.assertEqual(self.s1.k_word_frequencies(k=3, overlapping=False),
[expected1, expected2])
self.assertEqual(self.empty.k_word_frequencies(k=1), [])
def test_str(self):
"""str functions as expected
"""
exp1 = ">d1\nGATTACA\n>d2\nTTG\n"
self.assertEqual(str(self.s1), exp1)
exp2 = ">r1\nGAUUACA\n>r2\nUUG\n>r3\nU-----UGCC--\n"
self.assertEqual(str(self.s2), exp2)
exp4 = ""
self.assertEqual(str(self.empty), exp4)
def test_distances(self):
"""distances functions as expected
"""
s1 = SequenceCollection([DNA("ACGT", "d1"), DNA("ACGG", "d2")])
expected = [[0, 0.25], [0.25, 0]]
expected = DistanceMatrix(expected, ['d1', 'd2'])
actual = s1.distances(hamming)
self.assertEqual(actual, expected)
# alt distance function provided
def dumb_distance(s1, s2):
return 42.
expected = [[0, 42.], [42., 0]]
expected = DistanceMatrix(expected, ['d1', 'd2'])
actual = s1.distances(dumb_distance)
self.assertEqual(actual, expected)
def test_distribution_stats(self):
"""distribution_stats functions as expected
"""
actual1 = self.s1.distribution_stats()
self.assertEqual(actual1[0], 2)
self.assertAlmostEqual(actual1[1], 5.0, 3)
self.assertAlmostEqual(actual1[2], 2.0, 3)
actual2 = self.s2.distribution_stats()
self.assertEqual(actual2[0], 3)
self.assertAlmostEqual(actual2[1], 7.333, 3)
self.assertAlmostEqual(actual2[2], 3.682, 3)
actual3 = self.s3.distribution_stats()
self.assertEqual(actual3[0], 5)
self.assertAlmostEqual(actual3[1], 6.400, 3)
self.assertAlmostEqual(actual3[2], 3.323, 3)
actual4 = self.empty.distribution_stats()
self.assertEqual(actual4[0], 0)
self.assertEqual(actual4[1], 0.0)
self.assertEqual(actual4[2], 0.0)
def test_degap(self):
"""degap functions as expected
"""
expected = [(id_, seq.replace('.', '').replace('-', ''))
for id_, seq in self.seqs2_t]
expected = SequenceCollection.from_fasta_records(expected, RNASequence)
actual = self.s2.degap()
self.assertEqual(actual, expected)
def test_get_seq(self):
"""getseq functions asexpected
"""
self.assertEqual(self.s1.get_seq('d1'), self.d1)
self.assertEqual(self.s1.get_seq('d2'), self.d2)
def test_ids(self):
"""ids functions as expected
"""
self.assertEqual(self.s1.ids(), ['d1', 'd2'])
self.assertEqual(self.s2.ids(), ['r1', 'r2', 'r3'])
self.assertEqual(self.s3.ids(), ['d1', 'd2', 'r1', 'r2', 'r3'])
self.assertEqual(self.empty.ids(), [])
def test_int_map(self):
"""int_map functions as expected
"""
expected1 = {"1": self.d1, "2": self.d2}
expected2 = {"1": "d1", "2": "d2"}
self.assertEqual(self.s1.int_map(), (expected1, expected2))
expected1 = {"h-1": self.d1, "h-2": self.d2}
expected2 = {"h-1": "d1", "h-2": "d2"}
self.assertEqual(self.s1.int_map(prefix='h-'), (expected1, expected2))
def test_is_empty(self):
"""is_empty functions as expected
"""
self.assertFalse(self.s1.is_empty())
self.assertFalse(self.s2.is_empty())
self.assertFalse(self.s3.is_empty())
self.assertTrue(self.empty.is_empty())
def test_is_valid(self):
"""is_valid functions as expected
"""
self.assertTrue(self.s1.is_valid())
self.assertTrue(self.s2.is_valid())
self.assertTrue(self.s3.is_valid())
self.assertTrue(self.empty.is_valid())
self.assertFalse(self.invalid_s1.is_valid())
def test_iteritems(self):
"""iteritems functions as expected
"""
self.assertEqual(list(self.s1.iteritems()),
[(s.id, s) for s in self.s1])
def test_lower(self):
"""lower functions as expected
"""
self.assertEqual(self.s1.lower(), self.s1_lower)
def test_sequence_count(self):
"""num_seqs functions as expected
"""
self.assertEqual(self.s1.sequence_count(), 2)
self.assertEqual(self.s2.sequence_count(), 3)
self.assertEqual(self.s3.sequence_count(), 5)
self.assertEqual(self.empty.sequence_count(), 0)
def test_sequence_lengths(self):
"""sequence_lengths functions as expected
"""
self.assertEqual(self.s1.sequence_lengths(), [7, 3])
self.assertEqual(self.s2.sequence_lengths(), [7, 3, 12])
self.assertEqual(self.s3.sequence_lengths(), [7, 3, 7, 3, 12])
self.assertEqual(self.empty.sequence_lengths(), [])
def test_to_fasta(self):
"""to_fasta functions as expected
"""
exp1 = ">d1\nGATTACA\n>d2\nTTG\n"
self.assertEqual(self.s1.to_fasta(), exp1)
exp2 = ">r1\nGAUUACA\n>r2\nUUG\n>r3\nU-----UGCC--\n"
self.assertEqual(self.s2.to_fasta(), exp2)
def test_toFasta(self):
with warnings.catch_warnings():
warnings.simplefilter("ignore")
exp = ">d1\nGATTACA\n>d2\nTTG\n"
self.assertEqual(self.s1.toFasta(), exp)
def test_upper(self):
"""upper functions as expected
"""
self.assertEqual(self.s1_lower.upper(), self.s1)