def test_to_phylip_no_positions(self):
d1 = DNASequence('', id="d1")
d2 = DNASequence('', id="d2")
a = Alignment([d1, d2])
with self.assertRaises(SequenceCollectionError):
npt.assert_warns(UserWarning, a.to_phylip)
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 setUp(self):
self.d1 = DNASequence('..ACC-GTTGG..', id="d1")
self.d2 = DNASequence('TTACCGGT-GGCC', id="d2")
self.d3 = DNASequence('.-ACC-GTTGC--', id="d3")
self.r1 = RNASequence('UUAU-', id="r1")
self.r2 = RNASequence('ACGUU', id="r2")
self.seqs1 = [self.d1, self.d2, self.d3]
self.seqs2 = [self.r1, self.r2]
self.seqs1_t = [('d1', '..ACC-GTTGG..'), ('d2', 'TTACCGGT-GGCC'),
('d3', '.-ACC-GTTGC--')]
self.seqs2_t = [('r1', 'UUAU-'), ('r2', 'ACGUU')]
self.a1 = Alignment(self.seqs1)
self.a2 = Alignment(self.seqs2)
self.a3 = Alignment(self.seqs2,
score=42.0,
start_end_positions=[(0, 3), (5, 9)])
self.a4 = Alignment(self.seqs2,
score=-42.0,
start_end_positions=[(1, 4), (6, 10)])
# no sequences
self.empty = Alignment([])
# sequences, but no positions
self.no_positions = Alignment([RNA('', id='a'), RNA('', id='b')])
def test_reverse_complement(self):
self.assertEqual(self.b1.reverse_complement(), DNASequence("TGTAATC"))
self.assertEqual(self.b2.reverse_complement(),
DNASequence("GGTACCGGT"))
self.assertRaises(BiologicalSequenceError, self.b3.reverse_complement)
self.assertEqual(self.b4.reverse_complement(),
DNASequence("NVHDBMRSWYK"))
def setUp(self):
"""Setup for Fasta tests."""
self.strings = ['AAAA', 'CCCC', 'gggg', 'uuuu']
self.fasta_no_label = '>0\nAAAA\n>1\nCCCC\n>2\ngggg\n>3\nuuuu'
self.fasta_with_label =\
'>1st\nAAAA\n>2nd\nCCCC\n>3rd\nGGGG\n>4th\nUUUU'
self.fasta_with_label_lw2 =\
'>1st\nAA\nAA\n>2nd\nCC\nCC\n>3rd\nGG\nGG\n>4th\nUU\nUU'
self.alignment_dict = {
'1st': 'AAAA',
'2nd': 'CCCC',
'3rd': 'GGGG',
'4th': 'UUUU'
}
self.sequence_objects_a = [
DNASequence('ACTCGAGATC', 'seq1'),
DNASequence('GGCCT', 'seq2')
]
self.sequence_objects_b = [
BiologicalSequence('ACTCGAGATC', 'seq1'),
BiologicalSequence('GGCCT', 'seq2')
]
seqs = [
DNASequence("ACC--G-GGTA..", id="seq1"),
DNASequence("TCC--G-GGCA..", id="seqs2")
]
self.alignment = Alignment(seqs)
def test_to_phylip_unequal_sequence_lengths(self):
d1 = DNASequence('A-CT', id="d1")
d2 = DNASequence('TTA', id="d2")
d3 = DNASequence('.-AC', id="d3")
a = Alignment([d1, d2, d3])
with self.assertRaises(SequenceCollectionError):
npt.assert_warns(UserWarning, a.to_phylip)
def test_nondegenerates_mixed_degens(self):
exp = [
DNASequence('AGC'),
DNASequence('AGT'),
DNASequence('GGC'),
DNASequence('GGT')
]
obs = sorted(DNASequence('RGY').nondegenerates(), key=str)
self.assertEqual(obs, exp)
def test_nondegenerates_gap_mixed_case(self):
exp = [
DNASequence('-A.a'),
DNASequence('-A.c'),
DNASequence('-C.a'),
DNASequence('-C.c')
]
obs = sorted(DNASequence('-M.m').nondegenerates(), key=str)
self.assertEqual(obs, exp)
def test_majority_consensus_constructor(self):
d1 = DNASequence('TTT', id="d1")
d2 = DNASequence('TT-', id="d2")
d3 = DNASequence('TC-', id="d3")
a1 = Alignment([d1, d2, d3])
obs = npt.assert_warns(UserWarning, a1.majority_consensus,
constructor=str)
self.assertEqual(obs, 'TT-')
def test_validate_lengths(self):
self.assertTrue(self.a1._validate_lengths())
self.assertTrue(self.a2._validate_lengths())
self.assertTrue(self.empty._validate_lengths())
self.assertTrue(Alignment([
DNASequence('TTT', id="d1")])._validate_lengths())
self.assertFalse(Alignment([
DNASequence('TTT', id="d1"),
DNASequence('TT', id="d2")])._validate_lengths())
def test_subalignment(self):
"""subalignment functions as expected
"""
# keep seqs by ids
actual = self.a1.subalignment(seqs_to_keep=['d1', 'd3'])
expected = Alignment([self.d1, self.d3])
self.assertEqual(actual, expected)
# keep seqs by indices
actual = self.a1.subalignment(seqs_to_keep=[0, 2])
expected = Alignment([self.d1, self.d3])
self.assertEqual(actual, expected)
# keep seqs by ids (invert)
actual = self.a1.subalignment(seqs_to_keep=['d1', 'd3'],
invert_seqs_to_keep=True)
expected = Alignment([self.d2])
self.assertEqual(actual, expected)
# keep seqs by indices (invert)
actual = self.a1.subalignment(seqs_to_keep=[0, 2],
invert_seqs_to_keep=True)
expected = Alignment([self.d2])
self.assertEqual(actual, expected)
# keep positions
actual = self.a1.subalignment(positions_to_keep=[0, 2, 3])
d1 = DNASequence('.AC', id="d1")
d2 = DNASequence('TAC', id="d2")
d3 = DNASequence('.AC', id="d3")
expected = Alignment([d1, d2, d3])
self.assertEqual(actual, expected)
# keep positions (invert)
actual = self.a1.subalignment(positions_to_keep=[0, 2, 3],
invert_positions_to_keep=True)
d1 = DNASequence('.C-GTTGG..', id="d1")
d2 = DNASequence('TCGGT-GGCC', id="d2")
d3 = DNASequence('-C-GTTGC--', id="d3")
expected = Alignment([d1, d2, d3])
self.assertEqual(actual, expected)
# keep seqs and positions
actual = self.a1.subalignment(seqs_to_keep=[0, 2],
positions_to_keep=[0, 2, 3])
d1 = DNASequence('.AC', id="d1")
d3 = DNASequence('.AC', id="d3")
expected = Alignment([d1, d3])
self.assertEqual(actual, expected)
# keep seqs and positions (invert)
actual = self.a1.subalignment(seqs_to_keep=[0, 2],
positions_to_keep=[0, 2, 3],
invert_seqs_to_keep=True,
invert_positions_to_keep=True)
d2 = DNASequence('TCGGT-GGCC', id="d2")
expected = Alignment([d2])
self.assertEqual(actual, expected)
def test_to_phylip(self):
d1 = DNASequence('..ACC-GTTGG..', id="d1")
d2 = DNASequence('TTACCGGT-GGCC', id="d2")
d3 = DNASequence('.-ACC-GTTGC--', id="d3")
a = Alignment([d1, d2, d3])
phylip_str, id_map = npt.assert_warns(DeprecationWarning,
a.to_phylip,
map_labels=False)
self.assertEqual(id_map, {'d1': 'd1', 'd3': 'd3', 'd2': 'd2'})
expected = "\n".join([
"3 13", "d1 ..ACC-GTTGG..", "d2 TTACCGGT-GGCC", "d3 .-ACC-GTTGC--"
])
self.assertEqual(phylip_str, expected)
def test_to_phylip_map_labels(self):
"""to_phylip functions as expected with label mapping
"""
d1 = DNASequence('..ACC-GTTGG..', id="d1")
d2 = DNASequence('TTACCGGT-GGCC', id="d2")
d3 = DNASequence('.-ACC-GTTGC--', id="d3")
a = Alignment([d1, d2, d3])
phylip_str, id_map = a.to_phylip(map_labels=True, label_prefix="s")
self.assertEqual(id_map, {'s1': 'd1', 's3': 'd3', 's2': 'd2'})
expected = "\n".join([
"3 13", "s1 ..ACC-GTTGG..", "s2 TTACCGGT-GGCC", "s3 .-ACC-GTTGC--"
])
self.assertEqual(phylip_str, expected)
def test_init_validate(self):
"""initialization with validation functions as expected
"""
Alignment(self.seqs1, validate=True)
# invalid DNA character
invalid_seqs1 = [self.d1, self.d2, self.d3,
DNASequence('.-ACC-GTXGC--', id="i1")]
self.assertRaises(SequenceCollectionError, Alignment,
invalid_seqs1, validate=True)
# invalid lengths (they're not all equal)
invalid_seqs2 = [self.d1, self.d2, self.d3,
DNASequence('.-ACC-GTGC--', id="i2")]
self.assertRaises(SequenceCollectionError, Alignment,
invalid_seqs2, validate=True)
def test_is_valid(self):
"""is_valid functions as expected
"""
self.assertTrue(self.a1.is_valid())
self.assertTrue(self.a2.is_valid())
self.assertTrue(self.empty.is_valid())
# invalid because of length mismatch
d1 = DNASequence('..ACC-GTTGG..', id="d1")
d2 = DNASequence('TTACCGGT-GGC', id="d2")
self.assertFalse(Alignment([d1, d2]).is_valid())
# invalid because of invalid charaters
d1 = DNASequence('..ACC-GTXGG..', id="d1")
d2 = DNASequence('TTACCGGT-GGCC', id="d2")
self.assertFalse(Alignment([d1, d2]).is_valid())
def test_to_phylip_map_labels(self):
d1 = DNASequence('..ACC-GTTGG..', id="d1")
d2 = DNASequence('TTACCGGT-GGCC', id="d2")
d3 = DNASequence('.-ACC-GTTGC--', id="d3")
a = Alignment([d1, d2, d3])
phylip_str, id_map = npt.assert_warns(UserWarning, a.to_phylip,
map_labels=True,
label_prefix="s")
self.assertEqual(id_map, {'s1': 'd1',
's3': 'd3',
's2': 'd2'})
expected = "\n".join(["3 13",
"s1 ..ACC-GTTGG..",
"s2 TTACCGGT-GGCC",
"s3 .-ACC-GTTGC--"])
self.assertEqual(phylip_str, expected)
def generator():
yield BiologicalSequence('ACGT',
id='',
description='',
quality=range(4))
yield RNASequence('GAU', id=' foo \t\t bar ', description='')
yield DNASequence('TAG', id='', description='foo\n\n bar\n')
yield BiologicalSequence('A',
id='foo',
description='bar baz',
quality=[42])
def test_init_validate(self):
Alignment(self.seqs1, validate=True)
# invalid DNA character
invalid_seqs1 = [
self.d1, self.d2, self.d3,
DNASequence('.-ACC-GTXGC--', id="i1")
]
self.assertRaises(SequenceCollectionError,
Alignment,
invalid_seqs1,
validate=True)
def test_majority_consensus(self):
d1 = DNASequence('TTT', id="d1")
d2 = DNASequence('TT-', id="d2")
d3 = DNASequence('TC-', id="d3")
a1 = Alignment([d1, d2, d3])
self.assertTrue(a1.majority_consensus().equals(DNASequence('TT-')))
d1 = DNASequence('T', id="d1")
d2 = DNASequence('A', id="d2")
a1 = Alignment([d1, d2])
self.assertTrue(a1.majority_consensus() in
[DNASequence('T'), DNASequence('A')])
self.assertEqual(self.empty.majority_consensus(), '')
def setUp(self):
"""Setup for stockholm tests."""
self.seqs = [DNASequence("ACC-G-GGTA", id="seq1"),
DNASequence("TCC-G-GGCA", id="seq2")]
self.GF = OrderedDict([
("AC", "RF00360"),
("BM", ["cmbuild -F CM SEED",
"cmsearch -Z 274931 -E 1000000"]),
("SQ", "9"),
("RT", ["TITLE1", "TITLE2"]),
("RN", ["[1]", "[2]"]),
("RA", ["Auth1;", "Auth2;"]),
("RL", ["J Mol Biol", "Cell"]),
("RM", ["11469857", "12007400"]),
('RN', ['[1]', '[2]'])
])
self.GS = {"AC": OrderedDict([("seq1", "111"), ("seq2", "222")])}
self.GR = {"SS": OrderedDict([("seq1", "1110101111"),
("seq2", "0110101110")])}
self.GC = {"SS_cons": "(((....)))"}
self.st = StockholmAlignment(self.seqs, gc=self.GC, gf=self.GF,
gs=self.GS, gr=self.GR)
def setUp(self):
self.empty = DNASequence('')
self.b1 = DNASequence('GATTACA')
self.b2 = DNASequence('ACCGGTACC',
id="test-seq-2",
description="A test sequence")
self.b3 = DNASequence('ACCGGUACC',
id="bad-seq-1",
description="Not a DNA sequence")
self.b4 = DNASequence('MRWSYKVHDBN',
id="degen",
description="All of the degenerate bases")
self.b5 = DNASequence('.G--ATTAC-A...')
def test_is_reverse_complement(self):
self.assertFalse(self.b1.is_reverse_complement(self.b1))
self.assertTrue(self.b1.is_reverse_complement(DNASequence('TGTAATC')))
self.assertTrue(
self.b4.is_reverse_complement(DNASequence('NVHDBMRSWYK')))
def missing_qual_gen():
for seq in (RNASequence('A',
quality=[42]), BiologicalSequence('AG'),
DNASequence('GG', quality=[41, 40])):
yield seq
def blank_seq_gen():
for seq in (DNASequence('A'), BiologicalSequence(''),
RNASequence('GG')):
yield seq
def test_init_not_equal_lengths(self):
invalid_seqs = [
self.d1, self.d2, self.d3,
DNASequence('.-ACC-GTGC--', id="i2")
]
self.assertRaises(AlignmentError, Alignment, invalid_seqs)
def test_nondegenerates_all_degens(self):
# Same chars.
exp = [
DNASequence('CC'),
DNASequence('CG'),
DNASequence('GC'),
DNASequence('GG')
]
# Sort based on sequence string, as order is not guaranteed.
obs = sorted(DNASequence('SS').nondegenerates(), key=str)
self.assertEqual(obs, exp)
# Different chars.
exp = [
DNASequence('AC'),
DNASequence('AG'),
DNASequence('GC'),
DNASequence('GG')
]
obs = sorted(DNASequence('RS').nondegenerates(), key=str)
self.assertEqual(obs, exp)
# Odd number of chars.
obs = list(DNASequence('NNN').nondegenerates())
self.assertEqual(len(obs), 4**3)
def test_nondegenerates_invalid(self):
with self.assertRaises(BiologicalSequenceError):
list(DNASequence('AZA').nondegenerates())
def test_complement(self):
self.assertEqual(self.b1.complement(), DNASequence("CTAATGT"))
self.assertEqual(self.b2.complement(), DNASequence("TGGCCATGG"))
self.assertRaises(BiologicalSequenceError, self.b3.complement)
self.assertEqual(self.b4.complement(), DNASequence("KYWSRMBDHVN"))
self.assertEqual(self.b5.complement(), DNASequence(".C--TAATG-T..."))
