def test_reverse_complement(self):
self.assertEqual(self.b1.reverse_complement(), RNASequence("UGUAAUC"))
self.assertEqual(self.b2.reverse_complement(),
RNASequence("GGUACCGGU"))
self.assertRaises(BiologicalSequenceError, self.b3.reverse_complement)
self.assertEqual(self.b4.reverse_complement(),
RNASequence("NVHDBMRSWYK"))
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_nondegenerates_gap_mixed_case(self):
exp = [
RNASequence('-A.a'),
RNASequence('-A.c'),
RNASequence('-C.a'),
RNASequence('-C.c')
]
obs = sorted(RNASequence('-M.m').nondegenerates(), key=str)
self.assertEqual(obs, exp)
def test_nondegenerates_mixed_degens(self):
exp = [
RNASequence('AGC'),
RNASequence('AGU'),
RNASequence('GGC'),
RNASequence('GGU')
]
obs = sorted(RNASequence('RGY').nondegenerates(), key=str)
self.assertEqual(obs, exp)
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.empty = Alignment([])
def test_omit_gap_positions(self):
"""omitting gap positions functions as expected
"""
expected = self.a2
self.assertEqual(self.a2.omit_gap_positions(1.0), expected)
self.assertEqual(self.a2.omit_gap_positions(0.51), expected)
r1 = RNASequence('UUAU', id="r1")
r2 = RNASequence('ACGU', id="r2")
expected = Alignment([r1, r2])
self.assertEqual(self.a2.omit_gap_positions(0.49), expected)
r1 = RNASequence('UUAU', id="r1")
r2 = RNASequence('ACGU', id="r2")
expected = Alignment([r1, r2])
self.assertEqual(self.a2.omit_gap_positions(0.0), expected)
self.assertEqual(self.empty.omit_gap_positions(0.0), self.empty)
self.assertEqual(self.empty.omit_gap_positions(0.49), self.empty)
self.assertEqual(self.empty.omit_gap_positions(1.0), self.empty)
def test_iter_positions(self):
"""iter_positions functions as expected
"""
actual = list(self.a2.iter_positions())
expected = [[RNASequence(j) for j in i]
for i in ['UA', 'UC', 'AG', 'UU', '-U']]
self.seqs2_t = [('r1', 'UUAU-'), ('r2', 'ACGUU')]
self.assertEqual(actual, expected)
actual = list(self.a2.iter_positions(constructor=str))
expected = [list('UA'), list('UC'), list('AG'), list('UU'), list('-U')]
self.seqs2_t = [('r1', 'UUAU-'), ('r2', 'ACGUU')]
self.assertEqual(actual, expected)
def setUp(self):
self.empty = RNASequence('')
self.b1 = RNASequence('GAUUACA')
self.b2 = RNASequence('ACCGGUACC',
id="test-seq-2",
description="A test sequence")
self.b3 = RNASequence('ACCGGTACC',
id="bad-seq-1",
description="Not a RNA sequence")
self.b4 = RNASequence('MRWSYKVHDBN',
id="degen",
description="All of the degenerate bases")
self.b5 = RNASequence('.G--AUUAC-A...')
def test_nondegenerates_all_degens(self):
# Same chars.
exp = [
RNASequence('CC'),
RNASequence('CG'),
RNASequence('GC'),
RNASequence('GG')
]
# Sort based on sequence string, as order is not guaranteed.
obs = sorted(RNASequence('SS').nondegenerates(), key=str)
self.assertEqual(obs, exp)
# Different chars.
exp = [
RNASequence('AC'),
RNASequence('AG'),
RNASequence('GC'),
RNASequence('GG')
]
obs = sorted(RNASequence('RS').nondegenerates(), key=str)
self.assertEqual(obs, exp)
# Odd number of chars.
obs = list(RNASequence('NNN').nondegenerates())
self.assertEqual(len(obs), 4**3)
def test_nondegenerates_invalid(self):
with self.assertRaises(BiologicalSequenceError):
list(RNASequence('AZA').nondegenerates())
def test_is_reverse_complement(self):
self.assertFalse(self.b1.is_reverse_complement(self.b1))
self.assertTrue(self.b1.is_reverse_complement(RNASequence('UGUAAUC')))
self.assertTrue(
self.b4.is_reverse_complement(RNASequence('NVHDBMRSWYK')))
def test_complement(self):
self.assertEqual(self.b1.complement(), RNASequence("CUAAUGU"))
self.assertEqual(self.b2.complement(), RNASequence("UGGCCAUGG"))
self.assertRaises(BiologicalSequenceError, self.b3.complement)
self.assertEqual(self.b4.complement(), RNASequence("KYWSRMBDHVN"))
self.assertEqual(self.b5.complement(), RNASequence(".C--UAAUG-U..."))
