本文整理汇总了Python中skbio.Alignment.majority_consensus方法的典型用法代码示例。如果您正苦于以下问题：Python Alignment.majority_consensus方法的具体用法？Python Alignment.majority_consensus怎么用？Python Alignment.majority_consensus使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类skbio.Alignment的用法示例。
在下文中一共展示了Alignment.majority_consensus方法的6个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: test_majority_consensus
# 需要导入模块: from skbio import Alignment [as 别名]
# 或者: from skbio.Alignment import majority_consensus [as 别名]
def test_majority_consensus(self):
# empty cases
self.assertEqual(
self.empty.majority_consensus(), Sequence(''))
self.assertEqual(
self.no_positions.majority_consensus(), RNA(''))
# alignment where all sequences are the same
aln = Alignment([DNA('AG', metadata={'id': 'a'}),
DNA('AG', metadata={'id': 'b'})])
self.assertEqual(aln.majority_consensus(), DNA('AG'))
# no ties
d1 = DNA('TTT', metadata={'id': "d1"})
d2 = DNA('TT-', metadata={'id': "d2"})
d3 = DNA('TC-', metadata={'id': "d3"})
a1 = Alignment([d1, d2, d3])
self.assertEqual(a1.majority_consensus(), DNA('TT-'))
# ties
d1 = DNA('T', metadata={'id': "d1"})
d2 = DNA('A', metadata={'id': "d2"})
a1 = Alignment([d1, d2])
self.assertTrue(a1.majority_consensus() in
[DNA('T'), DNA('A')])示例2: test_majority_consensus
# 需要导入模块: from skbio import Alignment [as 别名]
# 或者: from skbio.Alignment import majority_consensus [as 别名]
def test_majority_consensus(self):
# empty cases
self.assertTrue(
self.empty.majority_consensus().equals(Sequence('')))
self.assertTrue(
self.no_positions.majority_consensus().equals(RNA('')))
# alignment where all sequences are the same
aln = Alignment([DNA('AG', id='a'),
DNA('AG', id='b')])
self.assertTrue(aln.majority_consensus().equals(DNA('AG')))
# no ties
d1 = DNA('TTT', id="d1")
d2 = DNA('TT-', id="d2")
d3 = DNA('TC-', id="d3")
a1 = Alignment([d1, d2, d3])
self.assertTrue(a1.majority_consensus().equals(DNA('TT-')))
# ties
d1 = DNA('T', id="d1")
d2 = DNA('A', id="d2")
a1 = Alignment([d1, d2])
self.assertTrue(a1.majority_consensus() in
[DNA('T'), DNA('A')])示例3: test_majority_consensus
# 需要导入模块: from skbio import Alignment [as 别名]
# 或者: from skbio.Alignment import majority_consensus [as 别名]
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(), '')示例4: test_majority_consensus
# 需要导入模块: from skbio import Alignment [as 别名]
# 或者: from skbio.Alignment import majority_consensus [as 别名]
def test_majority_consensus(self):
"""majority_consensus functions as expected
"""
d1 = DNASequence("TTT", id="d1")
d2 = DNASequence("TT-", id="d2")
d3 = DNASequence("TC-", id="d3")
a1 = Alignment([d1, d2, d3])
self.assertEqual(a1.majority_consensus(), 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(), "")示例5: AlignmentTests
# 需要导入模块: from skbio import Alignment [as 别名]
# 或者: from skbio.Alignment import majority_consensus [as 别名]
#.........这里部分代码省略.........
obs = self.a1.subalignment(positions_to_keep=None,
invert_positions_to_keep=True)
self.assertEqual(obs, exp)
def test_init_not_equal_lengths(self):
invalid_seqs = [self.d1, self.d2, self.d3,
DNA('.-ACC-GTGC--', metadata={'id': "i2"})]
self.assertRaises(AlignmentError, Alignment,
invalid_seqs)
def test_init_equal_lengths(self):
seqs = [self.d1, self.d2, self.d3]
Alignment(seqs)
def test_iter_positions(self):
actual = list(self.a2.iter_positions())
expected = [
[RNA('U', metadata={'id': 'r1'}), RNA('A', metadata={'id': 'r2'})],
[RNA('U', metadata={'id': 'r1'}), RNA('C', metadata={'id': 'r2'})],
[RNA('A', metadata={'id': 'r1'}), RNA('G', metadata={'id': 'r2'})],
[RNA('U', metadata={'id': 'r1'}), RNA('U', metadata={'id': 'r2'})],
[RNA('-', metadata={'id': 'r1'}), RNA('U', metadata={'id': 'r2'})]
]
self.assertEqual(actual, expected)
actual = list(self.a2.iter_positions(constructor=str))
expected = [list('UA'),
list('UC'),
list('AG'),
list('UU'),
list('-U')]
self.assertEqual(actual, expected)
def test_majority_consensus(self):
# empty cases
self.assertEqual(
self.empty.majority_consensus(), Sequence(''))
self.assertEqual(
self.no_positions.majority_consensus(), RNA(''))
# alignment where all sequences are the same
aln = Alignment([DNA('AG', metadata={'id': 'a'}),
DNA('AG', metadata={'id': 'b'})])
self.assertEqual(aln.majority_consensus(), DNA('AG'))
# no ties
d1 = DNA('TTT', metadata={'id': "d1"})
d2 = DNA('TT-', metadata={'id': "d2"})
d3 = DNA('TC-', metadata={'id': "d3"})
a1 = Alignment([d1, d2, d3])
self.assertEqual(a1.majority_consensus(), DNA('TT-'))
# ties
d1 = DNA('T', metadata={'id': "d1"})
d2 = DNA('A', metadata={'id': "d2"})
a1 = Alignment([d1, d2])
self.assertTrue(a1.majority_consensus() in
[DNA('T'), DNA('A')])
def test_omit_gap_positions(self):
expected = self.a2
self.assertEqual(self.a2.omit_gap_positions(1.0), expected)
self.assertEqual(self.a2.omit_gap_positions(0.51), expected)
r1 = RNA('UUAU', metadata={'id': "r1"})
r2 = RNA('ACGU', metadata={'id': "r2"})示例6: AlignmentTests
# 需要导入模块: from skbio import Alignment [as 别名]
# 或者: from skbio.Alignment import majority_consensus [as 别名]
#.........这里部分代码省略.........
"""
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_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 test_majority_consensus(self):
"""majority_consensus functions as expected
"""
d1 = DNASequence('TTT', id="d1")
d2 = DNASequence('TT-', id="d2")
d3 = DNASequence('TC-', id="d3")
a1 = Alignment([d1, d2, d3])
self.assertEqual(a1.majority_consensus(), 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 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)