本文整理汇总了Python中skbio.Alignment.omit_gap_sequences方法的典型用法代码示例。如果您正苦于以下问题：Python Alignment.omit_gap_sequences方法的具体用法？Python Alignment.omit_gap_sequences怎么用？Python Alignment.omit_gap_sequences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.omit_gap_sequences方法的3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_omit_gap_sequences
# 需要导入模块: from skbio import Alignment [as 别名]
# 或者: from skbio.Alignment import omit_gap_sequences [as 别名]
def test_omit_gap_sequences(self):
expected = self.a2
self.assertEqual(self.a2.omit_gap_sequences(1.0), expected)
self.assertEqual(self.a2.omit_gap_sequences(0.20), expected)
expected = Alignment([self.r2])
self.assertEqual(self.a2.omit_gap_sequences(0.19), expected)
self.assertEqual(self.empty.omit_gap_sequences(0.0), self.empty)
self.assertEqual(self.empty.omit_gap_sequences(0.2), self.empty)
self.assertEqual(self.empty.omit_gap_sequences(1.0), self.empty)
# Test to ensure floating point precision bug isn't present. See the
# tests for Alignment.position_frequencies for more details.
aln = Alignment([DNA('.' * 33, id='abc'), DNA('-' * 33, id='def')])
self.assertEqual(aln.omit_gap_sequences(1 - np.finfo(float).eps),
Alignment([]))示例2: AlignmentTests
# 需要导入模块: from skbio import Alignment [as 别名]
# 或者: from skbio.Alignment import omit_gap_sequences [as 别名]
#.........这里部分代码省略.........
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"})
expected = Alignment([r1, r2])
self.assertEqual(self.a2.omit_gap_positions(0.49), expected)
r1 = RNA('UUAU', metadata={'id': "r1"})
r2 = RNA('ACGU', metadata={'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)
# Test to ensure floating point precision bug isn't present. See the
# tests for Alignment.position_frequencies for more details.
seqs = []
for i in range(33):
seqs.append(DNA('-.', metadata={'id': str(i)}))
aln = Alignment(seqs)
self.assertEqual(aln.omit_gap_positions(1 - np.finfo(float).eps),
Alignment([DNA('', metadata={'id': str(i)})
for i in range(33)]))
def test_omit_gap_sequences(self):
expected = self.a2
self.assertEqual(self.a2.omit_gap_sequences(1.0), expected)
self.assertEqual(self.a2.omit_gap_sequences(0.20), expected)
expected = Alignment([self.r2])
self.assertEqual(self.a2.omit_gap_sequences(0.19), expected)
self.assertEqual(self.empty.omit_gap_sequences(0.0), self.empty)
self.assertEqual(self.empty.omit_gap_sequences(0.2), self.empty)
self.assertEqual(self.empty.omit_gap_sequences(1.0), self.empty)
# Test to ensure floating point precision bug isn't present. See the
# tests for Alignment.position_frequencies for more details.
aln = Alignment([DNA('.' * 33, metadata={'id': 'abc'}),
DNA('-' * 33, metadata={'id': 'def'})])
self.assertEqual(aln.omit_gap_sequences(1 - np.finfo(float).eps),
Alignment([]))
def test_position_counters(self):
self.assertEqual(self.empty.position_counters(), [])
self.assertEqual(self.no_positions.position_counters(), [])
expected = [Counter({'U': 1, 'A': 1}),
Counter({'U': 1, 'C': 1}),
Counter({'A': 1, 'G': 1}),
Counter({'U': 2}),
Counter({'-': 1, 'U': 1})]
self.assertEqual(self.a2.position_counters(), expected)
def test_position_frequencies(self):
self.assertEqual(self.empty.position_frequencies(), [])示例3: AlignmentTests
# 需要导入模块: from skbio import Alignment [as 别名]
# 或者: from skbio.Alignment import omit_gap_sequences [as 别名]
#.........这里部分代码省略.........
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)
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_omit_gap_sequences(self):
"""omitting gap sequences functions as expected
"""
expected = self.a2
self.assertEqual(self.a2.omit_gap_sequences(1.0), expected)
self.assertEqual(self.a2.omit_gap_sequences(0.20), expected)
expected = Alignment([self.r2])
self.assertEqual(self.a2.omit_gap_sequences(0.19), expected)
self.assertEqual(self.empty.omit_gap_sequences(0.0), self.empty)
self.assertEqual(self.empty.omit_gap_sequences(0.2), self.empty)
self.assertEqual(self.empty.omit_gap_sequences(1.0), self.empty)
def test_position_counters(self):
"""position_counters functions as expected
"""
expected = [Counter({'U': 1, 'A': 1}),
Counter({'U': 1, 'C': 1}),
Counter({'A': 1, 'G': 1}),
Counter({'U': 2}),
Counter({'-': 1, 'U': 1})]
self.assertEqual(self.a2.position_counters(), expected)
self.assertEqual(self.empty.position_counters(), [])
def test_position_frequencies(self):
"""computing position frequencies functions as expected
"""
expected = [defaultdict(int, {'U': 0.5, 'A': 0.5}),
defaultdict(int, {'U': 0.5, 'C': 0.5}),
defaultdict(int, {'A': 0.5, 'G': 0.5}),
defaultdict(int, {'U': 1.0}),