本文整理汇总了Python中skbio.SequenceCollection.degap方法的典型用法代码示例。如果您正苦于以下问题：Python SequenceCollection.degap方法的具体用法？Python SequenceCollection.degap怎么用？Python SequenceCollection.degap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.SequenceCollection的用法示例。
在下文中一共展示了SequenceCollection.degap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: SequenceCollectionTests
# 需要导入模块: from skbio import SequenceCollection [as 别名]
# 或者: from skbio.SequenceCollection import degap [as 别名]
#.........这里部分代码省略.........
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"),示例2: SequenceCollectionTests
# 需要导入模块: from skbio import SequenceCollection [as 别名]
# 或者: from skbio.SequenceCollection import degap [as 别名]
#.........这里部分代码省略.........
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()示例3: SequenceCollectionTests
# 需要导入模块: from skbio import SequenceCollection [as 别名]
# 或者: from skbio.SequenceCollection import degap [as 别名]
#.........这里部分代码省略.........
# 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"}