本文整理汇总了Python中skbio.core.alignment.SequenceCollection.distribution_stats方法的典型用法代码示例。如果您正苦于以下问题：Python SequenceCollection.distribution_stats方法的具体用法？Python SequenceCollection.distribution_stats怎么用？Python SequenceCollection.distribution_stats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.core.alignment.SequenceCollection的用法示例。
在下文中一共展示了SequenceCollection.distribution_stats方法的1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.core.alignment import SequenceCollection [as 别名]
# 或者: from skbio.core.alignment.SequenceCollection import distribution_stats [as 别名]
#.........这里部分代码省略.........
"""k_word_frequencies functions as expected
"""
expected1 = defaultdict(int)
expected1['A'] = 3/7.
expected1['C'] = 1/7.
expected1['G'] = 1/7.
expected1['T'] = 2/7.
expected2 = defaultdict(int)
expected2['G'] = 1/3.
expected2['T'] = 2/3.
self.assertEqual(self.s1.k_word_frequencies(k=1),
[expected1, expected2])
expected1 = defaultdict(int)
expected1['GAT'] = 1/2.
expected1['TAC'] = 1/2.
expected2 = defaultdict(int)
expected2['TTG'] = 1/1.
self.assertEqual(self.s1.k_word_frequencies(k=3, overlapping=False),
[expected1, expected2])
self.assertEqual(self.empty.k_word_frequencies(k=1), [])
def test_str(self):
"""str functions as expected
"""
exp1 = ">d1\nGATTACA\n>d2\nTTG\n"
self.assertEqual(str(self.s1), exp1)
exp2 = ">r1\nGAUUACA\n>r2\nUUG\n>r3\nU-----UGCC--\n"
self.assertEqual(str(self.s2), exp2)
exp4 = ""
self.assertEqual(str(self.empty), exp4)
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):