本文整理汇总了Python中cogent.core.profile.Profile.columnUncertainty方法的典型用法代码示例。如果您正苦于以下问题：Python Profile.columnUncertainty方法的具体用法？Python Profile.columnUncertainty怎么用？Python Profile.columnUncertainty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cogent.core.profile.Profile的用法示例。
在下文中一共展示了Profile.columnUncertainty方法的2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_columnUncertainty
# 需要导入模块: from cogent.core.profile import Profile [as 别名]
# 或者: from cogent.core.profile.Profile import columnUncertainty [as 别名]
def test_columnUncertainty(self):
"""columnUncertainty: should handle full and empty profiles
"""
p = Profile(array([[0.25, 0.5], [0.25, 0.5], [0.25, 0], [0.25, 0]]), "AB")
self.assertEqual(p.columnUncertainty(), [2, 1])
# for empty cols nothing is returned as the uncertainty
self.assertEqual(self.empty.columnUncertainty().tolist(), [])
p = Profile(array([[], [], []]), "")
self.assertEqual(p.columnUncertainty().tolist(), [])
# doesn't work on 1D array
self.assertRaises(ProfileError, self.oned.columnUncertainty)示例2: ProfileTests
# 需要导入模块: from cogent.core.profile import Profile [as 别名]
# 或者: from cogent.core.profile.Profile import columnUncertainty [as 别名]
#.........这里部分代码省略.........
p4 = Profile(array([[1, 0, 0, 0], [0, 1, 0, 0]]), "TCAG")
p5 = Profile(array([[1, 0, 0, 0], [0, 1, 0, 0], [0, 0, 0, 1]]), "AGTC")
# works on normal valid data
self.assertFloatEqual(self.score2.score(p1, offset=0), [0.55, 1.25, 0.45])
self.assertFloatEqual(self.score2.score(p2, offset=0), [1.49, 1.043, 0.483], 1e-3)
# works with different offset
self.assertFloatEqual(self.score2.score(p1, offset=1), [1.25, 0.45])
self.assertFloatEqual(self.score2.score(p1, offset=2), [0.45])
# raises error on invalid offset
self.assertRaises(ProfileError, self.score2.score, p1, offset=3)
# works on profile of minimal length
self.assertFloatEqual(self.score2.score(p3, offset=0), [0.6])
# raises error when profile is too short
self.assertRaises(ProfileError, self.score2.score, p4, offset=0)
# raises error on empty profile
self.assertRaises(ProfileError, self.empty.score, p1)
# raises error when character order doesn't match
self.assertRaises(ProfileError, self.score2.score, p5)
def test_rowUncertainty(self):
"""rowUncertainty: should handle full and empty profiles
"""
p = Profile(array([[0.25, 0.25, 0.25, 0.25], [0.5, 0.5, 0, 0]]), "ABCD")
self.assertEqual(p.rowUncertainty(), [2, 1])
# for empty rows 0 is returned as the uncertainty
self.assertEqual(self.empty.rowUncertainty().tolist(), [])
p = Profile(array([[], [], []]), "")
self.assertEqual(p.rowUncertainty().tolist(), [])
# doesn't work on 1D array
self.assertRaises(ProfileError, self.oned.rowUncertainty)
def test_columnUncertainty(self):
"""columnUncertainty: should handle full and empty profiles
"""
p = Profile(array([[0.25, 0.5], [0.25, 0.5], [0.25, 0], [0.25, 0]]), "AB")
self.assertEqual(p.columnUncertainty(), [2, 1])
# for empty cols nothing is returned as the uncertainty
self.assertEqual(self.empty.columnUncertainty().tolist(), [])
p = Profile(array([[], [], []]), "")
self.assertEqual(p.columnUncertainty().tolist(), [])
# doesn't work on 1D array
self.assertRaises(ProfileError, self.oned.columnUncertainty)
def test_rowDegeneracy(self):
"""rowDegneracy: should work as expected"""
p1 = self.consensus
p2 = self.not_same_value
self.assertEqual(p1.rowDegeneracy(), [1, 1, 1, 2, 1])
self.assertEqual(p1.rowDegeneracy(cutoff=0.5), [1, 1, 1, 2, 1])
self.assertEqual(p1.rowDegeneracy(cutoff=0.75), [1, 2, 1, 3, 2])
# when a row seems to add up to the cutoff value, it's not
# always found because of floating point error. E.g. second row
# in this example
self.assertEqual(p1.rowDegeneracy(cutoff=1), [2, 4, 1, 4, 2])
# when the cutoff can't be found, the number of columns in the
# profile is returned (for each row)
self.assertEqual(p1.rowDegeneracy(cutoff=1.5), [4, 4, 4, 4, 4])
self.assertEqual(p2.rowDegeneracy(cutoff=0.95), [4, 2, 4, 1])
self.assertEqual(p2.rowDegeneracy(cutoff=1.4), [4, 3, 4, 1])
self.assertEqual(self.empty.rowDegeneracy(), [])