本文整理汇总了Python中cogent.core.profile.Profile.toLogOddsMatrix方法的典型用法代码示例。如果您正苦于以下问题：Python Profile.toLogOddsMatrix方法的具体用法？Python Profile.toLogOddsMatrix怎么用？Python Profile.toLogOddsMatrix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.toLogOddsMatrix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_toLogOddsMatrix
# 需要导入模块: from cogent.core.profile import Profile [as 别名]
# 或者: from cogent.core.profile.Profile import toLogOddsMatrix [as 别名]
def test_toLogOddsMatrix(self):
"""toLogOddsMatrix: should work as expected"""
# This test can be short, because it mainly depends on toOddsMatrix
# for which everything has been tested
p = Profile(
array(
[
[0.1, 0.3, 0.5, 0.1],
[0.25, 0.25, 0.25, 0.25],
[0.05, 0.8, 0.05, 0.1],
[0.7, 0.1, 0.1, 0.1],
[0.6, 0.15, 0.05, 0.2],
]
),
Alphabet="ACTG",
)
p_exp = Profile(
array(
[
[-1.322, 0.263, 1.0, -1.322],
[0.0, 0.0, 0.0, 0.0],
[-2.322, 1.678, -2.322, -1.322],
[1.485, -1.322, -1.322, -1.322],
[1.263, -0.737, -2.322, -0.322],
]
),
Alphabet="ACTG",
)
self.assertFloatEqual(p.toLogOddsMatrix().Data, p_exp.Data, eps=1e-3)
# works on empty matrix
self.assertEqual(self.empty.toLogOddsMatrix().Data.tolist(), [[]])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 toLogOddsMatrix [as 别名]
#.........这里部分代码省略.........
p = Profile(
array(
[
[0.1, 0.3, 0.5, 0.1],
[0.25, 0.25, 0.25, 0.25],
[0.05, 0.8, 0.05, 0.1],
[0.7, 0.1, 0.1, 0.1],
[0.6, 0.15, 0.05, 0.2],
]
),
Alphabet="ACTG",
)
p_exp = Profile(
array([[0.4, 1.2, 2, 0.4], [1, 1, 1, 1], [0.2, 3.2, 0.2, 0.4], [2.8, 0.4, 0.4, 0.4], [2.4, 0.6, 0.2, 0.8]]),
Alphabet="ACTG",
)
self.assertEqual(p.toOddsMatrix().Data, p_exp.Data)
assert p.Alphabet is p.toOddsMatrix().Alphabet
self.assertEqual(p.toOddsMatrix([0.25, 0.25, 0.25, 0.25]).Data, p_exp.Data)
# fails if symbol_freqs has wrong size
self.assertRaises(ProfileError, p.toOddsMatrix, [0.25, 0.25, 0.25, 0.25, 0.25, 0.25])
self.assertRaises(ProfileError, self.zero_entry.toOddsMatrix, [0.1, 0.2, 0.3])
# works on empty profile
self.assertEqual(self.empty.toOddsMatrix().Data.tolist(), [[]])
# works with different input
self.assertEqual(self.zero_entry.toOddsMatrix().Data, array([[1.2, 0.8, 0, 2], [0, 0, 3.2, 0.8]]))
self.assertFloatEqual(
self.zero_entry.toOddsMatrix([0.1, 0.2, 0.3, 0.4]).Data, array([[3, 1, 0, 1.25], [0, 0, 2.667, 0.5]]), 1e-3
)
# fails when one of the background frequencies is 0
self.assertRaises(ProfileError, self.zero_entry.toOddsMatrix, [0.1, 0.2, 0.3, 0])
def test_toLogOddsMatrix(self):
"""toLogOddsMatrix: should work as expected"""
# This test can be short, because it mainly depends on toOddsMatrix
# for which everything has been tested
p = Profile(
array(
[
[0.1, 0.3, 0.5, 0.1],
[0.25, 0.25, 0.25, 0.25],
[0.05, 0.8, 0.05, 0.1],
[0.7, 0.1, 0.1, 0.1],
[0.6, 0.15, 0.05, 0.2],
]
),
Alphabet="ACTG",
)
p_exp = Profile(
array(
[
[-1.322, 0.263, 1.0, -1.322],
[0.0, 0.0, 0.0, 0.0],
[-2.322, 1.678, -2.322, -1.322],
[1.485, -1.322, -1.322, -1.322],
[1.263, -0.737, -2.322, -0.322],
]
),
Alphabet="ACTG",
)
self.assertFloatEqual(p.toLogOddsMatrix().Data, p_exp.Data, eps=1e-3)
# works on empty matrix
self.assertEqual(self.empty.toLogOddsMatrix().Data.tolist(), [[]])
def test__score_indices(self):