本文整理汇总了Python中cogent.core.profile.Profile._score_profile方法的典型用法代码示例。如果您正苦于以下问题：Python Profile._score_profile方法的具体用法？Python Profile._score_profile怎么用？Python Profile._score_profile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._score_profile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: ProfileTests
# 需要导入模块: from cogent.core.profile import Profile [as 别名]
# 或者: from cogent.core.profile.Profile import _score_profile [as 别名]
#.........这里部分代码省略.........
[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):
"""_score_indices: should work on valid input"""
self.assertEqual(self.score1._score_indices(array([0, 1, 1, 3, 0, 3]), offset=0), [6, 2, -3, 0])
self.assertFloatEqual(
self.score2._score_indices(array([3, 1, 2, 0, 2, 2, 3]), offset=0), [0.3, 1.4, 0.8, 1.4, 1.7]
)
self.assertFloatEqual(self.score2._score_indices(array([3, 1, 2, 0, 2, 2, 3]), offset=3), [1.4, 1.7])
# Errors will be raised on invalid input. Errors are not handled
# in this method. Validation of the input is done elsewhere
self.assertRaises(IndexError, self.score2._score_indices, array([3, 1, 63, 0, 4, 2, 3]), offset=3)
def test__score_profile(self):
"""_score_profile: should work on valid input"""
p1 = Profile(
array([[1, 0, 0, 0], [0, 1, 0, 0], [0, 0, 0.5, 0.5], [0, 0, 0, 1], [0.25, 0.25, 0.25, 0.25]]), "TCAG"
)
p2 = Profile(
array(
[[0, 1, 0, 0], [0.2, 0, 0.8, 0], [0, 0, 0.5, 0.5], [1 / 3, 1 / 3, 0, 1 / 3], [0.25, 0.25, 0.25, 0.25]]
),
"TCAG",
)
self.assertFloatEqual(self.score2._score_profile(p1, offset=0), [0.55, 1.25, 0.45])
self.assertFloatEqual(self.score2._score_profile(p1, offset=2), [0.45])
self.assertFloatEqual(self.score2._score_profile(p2, offset=0), [1.49, 1.043, 0.483], 1e-3)
# Errors will be raised on invalid input. Errors are not handled
# in this method. Validation of the input is done elsewhere
# In this case you don't get an error, but for sure an unexpected
# result
self.assertFloatEqual(self.score2._score_profile(p1, offset=3).tolist(), [])
def test_score_sequence(self):
"""score: should work correctly for Sequence as input
"""
# works on normal valid data
s1 = self.score1.score("ATTCAC", offset=0)
self.assertEqual(s1, [6, 2, -3, 0])
self.assertFloatEqual(self.score2.score("TCAAGT", offset=0), [0.5, 1.6, 1.7, 0.5])
# works with different offset
self.assertFloatEqual(self.score2.score("TCAAGT", offset=2), [1.7, 0.5])
self.assertFloatEqual(self.score2.score("TCAAGT", offset=3), [0.5])
# raises error on invalid offset