本文整理汇总了Python中cogent.LoadTree.getConnectingNode方法的典型用法代码示例。如果您正苦于以下问题：Python LoadTree.getConnectingNode方法的具体用法？Python LoadTree.getConnectingNode怎么用？Python LoadTree.getConnectingNode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.LoadTree的用法示例。
在下文中一共展示了LoadTree.getConnectingNode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: LikelihoodFunctionTests
# 需要导入模块: from cogent import LoadTree [as 别名]
# 或者: from cogent.LoadTree import getConnectingNode [as 别名]
class LikelihoodFunctionTests(TestCase):
"""tests for a tree analysis class. Various tests to create a tree analysis class,
set parameters, and test various functions.
"""
def setUp(self):
self.submodel = Nucleotide(
do_scaling=True, model_gaps=False, equal_motif_probs=True,
predicates = {'beta': 'transition'})
self.data = LoadSeqs(
filename = os.path.join(data_path, 'brca1_5.paml'),
moltype = self.submodel.MolType)
self.tree = LoadTree(
filename = os.path.join(data_path, 'brca1_5.tree'))
def _makeLikelihoodFunction(self, **kw):
lf = self.submodel.makeLikelihoodFunction(self.tree, **kw)
lf.setParamRule('beta', is_independent=True)
lf.setAlignment(self.data)
return lf
def _setLengthsAndBetas(self, likelihood_function):
for (species, length) in [
("DogFaced", 0.1),
("NineBande", 0.2),
("Human", 0.3),
("HowlerMon", 0.4),
("Mouse", 0.5)]:
likelihood_function.setParamRule("length", value=length,
edge=species, is_constant=True)
for (species1, species2, length) in [
("Human", "HowlerMon", 0.7),
("Human", "Mouse", 0.6)]:
LCA = self.tree.getConnectingNode(species1, species2).Name
likelihood_function.setParamRule("length", value=length,
edge=LCA, is_constant=True)
likelihood_function.setParamRule("beta", value=4.0, is_constant=True)
def test_information_criteria(self):
"""test get information criteria from a model."""
lf = self._makeLikelihoodFunction()
nfp = lf.getNumFreeParams()
lnL = lf.getLogLikelihood()
l = len(self.data)
self.assertFloatEqual(lf.getAic(), aic(lnL, nfp))
self.assertFloatEqual(lf.getAic(second_order=True),
aic(lnL, nfp, l))
self.assertFloatEqual(lf.getBic(), bic(lnL, nfp, l))
def test_result_str(self):
# actualy more a test of self._setLengthsAndBetas()
likelihood_function = self._makeLikelihoodFunction()
self._setLengthsAndBetas(likelihood_function)
self.assertEqual(str(likelihood_function), \
"""Likelihood Function Table\n\
======
beta
------
4.0000
------
=============================
edge parent length
-----------------------------
Human edge.0 0.3000
HowlerMon edge.0 0.4000
edge.0 edge.1 0.7000
Mouse edge.1 0.5000
edge.1 root 0.6000
NineBande root 0.2000
DogFaced root 0.1000
-----------------------------
===============
motif mprobs
---------------
T 0.2500
C 0.2500
A 0.2500
G 0.2500
---------------""")
likelihood_function = self._makeLikelihoodFunction(digits=2,space=2)
self.assertEqual(str(likelihood_function), \
"""Likelihood Function Table\n\
===============================
edge parent length beta
-------------------------------
Human edge.0 1.00 1.00
HowlerMon edge.0 1.00 1.00
edge.0 edge.1 1.00 1.00
Mouse edge.1 1.00 1.00
edge.1 root 1.00 1.00
NineBande root 1.00 1.00
DogFaced root 1.00 1.00
-------------------------------
=============
motif mprobs
-------------
#.........这里部分代码省略.........