本文整理汇总了Python中Tree.make_tree_binary方法的典型用法代码示例。如果您正苦于以下问题：Python Tree.make_tree_binary方法的具体用法？Python Tree.make_tree_binary怎么用？Python Tree.make_tree_binary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Tree的用法示例。
在下文中一共展示了Tree.make_tree_binary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: __init__
# 需要导入模块: import Tree [as 别名]
# 或者: from Tree import make_tree_binary [as 别名]
def __init__(self, msa, tree, single_model, paired_model, treat_gap_as_missing):
"""
Input:
msa --- MSA object (the alignment)
tree --- initially is the starting tree (dendropy.Tree)
single/paired model -- EvoModel.{single|paired}model objects
Also has the following attributes:
single_cols --- list of unpaired positions
paired_cols --- list of paired positions (i, j)
order --- postorder traversal (often changes! beware!)
like --- positive log likelihood (often changes! beware!)
nnode, ncol, nbase for single/paired parameters...
NOTE: ENFORCES tree TO BE BINARY
"""
self.msa = msa
self.tree = tree
self.single_model = single_model
self.paired_model = paired_model
self.treat_gap_as_missing = treat_gap_as_missing
self.log_freq_single = log(self.single_model.Frequency)
self.log_freq_paired = log(self.paired_model.Frequency)
self.single_cols = msa.single_cols()
self.paired_cols = msa.BP.items()
self.paired_cols.sort()
self.nnode = 2*msa.nseq + 1
self.ncol = len(self.single_cols)
self.nbase = 5
self.nnode_p = self.nnode
self.ncol_p = len(self.paired_cols)
self.nbase_p = 25
Tree.make_tree_binary(self.tree) # must preceded self.order!
self.order = Tree.postorder_assign_then_traverse(tree, list(msa.ids))
self.like = None # should be the positive log likelihood
self.S = None # likelihood matrix for single positions
self.P = None # likelihood matrix for paired positions