本文整理汇总了Python中Bio.Phylo.Consensus._equal_topology方法的典型用法代码示例。如果您正苦于以下问题：Python Consensus._equal_topology方法的具体用法？Python Consensus._equal_topology怎么用？Python Consensus._equal_topology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Bio.Phylo.Consensus的用法示例。
在下文中一共展示了Consensus._equal_topology方法的6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_majority_consensus
# 需要导入模块: from Bio.Phylo import Consensus [as 别名]
# 或者: from Bio.Phylo.Consensus import _equal_topology [as 别名]
def test_majority_consensus(self):
ref_trees = Phylo.parse('./TreeConstruction/majority_ref.tre', 'newick')
ref_tree = next(ref_trees)
consensus_tree = Consensus.majority_consensus(self.trees)
self.assertTrue(Consensus._equal_topology(consensus_tree, ref_tree))
ref_tree = next(ref_trees)
consensus_tree = Consensus.majority_consensus(self.trees, 1)
self.assertTrue(Consensus._equal_topology(consensus_tree, ref_tree))示例2: test_majority_consensus
# 需要导入模块: from Bio.Phylo import Consensus [as 别名]
# 或者: from Bio.Phylo.Consensus import _equal_topology [as 别名]
def test_majority_consensus(self):
# three trees
# ref_tree = open('./TreeConstruction/majority_ref.tre')
ref_tree = list(Phylo.parse("./TreeConstruction/majority_ref.tre", "newick"))
consensus_tree = Consensus.majority_consensus(self.trees)
# tree_file = StringIO()
# Phylo.write(consensus_tree, tree_file, 'newick')
self.assertTrue(Consensus._equal_topology(consensus_tree, ref_tree[0]))
consensus_tree = Consensus.majority_consensus(self.trees, 1)
# tree_file = StringIO()
# Phylo.write(consensus_tree, tree_file, 'newick')
self.assertTrue(Consensus._equal_topology(consensus_tree, ref_tree[1]))示例3: test_built_tree
# 需要导入模块: from Bio.Phylo import Consensus [as 别名]
# 或者: from Bio.Phylo.Consensus import _equal_topology [as 别名]
def test_built_tree(self):
tree = self.constructor.build_tree(self.aln)
self.assertTrue(isinstance(tree, BaseTree.Tree))
# tree_file = StringIO()
# Phylo.write(tree, tree_file, 'newick')
ref_tree = Phylo.read('./TreeConstruction/nj.tre', 'newick')
self.assertTrue(Consensus._equal_topology(tree, ref_tree))示例4: test_strict_consensus
# 需要导入模块: from Bio.Phylo import Consensus [as 别名]
# 或者: from Bio.Phylo.Consensus import _equal_topology [as 别名]
def test_strict_consensus(self):
ref_trees = list(Phylo.parse('./TreeConstruction/strict_refs.tre', 'newick'))
# three trees
consensus_tree = Consensus.strict_consensus(self.trees)
# tree_file = StringIO()
# Phylo.write(consensus_tree, tree_file, 'newick')
self.assertTrue(Consensus._equal_topology(consensus_tree, ref_trees[0]))
# tree 1 and tree 2
consensus_tree = Consensus.strict_consensus(self.trees[:2])
# tree_file = StringIO()
# Phylo.write(consensus_tree, tree_file, 'newick')
self.assertTrue(Consensus._equal_topology(consensus_tree, ref_trees[1]))
# tree 1 and tree 3
consensus_tree = Consensus.strict_consensus(self.trees[::2])
# tree_file = StringIO()
# Phylo.write(consensus_tree, tree_file, 'newick')
self.assertTrue(Consensus._equal_topology(consensus_tree, ref_trees[2]))示例5: test_adam_consensus
# 需要导入模块: from Bio.Phylo import Consensus [as 别名]
# 或者: from Bio.Phylo.Consensus import _equal_topology [as 别名]
def test_adam_consensus(self):
# ref_trees = open('./TreeConstruction/adam_refs.tre')
ref_trees = list(Phylo.parse("./TreeConstruction/adam_refs.tre", "newick"))
# three trees
consensus_tree = Consensus.adam_consensus(self.trees)
# tree_file = '/home/yeyanbo/adam.tres'
# tree_file = StringIO()
# Phylo.write(consensus_tree, tree_file, 'newick')
self.assertTrue(Consensus._equal_topology(consensus_tree, ref_trees[0]))
# tree 1 and tree 2
consensus_tree = Consensus.adam_consensus(self.trees[:2])
# tree_file = StringIO()
# Phylo.write(consensus_tree, tree_file, 'newick')
self.assertTrue(Consensus._equal_topology(consensus_tree, ref_trees[1]))
# tree 1 and tree 3
consensus_tree = Consensus.adam_consensus(self.trees[::2])
# tree_file = StringIO()
# Phylo.write(consensus_tree, tree_file, 'newick')
self.assertTrue(Consensus._equal_topology(consensus_tree, ref_trees[2]))示例6: test_nj
# 需要导入模块: from Bio.Phylo import Consensus [as 别名]
# 或者: from Bio.Phylo.Consensus import _equal_topology [as 别名]
def test_nj(self):
tree = self.constructor.nj(self.dm)
self.assertTrue(isinstance(tree, BaseTree.Tree))
# tree_file = StringIO()
# Phylo.write(tree, tree_file, 'newick')
ref_tree = Phylo.read('./TreeConstruction/nj.tre', 'newick')
self.assertTrue(Consensus._equal_topology(tree, ref_tree))
# ref_tree.close()
# create a matrix of length 2
calculator = DistanceCalculator('blosum62')
self.min_dm = calculator.get_distance(self.aln)
for i in range(len(self.min_dm) - 2):
del self.min_dm[len(self.min_dm) - 1]
min_tree = self.constructor.nj(self.min_dm)
self.assertTrue(isinstance(min_tree, BaseTree.Tree))
ref_min_tree = Phylo.read('./TreeConstruction/nj_min.tre', 'newick')
self.assertTrue(Consensus._equal_topology(min_tree, ref_min_tree))