本文整理汇总了Python中Bio.Phylo.Consensus类的典型用法代码示例。如果您正苦于以下问题：Python Consensus类的具体用法？Python Consensus怎么用？Python Consensus使用的例子？那么恭喜您, 这里精选的类代码示例或许可以为您提供帮助。
在下文中一共展示了Consensus类的12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
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
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
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_get_support
def test_get_support(self):
support_tree = Consensus.get_support(self.trees[0], self.trees)
clade = support_tree.common_ancestor([support_tree.find_any(name="Beta"), support_tree.find_any(name="Gamma")])
self.assertEqual(clade.confidence, 2 * 100.0 / 3)
clade = support_tree.common_ancestor([support_tree.find_any(name="Alpha"), support_tree.find_any(name="Beta")])
self.assertEqual(clade.confidence, 3 * 100.0 / 3)
clade = support_tree.common_ancestor([support_tree.find_any(name="Delta"), support_tree.find_any(name="Epsilon")])
self.assertEqual(clade.confidence, 2 * 100.0 / 3)示例5: test_count_clades
def test_count_clades(self):
bitstr_counts = Consensus._count_clades(self.trees)
self.assertEqual(len(bitstr_counts), 6)
self.assertEqual(bitstr_counts[_BitString('11111')][0], 3)
self.assertEqual(bitstr_counts[_BitString('11000')][0], 2)
self.assertEqual(bitstr_counts[_BitString('00111')][0], 3)
self.assertEqual(bitstr_counts[_BitString('00110')][0], 2)
self.assertEqual(bitstr_counts[_BitString('00011')][0], 1)
self.assertEqual(bitstr_counts[_BitString('01111')][0], 1)示例6: test_nj
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))示例7: test_strict_consensus
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8: test_adam_consensus
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9: test_bootstrap_consensus
def test_bootstrap_consensus(self):
calculator = DistanceCalculator('blosum62')
constructor = DistanceTreeConstructor(calculator, 'nj')
tree = Consensus.bootstrap_consensus(self.msa, 100, constructor, Consensus.majority_consensus)
self.assertTrue(isinstance(tree, BaseTree.Tree))
Phylo.write(tree, os.path.join(temp_dir, 'bootstrap_consensus.tre'), 'newick')示例10: test_bootstrap_trees
def test_bootstrap_trees(self):
calculator = DistanceCalculator('blosum62')
constructor = DistanceTreeConstructor(calculator)
trees = list(Consensus.bootstrap_trees(self.msa, 100, constructor))
self.assertEqual(len(trees), 100)
self.assertTrue(isinstance(trees[0], BaseTree.Tree))示例11: test_bootstrap
def test_bootstrap(self):
msa_list = list(Consensus.bootstrap(self.msa, 100))
self.assertEqual(len(msa_list), 100)
self.assertEqual(len(msa_list[0]), len(self.msa))
self.assertEqual(len(msa_list[0][0]), len(self.msa[0]))示例12: test_bootstrap_consensus
def test_bootstrap_consensus(self):
calculator = DistanceCalculator("blosum62")
constructor = DistanceTreeConstructor(calculator, "nj")
tree = Consensus.bootstrap_consensus(self.msa, 100, constructor, Consensus.majority_consensus)
self.assertTrue(isinstance(tree, BaseTree.Tree))
Phylo.write(tree, "./TreeConstruction/bootstrap_consensus.tre", "newick")