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))
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]))
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_mcmc = Consensus.majority_consensus(self.mcmc_trees, mcmc=True) # self.assertTrue(Consensus._equal_topology(consensus_tree_mcmc, ref_tree)) ref_tree = next(ref_trees) consensus_tree = Consensus.majority_consensus(self.trees, 1) self.assertTrue(Consensus._equal_topology(consensus_tree, ref_tree)) consensus_tree_mcmc = Consensus.majority_consensus(self.mcmc_trees, 1, mcmc=True) self.assertTrue(Consensus._equal_topology(consensus_tree_mcmc, ref_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))
def test_upgma(self): tree = self.constructor.upgma(self.dm) self.assertTrue(isinstance(tree, BaseTree.Tree)) # tree_file = StringIO() # Phylo.write(tree, tree_file, 'newick') ref_tree = Phylo.read("./TreeConstruction/upgma.tre", "newick") self.assertTrue(Consensus._equal_topology(tree, ref_tree))
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]))
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]))
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]))
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))
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))
def test_adam_consensus(self): 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])) consensus_tree_mcmc = Consensus.adam_consensus(self.mcmc_trees, mcmc=True) self.assertTrue(Consensus._equal_topology(consensus_tree_mcmc, 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])) consensus_tree_mcmc = Consensus.adam_consensus(self.mcmc_trees[:2], mcmc=True) # 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]))
def test_maximum_clade_probability_consensus(self): ref_trees = list(Phylo.parse("./TreeConstruction/maximum_clade_probability_ref.tre", "newick")) consensus_tree = Consensus.maximum_clade_probability_consensus(self.trees)[0] self.assertTrue(Consensus._equal_topology(consensus_tree, ref_trees[0])) consensus_tree_mcmc = Consensus.maximum_clade_probability_consensus(self.mcmc_trees, mcmc=True)[0] self.assertTrue(Consensus._equal_topology(consensus_tree_mcmc, ref_trees[0]))