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):
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_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]))
