# Copyright (C) 2013 by Yanbo Ye (yeyanbo289@gmail.com) # This code is part of the Biopython distribution and governed by its # license. Please see the LICENSE file that should have been included # as part of this package. """Unit tests for the Bio.Phylo.Consensus module.""" import os import unittest import tempfile # from io import StringIO from Bio import AlignIO from Bio import Phylo from Bio.Phylo import BaseTree from Bio.Phylo.TreeConstruction import DistanceCalculator from Bio.Phylo.TreeConstruction import DistanceTreeConstructor from Bio.Phylo import Consensus from Bio.Phylo.Consensus import _BitString temp_dir = tempfile.mkdtemp() class BitStringTest(unittest.TestCase): """Test for _BitString class.""" def test_bitstring(self): bitstr1 = _BitString("0011") bitstr2 = _BitString("0101") bitstr3 = _BitString("0001") bitstr4 = _BitString("0010") self.assertRaises(TypeError, _BitString, "10O1") self.assertEqual(bitstr1 & bitstr2, _BitString("0001")) self.assertEqual(bitstr1 | bitstr2, _BitString("0111")) self.assertEqual(bitstr1 ^ bitstr2, _BitString("0110")) self.assertFalse(bitstr1.contains(bitstr2)) self.assertTrue(bitstr1.contains(bitstr1)) self.assertTrue(bitstr1.contains(bitstr3)) self.assertTrue(bitstr1.contains(bitstr4)) self.assertFalse(bitstr1.independent(bitstr2)) self.assertFalse(bitstr1.independent(bitstr4)) self.assertTrue(bitstr2.independent(bitstr4)) self.assertTrue(bitstr3.independent(bitstr4)) self.assertFalse(bitstr1.iscompatible(bitstr2)) self.assertTrue(bitstr1.iscompatible(bitstr3)) self.assertTrue(bitstr1.iscompatible(bitstr4)) self.assertTrue(bitstr2.iscompatible(bitstr4)) self.assertTrue(bitstr3.iscompatible(bitstr4)) class ConsensusTest(unittest.TestCase): """Test for consensus methods.""" def setUp(self): self.trees = list(Phylo.parse("./TreeConstruction/trees.tre", "newick")) def test_count_clades(self): bitstr_counts, len_trees = Consensus._count_clades(self.trees) self.assertEqual(len_trees, len(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) 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])) # tree_file.close() 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_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])) # 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])) # tree_file.close() 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) class BootstrapTest(unittest.TestCase): """Test for bootstrap methods.""" def setUp(self): self.msa = AlignIO.read("TreeConstruction/msa.phy", "phylip") 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])) 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.assertIsInstance(trees[0], BaseTree.Tree) def test_bootstrap_consensus(self): calculator = DistanceCalculator("blosum62") constructor = DistanceTreeConstructor(calculator, "nj") tree = Consensus.bootstrap_consensus( self.msa, 100, constructor, Consensus.majority_consensus ) self.assertIsInstance(tree, BaseTree.Tree) Phylo.write(tree, os.path.join(temp_dir, "bootstrap_consensus.tre"), "newick") if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)