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# 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 unittest
# from Bio._py3k 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
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.assertTrue(isinstance(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.assertTrue(isinstance(tree, BaseTree.Tree))
Phylo.write(tree, './TreeConstruction/bootstrap_consensus.tre', 'newick')
if __name__ == '__main__':
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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