text: # 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.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, os.path.join(temp_dir, "bootstrap_consensus.tre"), "newick")
  
  
  if __name__ == "__main__":
      runner = unittest.TextTestRunner(verbosity=2)
      unittest.main(testRunner=runner)
  