#! /usr/bin/env python ############################################################################## ## DendroPy Phylogenetic Computing Library. ## ## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder. ## All rights reserved. ## ## See "LICENSE.rst" for terms and conditions of usage. ## ## If you use this work or any portion thereof in published work, ## please cite it as: ## ## Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library ## for phylogenetic computing. Bioinformatics 26: 1569-1571. ## ############################################################################## import unittest import dendropy import json from dendropy.test.support import pathmap from dendropy.test.support import dendropytest def generate_bipartitions( trees, generation_mode="from-trees", is_rooted=None): if is_rooted is None: is_rooted = trees[0].is_rooted if generation_mode == "all": bipartitions = [] all_taxa_bitmask = trees.taxon_namespace.all_taxa_bitmask() for s in range(1, all_taxa_bitmask): b = dendropy.Bipartition( leafset_bitmask=s, tree_leafset_bitmask=all_taxa_bitmask, is_rooted=is_rooted, compile_bipartition=True) bipartitions.append(b) elif generation_mode == "from-trees": bipartitions = [] for tree in trees: bipartitions.extend(tree.encode_bipartitions()) else: raise ValueError(generation_mode) unique_bipartitions = {} for b in bipartitions: if is_rooted: unique_bipartitions[b.leafset_bitmask] = b else: unique_bipartitions[b.split_bitmask] = b unique_bipartitions_keys = sorted(unique_bipartitions.keys()) bipartitions = [] for key in unique_bipartitions_keys: unique_bipartitions[key].is_mutable = False bipartitions.append(unique_bipartitions[key]) return bipartitions class TestSplitCompatibility(dendropytest.ExtendedTestCase): def test_compatibility(self): regimes = ( ("dendropy-test-trees-n12-x2.nexus", "all"), ("dendropy-test-trees-n33-unrooted-x100a.nexus", "from-trees"), ("dendropy-test-trees-n10-rooted-treeshapes.nexus", "all"), ) for trees_filename_idx, (trees_filename, bipartition_generation_mode) in enumerate(regimes): trees_filepath = pathmap.tree_source_path(trees_filename) trees = dendropy.TreeList.get_from_path( trees_filepath, "nexus",) bipartitions = generate_bipartitions(trees, bipartition_generation_mode, is_rooted=trees[0].is_rooted) # for bipartition1_idx, bipartition1 in enumerate(bipartitions): for bipartition1_idx, bipartition1 in enumerate(bipartitions): for tree_idx, tree in enumerate(trees): compatible_bipartitions = set() incompatible_bipartitions = set() bipartition_encoding = tree.encode_bipartitions() for biparition2_idx, bipartition2 in enumerate(bipartition_encoding): if bipartition2.is_compatible_with(bipartition1): self.assertTrue(bipartition1.is_compatible_with(bipartition2)) compatible_bipartitions.add(bipartition2) else: self.assertFalse(bipartition1.is_compatible_with(bipartition2)) incompatible_bipartitions.add(bipartition2) is_compatible = tree.is_compatible_with_bipartition(bipartition1) self.assertEqual(len(compatible_bipartitions) + len(incompatible_bipartitions), len(bipartition_encoding)) if is_compatible: self.assertEqual(len(incompatible_bipartitions), 0, "Tree {} of '{}': bipartition {} (leafset = {}, index = {}) found compatible with tree, but is incompatible with following bipartitions on tree: {}". format( tree_idx, trees_filename, bipartition1.split_as_bitstring(), bipartition1.leafset_as_bitstring(), bipartition1_idx, [b.split_as_bitstring() for b in incompatible_bipartitions], )) self.assertEqual(len(compatible_bipartitions), len(bipartition_encoding)) else: self.assertTrue(len(incompatible_bipartitions) > 0, "Tree {} of '{}': bipartition {} (leafset = {}, index = {}) found incompatible with tree, but is compatible with all bipartitions on tree: {}". format( tree_idx, trees_filename, bipartition1.split_as_bitstring(), bipartition1.leafset_as_bitstring(), bipartition1_idx, [b.split_as_bitstring() for b in compatible_bipartitions], )) # def test_compatibility(self): # regime_source_names = ( # ("dendropy-test-trees-n10-rooted-treeshapes.nexus", "dendropy-test-trees-n10-rooted-treeshapes.split-compatibilities-all.json", ), # ) # for tree_filename, ref_filename in regime_source_names: # with open(pathmap.tree_source_path(ref_filename), "r") as src: # regimed = json.load(src) # bipartitions = {} # for bidx in regimed["bipartitions"]: # bdesc = regimed["bipartitions"][bidx] # b = dendropy.Bipartition( # leafset_bitmask=bdesc["leafset_bitmask"], # tree_leafset_bitmask=bdesc["tree_leafset_bitmask"], # is_rooted=bdesc["is_rooted"]) # bipartitions[int(bidx)] = b # bipartition_indexes = sorted(bipartitions.keys()) # tree_data = {} # for tree_idx in regimed["trees"]: # i = int(tree_idx) # tree_data[i] = {} # tree_data[i]["compatible_bipartitions"] = set([int(j) for j in regimed["trees"][tree_idx]["compatible_bipartitions"]]) # tree_data[i]["incompatible_bipartitions"] = set([int(j) for j in regimed["trees"][tree_idx]["incompatible_bipartitions"]]) # trees = dendropy.TreeList.get_from_path( # pathmap.tree_source_path(tree_filename), # "nexus") # for tree_idx, tree in enumerate(trees): # tree_bipartitions = tree.encode_bipartitions() # for bipartition_idx in bipartition_indexes: # is_compatible = tree.is_compatible_with_bipartition(bipartition) # bipartition = bipartitions[bipartition_idx] # if bipartition_idx in tree_data[tree_idx]["compatible_bipartitions"]: # expected_is_compatible = True # elif bipartition_idx in tree_data[tree_idx]["incompatible_bipartitions"]: # expected_is_compatible = False # else: # raise Exception("Bipartition {} ('{}') not reported for tree {}".format(bipartition_idx, bipartition.split_as_bitstring(), tree_idx)) # self.assertIs(is_compatible, expected_is_compatible, # "Bipartition {} ('{}') for tree {} in '{}': expected '{}' for compatibility but instead observed '{}'".format( # bipartition_idx, # bipartition.split_as_bitstring(), # tree_idx, # tree_filename, # expected_is_compatible, # is_compatible, # )) if __name__ == "__main__": unittest.main()