def test_majority_rule(self):
trees = [
TreeNode.from_newick("(A,(B,(H,(D,(J,(((G,E),(F,I)),C))))));"),
TreeNode.from_newick("(A,(B,(D,((J,H),(((G,E),(F,I)),C)))));"),
TreeNode.from_newick("(A,(B,(D,(H,(J,(((G,E),(F,I)),C))))));"),
TreeNode.from_newick("(A,(B,(E,(G,((F,I),((J,(H,D)),C))))));"),
TreeNode.from_newick("(A,(B,(E,(G,((F,I),(((J,H),D),C))))));"),
TreeNode.from_newick("(A,(B,(E,((F,I),(G,((J,(H,D)),C))))));"),
TreeNode.from_newick("(A,(B,(E,((F,I),(G,(((J,H),D),C))))));"),
TreeNode.from_newick("(A,(B,(E,((G,(F,I)),((J,(H,D)),C)))));"),
TreeNode.from_newick("(A,(B,(E,((G,(F,I)),(((J,H),D),C)))));")]
exp = TreeNode.from_newick("(((E,(G,(F,I),(C,(D,J,H)))),B),A);")
obs = majority_rule(trees)
self.assertEqual(exp.compare_subsets(obs[0]), 0.0)
self.assertEqual(len(obs), 1)
tree = obs[0]
exp_supports = sorted([9.0, 9.0, 9.0, 6.0, 6.0, 6.0])
obs_supports = sorted([n.support for n in tree.non_tips()])
self.assertEqual(obs_supports, exp_supports)
obs = majority_rule(trees, weights=np.ones(len(trees)) * 2)
self.assertEqual(exp.compare_subsets(obs[0]), 0.0)
self.assertEqual(len(obs), 1)
tree = obs[0]
exp_supports = sorted([18.0, 18.0, 12.0, 18.0, 12.0, 12.0])
obs_supports = sorted([n.support for n in tree.non_tips()])
with self.assertRaises(ValueError):
majority_rule(trees, weights=[1, 2])
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
trees = load_tree_files(opts.input_dir)
# this retains the default behavior from PyCogent's majority_rule function
if opts.strict:
cutoff = 0.5
else:
cutoff = 0.0
consensus = majority_rule(trees=trees, cutoff=cutoff)[0]
f = open(opts.output_fname, 'w')
f.write(consensus.to_newick(with_distances=True))
f.close()
def test_majority_rule_multiple_trees(self):
trees = [
TreeNode.from_newick("((a,b),(c,d),(e,f))"),
TreeNode.from_newick("(a,(c,d),b,(e,f))"),
TreeNode.from_newick("((c,d),(e,f),b)"),
TreeNode.from_newick("(a,(c,d),(e,f))")]
trees = majority_rule(trees)
self.assertEqual(len(trees), 4)
exp = set([
frozenset(['a']),
frozenset(['b']),
frozenset([None, 'c', 'd']),
frozenset([None, 'e', 'f'])])
obs = set([frozenset([n.name for n in t.traverse()]) for t in trees])
self.assertEqual(obs, exp)
