def process_tree(tree, stree, gene2species):
#==============================
# process
if options.hist or options.hashes:
# count topology
hashes.append(phylo.hash_tree(tree, gene2species))
elif options.histsplit:
# count splits
for leaf in tree.leaves():
tree.rename(leaf.name, gene2species(leaf.name))
splits.extend(phylo.find_splits(tree))
elif options.dump:
# dump mode
dump_tree(tree)
elif options.events:
# add event labels
assert stree is not None and gene2species is not None
phylo.count_dup_loss_tree(tree, stree, gene2species)
else:
# default mode: display tree
display_tree(tree, options, gene2species=gene2species, stree=stree)
def process_tree(tree, stree, gene2species):
#==============================
# process
if options.hist or options.hashes:
# count topology
hashes.append(phylo.hash_tree(tree, gene2species))
elif options.histsplit:
# count splits
for leaf in tree.leaves():
tree.rename(leaf.name, gene2species(leaf.name))
splits.extend(phylo.find_splits(tree))
elif options.dump:
# dump mode
dump_tree(tree)
elif options.events:
# add event labels
assert stree is not None and gene2species is not None
phylo.count_dup_loss_tree(tree, stree, gene2species)
else:
# default mode: display tree
display_tree(tree, options, gene2species=gene2species, stree=stree)
def test(self):
tree1 = parse_newick("((a,b),c)")
tree2 = parse_newick("(c,(a,b))")
assert (phylo.find_splits(tree1, rooted=True) ==
phylo.find_splits(tree2, rooted=True))
tree1 = parse_newick("((a,b),(c,d))")
tree2 = parse_newick("(((c,d),a),b)")
assert (phylo.find_splits(tree1) ==
phylo.find_splits(tree2))
assert phylo.robinson_foulds_error(tree1, tree2) == 0.0
tree1 = parse_newick("(((a,b),(c,d)),(e,f))")
tree2 = parse_newick("(((a,c),(b,d)),(e,f))")
self.assertAlmostEqual(phylo.robinson_foulds_error(tree1, tree2), 2/3.)
def test(self):
tree1 = parse_newick("((a,b),c)")
tree2 = parse_newick("(c,(a,b))")
assert (phylo.find_splits(tree1, rooted=True) == phylo.find_splits(
tree2, rooted=True))
tree1 = parse_newick("((a,b),(c,d))")
tree2 = parse_newick("(((c,d),a),b)")
assert (phylo.find_splits(tree1) == phylo.find_splits(tree2))
assert phylo.robinson_foulds_error(tree1, tree2) == 0.0
tree1 = parse_newick("(((a,b),(c,d)),(e,f))")
tree2 = parse_newick("(((a,c),(b,d)),(e,f))")
self.assertAlmostEqual(phylo.robinson_foulds_error(tree1, tree2),
2 / 3.)
