def test_create_new_tree(self):
starting_root = "{};"
first_leaf = "{A};"
phy_tree = PhyTree(loads(starting_root))
phy_tree.add_to_group("A", "{}")
compare_nodes(self, phy_tree.get_newick()[0], loads(first_leaf)[0])
def test_add_second_level(self):
starting_point = "({A},{B}){A B};"
expected_tree = "({A},({B},{C}){B C}){A B C};"
phy_tree = PhyTree(loads(starting_point))
phy_tree.add_to_group("C", "{B}")
compare_nodes(self, phy_tree.get_newick()[0], loads(expected_tree)[0])
def choose_action(tree: str, action_name: str, optional: str = None):
if action_name in ["--update", "-u"]:
update(tree)
elif action_name in ["--show", "-sh"]:
phy_tree: PhyTree
if re.match(r'[\S]*\.newick$', tree):
phy_tree = load_tree(tree)
elif re.match(r'\([\S ]+\}\;$', tree):
phy_tree = PhyTree()
try:
phy_tree.parse_string(tree)
except ValueError as e:
print(e)
exit()
else:
print("Post tree as a filename or string")
exit()
visualize_tree(phy_tree.get_newick()[0])
elif action_name in ["--create", "-c"]:
create(tree)
elif action_name in ["--random-tree", "-r"]:
if optional is None:
random_tree(tree)
else:
random_tree(tree, int(optional))
elif action_name in ["--cut"]:
cut(tree)
else:
print("Wrong name function")
def test_add_leaf_append_group(self):
old_tree = "(({A},{B}){A B},{C}){A B C};"
new_tree = "(({A},{B},{X}){A B X},{C}){A B C X};"
olf_phy, new_phy = PhyTree(), PhyTree()
olf_phy.parse_string(old_tree)
new_phy.parse_string(new_tree)
olf_phy.add_to_group("X", "{A B}")
old_newick, new_newick = olf_phy.get_newick(), new_phy.get_newick()
compare_nodes(self, old_newick[0], new_newick[0])
def modify(file_name: str, tree: PhyTree):
finished = False
while not finished:
print("Tree has following groups:")
print(tree.get_nodes())
print("Add leaf:")
node = input()
if re.match(r"[{} ]", node):
print("Leaf name can not include {, }, and space")
continue
print(f"Add leaf '{node}' to group:")
group = input()
if not re.match(r'[{}]', group):
print("Target group has to be enclosed by {} brackets")
continue
current_structure = dumps(tree.get_newick())
try:
tree.add_to_group(node, group)
except ValueError as e:
print(e)
tree.parse_string(current_structure)
finished = ask_if_finished()
tree.save(file_name)