def consensus_tree():
trees = []
add_trees = True
while add_trees:
try:
phy_tree = PhyTree()
path = input("Tree's path: ")
if os.path.isdir(path):
files = os.listdir(path)
for f in files:
p = PhyTree()
p.load_file(path + f)
trees.append(p)
break
else:
phy_tree.load_file(path)
except ValueError as e:
print(e)
continue
trees.append(phy_tree)
add_trees = not ask_if_finished()
print("Threshold:")
threshold = get_float()
result = consensus(trees, threshold)
path = input("Save as: ")
result.save(path)
def rf_distance_cmd():
print("First tree:")
left = get_file_path()
print("Second tree:")
right = get_file_path()
left_tree = PhyTree()
left_tree.load_file(left)
right_tree = PhyTree()
right_tree.load_file(right)
distance = rf_distance(left_tree, right_tree)
print(f"Distance: {distance}")
def cut(file_name: str):
if not os.path.isfile(file_name):
print("Given file has to exist.")
return
tree = PhyTree()
tree.load_file(file_name)
wanted_leaves = set()
choose_leaves = True
while choose_leaves:
print(f"Chosen leaves: {wanted_leaves}")
leaf = input("Add leaf: ")
if leaf not in tree.leaves:
print(f"{leaf} was not among the tree's leaves")
continue
if leaf in wanted_leaves:
print(f"{leaf} is already among wanted leaves")
continue
wanted_leaves.add(leaf)
choose_leaves = not ask_if_finished()
cutter = TreeCutter()
cutter.attach_tree(tree)
cutter.choose_leaves(wanted_leaves)
new_tree = cutter.cut()
new_tree.save(file_name)
def update(file_name: str):
tree = PhyTree()
tree.load_file(file_name)
modify(file_name, tree)