def save_as_nexus(self):
save_as_nexus(self.tree.tree, self.output_path + "_timeTree.nex")
return node
def traverse_and_resolve_first(tree):
for clade in tree.find_clades(terminal=False, order="preorder"):
if len(clade.clades) != 2:
print("resolving ", clade.name, " with ", len(clade.clades), " children using temporal data")
clade = ladderise_node(clade)
return True
return False
## fn start
polytomies_exist = True; # stopping condition
while polytomies_exist:
polytomies_exist = traverse_and_resolve_first(tree)
assert(tree.is_bifurcating())
tree.ladderize()
if __name__=="__main__":
params = collect_args()
outfile = params.outfile if params.outfile != None else params.tree.split(".json")[0]+".nex"
json_fh = open(params.tree, "r")
json_dict = json.load(json_fh)
tree = json_to_tree(json_dict)
if params.resolve:
resolve_polytomies(tree)
if params.temporal:
save_as_nexus(tree, outfile, "num_date")
else:
save_as_nexus(tree, outfile, "div")
return node
def traverse_and_resolve_first(tree):
for clade in tree.find_clades(terminal=False, order="preorder"):
if len(clade.clades) != 2:
print("resolving ", clade.name, " with ", len(clade.clades), " children using temporal data")
clade = ladderise_node(clade)
return True
return False
## fn start
polytomies_exist = True; # stopping condition
while polytomies_exist:
polytomies_exist = traverse_and_resolve_first(tree)
assert(tree.is_bifurcating())
tree.ladderize()
if __name__=="__main__":
params = collect_args()
outfile = params.outfile if params.outfile != None else params.tree.split(".json")[0]+".nex"
json_fh = open(params.tree, "r")
json_dict = json.load(json_fh)
tree = json_to_tree(json_dict)
if params.resolve:
resolve_polytomies(tree)
if params.temporal:
save_as_nexus(tree, outfile, "num_date")
else:
save_as_nexus(tree, outfile, "div")