def main(arguments):
prune = False
if arguments.url:
tree = Tree().get(url=arguments.url,
schema="newick",
preserve_underscores=True)
elif arguments.path:
tree = Tree().get(path=arguments.path,
schema="newick",
preserve_underscores=True)
else:
raise ValueError(
"No input argument found. Please specify either --url or --path")
if arguments.rename is not None:
tree, prune_list = rename_tree(tree, arguments.rename)
tree = collapse_polytomies(tree, arguments.limit)
if prune:
PareTree_wrapper(tree, prune_list, arguments.output)
else:
tree.write(path=arguments.output, schema="newick")
