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import argparse
import Bio.Phylo
import deepdiff
from augur.argparse_ import ExtendOverwriteDefault
def clade_to_items(clade, attrs=("name", "branch_length")):
"""Recursively convert a clade of a tree to a list of nested lists according to
the topology of the clade with the requested attributes per node.
Examples
--------
>>> from io import StringIO
>>> treedata = "(A, (B, C), (D, E))"
>>> handle = StringIO(treedata)
>>> tree = Bio.Phylo.read(handle, "newick")
>>> clade_to_items(tree.root)
[[None, None], [['A', None]], [[None, None], [['B', None]], [['C', None]]], [[None, None], [['D', None]], [['E', None]]]]
"""
items = [[
getattr(clade, attr)
for attr in attrs
]]
for child in clade.clades:
items.extend([clade_to_items(child)])
return items
if __name__ == "__main__":
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument("first_tree", help="first Newick tree to compare")
parser.add_argument("second_tree", help="second Newick tree to compare")
parser.add_argument("--attributes", nargs="+", action=ExtendOverwriteDefault, default=["name", "branch_length"], help="node attributes to include in comparison")
parser.add_argument("--significant-digits", type=int, default=5, help="number of significant digits to use when comparing branch lengths")
args = parser.parse_args()
first_tree = Bio.Phylo.read(args.first_tree, "newick")
second_tree = Bio.Phylo.read(args.second_tree, "newick")
first_tree_items = clade_to_items(first_tree.root, attrs=args.attributes)
second_tree_items = clade_to_items(second_tree.root, attrs=args.attributes)
print(
deepdiff.DeepDiff(
first_tree_items,
second_tree_items,
significant_digits=args.significant_digits
)
)
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