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# Copyright (C) 2013 by Ben Morris (ben@bendmorris.com)
# based on code by Eric Talevich (eric.talevich@gmail.com)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Unit tests for the NeXML and NeXMLIO modules."""
import os
import tempfile
import unittest
from io import BytesIO
from Bio import Phylo
# Example NeXML files
nexml_files = (
"characters.xml",
"edgelabels.xml",
"meta_taxa.xml",
"meta_types.xml",
"nexml.xml",
"phenoscape.xml",
"sets.xml",
"taxa.xml",
"timetree.xml",
"tolweb.xml",
"treebase-record.xml",
"trees-uris.xml",
"trees.xml",
)
tree_counts = {
"taxa.xml": 0,
"timetree.xml": 38,
"phenoscape.xml": 0,
"nexml.xml": 0,
"meta_types.xml": 0,
"meta_taxa.xml": 0,
"trees.xml": 2,
"characters.xml": 0,
}
class ParseTests(unittest.TestCase):
"""Tests for proper parsing of example NeXML files."""
def test_parse(self):
"""Extract and count phylogenetic trees using Phylo.parse."""
for filename in nexml_files:
count = tree_counts.get(filename, 1)
path = os.path.join("NeXML", filename)
msg = "Failed parser test for %s" % path
trees = list(Phylo.parse(path, "nexml"))
self.assertEqual(len(trees), count, msg=msg)
class WriterTests(unittest.TestCase):
"""NeXML writer tests."""
def check(self, path):
"""Parse, rewrite and retest an example phylogeny file."""
msg = "Failed NeXMLIO writer test for %s" % path
# Using Phylo.NeXMLIO directly, binary mode handles
with open(path, "rb") as stream:
t1 = next(Phylo.NeXMLIO.Parser(stream).parse())
stream = BytesIO()
Phylo.NeXMLIO.write([t1], stream)
stream.seek(0)
t2 = next(Phylo.NeXMLIO.Parser(stream).parse())
self.compare(t1, t2, msg)
# Using Phylo.parse/write, using filenames
msg = "Failed Phylo API writer test for %s" % path
t1 = next(Phylo.parse(path, "nexml"))
tmp = tempfile.NamedTemporaryFile().name
Phylo.write([t1], tmp, "nexml")
t2 = next(Phylo.parse(tmp, "nexml"))
self.compare(t1, t2, msg)
os.remove(tmp)
def compare(self, t1, t2, msg=None):
"""Compare two trees."""
for prop_name in ("name", "branch_length", "confidence"):
p1 = sorted(
getattr(n, prop_name)
for n in t1.get_terminals()
if getattr(n, prop_name)
)
p2 = sorted(
getattr(n, prop_name)
for n in t2.get_terminals()
if getattr(n, prop_name)
)
self.assertEqual(p1, p2, msg=msg)
def test_write(self):
"""Test for serialization of objects to NeXML format."""
for filename in nexml_files:
count = tree_counts.get(filename, 1)
if count > 0:
path = os.path.join("NeXML", filename)
self.check(path)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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