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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
import Bio.Phylo as bp
from Bio.Phylo import NeXML, NeXMLIO
# 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,
}
# Temporary file name for Writer tests below
DUMMY = tempfile.mktemp()
# ---------------------------------------------------------
# Parser tests
def _test_parse_factory(source):
"""Generate a test method for parse()ing the given source.
The generated function extracts each phylogenetic tree using the parse()
function and counts the total number of trees extracted.
"""
filename = os.path.join('NeXML/', source)
if source in tree_counts:
count = tree_counts[source]
else:
count = 1
def test_parse(self):
trees = list(bp._io.parse(filename, 'nexml'))
self.assertEqual(len(trees), count)
test_parse.__doc__ = "Parse the phylogenies in %s." % source
return test_parse
def _test_write_factory(source):
"""Tests for serialization of objects to NeXML format.
Modifies the globally defined filenames in order to run the other parser
tests on files (re)generated by NeXMLIO's own writer.
"""
filename = os.path.join('NeXML/', source)
if source in tree_counts:
count = tree_counts[source]
else:
count = 1
def test_write(self):
"""Parse, rewrite and retest an example file."""
with open(filename, 'rb') as infile:
t1 = next(NeXMLIO.Parser(infile).parse())
with open(DUMMY, 'w+b') as outfile:
NeXMLIO.write([t1], outfile)
with open(DUMMY, 'rb') as infile:
t2 = next(NeXMLIO.Parser(infile).parse())
def assert_property(prop_name):
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)
for prop_name in ('name', 'branch_length', 'confidence'):
assert_property(prop_name)
test_write.__doc__ = "Write and re-parse the phylogenies in %s." % source
return test_write
class ParseTests(unittest.TestCase):
"""Tests for proper parsing of example NeXML files."""
for n, ex in enumerate(nexml_files):
parse_test = _test_parse_factory(ex)
parse_test.__name__ = 'test_parse_%s' % n
setattr(ParseTests, parse_test.__name__, parse_test)
class WriterTests(unittest.TestCase):
pass
for n, ex in enumerate(nexml_files):
count = 1
if ex in tree_counts:
count = tree_counts[ex]
if count > 0:
write_test = _test_write_factory(ex)
write_test.__name__ = 'test_write_%s' % n
setattr(WriterTests, write_test.__name__, write_test)
if __name__ == '__main__':
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
# Clean up the temporary file
if os.path.exists(DUMMY):
os.remove(DUMMY)
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