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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 CDAO and CDAOIO modules."""
import os
import tempfile
import unittest
from Bio import MissingExternalDependencyError
import Bio.Phylo as bp
from Bio.Phylo import CDAO
try:
from Bio.Phylo import CDAOIO
except ImportError:
raise MissingExternalDependencyError(
"Install RDFlib if you want to use the CDAO tree format."
) from None
# Example CDAO files
cdao_files = ("test.cdao",)
# 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.
"""
filename = os.path.join("CDAO/", source)
def test_parse(self):
trees = list(bp._io.parse(filename, "cdao"))
test_parse.__doc__ = "Parse the phylogenies in %s." % source
return test_parse
def _test_write_factory(source):
"""Test for serialization of objects to CDAO format.
Modifies the globally defined filenames in order to run the other parser
tests on files (re)generated by CDAOIO's own writer.
"""
filename = os.path.join("CDAO/", source)
def test_write(self):
"""Parse, rewrite and retest an example file."""
with open(filename) as infile:
t1 = next(CDAOIO.Parser(infile).parse())
with open(DUMMY, "w") as outfile:
CDAOIO.write([t1], outfile)
with open(DUMMY) as infile:
t2 = next(CDAOIO.Parser(infile).parse())
for prop_name in ("name", "branch_length", "confidence"):
p1 = [getattr(n, prop_name) for n in t1.get_terminals()]
p2 = [getattr(n, prop_name) for n in t2.get_terminals()]
if p1 == p2:
pass
else:
# Can't sort lists with None on Python 3 ...
self.assertNotIn(
None, p1, "Bad input values for %s: %r" % (prop_name, p1)
)
self.assertNotIn(
None, p2, "Bad output values for %s: %r" % (prop_name, p2)
)
self.assertEqual(sorted(p1), sorted(p2))
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 CDAO files."""
for n, ex in enumerate(cdao_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(cdao_files):
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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