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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
import Bio.Phylo as bp
from Bio import MissingExternalDependencyError
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.NamedTemporaryFile(delete=False).name
# ---------------------------------------------------------
# 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__ = f"Parse the phylogenies in {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, f"Bad input values for {prop_name}: {p1!r}")
self.assertNotIn(None, p2, f"Bad output values for {prop_name}: {p2!r}")
self.assertEqual(sorted(p1), sorted(p2))
test_write.__doc__ = f"Write and re-parse the phylogenies in {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__ = f"test_parse_{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__ = f"test_write_{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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