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# Copyright (C) 2012 by Eric Talevich.
# 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 Bio.Phylo.Applications wrappers."""
import os
import unittest
import warnings
from Bio import BiopythonDeprecationWarning
from Bio import MissingExternalDependencyError
from Bio import Phylo
with warnings.catch_warnings():
warnings.simplefilter("ignore", category=BiopythonDeprecationWarning)
from Bio.Phylo.Applications import RaxmlCommandline
raxml_exe = None
try:
from subprocess import getoutput
output = getoutput("raxmlHPC -v")
if "not found" not in output and "not recognized" not in output:
if "This is RAxML" in output:
raxml_exe = "raxmlHPC"
except FileNotFoundError:
pass
if not raxml_exe:
raise MissingExternalDependencyError(
"Install RAxML (binary raxmlHPC) if you want"
" to test the Bio.Phylo.Applications wrapper."
)
# Example Phylip file with 4 aligned protein sequences
EX_PHYLIP = "Phylip/interlaced2.phy"
class AppTests(unittest.TestCase):
"""Tests for application wrappers."""
def test_raxml(self):
"""Run RAxML using the wrapper."""
cmd = RaxmlCommandline(
raxml_exe, sequences=EX_PHYLIP, model="PROTCATWAG", name="test"
)
# The parsimony seed should be set automatically
self.assertIn("-p", str(cmd))
# Smoke test
try:
out, err = cmd()
self.assertGreater(len(out), 0)
self.assertEqual(len(err), 0)
# Check the output tree
tree = Phylo.read("RAxML_result.test", "newick")
self.assertEqual(tree.count_terminals(), 4)
finally:
# Remove RAxML-generated files, or RAxML will complain bitterly
# during the next run
for fname in [
"RAxML_info.test",
"RAxML_log.test",
"RAxML_parsimonyTree.test",
"RAxML_result.test",
# Present in 7.2.X+ but not 7.0.4:
"RAxML_bestTree.test",
]:
if os.path.isfile(fname):
os.remove(fname)
# ---------------------------------------------------------
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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