mirror of
https://github.com/biopython/biopython.git
synced 2025-10-20 13:43:47 +08:00
de0bb21fb3
$ ruff check --fix --select=I \ --config=lint.isort.force-single-line=true \ --config=lint.isort.order-by-type=false \ BioSQL/ Bio/ Tests/ Scripts/ Doc/ setup.py Using ruff version 0.4.10
80 lines
2.4 KiB
Python
80 lines
2.4 KiB
Python
# 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)
|