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# Copyright 2007 by Tiago Antao <tiagoantao@gmail.com>. All rights reserved.
# 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.
import os
import unittest
import warnings
from Bio import MissingExternalDependencyError
from Bio import BiopythonDeprecationWarning
with warnings.catch_warnings():
warnings.simplefilter("ignore", BiopythonDeprecationWarning)
from Bio.PopGen import SimCoal
from Bio.PopGen.SimCoal.Controller import SimCoalController
# Tests simcoal related code. Note: this case requires simcoal
# test_PopGen_SimCoal_nodepend tests code that does not require simcoal
found = False
for path in os.environ['PATH'].split(os.pathsep):
try:
for filename in os.listdir(path):
if filename == "simcoal2" \
or (filename.lower() == "simcoal2.exe"):
found = True
simcoal_dir = path
except os.error:
pass # Path doesn't exist - correct to pass
if not found:
raise MissingExternalDependencyError(
"Install SIMCOAL2 if you want to use Bio.PopGen.SimCoal.")
class AppTest(unittest.TestCase):
"""Tests simcoal execution via biopython.
"""
def setUp(self):
self.tidy()
def tearDown(self):
self.tidy()
def tidy(self):
if not os.path.isdir(os.path.join('PopGen', 'simple')):
# Unit test must have failed to invoke simcaol,
# and thus it never created the directory.
return
for file in os.listdir(os.path.join('PopGen', 'simple')):
os.remove(os.sep.join(['PopGen', 'simple', file]))
os.rmdir(os.path.join('PopGen', 'simple'))
def test_simcoal(self):
"""Test simcoal execution.
"""
ctrl = SimCoalController(simcoal_dir)
ctrl.run_simcoal('simple.par', 50, par_dir='PopGen')
assert os.path.isdir(os.path.join('PopGen', 'simple')), \
"Output directory not created!"
assert(len(os.listdir(os.path.join('PopGen', 'simple'))) == 52)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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