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test_PopGen_SimCoal.py

# 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
from Bio.PopGen import SimCoal
from Bio.PopGen.SimCoal.Controller import SimCoalController
from Bio import MissingExternalDependencyError

#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.startswith('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.")


00030 class AppTest(unittest.TestCase):
    """Tests simcoal execution via biopython.
    """
    def tearDown(self):
        if not os.path.isdir(os.path.join('PopGen', 'simple')) :
            #Unit test must have failed to invoke simcaol,
            #and this 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'))

00042     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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