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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 commands
import os
import shutil
import sys
import tempfile
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:
list = os.listdir(path)
for file in os.listdir(path):
if file.startswith('simcoal2'):
found = True
simcoal_dir = path
except os.error:
pass #Path doesn't exist - correct to pass
if not found:
raise MissingExternalDependencyError("SimCoal not found (not a problem if you do not intend to use it).")
def run_tests(argv):
test_suite = testing_suite()
runner = unittest.TextTestRunner(sys.stdout, verbosity = 2)
runner.run(test_suite)
def testing_suite():
"""Generate the suite of tests.
"""
print "Running simcoal tests, which might take some time, please wait"
test_suite = unittest.TestSuite()
test_loader = unittest.TestLoader()
test_loader.testMethodPrefix = 't_'
tests = [AppTest]
for test in tests:
cur_suite = test_loader.loadTestsFromTestCase(test)
test_suite.addTest(cur_suite)
return test_suite
class AppTest(unittest.TestCase):
"""Tests simcoal execution via biopython.
"""
def tearDown(self):
for file in os.listdir('PopGen' + os.sep + 'simple'):
os.remove(os.sep.join(['PopGen', 'simple', file]))
os.rmdir('PopGen' + os.sep + 'simple')
def t_simcoal(self):
"""Test simcoal execution.
"""
ctrl = SimCoalController(simcoal_dir)
ctrl.run_simcoal('simple.par', 50, par_dir = 'PopGen')
assert( len(os.listdir('PopGen' + os.sep + 'simple')) == 52)
if __name__ == "__main__":
sys.exit(run_tests(sys.argv))
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