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# Copyright 2006 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.Template import generate_simcoal_from_template
#Tests simcoal related code. Note: this case doesn't require simcoal
#test_PopGen_SimCoal tests code that requires simcoal
class TemplateTest(unittest.TestCase):
def test_template_full(self):
"""Full template creation test
"""
generate_simcoal_from_template('simple',
[(1, [('SNP', [24, 0.0005, 0.0])])],
[('sample_size', [30]),
('pop_size', [100])],
'PopGen')
#Confirm the files match (ignoring any switch of line endings
#possible if the input file used a different OS convention)
handle = open(os.path.join('PopGen', 'simple.par'), "rU")
old = handle.readlines()
handle.close()
handle = open(os.path.join('PopGen', 'simple_100_30.par'))
new = handle.readlines()
handle.close()
assert old==new, "Error - Old:\n%s\n\nNew:\n%s\n" % (old, new)
#assert(os.stat('PopGen' + os.sep + 'simple.par').st_size ==
# os.stat('PopGen' + os.sep + 'simple_100_30.par').st_size)
def tearDown(self):
if os.path.isfile(os.path.join('PopGen', 'tmp.par')):
#This is a temp file create by the Bio.PopGen.SimCoal.Template
#function generate_simcoal_from_template
os.remove(os.path.join('PopGen', 'tmp.par'))
if os.path.isfile(os.path.join('PopGen', 'simple_100_30.par')):
#This won't exist if the template generation failed:
os.remove(os.path.join('PopGen', 'simple_100_30.par'))
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity = 2)
unittest.main(testRunner=runner)
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