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# Copyright 2006 by Tiago Antao <>. 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.
from Bio._py3k import _universal_read_mode
import os
import unittest
import warnings
from Bio import BiopythonDeprecationWarning
with warnings.catch_warnings():
warnings.simplefilter("ignore", BiopythonDeprecationWarning)
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
[(1, [('SNP', [24, 0.0005, 0.0])])],
[('sample_size', [30]),
('pop_size', [100])],
# Confirm the files match (ignoring any switch of line endings
# possible if the input file used a different OS convention)
with open(os.path.join('PopGen', 'simple.par'), _universal_read_mode) as handle:
old = handle.readlines()
with open(os.path.join('PopGen', 'simple_100_30.par')) as handle:
new = handle.readlines()
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)