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# Copyright 2010 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.
from __future__ import print_function
import os
import shutil
import tempfile
import unittest
import warnings
from Bio import MissingExternalDependencyError
from Bio import BiopythonDeprecationWarning
with warnings.catch_warnings():
warnings.simplefilter("ignore", BiopythonDeprecationWarning)
from Bio.PopGen import FDist
from Bio.PopGen.FDist import Controller
# Tests DFDist related code. Note: this case requires Dfdist (four binaries)
# test_PopGen_FDist_nodepend tests code that does not require fdist2 or Dfdist
def is_pypy():
import platform
try:
if platform.python_implementation() == 'PyPy':
return True
except AttributeError:
# New in Python 2.6, not in Jython yet either
pass
return False
wanted = dict()
for path in os.environ['PATH'].split(os.pathsep):
try:
list = os.listdir(path)
for file in os.listdir(path):
for f in ['Dfdist', 'Ddatacal', 'pv2', 'cplot2']:
if file == f or file.lower() == f.lower() + ".exe":
wanted[f] = file
except os.error:
pass # Path doesn't exist - correct to pass
if len(wanted) != 4:
raise MissingExternalDependencyError(
"Install Dfdist, Ddatacal, pv2 and cplot2 if you want to use DFDist with Bio.PopGen.FDist.")
del wanted
import sys
if not is_pypy() and sys.version_info[0] == 3 and sys.version_info < (3, 2, 4):
raise MissingExternalDependencyError("Under Python 3, please use Python 3.2.4"
" onwards for this test - see http://bugs.python.org/issue16903")
class AppTest(unittest.TestCase):
"""Tests the Dfdist suite of applications.
"""
def _copyfile(self, inname, outname):
shutil.copyfile(
'PopGen' + os.sep + inname,
self.dirname + os.sep + outname)
def setUp(self):
self.ctrl = Controller.FDistController()
self.dirname = tempfile.mkdtemp()
self._copyfile('data_dfst_outfile', 'data_fst_outfile')
self._copyfile('dfdist1', 'infile')
self._copyfile('dout.dat', 'out.dat')
self._copyfile('dout.cpl', 'out.cpl')
def tearDown(self):
# Not sure how exactly, but its possible the temp directory
# may not (still) exist.
if os.path.isdir(self.dirname):
for file in os.listdir(self.dirname):
os.remove(self.dirname + os.sep + file)
os.rmdir(self.dirname)
def test_ddatacal(self):
"""Test Ddatacal execution.
"""
fst, samp_size, loci, pops, F, obs = \
self.ctrl.run_datacal(data_dir=self.dirname, version=2)
self.assertTrue(fst - 0.23 < 0.02)
self.assertEqual(samp_size, 32)
self.assertEqual(loci, 300)
self.assertEqual(pops, 2)
self.assertTrue(F - 0.11 < 0.01)
self.assertEqual(obs, 300)
def test_dfdist(self):
"""Test Dfdist execution.
"""
# The number of simulations in real life should be at least 10000,
# see the fdist2 documentation.
fst = self.ctrl.run_fdist(npops=15, nsamples=10, fst=0.1,
sample_size=20, mut=0, num_sims=100,
data_dir=self.dirname, is_dominant=True)
self.assertTrue(abs(fst - 0.1) < 0.03,
"Stochastic result, expected %f close to 0.1" % fst)
def atest_dfdist_force_fst(self):
"""Test dfdist execution approximating Fst.
THIS IS TOO SLOW
"""
# The number of simulations in real life should be at least 10000,
# see the fdist2 documentation.
fst = self.ctrl.run_fdist_force_fst(npops=15, nsamples=10,
fst=0.1,
sample_size=20, mut=0, num_sims=100,
data_dir=self.dirname, is_dominant=True)
self.assertTrue(abs(fst - 0.09) < 0.05,
"Stochastic result, expected %f close to 0.09" % fst)
def test_cplot2(self):
"""Test cplot2 execution.
"""
cpl_interval = self.ctrl.run_cplot(data_dir=self.dirname, version=2)
self.assertEqual(len(cpl_interval), 300)
def test_pv2(self):
"""Test pv2 execution.
"""
pv_data = self.ctrl.run_pv(data_dir=self.dirname, version=2)
self.assertEqual(len(pv_data), 300)
if __name__ == "__main__":
print("Running fdist tests, which might take some time, please wait")
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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