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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 commands
import os
import shutil
import tempfile
import unittest
from Bio.PopGen import FDist
from Bio.PopGen.FDist import Controller
from Bio import MissingExternalDependencyError
#Tests fdist related code. Note: this case requires fdist
#test_PopGen_FDist_nodepend tests code that does not require fdist
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('fdist2'):
found = True
except os.error:
pass #Path doesn't exist - correct to pass
if not found:
raise MissingExternalDependencyError(\
"Install FDist if you want to use Bio.PopGen.FDist.")
class AppTest(unittest.TestCase):
"""Tests the fdist 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_fst_outfile', 'data_fst_outfile')
self._copyfile('fdist1', 'infile')
self._copyfile('out.dat', 'out.dat')
self._copyfile('out.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_datacal(self):
"""Test datacal execution.
"""
fst, samp_size = self.ctrl.run_datacal(data_dir = self.dirname)
assert (fst - 0.44 < 0.01)
assert (samp_size == 11)
def test_fdist(self):
"""Test fdist 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)
assert(abs(fst - 0.1) < 0.02) #Stochastic result...
def test_fdist_force_fst(self):
"""Test fdist execution approximating Fst.
"""
#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)
assert(abs(fst - 0.09) < 0.05) #Stochastic result...
def test_cplot(self):
"""Test cplot execution.
"""
cpl_interval =self.ctrl.run_cplot(data_dir = self.dirname)
assert(len(cpl_interval) == 8)
def test_pv(self):
"""Test pv execution.
"""
pv_data = self.ctrl.run_pv(data_dir = self.dirname)
assert(len(pv_data) == 4)
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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