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dfdist support

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1 parent 065e235 commit 6eb8b98e8cce2d5e0b2f97d30b0e0b0dc3db7525 @tiagoantao tiagoantao committed with peterjc Aug 20, 2010
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  1. +300 −0 Tests/PopGen/data_dfst_outfile
  2. +1,204 −0 Tests/PopGen/dfdist1
  3. +300 −0 Tests/PopGen/dout.cpl
  4. +50,000 −0 Tests/PopGen/dout.dat
  5. +105 −0 Tests/test_PopGen_DFDist.py
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300 Tests/PopGen/data_dfst_outfile
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View
300 Tests/PopGen/dout.cpl
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105 Tests/test_PopGen_DFDist.py
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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.
+
+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('Dfdist'):
+ 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_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_datacal(self):
+ """Test datacal execution.
+ """
+ fst, samp_size, loci, pops, F, obs = \
+ self.ctrl.run_datacal(data_dir = self.dirname, version=2)
+ assert (fst - 0.23 < 0.02)
+ assert (samp_size == 32)
+ assert (loci == 300)
+ assert (pops == 2)
+ assert (F - 0.11 < 0.01)
+ assert (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)
+ assert(abs(fst - 0.1) < 0.02) #Stochastic result...
+
+ def test_dfdist_force_fst(self):
+ """Test dfdist 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, is_dominant=True)
+ 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, version=2)
+ assert (len(cpl_interval)==300)
+
+ def test_pv(self):
+ """Test pv execution.
+ """
+ pv_data = self.ctrl.run_pv(data_dir = self.dirname, version=2)
+ assert(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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