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# Copyright 2009 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.
"""Test GenePop."""
import os
import unittest
from Bio import MissingExternalDependencyError
from Bio.PopGen.GenePop.Controller import GenePopController
# Tests genepop related code. Note: this case requires genepop
# test_PopGen_GenePop_nodepend tests code that does not require genepop
found = False
for path in os.environ["PATH"].split(os.pathsep):
try:
for filename in os.listdir(path):
if filename.startswith("Genepop"):
found = True
except os.error:
pass # Path doesn't exist - correct to pass
if not found:
raise MissingExternalDependencyError(
"Install GenePop if you want to use Bio.PopGen.GenePop."
)
class AppTest(unittest.TestCase):
"""Tests genepop execution via biopython."""
def test_allele_genotype_frequencies(self):
"""Test genepop execution on basic allele and genotype frequencies."""
ctrl = GenePopController()
path = os.path.join("PopGen", "big.gen")
pop_iter, locus_iter = ctrl.calc_allele_genotype_freqs(path)
# print("%s %s" % (pop, loci))
# for popc in pop_iter:
# pop_name, loci_content = popc
# print(pop_name)
# for locus in loci_content:
# geno_list, hets, freq_fis = loci_content[locus]
# print(locus)
# print(hets)
# print(freq_fis)
# print(geno_list)
# print("")
def test_calc_diversities_fis_with_identity(self):
"""Test calculations of diversities."""
ctrl = GenePopController()
path = os.path.join("PopGen", "big.gen")
iter, avg_fis, avg_Qintra = ctrl.calc_diversities_fis_with_identity(path)
liter = list(iter)
self.assertEqual(len(liter), 37)
self.assertEqual(liter[0][0], "Locus1")
self.assertEqual(len(avg_fis), 10)
self.assertEqual(len(avg_Qintra), 10)
def test_estimate_nm(self):
"""Test Nm estimation."""
ctrl = GenePopController()
path = os.path.join("PopGen", "big.gen")
(
mean_sample_size,
mean_priv_alleles,
mig10,
mig25,
mig50,
mig_corrected,
) = ctrl.estimate_nm(path)
self.assertAlmostEqual(mean_sample_size, 28.0)
self.assertAlmostEqual(mean_priv_alleles, 0.016129)
self.assertAlmostEqual(mig10, 52.5578)
self.assertAlmostEqual(mig25, 15.3006)
self.assertAlmostEqual(mig50, 8.94583)
self.assertAlmostEqual(mig_corrected, 13.6612)
def test_fst_all(self):
"""Test genepop execution on all fst."""
ctrl = GenePopController()
path = os.path.join("PopGen", "c2line.gen")
(allFis, allFst, allFit), itr = ctrl.calc_fst_all(path)
results = list(itr)
self.assertEqual(len(results), 3)
self.assertEqual(results[0][0], "136255903")
self.assertAlmostEqual(results[1][3], 0.335846)
def test_haploidy(self):
"""Test haploidy."""
ctrl = GenePopController()
path = os.path.join("PopGen", "haplo.gen")
(allFis, allFst, allFit), itr = ctrl.calc_fst_all(path)
litr = list(itr)
self.assertNotIsInstance(allFst, int)
self.assertEqual(len(litr), 37)
self.assertEqual(litr[36][0], "Locus37")
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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