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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.
from __future__ import print_function
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()
pop_iter, locus_iter = ctrl.calc_allele_genotype_freqs("PopGen" + os.sep + "big.gen")
# 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()
iter, avg_fis, avg_Qintra = ctrl.calc_diversities_fis_with_identity(
"PopGen" + os.sep + "big.gen")
liter = list(iter)
assert len(liter) == 37
assert liter[0][0] == "Locus1"
assert len(avg_fis) == 10
assert len(avg_Qintra) == 10
def test_estimate_nm(self):
"""Test Nm estimation.
"""
ctrl = GenePopController()
mean_sample_size, mean_priv_alleles, mig10, mig25, mig50, mig_corrected =\
ctrl.estimate_nm("PopGen" + os.sep + "big.gen")
assert (mean_sample_size, mean_priv_alleles, mig10, mig25, mig50, mig_corrected) == \
(28.0, 0.016129, 52.5578, 15.3006, 8.94583, 13.6612)
def test_fst_all(self):
"""Test genepop execution on all fst.
"""
ctrl = GenePopController()
(allFis, allFst, allFit), itr = ctrl.calc_fst_all("PopGen" + os.sep + "c2line.gen")
results = list(itr)
assert (len(results) == 3)
assert (results[0][0] == "136255903")
assert (results[1][3] - 0.33 < 0.01)
def test_haploidy(self):
"""Test haploidy.
"""
ctrl = GenePopController()
(allFis, allFst, allFit), itr = ctrl.calc_fst_all("PopGen" + os.sep + "haplo.gen")
litr = list(itr)
assert not isinstance(allFst, int)
assert len(litr) == 37
assert litr[36][0] == "Locus37"
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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