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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.
import os
import unittest
from Bio import MissingExternalDependencyError
from Bio.PopGen.GenePop.EasyController import EasyController
# Tests genepop related code for easy contorller. Note: this 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.")
cur_dir = os.path.abspath(".") # Tests directory
class AppTest(unittest.TestCase):
"""Tests genepop execution via biopython using EasyController.
"""
def setUp(self):
# Genepop likes to be on the directory where the file is.
os.chdir("PopGen")
self.ctrl = EasyController("big.gen")
def tearDown(self):
os.chdir(cur_dir)
def test_basic_info(self):
"""Test basic info.
"""
pops, loci = self.ctrl.get_basic_info()
self.assertEqual(len(pops), 10)
self.assertEqual(len(loci), 37)
def test_get_heterozygosity_info(self):
"""Test heterozygosity info.
"""
hz_info = self.ctrl.get_heterozygosity_info(0, "Locus2")
self.assertEqual(hz_info[1], 24)
self.assertEqual(hz_info[3], 7)
def test_get_alleles(self):
"""Test get alleles.
"""
# Returns keys of a dict, so order is Python implementation dependent
self.assertEqual(set(self.ctrl.get_alleles(0, "Locus3")), set([3, 20]))
def test_get_alleles_all_pops(self):
"""Test get alleles for all populations.
"""
self.assertEqual(self.ctrl.get_alleles_all_pops("Locus4"), [1, 3])
def test_get_fis(self):
"""Test get Fis.
"""
alleles, overall = self.ctrl.get_fis(0, "Locus2")
self.assertEqual(alleles[3][0], 55)
self.assertEqual(overall[0], 62)
def test_get_allele_frequency(self):
"""Test allele frequency.
"""
tot_genes, alleles = self.ctrl.get_allele_frequency(0, "Locus2")
self.assertEqual(tot_genes, 62)
self.assertTrue(abs(alleles[20] - 0.113) < 0.05)
def test_get_genotype_count(self):
"""Test genotype count.
"""
self.assertEqual(len(self.ctrl.get_genotype_count(0, "Locus2")), 3)
def test_estimate_nm(self):
"""Test Nm estimation.
"""
nms = self.ctrl.estimate_nm()
self.assertEqual(nms[0], 28.0)
def test_hwe_excess(self):
"""Test Hardy-Weinberg Equilibrium.
"""
hwe_excess = self.ctrl.test_hw_pop(0, "excess")
self.assertEqual(hwe_excess["Locus1"], (0.4955, None, -0.16, -0.1623, 5))
# These tests are frequently failing, possibly due to a Genepop problem.
# def test_get_avg_fst_pair_locus(self):
# """Test get average Fst for pairwise pops on a locus.
# """
# self.assertEqual(len(self.ctrl.get_avg_fst_pair_locus("Locus4")), 45)
#
# def test_get_avg_fst_pair(self):
# """Test get pairwise Fst.
# """
# pop_fis = self.ctrl.get_avg_fst_pair()
# self.assertEqual(len(pop_fis), 45)
def test_get_avg_fis(self):
"""Test average Fis.
"""
self.ctrl.get_avg_fis()
def test_get_multilocus_f_stats(self):
"""Test multilocus F stats.
"""
mf = self.ctrl.get_multilocus_f_stats()
self.assertEqual(len(mf), 3)
self.assertTrue(mf[0] < 0.1)
def test_get_f_stats(self):
"""Test F stats.
"""
fs = self.ctrl.get_f_stats("Locus2")
self.assertEqual(len(fs), 5)
self.assertTrue(fs[0] < 0)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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