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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.")
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("..")
def test_basic_info(self):
"""Test basic info.
"""
pops, loci = self.ctrl.get_basic_info()
assert len(pops) == 10
assert len(loci) == 37
def test_get_heterozygosity_info(self):
"""Test heterozygosity info.
"""
hz_info = self.ctrl.get_heterozygosity_info(0, "Locus2")
assert hz_info[1] == 24
assert hz_info[3] == 7
def test_get_alleles(self):
"""Test get alleles.
"""
assert self.ctrl.get_alleles(0,"Locus3") == [3, 20]
def test_get_alleles_all_pops(self):
"""Test get alleles for all populations.
"""
assert 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")
assert alleles[3][0] == 55
assert overall[0] == 62
def test_get_allele_frequency(self):
"""Test allele frequency.
"""
tot_genes, alleles = self.ctrl.get_allele_frequency(0,"Locus2")
assert tot_genes == 62
assert abs(alleles[20] - 0.113) < 0.05
def test_get_genotype_count(self):
"""Test genotype count.
"""
assert len(self.ctrl.get_genotype_count(0,"Locus2")) == 3
def test_estimate_nm(self):
"""Test Nm estimation.
"""
nms = self.ctrl.estimate_nm()
assert nms[0] == 28.0
def test_get_avg_fst_pair_locus(self):
"""Test get average Fst for pairwise pops on a locus.
"""
assert 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()
assert 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()
assert len(mf) == 3
assert mf[0]<0.1
def test_get_f_stats(self):
"""Test F stats.
"""
fs = self.ctrl.get_f_stats("Locus2")
assert len(fs)==5
assert fs[0]<0
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity = 2)
unittest.main(testRunner=runner)
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