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)
def setUp(self):
# Genepop likes to be on the directory where the file is.
os.chdir("PopGen")
self.ctrl = EasyController("big.gen")
def setUp(self):
"""Change working directory."""
# Genepop likes to be on the directory where the file is.
os.chdir("PopGen")
self.ctrl = EasyController("big.gen")
class AppTest(unittest.TestCase):
"""Tests genepop execution via biopython using EasyController."""
def setUp(self):
"""Change working directory."""
# Genepop likes to be on the directory where the file is.
os.chdir("PopGen")
self.ctrl = EasyController("big.gen")
def tearDown(self):
"""Restore working directory."""
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.assertCountEqual(self.ctrl.get_alleles(0, "Locus3"), [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.assertLess(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.assertLess(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.assertLess(fs[0], 0)
def filehandler(infile):
"""Doc here"""
filehandle = EasyController(infile)
return filehandle
if len(sys.argv) != 3:
print("python %s startGen endGen" % (sys.argv[0],))
sys.exit(-1)
startGen = int(sys.argv[1])
endGen = int(sys.argv[2])
fName = "/tmp/hz%s.txt" % (str(os.getpid()))
f = open(fName, "w")
l = sys.stdin.readline()
while l != "":
f.write(l)
l = sys.stdin.readline()
f.close()
ctrl = EasyController(fName)
pop_list, loci_list = ctrl.get_basic_info()
numPops = len(pop_list)
for pop in range(numPops):
for locus in loci_list:
# expho, obsho, exphe, obshe = ctrl.get_heterozygosity_info(pop, locus)
# print float(exphe)/(exphe+expho),
obs, freqs = ctrl.get_allele_frequency(pop, locus)
ho = 0.0
for freq in list(freqs.values()):
ho += freq**2
print(1-ho, end=' ')
print()
os.remove(fName)
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