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_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"
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_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_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_haploidy(self):
"""Test haploidy.
"""
ctrl = GenePopController()
(allFis, allFst,
allFit), itr = ctrl.calc_fst_all("PopGen" + os.sep + "haplo.gen")
litr = list(itr)
assert not type(allFst) == int
assert len(litr) == 37
assert litr[36][0] == "Locus37"
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_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_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_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")
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 + "controller1.gen")
