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")