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)
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)