def test_predict_deleterious_probability_vcf(self): #init self.init_test('predict_deleterious_probability_vcf') test_file = os.path.join(self.data_dir, 'test_test_combivep.vcf') output_file = os.path.join(self.working_dir, 'vcf_output.txt') #run test predict_deleterious_probability(test_file, params_file=combivep_settings.COMBIVEP_CENTRAL_TEST_PARAMETER_FILE, file_type=combivep_settings.FILE_TYPE_VCF, config_file=combivep_settings.COMBIVEP_CENTRAL_TEST_CONFIGURATION_FILE, output_file=output_file, ) self.assertTrue(os.path.exists(output_file), msg='Predictor does not functional properly') f = open(output_file, 'r') self.assertEqual(f.readline().strip(), '#CHROM\tPOS\tREF\tALT\tACTUAL_DELETERIOUS_EFFECT\tPREDICTED_DELETERIOUS_PROBABILITY') self.assertEqual(f.readline().strip(), '3\t361508\tC\tT\tNone\t0.024209\t0.0\t0\t0.950380\t0.000019\t-2.66\t0.0001') f.close()
def test_predict_deleterious_probability_cbv(self): #init # self.individual_debug = True self.init_test('predict_deleterious_probability_cbv') test_file = os.path.join(self.data_dir, 'test_test_combivep.cbv') output_file = os.path.join(self.working_dir, 'cbv_output.txt') #run test args = {} args["params_file"] = combivep_settings.COMBIVEP_CENTRAL_TEST_PARAMETER_FILE args["file_type"] = combivep_settings.FILE_TYPE_CBV args["config_file"] = combivep_settings.COMBIVEP_CENTRAL_TEST_CONFIGURATION_FILE args["output_file"] = output_file predict_deleterious_probability(test_file, **args ) self.assertTrue(os.path.exists(output_file), msg='Predictor does not functional properly') f = open(output_file, 'r') self.assertEqual(f.readline().strip(), '#CHROM\tPOS\tREF\tALT\tACTUAL_DELETERIOUS_EFFECT\tPREDICTED_DELETERIOUS_PROBABILITY') self.assertEqual(f.readline().strip(), '1\t35227264\tT\tC\t1\t0.968087\t0.96\t0.031\t1.000000\t0.838867\t4.45\t0.2605') f.close()
def test_predict_deleterious_probability_vcf(self): #init self.init_test('predict_deleterious_probability_vcf') test_file = os.path.join(self.data_dir, 'test_test_combivep.vcf') output_file = os.path.join(self.working_dir, 'vcf_output.txt') #run test kwargs = {} kwargs["params_file"] = cbv_const.CBV_SAMPLE_PARAM_FILE kwargs["file_type"] = cbv_const.FILE_TYPE_VCF kwargs["cfg_file"] = cbv_const.CBV_SAMPLE_CFG_FILE kwargs["output_file"] = output_file predict_deleterious_probability(test_file, **kwargs) self.assertTrue(os.path.exists(output_file), msg='Predictor does not functional properly') f = open(output_file, 'r') self.assertEqual(f.readline().strip(), "#"+"\t".join(cbv_const.PREDICTION_OUT_COLS_HEADER)) self.assertEqual(f.readline().strip(), '3\t361508\tC\tT\tNone\t0.0001\t0.024209\t0.0\t0\t0.950380\t0.000019\t-2.66') f.close()
def test_predict_deleterious_probability_cbv(self): #init self.init_test('predict_deleterious_probability_cbv') test_file = os.path.join(self.data_dir, 'test_test_combivep.cbv') output_file = os.path.join(self.working_dir, 'cbv_output.txt') #run test kwargs = {} kwargs["params_file"] = cbv_const.CBV_SAMPLE_PARAM_FILE kwargs["file_type"] = cbv_const.FILE_TYPE_CBV kwargs["cfg_file"] = cbv_const.CBV_SAMPLE_CFG_FILE kwargs["output_file"] = output_file predict_deleterious_probability(test_file, **kwargs) self.assertTrue(os.path.exists(output_file), msg='Predictor does not functional properly') f = open(output_file, 'r') self.assertEqual(f.readline().strip(), "#"+"\t".join(cbv_const.PREDICTION_OUT_COLS_HEADER)) self.assertEqual(f.readline().strip(), '1\t35227264\tT\tC\t1\t0.2605\t0.968087\t0.96\t0.031\t1.000000\t0.838867\t4.45') f.close()