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()
