diff options
| -rw-r--r-- | wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py | 47 |
1 files changed, 27 insertions, 20 deletions
diff --git a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py index 1b09afd6..fd45fd65 100644 --- a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py +++ b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py @@ -27,18 +27,39 @@ class TestGemmaMapping(unittest.TestCase): def setUp(self): pass + + + @mock.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output") + def test_run_gemma_first_run_loco_set_false(self, mock_parse_loco): + dataset = AttributeSetter( + {"group": AttributeSetter({"genofile": "genofile.geno"})}) + + output_files = "file1" + use_loco = False + mock_parse_loco.side_effect = None + mock_parse_loco.return_value = [] + this_trait = AttributeSetter({"name": "t1"}) + + result = run_gemma(this_trait=this_trait, this_dataset=dataset, samples=[], vals=[ + ], covariates="", use_loco=True, first_run=False, output_files=output_files) + + expected_results = ([], "file1") + self.assertEqual(expected_results, result) + + @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img") @mock.patch("wqflask.marker_regression.gemma_mapping.GEMMAOPTS", "-debug") @mock.patch("wqflask.marker_regression.gemma_mapping.GEMMA_WRAPPER_COMMAND", "ghc") @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/user/data/") @mock.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output") + @mock.patch("wqflask.marker_regression.gemma_mapping.logger") @mock.patch("wqflask.marker_regression.gemma_mapping.flat_files") @mock.patch("wqflask.marker_regression.gemma_mapping.gen_covariates_file") @mock.patch("wqflask.marker_regression.gemma_mapping.string.ascii_uppercase", "R") @mock.patch("wqflask.marker_regression.gemma_mapping.string.digits", "R") @mock.patch("wqflask.marker_regression.gemma_mapping.os") @mock.patch("wqflask.marker_regression.gemma_mapping.gen_pheno_txt_file") - def test_run_gemma_first_run_set_true(self, mock_gen_pheno_txt, mock_os, mock_gen_covar, mock_flat_files, mock_parse_loco): + def test_run_gemma_first_run_set_true(self, mock_gen_pheno_txt, mock_os, mock_gen_covar, mock_flat_files,mock_logger,mock_parse_loco): chromosomes = [] for i in range(1, 5): @@ -71,32 +92,18 @@ class TestGemmaMapping(unittest.TestCase): mock_gen_pheno_txt.assert_called_once() self.assertEqual(mock_flat_files.call_count, 4) + system_calls = [mock.call('ghc --json -- -debug -g /home/genotype/bimbam/file_geno.txt -p /home/user/data//gn2/trait1_dataset1_name_pheno.txt -a /home/genotype/bimbam/file_snps.txt -gk > /home/user/data//gn2/GP1_K_RRRRRR.json'), mock.call('ghc --json --input /home/user/data//gn2/GP1_K_RRRRRR.json -- -debug -a /home/genotype/bimbam/file_snps.txt -lmm 2 -g /home/genotype/bimbam/file_geno.txt -p /home/user/data//gn2/trait1_dataset1_name_pheno.txt > /home/user/data//gn2/GP1_GWA_RRRRRR.json')] mock_os.system.assert_has_calls(system_calls) - mock_os.path.isfile.assert_called_once_with(('/home/user/imgfile_output.assoc.txt') - ) - - mock_parse_loco.assert_called_once_with(dataset,"GP1_GWA_RRRRRR") + mock_os.path.isfile.assert_called_once_with(('/home/user/imgfile_output.assoc.txt')) - @mock.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output") - def test_run_gemma_first_run_loco_set_false(self, mock_parse_loco): - dataset = AttributeSetter( - {"group": AttributeSetter({"genofile": "genofile.geno"})}) + self.assertEqual(mock_logger.debug.call_count,2) + - output_files = "file1" - use_loco = False - mock_parse_loco.side_effect = None - mock_parse_loco.return_value = [] - this_trait = AttributeSetter({"name": "t1"}) - - result = run_gemma(this_trait=this_trait, this_dataset=dataset, samples=[], vals=[ - ], covariates="", use_loco=True, first_run=False, output_files=output_files) - - expected_results = ([], "file1") - self.assertEqual(expected_results, result) + mock_parse_loco.assert_called_once_with(dataset,"GP1_GWA_RRRRRR") @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/user/data") def test_gen_pheno_txt_file(self): |