diff options
| -rw-r--r-- | wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py | 70 |
1 files changed, 55 insertions, 15 deletions
diff --git a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py index 4a88509e..1b09afd6 100644 --- a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py +++ b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py @@ -1,4 +1,4 @@ -#test for wqflask/marker_regression/gemma_mapping.py +# test for wqflask/marker_regression/gemma_mapping.py import unittest import random from unittest import mock @@ -24,22 +24,62 @@ class TestGemmaMapping(unittest.TestCase): # def test_fail(self): # self.assertEqual(2,3) - @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/user/data") def setUp(self): - pass + pass - @mock.patch("wqflask.marker_regression.gemma_mapping.gen_pheno_txt_file") + @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.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") - def test_run_gemma_first_run_set_true(self, mock_gen_pheno, mock_os): - chromosomes = AttributeSetter({"chromosomes": "SA"}) - covariates = "XI:X2,X4:X3,X6:X7" - dataset_group = MockDatasetGroup({"genofile": "fileX"}) - dataset = AttributeSetter( - {"group": dataset_group, "name": "dataset1_name", "species": chromosomes}) + @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): + + chromosomes = [] + for i in range(1, 5): + chromosomes.append(AttributeSetter({"name": f"CH{i}"})) + + chromo = AttributeSetter({"chromosomes": chromosomes}) + + dataset_group = MockDatasetGroup( + {"name": "GP1", "genofile": "file_geno"}) + + dataset = AttributeSetter({"group": dataset_group, "name": "dataset1_name", + "species": AttributeSetter({"chromosomes": chromo})}) + trait = AttributeSetter({"name": "trait1"}) - mock_gen_pheno.side_effect = None - mock_gen_pheno.return_value = None + samples = [] + mock_gen_pheno_txt.side_effect = None + mock_gen_pheno_txt.return_value = None mock_os.path.isfile.return_value = True + mock_os.system.return_value = None + mock_os.system.side_effect = None + mock_gen_covar.side_effect = None + mock_gen_covar.return_value = None + mock_flat_files.return_value = "/home/genotype/bimbam" + mock_parse_loco.side_effect = None + mock_parse_loco.return_value = [] + results = run_gemma(this_trait=trait, this_dataset=dataset, samples=[ + ], vals=[], covariates="", use_loco=True) + # check results + self.assertEqual(results, ([], "GP1_GWA_RRRRRR")) + 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.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output") def test_run_gemma_first_run_loco_set_false(self, mock_parse_loco): @@ -130,7 +170,8 @@ X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4 """ with mock.patch("builtins.open", mock.mock_open(read_data=file)) as mock_open: results = parse_gemma_output(genofile_name="gema_file") - expected = [{'name': ' gn2', 'chr': 'X/Y', 'Mb': 2.1e-05, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, {'name': 'gn2', 'chr': 'X/Y', 'Mb': 0.021322, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, {'name': 'gn7', 'chr': 'X', 'Mb': 2.324424, 'p_value': 0.4, 'lod_score': 0.3979400086720376}, {'name': 'gn9', 'chr': 125, 'Mb': 0.433575, 'p_value': 0.67, 'lod_score': 0.17392519729917352}] + expected = [{'name': ' gn2', 'chr': 'X/Y', 'Mb': 2.1e-05, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, {'name': 'gn2', 'chr': 'X/Y', 'Mb': 0.021322, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, + {'name': 'gn7', 'chr': 'X', 'Mb': 2.324424, 'p_value': 0.4, 'lod_score': 0.3979400086720376}, {'name': 'gn9', 'chr': 125, 'Mb': 0.433575, 'p_value': 0.67, 'lod_score': 0.17392519729917352}] mock_open.assert_called_once_with( "/home/user/img/gema_file_output.assoc.txt") @@ -146,7 +187,7 @@ X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4 @mock.patch("builtins.open", mock.mock_open(read_data="chr\t")) def test_parse_gemma_output_empty_return(self): - #duplicate + # duplicate string_read = parse_gemma_output(genofile_name="hdf") # print(string_read) @@ -156,7 +197,6 @@ X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4 mock_os.path.isfile.return_value = False file_to_write = """{"files":["file_1","file_2"]}""" - @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") @mock.patch("wqflask.marker_regression.gemma_mapping.os") def test_parse_loco_output_file_not_found(self, mock_os): |