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| author | zsloan | 2021-04-28 14:44:03 -0500 |
|---|---|---|
| committer | GitHub | 2021-04-28 14:44:03 -0500 |
| commit | d31f2c4e4d57b927101fe9a33b4f540eef1385ae (patch) | |
| tree | cd633578dd208788fa9ef28ae4f15974abac9396 | |
| parent | 1a7bb988ee360b3ef48e22e25b419c375dccb9fa (diff) | |
| parent | 6e8afe5a6871a680778bfaed6b79c934b33d0307 (diff) | |
| download | genenetwork2-d31f2c4e4d57b927101fe9a33b4f540eef1385ae.tar.gz | |
Merge pull request #567 from zsloan/bug/fix_gemma_temptrait_covariates
Account for temp traits when adding covariates with GEMMA mapping
| -rw-r--r-- | wqflask/wqflask/marker_regression/gemma_mapping.py | 7 |
1 files changed, 6 insertions, 1 deletions
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index 83ebcdf9..06c9300a 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -146,7 +146,12 @@ def gen_covariates_file(this_dataset, covariates, samples): for covariate in covariate_list: this_covariate_data = [] trait_name = covariate.split(":")[0] - dataset_ob = create_dataset(covariate.split(":")[1]) + dataset_name = covariate.split(":")[1] + if dataset_name == "Temp": + temp_group = trait_name.split("_")[2] + dataset_ob = create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = temp_group) + else: + dataset_ob = create_dataset(covariate.split(":")[1]) trait_ob = create_trait(dataset=dataset_ob, name=trait_name, cellid=None) |