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| author | zsloan | 2022-09-13 00:35:09 +0000 |
|---|---|---|
| committer | zsloan | 2022-09-13 00:35:48 +0000 |
| commit | efb0d394630d06ecc81939ef1708dbd12b44ec77 (patch) | |
| tree | 10538db6df087ebe1c528cb6f56d7ea0f1d7a7f7 | |
| parent | 9cd9b91412734f8f084439690082f9e699ebd89e (diff) | |
| download | genenetwork2-efb0d394630d06ecc81939ef1708dbd12b44ec77.tar.gz | |
Fix bug where passing LOCO into the mapping API endpoint didn't work
| -rw-r--r-- | wqflask/wqflask/marker_regression/gemma_mapping.py | 3 |
1 files changed, 2 insertions, 1 deletions
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index 646728ba..8adca6e5 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -27,6 +27,7 @@ def generate_random_n_string(n): def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf=0.01, first_run=True, output_files=None): """Generates p-values for each marker using GEMMA""" + if this_dataset.group.genofile is not None: genofile_name = this_dataset.group.genofile[:-5] else: @@ -53,7 +54,7 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, chr_list_string = ",".join(this_chromosomes_name) if covariates != "": covar_filename = gen_covariates_file(this_dataset, covariates, samples) - if use_loco == "True": + if str(use_loco).lower() == "true": generate_k_command = (f"{GEMMA_WRAPPER_COMMAND} --json --loco " f"{chr_list_string} -- {GEMMAOPTS} " f"-g {flat_files('genotype/bimbam')}/" |