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| author | zsloan | 2021-08-10 19:01:47 +0000 |
|---|---|---|
| committer | zsloan | 2021-08-10 19:01:47 +0000 |
| commit | 162851e8f92ed6d01c25d4f6034bcac4986e8094 (patch) | |
| tree | 4961e3a21a663f1b215a65eccb605e075920813a | |
| parent | 3ae0ab231c529f765e48557dec7e336fa3bd9ede (diff) | |
| download | genenetwork2-162851e8f92ed6d01c25d4f6034bcac4986e8094.tar.gz | |
Replaced forward slashes with underscores in the hashed filenames used by GEMMA, since the forward slashes make the paths not work properly
| -rw-r--r-- | wqflask/wqflask/marker_regression/gemma_mapping.py | 4 |
1 files changed, 2 insertions, 2 deletions
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index efd8bba8..623ab87f 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -129,7 +129,7 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, def gen_pheno_txt_file(this_dataset, genofile_name, vals): """Generates phenotype file for GEMMA""" - filename = "PHENO_" + generate_hash_of_string(this_dataset.name + str(vals)) + filename = "PHENO_" + generate_hash_of_string(this_dataset.name + str(vals)).replace("/", "_") with open(f"{TEMPDIR}/gn2/{filename}.txt", "w") as outfile: for value in vals: @@ -169,7 +169,7 @@ def gen_covariates_file(this_dataset, covariates, samples): this_covariate_data.append("-9") covariate_data_object.append(this_covariate_data) - filename = "COVAR_" + generate_hash_of_string(this_dataset.name + str(covariate_data_object)) + filename = "COVAR_" + generate_hash_of_string(this_dataset.name + str(covariate_data_object)).replace("/", "_") with open((f"{flat_files('mapping')}/" f"{filename}.txt"), |