From 162851e8f92ed6d01c25d4f6034bcac4986e8094 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 10 Aug 2021 19:01:47 +0000
Subject: Replaced forward slashes with underscores in the hashed filenames
 used by GEMMA, since the forward slashes make the paths not work properly

---
 wqflask/wqflask/marker_regression/gemma_mapping.py | 4 ++--
 1 file 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"),
-- 
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