# HG changeset patch
# User luca_milaz
# Date 1726733219 0
# Node ID 80bfd8743ea614d970a6478b9578bb1af383b75b
# Parent  c5dbdbb64cefa61a3a1a98fa9f2d35644d29fb6e
Uploaded

diff -r c5dbdbb64cef -r 80bfd8743ea6 COBRAxy/custom_data_generator.py
--- a/COBRAxy/custom_data_generator.py	Thu Sep 19 08:03:37 2024 +0000
+++ b/COBRAxy/custom_data_generator.py	Thu Sep 19 08:06:59 2024 +0000
@@ -188,15 +188,11 @@
     bounds = generate_bounds(model)
     medium = get_medium(model)
 
-    rulesPath     = utils.FilePath("rules", "csv")
-    reactionsPath = utils.FilePath("reactions", "csv")
-    boundsPath = utils.FilePath("bounds", "csv")
-    mediumPath = utils.FilePath("medium", "csv")
 
-    save_as_csv(rules, rulesPath, ("ReactionID", "Rule"))
-    save_as_csv(reactions, reactionsPath, ("ReactionID", "Reaction"))
-    bounds.to_csv(boundsPath.show(), sep = '\t')
-    medium.to_csv(mediumPath.show(), sep = '\t')
+    save_as_csv(rules, ARGS.out_rules, ("ReactionID", "Rule"))
+    save_as_csv(reactions, ARGS.out_reactions, ("ReactionID", "Reaction"))
+    bounds.to_csv(ARGS.out_bounds, sep = '\t')
+    medium.to_csv(ARGS.out_medium, sep = '\t')
 
 
     # ^ Please if anyone works on this after updating python to 3.12 change the if/elif into a match statement!!