# HG changeset patch
# User luca_milaz
# Date 1728828413 0
# Node ID 58919e82d96e9226181c389a93364c1485ee92f9
# Parent  1629671d4ca60d8cfd3f62fe2f59c641989be3bd
Uploaded

diff -r 1629671d4ca6 -r 58919e82d96e COBRAxy/ras_to_bounds.py
--- a/COBRAxy/ras_to_bounds.py	Sun Oct 13 14:01:03 2024 +0000
+++ b/COBRAxy/ras_to_bounds.py	Sun Oct 13 14:06:53 2024 +0000
@@ -185,7 +185,11 @@
     '''
     for reaction, value in medium.items():
         if value is not None:
-            model.reactions.get_by_id(reaction).lower_bound = -float(value)
+            if(reaction != "EX_thbpt_e" and reaction != "EX_lac__L_e"):
+                model.reactions.get_by_id(reaction).lower_bound = -float(value)
+            if(reaction == "EX_lac__L_e"):
+                model.reactions.get_by_id(reaction).lower_bound = float(0.0)
+            
     
     # Perform Flux Variability Analysis (FVA)
     df_FVA = cobra.flux_analysis.flux_variability_analysis(model, fraction_of_optimum=0, processes=1).round(8)
@@ -199,7 +203,7 @@
         #Parallel(n_jobs=cpu_count())(delayed(process_ras_cell)(cellName, ras_row, model, rxns_ids, output_folder) for cellName, ras_row in ras.iterrows())
         for cellName, ras_row in ras.iterrows():
             process_ras_cell(cellName, ras_row, model, rxns_ids, output_folder)
-            break
+            break #just one cell for testing
     else:
         model_new = model.copy()
         apply_ras_bounds(model_new, pd.Series([1]*len(rxns_ids), index=rxns_ids), rxns_ids)