--- a/COBRAxy/flux_simulation_beta.py	Wed Sep 10 13:26:03 2025 +0000
+++ b/COBRAxy/flux_simulation_beta.py	Wed Sep 10 14:53:36 2025 +0000
@@ -80,6 +80,12 @@
                         required = True,
                         help = 'choose how many batches')
     
+    parser.add_argument('-opt', '--perc_opt',
+                        type = float,
+                        default=0.9,
+                        required = False,
+                        help = 'choose the fraction of optimality for FVA (0-1)')
+    
     parser.add_argument('-ot', '--output_type', 
                         type = str,
                         required = True,
@@ -359,7 +365,7 @@
             df_pFBA.index = [model_name]
             df_pFBA = df_pFBA.astype(float).round(6)
         elif(output_type == "FVA"):
-            fva = cobra.flux_analysis.flux_variability_analysis(model, fraction_of_optimum=0, processes=1).round(8)
+            fva = cobra.flux_analysis.flux_variability_analysis(model, fraction_of_optimum=ARGS.perc_opt, processes=1).round(8)
             columns = []
             for rxn in fva.index.to_list():
                 columns.append(rxn + "_min")