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changeset 107:58919e82d96e draft

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Uploaded
author luca_milaz
date Sun, 13 Oct 2024 14:06:53 +0000
parents 1629671d4ca6
children 22cebbdb4b6d
files COBRAxy/ras_to_bounds.py
diffstat 1 files changed, 6 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- 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)