Mercurial > repos > bimib > marea_2

changeset 125:4f889150f278 draft

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Uploaded
author luca_milaz
date Sun, 21 Jul 2024 20:04:28 +0000
parents 2590e2f60307
children 8d50cf0c3d5f
files marea_2/ras_to_bounds.py
diffstat 1 files changed, 27 insertions(+), 19 deletions(-) [+]
line wrap: on
line diff
--- a/marea_2/ras_to_bounds.py	Sun Jul 21 19:48:27 2024 +0000
+++ b/marea_2/ras_to_bounds.py	Sun Jul 21 20:04:28 2024 +0000
@@ -111,14 +111,28 @@
     for reaction in rxns_ids:
         model_new.reactions.get_by_id(reaction).lower_bound=float(df_FVA.loc[reaction,"minimum"])
         model_new.reactions.get_by_id(reaction).upper_bound=float(df_FVA.loc[reaction,"maximum"])
-    
-    if(ras is not None):#iterate over cells
-        for reaction in rxns_ids:
-            if reaction in ras.keys():
+        
+    for cellName, ras in ras.iterrows():
+        if(ras is not  None):
+            for reaction in rxns_ids:
+                if reaction in ras.keys():
+                    lower_bound=model_new.reactions.get_by_id(reaction).lower_bound
+                    upper_bound=model_new.reactions.get_by_id(reaction).upper_bound
+                    valMax=float((upper_bound)*ras[reaction])
+                    valMin=float((lower_bound)*ras[reaction])
+                    if upper_bound!=0 and lower_bound==0:
+                        model_new.reactions.get_by_id(reaction).upper_bound=valMax
+                    if upper_bound==0 and lower_bound!=0:
+                        model_new.reactions.get_by_id(reaction).lower_bound=valMin
+                    if upper_bound!=0 and lower_bound!=0:
+                        model_new.reactions.get_by_id(reaction).lower_bound=valMin
+                        model_new.reactions.get_by_id(reaction).upper_bound=valMax
+        else:
+            for reaction in rxns_ids:
                 lower_bound=model_new.reactions.get_by_id(reaction).lower_bound
                 upper_bound=model_new.reactions.get_by_id(reaction).upper_bound
-                valMax=float((upper_bound)*ras[reaction])
-                valMin=float((lower_bound)*ras[reaction])
+                valMax = float((upper_bound)*1)
+                valMin=float((lower_bound)*1)
                 if upper_bound!=0 and lower_bound==0:
                     model_new.reactions.get_by_id(reaction).upper_bound=valMax
                 if upper_bound==0 and lower_bound!=0:
@@ -126,15 +140,11 @@
                 if upper_bound!=0 and lower_bound!=0:
                     model_new.reactions.get_by_id(reaction).lower_bound=valMin
                     model_new.reactions.get_by_id(reaction).upper_bound=valMax
-    rxns = []
-    for reaction in model_new.reactions:
-        rxns.append(reaction.id)
-
-    bounds = pd.DataFrame(columns = ["lower_bound", "upper_bound"], index=rxns)
-
-    for reaction in model.reactions:
-        bounds.loc[reaction.id] = [reaction.lower_bound, reaction.upper_bound]
-    return bounds
+        bounds = pd.DataFrame(columns = ["lower_bound", "upper_bound"], index=rxns_ids)
+        for reaction in model.reactions:
+            bounds.loc[reaction.id] = [reaction.lower_bound, reaction.upper_bound]
+        bounds.to_csv(ARGS.output_folder + cellName, sep = '\t', index = False)
+    pass
 
 
 ############################# main ###########################################
@@ -157,7 +167,6 @@
             ARGS.input_ras,
             ARGS.out_log)
 
-    boundsPath = utils.FilePath("bounds", ".csv", prefix = ARGS.output_folder)
     mediumPath = utils.FilePath("medium", ".csv", prefix = ARGS.output_folder)
 
     if(ARGS.ras_selector == True):
@@ -183,11 +192,10 @@
         medium = medium[ARGS.medium_selector].to_dict()
 
     if(ARGS.ras_selector == True):
-        bounds = generate_bounds(model, medium, ras = ras)
+        generate_bounds(model, medium, ras = ras)
     else:
-        bounds = generate_bounds(model, medium)
+        generate_bounds(model, medium)
 
-    bounds.to_csv(boundsPath.show())
     medium.to_csv(mediumPath.show())
     pass