Mercurial > repos > bimib > cobraxy

changeset 210:3ca179b83574 draft

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Uploaded
author luca_milaz
date Thu, 28 Nov 2024 14:07:11 +0000
parents 00a66b9bc29e
children 4e368ecd4fb6
files COBRAxy/flux_simulation.py
diffstat 1 files changed, 5 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/COBRAxy/flux_simulation.py	Thu Nov 28 13:51:23 2024 +0000
+++ b/COBRAxy/flux_simulation.py	Thu Nov 28 14:07:11 2024 +0000
@@ -238,26 +238,24 @@
         model_input.reactions.get_by_id(rxn_index).lower_bound = row.lower_bound
         model_input.reactions.get_by_id(rxn_index).upper_bound = row.upper_bound
     
-    #name = '.'.join(cell_name.rsplit('.', 1)[:-1])
-    name = cell_name
     
     if ARGS.algorithm == 'OPTGP':
-        OPTGP_sampler(model_input, name, ARGS.n_samples, ARGS.thinning, ARGS.n_batches, ARGS.seed)
+        OPTGP_sampler(model_input, cell_name, ARGS.n_samples, ARGS.thinning, ARGS.n_batches, ARGS.seed)
 
     elif ARGS.algorithm == 'CBS':
-        CBS_sampler(model_input,  name, ARGS.n_samples, ARGS.n_batches, ARGS.seed)
+        CBS_sampler(model_input,  cell_name, ARGS.n_samples, ARGS.n_batches, ARGS.seed)
 
-    df_mean, df_median, df_quantiles = fluxes_statistics(name, ARGS.output_types)
+    df_mean, df_median, df_quantiles = fluxes_statistics(cell_name, ARGS.output_types)
 
     if("fluxes" not in ARGS.output_types):
-        os.remove(ARGS.output_path + "/"  +  name + '.csv')
+        os.remove(ARGS.output_path + "/"  +  cell_name + '.csv')
 
     returnList = []
     returnList.append(df_mean)
     returnList.append(df_median)
     returnList.append(df_quantiles)
 
-    df_pFBA, df_FVA, df_sensitivity = fluxes_analysis(model_input, name, ARGS.output_type_analysis)
+    df_pFBA, df_FVA, df_sensitivity = fluxes_analysis(model_input, cell_name, ARGS.output_type_analysis)
 
     if("pFBA" in ARGS.output_type_analysis):
         returnList.append(df_pFBA)