Mercurial > repos > bimib > cobraxy

comparison COBRAxy/ras_to_bounds.py @ 62:14076662f687 draft

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author luca_milaz
date Sun, 13 Oct 2024 08:08:33 +0000
parents 455e8945d02a
children 5302258f8262
comparison
equal deleted inserted replaced
61:455e8945d02a 62:14076662f687
182 rxn = model.reactions.get_by_id(reaction) 182 rxn = model.reactions.get_by_id(reaction)
183 rxn.lower_bound = float(df_FVA.loc[reaction, "minimum"]) 183 rxn.lower_bound = float(df_FVA.loc[reaction, "minimum"])
184 rxn.upper_bound = float(df_FVA.loc[reaction, "maximum"]) 184 rxn.upper_bound = float(df_FVA.loc[reaction, "maximum"])
185 185
186 if ras is not None: 186 if ras is not None:
187 Parallel(n_jobs=cpu_count())(delayed(process_ras_cell)(cellName, ras_row, model, rxns_ids, output_folder) for cellName, ras_row in ras.iterrows()) 187 #Parallel(n_jobs=cpu_count())(delayed(process_ras_cell)(cellName, ras_row, model, rxns_ids, output_folder) for cellName, ras_row in ras.iterrows())
188 for cellName, ras_row in ras.iterrows():
189 process_ras_cell(cellName, ras_row, model, rxns_ids, output_folder)
188 else: 190 else:
189 model_new = model.copy() 191 model_new = model.copy()
190 apply_ras_bounds(model_new, pd.Series([1]*len(rxns_ids), index=rxns_ids), rxns_ids) 192 apply_ras_bounds(model_new, pd.Series([1]*len(rxns_ids), index=rxns_ids), rxns_ids)
191 bounds = pd.DataFrame([(rxn.lower_bound, rxn.upper_bound) for rxn in model_new.reactions], index=rxns_ids, columns=["lower_bound", "upper_bound"]) 193 bounds = pd.DataFrame([(rxn.lower_bound, rxn.upper_bound) for rxn in model_new.reactions], index=rxns_ids, columns=["lower_bound", "upper_bound"])
192 bounds.to_csv(output_folder + "bounds.csv", sep='\t', index=True) 194 bounds.to_csv(output_folder + "bounds.csv", sep='\t', index=True)