Mercurial > repos > bimib > cobraxy

comparison COBRAxy/ras_to_bounds.py @ 118:6e1a6e480969 draft

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author luca_milaz
date Sun, 13 Oct 2024 16:32:08 +0000
parents 69190617d1ea
children 829ea241c3a1
comparison
equal deleted inserted replaced
117:69190617d1ea 118:6e1a6e480969
176 176
177 Returns: 177 Returns:
178 pd.DataFrame: DataFrame containing the bounds of reactions in the model. 178 pd.DataFrame: DataFrame containing the bounds of reactions in the model.
179 """ 179 """
180 rxns_ids = [rxn.id for rxn in model.reactions] 180 rxns_ids = [rxn.id for rxn in model.reactions]
181
182 warning(str(model.reactions.get_by_id("EX_Lcystin_e").lower_bound))
183 warning(str(model.reactions.get_by_id("EX_Lcystin_e").upper_bound))
184 181
185 # Set medium conditions 182 # Set medium conditions
186 for reaction, value in medium.items(): 183 for reaction, value in medium.items():
187 if value is not None: 184 if value is not None:
188 if(reaction != "EX_thbpt_e" and reaction != "EX_lac__L_e"): 185 if(reaction != "EX_thbpt_e" and reaction != "EX_lac__L_e"):
197 194
198 # Set FVA bounds 195 # Set FVA bounds
199 for reaction in rxns_ids: 196 for reaction in rxns_ids:
200 model.reactions.get_by_id(reaction).lower_bound = float(df_FVA.loc[reaction, "minimum"]) 197 model.reactions.get_by_id(reaction).lower_bound = float(df_FVA.loc[reaction, "minimum"])
201 model.reactions.get_by_id(reaction).upper_bound = float(df_FVA.loc[reaction, "maximum"]) 198 model.reactions.get_by_id(reaction).upper_bound = float(df_FVA.loc[reaction, "maximum"])
199
200 warning(str(model.reactions.get_by_id("EX_Lcystin_e").lower_bound))
201 warning(str(model.reactions.get_by_id("EX_Lcystin_e").upper_bound))
202 202
203 if ras is not None: 203 if ras is not None:
204 #Parallel(n_jobs=cpu_count())(delayed(process_ras_cell)(cellName, ras_row, model, rxns_ids, output_folder) for cellName, ras_row in ras.iterrows()) 204 #Parallel(n_jobs=cpu_count())(delayed(process_ras_cell)(cellName, ras_row, model, rxns_ids, output_folder) for cellName, ras_row in ras.iterrows())
205 for cellName, ras_row in ras.iterrows(): 205 for cellName, ras_row in ras.iterrows():
206 process_ras_cell(cellName, ras_row, model, rxns_ids, mediumRxns_ids, output_folder) 206 process_ras_cell(cellName, ras_row, model, rxns_ids, mediumRxns_ids, output_folder)