Mercurial > repos > bimib > cobraxy

comparison COBRAxy/ras_to_bounds.py @ 122:7e1ce04cf192 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author luca_milaz
date Mon, 14 Oct 2024 08:22:30 +0000
parents 567ffd4333d4
children 258ff4208e52
comparison
equal deleted inserted replaced
121:2121cc1aef45 122:7e1ce04cf192
121 rxns_ids (list of str): List of reaction IDs to which the scaling factors will be applied. 121 rxns_ids (list of str): List of reaction IDs to which the scaling factors will be applied.
122 mediumRxns_ids (list of str): List of reaction IDs in the medium. Their RAS is set to zero, but they are already set in the model. 122 mediumRxns_ids (list of str): List of reaction IDs in the medium. Their RAS is set to zero, but they are already set in the model.
123 Returns: 123 Returns:
124 None 124 None
125 """ 125 """
126 for reaction in rxns_ids: 126 for reaction in ras_row.index:
127 if reaction in ras_row.index and reaction not in mediumRxns_ids: 127 scaling_factor = ras_row[reaction]
128 scaling_factor = ras_row[reaction] 128 if(scaling_factor not in [np.nan, None]):
129 lower_bound=model.reactions.get_by_id(reaction).lower_bound 129 lower_bound=model.reactions.get_by_id(reaction).lower_bound
130 upper_bound=model.reactions.get_by_id(reaction).upper_bound 130 upper_bound=model.reactions.get_by_id(reaction).upper_bound
131 valMax=float((upper_bound)*scaling_factor) 131 valMax=float((upper_bound)*scaling_factor)
132 valMin=float((lower_bound)*scaling_factor) 132 valMin=float((lower_bound)*scaling_factor)
133 if upper_bound!=0 and lower_bound==0: 133 if upper_bound!=0 and lower_bound==0:
176 rxns_ids = [rxn.id for rxn in model.reactions] 176 rxns_ids = [rxn.id for rxn in model.reactions]
177 177
178 # Set medium conditions 178 # Set medium conditions
179 for reaction, value in medium.items(): 179 for reaction, value in medium.items():
180 if value is not None: 180 if value is not None:
181 ## SOLO ENGRO2
181 if(reaction != "EX_thbpt_e" and reaction != "EX_lac__L_e"): 182 if(reaction != "EX_thbpt_e" and reaction != "EX_lac__L_e"):
182 model.reactions.get_by_id(reaction).lower_bound = -float(value) 183 model.reactions.get_by_id(reaction).lower_bound = -float(value)
183 if(reaction == "EX_lac__L_e"): 184 if(reaction == "EX_lac__L_e"):
184 model.reactions.get_by_id(reaction).lower_bound = float(0.0) 185 model.reactions.get_by_id(reaction).lower_bound = float(0.0)
185 186
245 246
246 # Concatenate all ras DataFrames into a single DataFrame 247 # Concatenate all ras DataFrames into a single DataFrame
247 ras_combined = pd.concat(ras_list, axis=0) 248 ras_combined = pd.concat(ras_list, axis=0)
248 # Normalize the RAS values by max RAS 249 # Normalize the RAS values by max RAS
249 ras_combined = ras_combined.div(ras_combined.max(axis=0)) 250 ras_combined = ras_combined.div(ras_combined.max(axis=0))
250 ras_combined = ras_combined.fillna(0) 251 #ras_combined = ras_combined.fillna(0)
252 #il ras c'è per tutti o non c'è per nessuno
251 253
252 254
253 255
254 model_type :utils.Model = ARGS.model_selector 256 model_type :utils.Model = ARGS.model_selector
255 if model_type is utils.Model.Custom: 257 if model_type is utils.Model.Custom: