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comparison COBRAxy/ras_to_bounds.py @ 114:a7a079f6a4cd draft

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author luca_milaz
date Sun, 13 Oct 2024 15:57:26 +0000
parents 1961a091484c
children 867a965d6a57
comparison
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113:1961a091484c 114:a7a079f6a4cd
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 rxns_ids:
127 if reaction in ras_row.index and ras_row[reaction] not in mediumRxns_ids: 127 if reaction in ras_row.index and reaction not in mediumRxns_ids:
128 scaling_factor = ras_row[reaction] 128 scaling_factor = ras_row[reaction]
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)
190 190
191 # Set FVA bounds 191 # Set FVA bounds
192 for reaction in rxns_ids: 192 for reaction in rxns_ids:
193 model.reactions.get_by_id(reaction).lower_bound = float(df_FVA.loc[reaction, "minimum"]) 193 model.reactions.get_by_id(reaction).lower_bound = float(df_FVA.loc[reaction, "minimum"])
194 model.reactions.get_by_id(reaction).upper_bound = float(df_FVA.loc[reaction, "maximum"]) 194 model.reactions.get_by_id(reaction).upper_bound = float(df_FVA.loc[reaction, "maximum"])
195
196 #warning(str(model.reactions.get_by_id("EX_Lcystin_e").lower_bound))
197 195
198 if ras is not None: 196 if ras is not None:
199 #Parallel(n_jobs=cpu_count())(delayed(process_ras_cell)(cellName, ras_row, model, rxns_ids, output_folder) for cellName, ras_row in ras.iterrows()) 197 #Parallel(n_jobs=cpu_count())(delayed(process_ras_cell)(cellName, ras_row, model, rxns_ids, output_folder) for cellName, ras_row in ras.iterrows())
200 for cellName, ras_row in ras.iterrows(): 198 for cellName, ras_row in ras.iterrows():
201 process_ras_cell(cellName, ras_row, model, rxns_ids, mediumRxns_ids, output_folder) 199 process_ras_cell(cellName, ras_row, model, rxns_ids, mediumRxns_ids, output_folder)