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comparison COBRAxy/ras_to_bounds.py @ 111:22d2cf96d552 draft

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Uploaded
author luca_milaz
date Sun, 13 Oct 2024 15:46:36 +0000
parents 76e87d3b9e0e
children 4ea14da7043b
comparison
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110:76e87d3b9e0e 111:22d2cf96d552
175 rxns_ids = [rxn.id for rxn in model.reactions] 175 rxns_ids = [rxn.id for rxn in model.reactions]
176 176
177 # Set medium conditions 177 # Set medium conditions
178 for reaction, value in medium.items(): 178 for reaction, value in medium.items():
179 if value is not None: 179 if value is not None:
180 warning(str(reaction) + " " + str(value))
181 if(reaction != "EX_thbpt_e" and reaction != "EX_lac__L_e"): 180 if(reaction != "EX_thbpt_e" and reaction != "EX_lac__L_e"):
182 model.reactions.get_by_id(reaction).lower_bound = -float(value) 181 model.reactions.get_by_id(reaction).lower_bound = -float(value)
183 if(reaction == "EX_lac__L_e"): 182 if(reaction == "EX_lac__L_e"):
184 model.reactions.get_by_id(reaction).lower_bound = float(0.0) 183 model.reactions.get_by_id(reaction).lower_bound = float(0.0)
185 184
185 warning(str(model.reactions.get_by_id("EX_Lcystin_e").lower_bound))
186 186
187 # Perform Flux Variability Analysis (FVA) 187 # Perform Flux Variability Analysis (FVA)
188 df_FVA = cobra.flux_analysis.flux_variability_analysis(model, fraction_of_optimum=0, processes=1).round(8) 188 df_FVA = cobra.flux_analysis.flux_variability_analysis(model, fraction_of_optimum=0, processes=1).round(8)
189 189
190 # Set FVA bounds 190 # Set FVA bounds