Mercurial > repos > bimib > cobraxy
comparison COBRAxy/ras_to_bounds.py @ 112:4ea14da7043b draft
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| author | luca_milaz |
|---|---|
| date | Sun, 13 Oct 2024 15:48:44 +0000 |
| parents | 22d2cf96d552 |
| children | 1961a091484c |
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| 111:22d2cf96d552 | 112:4ea14da7043b |
|---|---|
| 180 if(reaction != "EX_thbpt_e" and reaction != "EX_lac__L_e"): | 180 if(reaction != "EX_thbpt_e" and reaction != "EX_lac__L_e"): |
| 181 model.reactions.get_by_id(reaction).lower_bound = -float(value) | 181 model.reactions.get_by_id(reaction).lower_bound = -float(value) |
| 182 if(reaction == "EX_lac__L_e"): | 182 if(reaction == "EX_lac__L_e"): |
| 183 model.reactions.get_by_id(reaction).lower_bound = float(0.0) | 183 model.reactions.get_by_id(reaction).lower_bound = float(0.0) |
| 184 | 184 |
| 185 warning(str(model.reactions.get_by_id("EX_Lcystin_e").lower_bound)) | |
| 186 | |
| 187 # Perform Flux Variability Analysis (FVA) | 185 # Perform Flux Variability Analysis (FVA) |
| 188 df_FVA = cobra.flux_analysis.flux_variability_analysis(model, fraction_of_optimum=0, processes=1).round(8) | 186 df_FVA = cobra.flux_analysis.flux_variability_analysis(model, fraction_of_optimum=0, processes=1).round(8) |
| 189 | 187 |
| 190 # Set FVA bounds | 188 # Set FVA bounds |
| 191 for reaction in rxns_ids: | 189 for reaction in rxns_ids: |
| 192 model.reactions.get_by_id(reaction).lower_bound = float(df_FVA.loc[reaction, "minimum"]) | 190 model.reactions.get_by_id(reaction).lower_bound = float(df_FVA.loc[reaction, "minimum"]) |
| 193 model.reactions.get_by_id(reaction).upper_bound = float(df_FVA.loc[reaction, "maximum"]) | 191 model.reactions.get_by_id(reaction).upper_bound = float(df_FVA.loc[reaction, "maximum"]) |
| 192 | |
| 193 warning(str(model.reactions.get_by_id("EX_Lcystin_e").lower_bound)) | |
| 194 | 194 |
| 195 if ras is not None: | 195 if ras is not None: |
| 196 #Parallel(n_jobs=cpu_count())(delayed(process_ras_cell)(cellName, ras_row, model, rxns_ids, output_folder) for cellName, ras_row in ras.iterrows()) | 196 #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 for cellName, ras_row in ras.iterrows(): | 197 for cellName, ras_row in ras.iterrows(): |
| 198 process_ras_cell(cellName, ras_row, model, rxns_ids, output_folder) | 198 process_ras_cell(cellName, ras_row, model, rxns_ids, output_folder) |