Mercurial > repos > bimib > cobraxy
comparison COBRAxy/utils/model_utils.py @ 430:f49c951c9fe6 draft
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| author | francesco_lapi |
|---|---|
| date | Wed, 10 Sep 2025 14:53:36 +0000 |
| parents | 4a385fdb9e58 |
| children | 06564187fba3 |
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| 429:0485c4b1943d | 430:f49c951c9fe6 |
|---|---|
| 252 reactions_added += 1 | 252 reactions_added += 1 |
| 253 | 253 |
| 254 | 254 |
| 255 print(f"Aggiunte {reactions_added} reazioni, saltate {reactions_skipped} reazioni") | 255 print(f"Aggiunte {reactions_added} reazioni, saltate {reactions_skipped} reazioni") |
| 256 | 256 |
| 257 # Imposta l'obiettivo di biomassa | 257 # set objective function |
| 258 set_biomass_objective(model) | 258 set_objective_from_csv(model, df, obj_col="ObjectiveCoefficient") |
| 259 | 259 |
| 260 # Imposta il medium | 260 # Imposta il medium |
| 261 set_medium_from_data(model, df) | 261 set_medium_from_data(model, df) |
| 262 | 262 |
| 263 print(f"Modello completato: {len(model.reactions)} reazioni, {len(model.metabolites)} metaboliti") | 263 print(f"Modello completato: {len(model.reactions)} reazioni, {len(model.metabolites)} metaboliti") |
| 264 | 264 |
| 359 | 359 |
| 360 return metabolites | 360 return metabolites |
| 361 | 361 |
| 362 | 362 |
| 363 | 363 |
| 364 def set_biomass_objective(model: cobraModel): | 364 def set_objective_from_csv(model: cobra.Model, df: pd.DataFrame, obj_col: str = "ObjectiveCoefficient"): |
| 365 """ | 365 """ |
| 366 Imposta la reazione di biomassa come obiettivo. | 366 Sets the model's objective function based on a column of coefficients in the CSV. |
| 367 """ | 367 Can be any reaction(s), not necessarily biomass. |
| 368 biomass_reactions = [r for r in model.reactions if 'biomass' in r.id.lower()] | 368 """ |
| 369 | 369 obj_dict = {} |
| 370 if biomass_reactions: | 370 |
| 371 model.objective = biomass_reactions[0].id | 371 for idx, row in df.iterrows(): |
| 372 print(f"Obiettivo impostato su: {biomass_reactions[0].id}") | 372 reaction_id = str(row['ReactionID']).strip() |
| 373 else: | 373 coeff = float(row[obj_col]) if pd.notna(row[obj_col]) else 0.0 |
| 374 print("Nessuna reazione di biomassa trovata") | 374 if coeff != 0: |
| 375 # Assicuriamoci che la reazione esista nel modello | |
| 376 if reaction_id in model.reactions: | |
| 377 obj_dict[model.reactions.get_by_id(reaction_id)] = coeff | |
| 378 else: | |
| 379 print(f"Warning: reaction {reaction_id} not found in model, skipping for objective.") | |
| 380 | |
| 381 if not obj_dict: | |
| 382 raise ValueError("No reactions found with non-zero objective coefficient.") | |
| 383 | |
| 384 # Imposta la funzione obiettivo | |
| 385 model.objective = obj_dict | |
| 386 print(f"Objective set with {len(obj_dict)} reactions.") | |
| 387 | |
| 388 | |
| 375 | 389 |
| 376 | 390 |
| 377 def set_medium_from_data(model: cobraModel, df: pd.DataFrame): | 391 def set_medium_from_data(model: cobraModel, df: pd.DataFrame): |
| 378 """ | 392 """ |
| 379 Imposta il medium basato sulla colonna InMedium. | 393 Imposta il medium basato sulla colonna InMedium. |