Mercurial > repos > bimib > cobraxy
comparison COBRAxy/metabolicModel2Tabular.py @ 506:ffc234ec80db draft
Uploaded
| author | francesco_lapi |
|---|---|
| date | Wed, 01 Oct 2025 13:19:03 +0000 |
| parents | 054c872e3880 |
| children | ca98c149ec61 |
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| 505:96f512dff490 | 506:ffc234ec80db |
|---|---|
| 330 reactions = modelUtils.generate_reactions(model, asParsed = False) | 330 reactions = modelUtils.generate_reactions(model, asParsed = False) |
| 331 bounds = modelUtils.generate_bounds(model) | 331 bounds = modelUtils.generate_bounds(model) |
| 332 medium = modelUtils.get_medium(model) | 332 medium = modelUtils.get_medium(model) |
| 333 objective_function = modelUtils.extract_objective_coefficients(model) | 333 objective_function = modelUtils.extract_objective_coefficients(model) |
| 334 | 334 |
| 335 if ARGS.name == "ENGRO2": | 335 compartments = modelUtils.generate_compartments(model) |
| 336 compartments = modelUtils.generate_compartments(model) | |
| 337 | 336 |
| 338 df_rules = pd.DataFrame(list(rules.items()), columns = ["ReactionID", "GPR"]) | 337 df_rules = pd.DataFrame(list(rules.items()), columns = ["ReactionID", "GPR"]) |
| 339 df_reactions = pd.DataFrame(list(reactions.items()), columns = ["ReactionID", "Formula"]) | 338 df_reactions = pd.DataFrame(list(reactions.items()), columns = ["ReactionID", "Formula"]) |
| 340 | 339 |
| 341 # Create DataFrame for translation issues | 340 # Create DataFrame for translation issues |
| 349 df_medium["InMedium"] = True | 348 df_medium["InMedium"] = True |
| 350 | 349 |
| 351 merged = df_reactions.merge(df_rules, on = "ReactionID", how = "outer") | 350 merged = df_reactions.merge(df_rules, on = "ReactionID", how = "outer") |
| 352 merged = merged.merge(df_bounds, on = "ReactionID", how = "outer") | 351 merged = merged.merge(df_bounds, on = "ReactionID", how = "outer") |
| 353 merged = merged.merge(objective_function, on = "ReactionID", how = "outer") | 352 merged = merged.merge(objective_function, on = "ReactionID", how = "outer") |
| 354 if ARGS.name == "ENGRO2": | 353 if compartments is not None: |
| 355 merged = merged.merge(compartments, on = "ReactionID", how = "outer") | 354 merged = merged.merge(compartments, on = "ReactionID", how = "outer") |
| 356 merged = merged.merge(df_medium, on = "ReactionID", how = "left") | 355 merged = merged.merge(df_medium, on = "ReactionID", how = "left") |
| 357 | 356 |
| 358 # Add translation issues column | 357 # Add translation issues column |
| 359 if not df_translation_issues.empty: | 358 if not df_translation_issues.empty: |