Mercurial > repos > bimib > cobraxy

comparison COBRAxy/metabolicModel2Tabular.py @ 506:ffc234ec80db draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author francesco_lapi
date Wed, 01 Oct 2025 13:19:03 +0000
parents 054c872e3880
children ca98c149ec61
comparison
equal deleted inserted replaced
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: