comparison COBRAxy/metabolicModel2Tabular.py @ 508:ca98c149ec61 draft

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507:20e135a73cad

                target_nomenclature=ARGS.gene_format,
                source_nomenclature=source_nomenclature,
                logger=logger
            )

    # generate data
    rules = modelUtils.generate_rules(model, asParsed = False)
    reactions = modelUtils.generate_reactions(model, asParsed = False)
    bounds = modelUtils.generate_bounds(model)
    medium = modelUtils.get_medium(model)
    objective_function = modelUtils.extract_objective_coefficients(model)
    
    compartments = modelUtils.generate_compartments(model)

    df_rules = pd.DataFrame(list(rules.items()), columns = ["ReactionID", "GPR"])
    df_reactions = pd.DataFrame(list(reactions.items()), columns = ["ReactionID", "Formula"])

    # Create DataFrame for translation issues
    df_translation_issues = pd.DataFrame([
        {"ReactionID": rxn_id, "TranslationIssues": issues}
        for rxn_id, issues in translation_issues.items()
    ])
    
    df_bounds = bounds.reset_index().rename(columns = {"index": "ReactionID"})
    df_medium = medium.rename(columns = {"reaction": "ReactionID"})
    df_medium["InMedium"] = True

    merged = df_reactions.merge(df_rules, on = "ReactionID", how = "outer")
    merged = merged.merge(df_bounds, on = "ReactionID", how = "outer")
    merged = merged.merge(objective_function, on = "ReactionID", how = "outer")
    if compartments is not None: 
        merged = merged.merge(compartments, on = "ReactionID", how = "outer")
    merged = merged.merge(df_medium, on = "ReactionID", how = "left")
    
    # Add translation issues column
    if not df_translation_issues.empty:
        merged = merged.merge(df_translation_issues, on = "ReactionID", how = "left")
        merged["TranslationIssues"] = merged["TranslationIssues"].fillna("")
    else:
        # Add empty TranslationIssues column if no issues found
        #merged["TranslationIssues"] = ""
        pass

    merged["InMedium"] = merged["InMedium"].fillna(False)

    merged = merged.sort_values(by = "InMedium", ascending = False)

    if not ARGS.out_tabular:
        raise utils.ArgsErr("out_tabular", "output path (--out_tabular) is required when output_format == tabular", ARGS.out_tabular)
    save_as_tabular_df(merged, ARGS.out_tabular)
    expected = ARGS.out_tabular

    # verify output exists and non-empty
    if not expected or not os.path.exists(expected) or os.path.getsize(expected) == 0:
        raise utils.DataErr(expected, "Output not created or empty")

508:ca98c149ec61

                target_nomenclature=ARGS.gene_format,
                source_nomenclature=source_nomenclature,
                logger=logger
            )

    # generate data using unified function
    if not ARGS.out_tabular:
        raise utils.ArgsErr("out_tabular", "output path (--out_tabular) is required when output_format == tabular", ARGS.out_tabular)
    
    merged = modelUtils.export_model_to_tabular(
        model=model,
        output_path=ARGS.out_tabular,
        translation_issues=translation_issues,
        include_objective=True,
        save_function=save_as_tabular_df
    )
    expected = ARGS.out_tabular

    # verify output exists and non-empty
    if not expected or not os.path.exists(expected) or os.path.getsize(expected) == 0:
        raise utils.DataErr(expected, "Output not created or empty")