comparison COBRAxy/fromCSVtoCOBRA_beta.py @ 454:3654c08668f1 draft

Uploaded

453:51f794fff930

    try:
        # Basic sanity checks
        if not os.path.exists(ARGS.input):
            logging.error('Input file not found: %s', ARGS.input)
            print(f"ERROR: Input file not found: {ARGS.input}", file=sys.stderr)
            sys.exit(2)

        out_dir = os.path.dirname(os.path.abspath(ARGS.output))
        if out_dir and not os.path.isdir(out_dir):
            try:
                os.makedirs(out_dir, exist_ok=True)
                logging.info('Created missing output directory: %s', out_dir)
            except Exception as e:
                logging.exception('Cannot create output directory: %s', out_dir)
                print(f"ERROR: Cannot create output directory: {out_dir}", file=sys.stderr)
                sys.exit(3)

        # Build the model from the CSV (NOTE: use ARGS.input here)
        model = modelUtils.build_cobra_model_from_csv(ARGS.input)

        # Save model in requested format

            cobra.io.save_matlab_model(model, ARGS.output)
        elif ARGS.format == "yaml":
            cobra.io.save_yaml_model(model, ARGS.output)
        else:
            logging.error('Unknown format requested: %s', ARGS.format)
            print(f"ERROR: Unknown format: {ARGS.format}", file=sys.stderr)
            sys.exit(4)

        logging.info('Model successfully written to %s (format=%s)', ARGS.output, ARGS.format)

    except Exception:
        # Log full traceback to the out_log so Galaxy users/admins can see what happened
        logging.exception('Unhandled exception in fromCSVtoCOBRA')
        traceback.print_exc(file=sys.stderr)
        sys.exit(1)


if __name__ == '__main__':
    main()

454:3654c08668f1

    try:
        # Basic sanity checks
        if not os.path.exists(ARGS.input):
            logging.error('Input file not found: %s', ARGS.input)

        out_dir = os.path.dirname(os.path.abspath(ARGS.output))
        if out_dir and not os.path.isdir(out_dir):
            try:
                os.makedirs(out_dir, exist_ok=True)
                logging.info('Created missing output directory: %s', out_dir)
            except Exception as e:
                logging.exception('Cannot create output directory: %s', out_dir)

        # Build the model from the CSV (NOTE: use ARGS.input here)
        model = modelUtils.build_cobra_model_from_csv(ARGS.input)

        # Save model in requested format

            cobra.io.save_matlab_model(model, ARGS.output)
        elif ARGS.format == "yaml":
            cobra.io.save_yaml_model(model, ARGS.output)
        else:
            logging.error('Unknown format requested: %s', ARGS.format)
            print(f"ERROR: Unknown format: {ARGS.format}")


        logging.info('Model successfully written to %s (format=%s)', ARGS.output, ARGS.format)

    except Exception:
        # Log full traceback to the out_log so Galaxy users/admins can see what happened
        logging.exception('Unhandled exception in fromCSVtoCOBRA')


if __name__ == '__main__':
    main()