comparison COBRAxy/custom_data_generator.py @ 393:52658ddcaa5d draft

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392:f73d57641124

                        help="Custom model file (JSON or XML)")
    parser.add_argument("--name", type=str, required=True,
                        help="Model name (default or custom)")
    
    parser.add_argument("--medium_selector", type=str, required=True,
                        help="Medium selection option (default/custom)")
    parser.add_argument("--medium", type=str,
                        help="Custom medium file if medium_selector=Custom")
    
    parser.add_argument("--out_tabular", type=str,
                        help="Output file for the merged dataset (CSV or XLSX)")
    
    parser.add_argument("--tool_dir", type=str, default=os.path.dirname(__file__),

        except Exception as e:
            # Wrap/normalize load errors as DataErr for consistency
            raise utils.DataErr(ARGS.model, f"failed loading built-in model: {e}")

    # Determine final model name: explicit --name overrides, otherwise use the model id
    model_name = ARGS.name if ARGS.name else ARGS.model

    # generate data
    rules = generate_rules(model, asParsed = False)
    reactions = generate_reactions(model, asParsed = False)
    bounds = generate_bounds(model)

393:52658ddcaa5d

                        help="Custom model file (JSON or XML)")
    parser.add_argument("--name", type=str, required=True,
                        help="Model name (default or custom)")
    
    parser.add_argument("--medium_selector", type=str, required=True,
                        help="Medium selection option")

    parser.add_argument("--gene_format", type=str, default="Default",
                        help="Gene nomenclature format: Default (original), ENSNG, HGNC_SYMBOL, HGNC_ID, ENTREZ")
    
    parser.add_argument("--out_tabular", type=str,
                        help="Output file for the merged dataset (CSV or XLSX)")
    
    parser.add_argument("--tool_dir", type=str, default=os.path.dirname(__file__),

        except Exception as e:
            # Wrap/normalize load errors as DataErr for consistency
            raise utils.DataErr(ARGS.model, f"failed loading built-in model: {e}")

    # Determine final model name: explicit --name overrides, otherwise use the model id
    
    model_name = ARGS.name if ARGS.name else ARGS.model
    
    
    if ARGS.name == "ENGRO2" and ARGS.medium_selector != "Default":
        df_mediums = pd.read_csv(ARGS.tool_dir + "/local/medium/medium.csv", index_col = 0)
        ARGS.medium_selector = ARGS.medium_selector.replace("_", " ")
        medium = df_mediums[[ARGS.medium_selector]]
        medium = medium[ARGS.medium_selector].to_dict()

        # Set all reactions to zero in the medium
        for rxn_id, _ in model.medium.items():
            model.reactions.get_by_id(rxn_id).lower_bound = float(0.0)
        
        # Set medium conditions
        for reaction, value in medium.items():
            if value is not None:
                model.reactions.get_by_id(reaction).lower_bound = -float(value)

    if ARGS.name == "ENGRO2" and ARGS.gene_format != "Default":
        utils.convert_genes(model, ARGS.gene_format)

    # generate data
    rules = generate_rules(model, asParsed = False)
    reactions = generate_reactions(model, asParsed = False)
    bounds = generate_bounds(model)