comparison COBRAxy/custom_data_generator_beta.py @ 444:06564187fba3 draft

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443:3d4e10546917

        # 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":
        logging.basicConfig(level=logging.INFO)
        logger = logging.getLogger(__name__)

        model = modelUtils.translate_model_genes(
            model=model,
            mapping_df= pd.read_csv(ARGS.tool_dir + "/local/mappings/genes_human.csv"),
            target_nomenclature=ARGS.gene_format.replace("HGNC_", "HGNC "),
            source_nomenclature='HGNC_ID',
            logger=logger
        )
        #model = modelUtils.convert_genes(model, ARGS.gene_format.replace("HGNC_", "HGNC "))
    
    if ARGS.name == "Recon" and ARGS.gene_format != "Default":
        logging.basicConfig(level=logging.INFO)
        logger = logging.getLogger(__name__)

        model = modelUtils.translate_model_genes(
            model=model,
            mapping_df= pd.read_csv(ARGS.tool_dir + "/local/mappings/genes_human.csv"),
            target_nomenclature=ARGS.gene_format.replace("HGNC_", "HGNC "),
            source_nomenclature='HGNC_symbol',
            logger=logger
        )

444:06564187fba3

        # 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":
    #    logging.basicConfig(level=logging.INFO)
    #    logger = logging.getLogger(__name__)

        #model = modelUtils.translate_model_genes(
        #    model=model,
        #    mapping_df= pd.read_csv(ARGS.tool_dir + "/local/mappings/genes_human.csv"), dtype={'entrez_id': str},
        #    target_nomenclature=ARGS.gene_format.replace("HGNC_", "HGNC "),
        #    source_nomenclature='HGNC_ID',
        #    logger=logger
        #)
        #model = modelUtils.convert_genes(model, ARGS.gene_format.replace("HGNC_", "HGNC "))
    
    if (ARGS.name == "Recon" or ARGS.name == "ENGRO2") and ARGS.gene_format != "Default":
        logging.basicConfig(level=logging.INFO)
        logger = logging.getLogger(__name__)

        model = modelUtils.translate_model_genes(
            model=model,
            mapping_df= pd.read_csv(ARGS.tool_dir + "/local/mappings/genes_human.csv", dtype={'entrez_id': str}),
            target_nomenclature=ARGS.gene_format.replace("HGNC_", "HGNC "),
            source_nomenclature='HGNC_symbol',
            logger=logger
        )