# HG changeset patch # User francesco_lapi # Date 1759244993 0 # Node ID 5397559097dc3568a9bc322c489761ae6f1b578b # Parent a92d21f92956b05d6e244e628dc796d86a85fbdc Uploaded diff -r a92d21f92956 -r 5397559097dc COBRAxy/metabolicModel2Tabular.py --- a/COBRAxy/metabolicModel2Tabular.py Tue Sep 30 15:00:21 2025 +0000 +++ b/COBRAxy/metabolicModel2Tabular.py Tue Sep 30 15:09:53 2025 +0000 @@ -237,30 +237,6 @@ logging.basicConfig(level=logging.INFO) logger = logging.getLogger(__name__) - tmp_check = [] - for g in model.genes[1:5]: # check first 3 genes only - tmp_check.append(modelUtils.gene_type(g.id, "Custom_model")) - - if len(set(tmp_check)) > 1: - raise utils.DataErr("Custom_model", "The custom model contains genes with mixed or unrecognized nomenclature. Please ensure all genes use the same recognized nomenclature before applying gene_format conversion.") - else: - source_nomenclature = tmp_check[0] - - if source_nomenclature != ARGS.gene_format: - model, translation_issues = 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, - source_nomenclature=source_nomenclature, - logger=logger - ) - - - - - if ARGS.name == "Custom_model" and ARGS.gene_format != "Default": - logger = logging.getLogger(__name__) - # Take a small, clean sample of gene IDs (skipping placeholders like 0) ids_sample = sample_valid_gene_ids(model.genes, limit=10) if not ids_sample: