Mercurial > repos > bimib > cobraxy

comparison COBRAxy/metabolicModel2Tabular.py @ 494:5397559097dc draft

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author francesco_lapi
date Tue, 30 Sep 2025 15:09:53 +0000
parents 4ed95023af20
children e19083971cc3
comparison
equal deleted inserted replaced
493:a92d21f92956 494:5397559097dc
233 logger=logger 233 logger=logger
234 ) 234 )
235 235
236 if ARGS.name == "Custom_model" and ARGS.gene_format != "Default": 236 if ARGS.name == "Custom_model" and ARGS.gene_format != "Default":
237 logging.basicConfig(level=logging.INFO) 237 logging.basicConfig(level=logging.INFO)
238 logger = logging.getLogger(__name__)
239
240 tmp_check = []
241 for g in model.genes[1:5]: # check first 3 genes only
242 tmp_check.append(modelUtils.gene_type(g.id, "Custom_model"))
243
244 if len(set(tmp_check)) > 1:
245 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.")
246 else:
247 source_nomenclature = tmp_check[0]
248
249 if source_nomenclature != ARGS.gene_format:
250 model, translation_issues = modelUtils.translate_model_genes(
251 model=model,
252 mapping_df= pd.read_csv(ARGS.tool_dir + "/local/mappings/genes_human.csv", dtype={'entrez_id': str}),
253 target_nomenclature=ARGS.gene_format,
254 source_nomenclature=source_nomenclature,
255 logger=logger
256 )
257
258
259
260
261 if ARGS.name == "Custom_model" and ARGS.gene_format != "Default":
262 logger = logging.getLogger(__name__) 238 logger = logging.getLogger(__name__)
263 239
264 # Take a small, clean sample of gene IDs (skipping placeholders like 0) 240 # Take a small, clean sample of gene IDs (skipping placeholders like 0)
265 ids_sample = sample_valid_gene_ids(model.genes, limit=10) 241 ids_sample = sample_valid_gene_ids(model.genes, limit=10)
266 if not ids_sample: 242 if not ids_sample: