Mercurial > repos > bimib > cobraxy

comparison COBRAxy/utils/model_utils.py @ 444:06564187fba3 draft

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author francesco_lapi
date Thu, 11 Sep 2025 09:03:10 +0000
parents f49c951c9fe6
children f8b1761eee37
comparison
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443:3d4e10546917 444:06564187fba3
442 return -1 442 return -1
443 rename_genes(model2,dict_genes) 443 rename_genes(model2,dict_genes)
444 444
445 return model2 445 return model2
446 446
447
448
449 # ---------- Utility helpers ---------- 447 # ---------- Utility helpers ----------
450 def _normalize_colname(col: str) -> str: 448 def _normalize_colname(col: str) -> str:
451 return col.strip().lower().replace(' ', '_') 449 return col.strip().lower().replace(' ', '_')
452 450
453 def _choose_columns(mapping_df: 'pd.DataFrame') -> Dict[str, str]: 451 def _choose_columns(mapping_df: 'pd.DataFrame') -> Dict[str, str]:
459 chosen = {} 457 chosen = {}
460 # possibili nomi per ciascuna categoria 458 # possibili nomi per ciascuna categoria
461 candidates = { 459 candidates = {
462 'ensg': ['ensg', 'ensembl_gene_id', 'ensembl'], 460 'ensg': ['ensg', 'ensembl_gene_id', 'ensembl'],
463 'hgnc_id': ['hgnc_id', 'hgnc', 'hgnc:'], 461 'hgnc_id': ['hgnc_id', 'hgnc', 'hgnc:'],
464 'hgnc_symbol': ['hgnc_symbol', 'hgnc_symbol', 'symbol'], 462 'hgnc_symbol': ['hgnc_symbol', 'hgnc symbol', 'symbol'],
465 'entrez_id': ['entrez', 'entrez_id', 'entrezgene'] 463 'entrez_id': ['entrez', 'entrez_id', 'entrezgene']
466 } 464 }
467 for key, names in candidates.items(): 465 for key, names in candidates.items():
468 for n in names: 466 for n in names:
469 if n in cols: 467 if n in cols: