Mercurial > repos > bimib > cobraxy

comparison COBRAxy/utils/general_utils.py @ 394:a0b53ccc73a8 draft

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Uploaded
author francesco_lapi
date Fri, 05 Sep 2025 13:05:29 +0000
parents f73d57641124
children f413b78d61bf
comparison
equal deleted inserted replaced
393:52658ddcaa5d 394:a0b53ccc73a8
14 14
15 import zipfile 15 import zipfile
16 import gzip 16 import gzip
17 import bz2 17 import bz2
18 from io import StringIO 18 from io import StringIO
19
20
19 21
20 class ValueErr(Exception): 22 class ValueErr(Exception):
21 def __init__(self, param_name, expected, actual): 23 def __init__(self, param_name, expected, actual):
22 super().__init__(f"Invalid value for {param_name}: expected {expected}, got {actual}") 24 super().__init__(f"Invalid value for {param_name}: expected {expected}, got {actual}")
23 25
697 raise Exception(f"Error during model extraction: {str(e)}") 699 raise Exception(f"Error during model extraction: {str(e)}")
698 700
699 701
700 702
701 def __str__(self) -> str: return self.value 703 def __str__(self) -> str: return self.value
704
705
706 def convert_genes(model,annotation):
707 from cobra.manipulation import rename_genes
708 model2=model.copy()
709 try:
710 dict_genes={gene.id:gene.notes[annotation] for gene in model2.genes}
711 except:
712 print("No annotation in gene dict!")
713 return -1
714 rename_genes(model2,dict_genes)
715
716 return model2