--- a/COBRAxy/ras_generator.py	Mon Sep 29 10:33:26 2025 +0000
+++ b/COBRAxy/ras_generator.py	Mon Sep 29 15:13:21 2025 +0000
@@ -106,97 +106,6 @@
             rules.append(value)
     return (ids, rules)
 
-############################ check_methods ####################################
-def gene_type(l :str, name :str) -> str:
-    """
-    Determine the type of gene ID.
-
-    Args:
-        l (str): The gene identifier to check.
-        name (str): The name of the dataset, used in error messages.
-
-    Returns:
-        str: The type of gene ID ('hugo_id', 'ensembl_gene_id', 'symbol', or 'entrez_id').
-
-    Raises:
-        sys.exit: If the gene ID type is not supported, the execution is aborted.
-    """
-    if check_hgnc(l):
-        return 'hugo_id'
-    elif check_ensembl(l):
-        return 'ensembl_gene_id'
-    elif check_symbol(l):
-        return 'symbol'
-    elif check_entrez(l):
-        return 'entrez_id'
-    else:
-        sys.exit('Execution aborted:\n' +
-                 'gene ID type in ' + name + ' not supported. Supported ID'+
-                 'types are: HUGO ID, Ensemble ID, HUGO symbol, Entrez ID\n')
-
-def check_hgnc(l :str) -> bool:
-    """
-    Check if a gene identifier follows the HGNC format.
-
-    Args:
-        l (str): The gene identifier to check.
-
-    Returns:
-        bool: True if the gene identifier follows the HGNC format, False otherwise.
-    """
-    if len(l) > 5:
-        if (l.upper()).startswith('HGNC:'):
-            return l[5:].isdigit()
-        else:
-            return False
-    else:
-        return False
-
-def check_ensembl(l :str) -> bool:
-    """
-    Check if a gene identifier follows the Ensembl format.
-
-    Args:
-        l (str): The gene identifier to check.
-
-    Returns:
-        bool: True if the gene identifier follows the Ensembl format, False otherwise.
-    """
-    return l.upper().startswith('ENS')
- 
-
-def check_symbol(l :str) -> bool:
-    """
-    Check if a gene identifier follows the symbol format.
-
-    Args:
-        l (str): The gene identifier to check.
-
-    Returns:
-        bool: True if the gene identifier follows the symbol format, False otherwise.
-    """
-    if len(l) > 0:
-        if l[0].isalpha() and l[1:].isalnum():
-            return True
-        else:
-            return False
-    else:
-        return False
-
-def check_entrez(l :str) -> bool:
-    """
-    Check if a gene identifier follows the Entrez ID format.
-
-    Args:
-        l (str): The gene identifier to check.
-
-    Returns:
-        bool: True if the gene identifier follows the Entrez ID format, False otherwise.
-    """ 
-    if len(l) > 0:
-        return l.isdigit()
-    else: 
-        return False
 
 ############################ gene #############################################
 def data_gene(gene: pd.DataFrame, type_gene: str, name: str, gene_custom: Optional[Dict[str, str]]) -> Dict[str, str]: