comparison COBRAxy/ras_generator.py @ 490:c6ea189ea7e9 draft

Uploaded

489:97eea560a10f

    for key, value in reactions.items():
            ids.append(key)
            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]:
    """
    Process gene data to ensure correct formatting and handle duplicates.

490:c6ea189ea7e9

    for key, value in reactions.items():
            ids.append(key)
            rules.append(value)
    return (ids, rules)


############################ gene #############################################
def data_gene(gene: pd.DataFrame, type_gene: str, name: str, gene_custom: Optional[Dict[str, str]]) -> Dict[str, str]:
    """
    Process gene data to ensure correct formatting and handle duplicates.