scout/utils/hgnc_id.py
def get_hgnc_id(gene_info, adapter):
    """Get the hgnc id for a gene

        The proprity order will be
        1. if there is a hgnc id this one will be choosen
        2. if the hgnc symbol matches a genes proper hgnc symbol
        3. if the symbol ony matches aliases on several genes one will be
           choosen at random

        Args:
            gene_info(dict)
            adapter

        Returns:
            true_id(int)
    """
    hgnc_id = gene_info.get('hgnc_id')
    hgnc_symbol = gene_info.get('hgnc_symbol')

    true_id = None

    if hgnc_id:
        true_id = int(hgnc_id)
    else:
        gene_result = adapter.hgnc_genes(hgnc_symbol)
        if gene_result.count() == 0:
            raise Exception("No gene could be found for {}".format(hgnc_symbol))
        for gene in gene_result:
            if hgnc_symbol.upper() == gene.hgnc_symbol.upper():
                true_id = gene.hgnc_id
        if not gene_info['hgnc_id']:
            true_id = gene.hgnc_id

    return true_id
def get_hgnc_id(gene_info, adapter):
    hgnc_id = gene_info.get('hgnc_id')
    hgnc_symbol = gene_info.get('hgnc_symbol')

    true_id = None

    if hgnc_id:
        true_id = int(hgnc_id)
    else:
        gene_result = adapter.hgnc_genes(hgnc_symbol)
        if gene_result.count() == 0:
            raise Exception("No gene could be found for {}".format(hgnc_symbol))
        for gene in gene_result:
            if hgnc_symbol.upper() == gene.hgnc_symbol.upper():
                true_id = gene.hgnc_id
        if not gene_info['hgnc_id']:
            true_id = gene.hgnc_id

    return true_id
def get_hgnc_id ( gene_info , adapter ) : hgnc_id = gene_info . get ( 'hgnc_id' ) hgnc_symbol = gene_info . get ( 'hgnc_symbol' ) true_id = None if hgnc_id : true_id = int ( hgnc_id ) else : gene_result = adapter . hgnc_genes ( hgnc_symbol ) if gene_result . count ( ) == 0 : raise Exception ( "No gene could be found for {}" . format ( hgnc_symbol ) ) for gene in gene_result : if hgnc_symbol . upper ( ) == gene . hgnc_symbol . upper ( ) : true_id = gene . hgnc_id if not gene_info [ 'hgnc_id' ] : true_id = gene . hgnc_id return true_id
Get the hgnc id for a gene

        The proprity order will be
        1. if there is a hgnc id this one will be choosen
        2. if the hgnc symbol matches a genes proper hgnc symbol
        3. if the symbol ony matches aliases on several genes one will be
           choosen at random

        Args:
            gene_info(dict)
            adapter

        Returns:
            true_id(int)
Get the hgnc id for a gene