def parse_genes(gene_file):
    """Select gene to exclude: where sgt column is not 'yes' 
    input: csv file with genes
    return: set of genes which should be exluded"""
    to_exlude = set()
    with open(gene_file) as lines:
        next(lines)
        for line in lines:
            gene, _, _, sgt = line.split('\t')
            if sgt.strip().lower() != 'yes':
                to_exlude.add(gene)
    return to_exlude