How to use the comparem.aai_calculator.AAICalculator function in comparem

Flag indicating if RBH should be written to file.
        output_dir : str
            Directory to store AAI results.
        """
        
        # read taxonomic identification of each genome
        taxonomy = {}
        if taxonomy_file:
            for line in open(taxonomy_file):
                genome_id, taxa_str = line.rstrip().split('\t')
                taxonomy[genome_id] = taxa_str

        # calculate AAI between query and target genomes
        aai_output_dir = os.path.join(output_dir, 'aai')
        make_sure_path_exists(aai_output_dir)
        aai_calculator = AAICalculator(self.cpus)
        aai_output_file, rbh_output_file = aai_calculator.run(query_gene_file,
                                                                target_gene_file,
                                                                sorted_hit_table,
                                                                evalue_threshold,
                                                                per_iden_threshold,
                                                                per_aln_len_threshold,
                                                                keep_rbhs,
                                                                aai_output_dir)

        # determine matches to each query genomes
        aai_results_file = os.path.join(aai_output_dir, 'aai_summary.tsv')
        with open(aai_results_file) as f:
            f.readline()
            
            hits = defaultdict(list)
            for line in f:

def aai(self, options):
        """AAI command"""
        check_file_exists(options.sorted_hit_table)
        make_sure_path_exists(options.output_dir)

        aai_calculator = AAICalculator(options.cpus)
        aai_output_file, rbh_output_file = aai_calculator.run(options.query_gene_file,
                                                                None,
                                                                options.sorted_hit_table,
                                                                options.evalue,
                                                                options.per_identity,
                                                                options.per_aln_len,
                                                                options.keep_rbhs,
                                                                options.output_dir)

        if rbh_output_file:
            self.logger.info('Identified reciprocal best hits written to: %s' % rbh_output_file)
            
        self.logger.info('AAI between genomes written to: %s' % aai_output_file)