How to use the refinem.reference.Reference function in refinem

def reference(self, options):
        """Reference command"""

        check_file_exists(options.scaffold_prot_file)
        check_file_exists(options.scaffold_stats_file)
        make_sure_path_exists(options.output_dir)

        ref_gene_files = self._genome_files(options.ref_genome_prot_dir, options.protein_ext)
        if not self._check_protein_seqs(ref_gene_files):
            self.logger.warning('All files must contain amino acid sequences.')
            sys.exit()

        reference = Reference(options.cpus, options.output_dir)
        reference_out = reference.run(options.scaffold_prot_file,
                                        options.scaffold_stats_file,
                                        ref_gene_files,
                                        options.db_file,
                                        options.evalue,
                                        options.per_identity,
                                        options.per_aln_len)

        self.logger.info('Results written to: ' + reference_out)

"""Compatible command"""

        check_file_exists(options.reference_file)
        check_file_exists(options.scaffold_stats_file)
        make_sure_path_exists(options.output_dir)

        # read scaffold statistics and calculate genome stats
        self.logger.info('Reading scaffold statistics.')
        scaffold_stats = ScaffoldStats()
        scaffold_stats.read(options.scaffold_stats_file)

        genome_stats = GenomeStats()
        genome_stats = genome_stats.run(scaffold_stats)

        # identify putative homologs to reference genomes
        reference = Reference(1, None)
        putative_homologs = reference.homology_check(options.reference_file,
                                                         options.min_genes,
                                                         float(options.perc_genes))

        # identify scaffolds compatible with bins
        outliers = Outliers()
        output_file = os.path.join(options.output_dir, 'compatible.tsv')
        outliers.compatible(putative_homologs, scaffold_stats, genome_stats,
                                      options.gc_perc, options.td_perc,
                                      options.cov_corr, options.cov_perc,
                                      options.report_type, output_file)

        self.logger.info('Results written to: ' + output_file)