How to use the refinem.genome_stats.GenomeStats function in refinem

def genome_stats(self, options):
        """Genomes statistics command"""
        
        check_file_exists(options.scaffold_stats_file)

        self.logger.info('Reading scaffold statistics.')
        scaffold_stats = ScaffoldStats(options.cpus)
        scaffold_stats.read(options.scaffold_stats_file)

        genome_stats = GenomeStats()
        genome_stats.run(scaffold_stats)
        genome_stats.write(options.output_file)

        self.logger.info('Genome statistic written to: %s' % options.output_file)

def compatible(self, options):
        """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)

def outliers(self, options):
        """Outlier command"""

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

        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 outliers
        outliers = Outliers()
        outlier_file = os.path.join(options.output_dir, 'outliers.tsv')
        outliers.identify(scaffold_stats, genome_stats,
                                      options.gc_perc, options.td_perc,
                                      options.cov_corr, options.cov_perc,
                                      options.report_type, outlier_file)
        self.logger.info('Outlier information written to: ' + outlier_file)

        # create outlier plots
        if options.create_plots:
            plot_dir = os.path.join(options.output_dir, 'plots')
            make_sure_path_exists(plot_dir)