How to use the comparem.codon_usage.CodonUsage function in comparem

def codon_usage(self, options):
        """Codon usage command"""

        gene_files = self._input_files(options.nucleotide_gene_files, options.file_ext)

        # calculate amino acid usage
        codon_usage = CodonUsage(options.cpus, options.keep_ambiguous)
        genome_codon_usage, codon_set, _mean_length = codon_usage.run(gene_files)

        # write out results
        self._write_usage_profile(genome_codon_usage, 
                                    codon_set, 
                                    options.counts, 
                                    options.output_file)

        self.logger.info('Codon usage written to: %s' % options.output_file)

def stop_usage(self, options):
        """Stop codon usage command"""

        gene_files = self._input_files(options.nucleotide_gene_files, options.file_ext)

        # calculate amino acid usage
        codon_usage = CodonUsage(options.cpus, keep_ambiguous=False, stop_codon_only=True)
        genome_codon_usage, codon_set, mean_gene_length = codon_usage.run(gene_files)

        # write out results
        if not options.mean_gene_length:
            self._write_usage_profile(genome_codon_usage, 
                                        codon_set, 
                                        options.counts, 
                                        options.output_file)
        else:
            fout = open(options.output_file, 'w')
            for codon in codon_set:
                fout.write('\t' + codon)
                if mean_gene_length:
                    fout.write('\t' + codon + ': avg. seq. length')
            fout.write('\n')