How to use the comparem.prodigal.ProdigalGeneFeatureParser function in comparem

# check if there is sufficient bases to calculate prodigal parameters
                if total_bases < 100000:
                    proc_str = 'meta'  # use best precalculated parameters
                else:
                    proc_str = 'single'  # estimate parameters from data

                cmd = 'prodigal -p %s -q -f gff -g %d -a %s -d %s -i %s > %s 2> /dev/null' % (proc_str,
                                                                                              translation_table,
                                                                                              aa_gene_file_tmp,
                                                                                              nt_gene_file_tmp,
                                                                                              genome_file,
                                                                                              gff_file_tmp)
                os.system(cmd)

                # determine coding density
                prodigalParser = ProdigalGeneFeatureParser(gff_file_tmp)

                codingBases = 0
                for seq_id, seq in seqs.iteritems():
                    codingBases += prodigalParser.coding_bases(seq_id)

                codingDensity = float(codingBases) / total_bases
                table_coding_density[translation_table] = codingDensity

            # determine best translation table
            best_translation_table = 11
            if (table_coding_density[4] - table_coding_density[11] > 0.05) and table_coding_density[4] > 0.7:
                best_translation_table = 4

            shutil.copyfile(os.path.join(tmp_dir, str(best_translation_table), genome_id + '.genes.faa'), aa_gene_file)
            shutil.copyfile(os.path.join(tmp_dir, str(best_translation_table), genome_id + '.genes.fna'), nt_gene_file)
            shutil.copyfile(os.path.join(tmp_dir, str(best_translation_table), genome_id + '.gff'), gff_file)