input: 
  def calculate_percent_rrna_mapping(htseq_counts: str, gtf: str) -> str:
      """ Calculate the percent of transcripts mapping to rRNA and MT genes given an HTseq_counts file and a GTF file.
      >>> calculate_percent_rrna_mapping("C17_3_S20_Aligned.out.srt.bam_htseq_combined_counts.txt", "/Users/malwina/Documents/CTR-Data/genomes/Mus_musculus/mm10/Mus_musculus.GRCm38.84.gtf")
      "Summary output file:		C17_3_S20_Aligned.out.srt.bam_htseq_combined_counts_rRNAmtRNACounts.txt"
      """
  
output:     rrna_mt_genes = set()
      with open(gtf, 'r') as gtf_file:
          for line in gtf_file:
              if line.startswith('#'):
                  continue
              fields = line.strip().split('\t')
              if fields[2] == 'gene':
                  gene_info = fields[8]
                  if 'gene_biotype "rRNA"' in gene_info or 'gene_biotype "Mt_rRNA"' in gene_info or 'gene_biotype "Mt_tRNA"' in gene_info:
                      gene_id = gene_info.split('gene_id "')[1].split('";')[0]
                      rrna_mt_genes.add(gene_id)
  
      total_count = 0
      rrna_mt_count = 0
      with open(htseq_counts, 'r') as htseq_file:
          for line in htseq_file:
              if line.startswith('__'):
                  continue
              gene_id, count = line.strip().split('\t')
              count = int(count)
              total_count += count
              if gene_id in rrna_mt_genes:
                  rrna_mt_count += count
  
      percent_rrna_mt = (rrna_mt_count / total_count) * 100
      output_file_name = htseq_counts.replace('.txt', '_rRNAmtRNACounts.txt')
      with open(output_file_name, 'w') as output_file:
          output_file.write(f"Total reads: {total_count}\n")
          output_file.write(f"rRNA and MT reads: {rrna_mt_count}\n")
          output_file.write(f"Percent rRNA and MT reads: {percent_rrna_mt:.2f}%\n")
  
      return f"Summary output file:\t\t{output_file_name}"