input: 
  def calculate_percent_rRNA_mapping(HTSEQ_COUNTS: str, GTF: str) -> str:
      """
      Calculate the percent of transcripts mapping to rRNA. This function takes an HTseq_counts file and an original 
      reference transcriptome aligned to, extracts all identifiers of genes/transcripts mapping to the rRNA and MT genes, 
      counts reads matching the rRNA identifiers, and writes the output files. The summary output file will be named 
      "HTseq_counts_file_rRNAmtRNACounts.txt".
      
      >>> calculate_percent_rRNA_mapping('/path/to/HTseq_counts/file', '/path/to/GTF/file')
      'HTseq_counts_file_rRNAmtRNACounts.txt'
      """
  
output:     
      rRNA_ids = set()
      MT_ids = set()
      total_reads = 0
      rRNA_reads = 0
  
      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].split(';')
                  gene_id = [x.strip().split(' ')[1].strip('"') for x in gene_info if 'gene_id' in x][0]
                  if 'rRNA' in fields[8]:
                      rRNA_ids.add(gene_id)
                  if 'MT' in fields[8]:
                      MT_ids.add(gene_id)
  
      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_reads += count
              if gene_id in rRNA_ids or gene_id in MT_ids:
                  rRNA_reads += count
  
      percent_rRNA = (rRNA_reads / total_reads) * 100
      output_file = HTSEQ_COUNTS.split('/')[-1] + '_rRNAmtRNACounts.txt'
  
      with open(output_file, 'w') as out_file:
          out_file.write(f"Total reads: {total_reads}\n")
          out_file.write(f"rRNA/MT reads: {rRNA_reads}\n")
          out_file.write(f"Percent rRNA/MT: {percent_rRNA:.2f}%\n")
  
      return output_file
  