input: 
  def calculate_percent_rRNA_mapping(htseq_counts, gtf_file):
      """
      Calculate the percentage of transcripts mapping to rRNA and MT genes from HTseq_counts and GTF file.
      
      Parameters:
      htseq_counts (str): Path to the HTseq_counts file.
      gtf_file (str): Path to the GTF file.
      
      Returns:
      str: A string containing the summary output file name and the percentage of rRNA and MT mapped reads.
      
      Example:
      >>> calculate_percent_rRNA_mapping('/path/to/HTseq_counts/file', '/path/to/GTF/file')
      'Summary output file: /path/to/HTseq_counts/file_rRNAmtRNACounts.txt\n Percent rRNA mapped reads: 10.5%\n Percent MT mapped reads: 5.3%'
      """
  
output:     rRNA_genes = set()
      MT_genes = set()
      
      with open(gtf_file, 'r') as gtf:
          for line in gtf:
              if line.startswith('#'):
                  continue
              fields = line.strip().split('\t')
              if fields[2] == 'gene':
                  attributes = fields[8].split(';')
                  gene_id = None
                  gene_type = None
                  for attr in attributes:
                      if 'gene_id' in attr:
                          gene_id = attr.split()[1].strip('"')
                      if 'gene_type' in attr:
                          gene_type = attr.split()[1].strip('"')
                  if gene_type == 'rRNA':
                      rRNA_genes.add(gene_id)
                  elif gene_type == 'Mt_rRNA' or gene_type == 'Mt_tRNA':
                      MT_genes.add(gene_id)
      
      rRNA_counts = 0
      MT_counts = 0
      total_counts = 0
      
      with open(htseq_counts, 'r') as counts:
          for line in counts:
              if line.startswith('__'):
                  continue
              gene_id, count = line.strip().split('\t')
              count = int(count)
              total_counts += count
              if gene_id in rRNA_genes:
                  rRNA_counts += count
              elif gene_id in MT_genes:
                  MT_counts += count
      
      percent_rRNA = (rRNA_counts / total_counts) * 100
      percent_MT = (MT_counts / total_counts) * 100
      
      output_file = f"{htseq_counts}_rRNAmtRNACounts.txt"
      summary = f"Summary output file: {output_file}\n Percent rRNA mapped reads: {percent_rRNA:.1f}%\n Percent MT mapped reads: {percent_MT:.1f}%"
      
      return summary