code: def _prepare_inputs(ma_fn, bam_file, out_dir):
      
      fixed_fa = os.path.join(out_dir, "file_reads.fa")
      count_name =dict()
      with file_transaction(fixed_fa) as out_tx:
          with open(out_tx, 'w') as out_handle:
              with open(ma_fn) as in_handle:
                  h = next(in_handle)
                  for line in in_handle:
                      cols = line.split("\t")
                      name_with_counts = "%s_x%s" % (cols[0], sum(map(int, cols[2:])))
                      count_name[cols[0]] = name_with_counts
                      out_handle.write(">%s\n%s\n" % (name_with_counts, cols[1]))
      fixed_bam = os.path.join(out_dir, "align.bam")
      bam_handle = pysam.AlignmentFile(bam_file, "rb")
      with pysam.AlignmentFile(fixed_bam, "wb", template=bam_handle) as out_handle:
          for read in bam_handle.fetch():
              read.query_name = count_name[read.query_name]
              out_handle.write(read)
  
      return fixed_fa, fixed_bam
docs: Convert to fastq with counts