docs: def get_rna_counts(rna_file, transcript_name):
      """Get coverage for a given RNA BAM file, return read counts. """
      # check if the RNA file exists
      if not os.path.exists(rna_file):
          msg = 'RNA-Seq BAM file "{}" does not exist'.format(rna_file)
          logging.error(msg)
          raise OSError(msg)
      rna_counts = {}
  
      cov_file = tempfile.NamedTemporaryFile(delete=False)
      try:
          subprocess.check_call(
              ['bedtools', 'genomecov', '-ibam', rna_file,
               '-bg'], stdout=cov_file)
      except subprocess.CalledProcessError as e:
          # needs testing
          raise ribocore.RNACountsError('Could not generate coverage for RNA BAM file. \n{}\n'.format(e))
      for line in open(cov_file.name):
          line = line.split()
          if line[0] == transcript_name:
              position, count = int(line[1]) + 1, int(line[3])
              rna_counts[position] = count
      cov_file.close()
      os.unlink(cov_file.name)
      return rna_counts