code: def create_splicesites_file(gtf_file, align_dir, data):
      
      out_file = os.path.join(align_dir, "ref-transcripts-splicesites.txt")
      if file_exists(out_file):
          return out_file
      safe_makedir(align_dir)
      hisat2_ss = config_utils.get_program("hisat2_extract_splice_sites.py", data)
      cmd = "{hisat2_ss} {gtf_file} > {tx_out_file}"
      message = "Creating hisat2 splicesites file from %s." % gtf_file
      with file_transaction(out_file) as tx_out_file:
          do.run(cmd.format(**locals()), message)
      return out_file
docs: if not pre-created, make a splicesites file to use with hisat2