code: def run_RNAplfold(input_fasta, tmpdir, W=240, L=160, U=1):
      
  
      profiles = RNAplfold_PROFILES_EXECUTE
      for i, P in enumerate(profiles):
          print("running {P}_RNAplfold... ({i}/{N})".format(P=P, i=i + 1, N=len(profiles)))
  
          command = "{bin}/{P}_RNAplfold".format(bin=RNAplfold_BIN_DIR, P=P)
          file_out = "{tmp}/{P}_profile.fa".format(tmp=tmpdir, P=P)
          args = " -W {W} -L {L} -u {U} < {fa} > {file_out}".format(W=W, L=L, U=U, fa=input_fasta, file_out=file_out)
  
          os.system(command + args)
  
          # check if the file is empty
          if os.path.getsize(file_out) == 0:
              raise Exception("command wrote an empty file: {0}".format(file_out))
      print("done!")
docs: Arguments:
         W, Int: span - window length
         L, Int, maxiumm span
         U, Int, size of unpaired region