def _hmm_command(self, input_pipe, pairs_to_run):
element = pairs_to_run.pop()<EOL>hmmsearch_cmd = self._individual_hmm_command(element[<NUM_LIT:0>][<NUM_LIT:0>],<EOL>element[<NUM_LIT:0>][<NUM_LIT:1>],<EOL>element[<NUM_LIT:1>])<EOL>while len(pairs_to_run) > <NUM_LIT:0>:<EOL><INDENT>element = pairs_to_run.pop()<EOL>hmmsearch_cmd = "<STR_LIT>" % (self._individual_hmm_command(element[<NUM_LIT:0>][<NUM_LIT:0>],<EOL>element[<NUM_LIT:0>][<NUM_LIT:1>],<EOL>element[<NUM_LIT:1>]),<EOL>hmmsearch_cmd)<EOL><DEDENT>hmmsearch_cmd = "<STR_LIT>" % (input_pipe, hmmsearch_cmd)<EOL>return hmmsearch_cmd<EOL>
r"""INTERNAL method for getting cmdline for running a batch of HMMs.

        Parameters
        ----------
        input_pipe: as hmmsearch
        pairs_to_run: list
            list with 2 members: (1) list of hmm and output file, (2) number of
            CPUs to use when searching

        Returns
        -------
        A string command to be run with bash