Generate hmm with hhbuild,
        output to file. Also stores query names.

def run_hmmbuild(self):

        '''
        Generate hmm with hhbuild,
        output to file. Also stores query names.
        '''

        for alignment in self.alignment_list:

            print 'building Hmm for', alignment

            alignment_full_path = self.alignment_dir + alignment
            query_name = alignment.split("_")[0]
            self.query_names.append(query_name)

            new_hmm= self.hmm_dir + query_name + ".hmm"

            hmmbuild_output = subprocess.call(["hmmbuild", new_hmm,
             alignment_full_path])

        print 'hhbuild complete for', self.query_names