def run_hmmbuild(self):
for alignment in self.alignment_list:<EOL><INDENT>print('<STR_LIT>', alignment)<EOL>alignment_full_path = self.alignment_dir + alignment<EOL>query_name = alignment.split("<STR_LIT:_>")[<NUM_LIT:0>]<EOL>self.query_names.append(query_name)<EOL>new_hmm= self.hmm_dir + query_name + "<STR_LIT>"<EOL>hmmbuild_output = subprocess.call(["<STR_LIT>", new_hmm,<EOL>alignment_full_path])<EOL><DEDENT>print('<STR_LIT>', self.query_names)<EOL>
Generate hmm with hhbuild,
output to file. Also stores query names.