def template_align(self, ref_path):
<EOL>sh.mothur("<STR_LIT>" % (self.path, ref_path))<EOL>shutil.move(self.path[:-<NUM_LIT:6>] + '<STR_LIT>',        self.p.aligned)<EOL>shutil.move(self.path[:-<NUM_LIT:6>] + '<STR_LIT>', self.p.report)<EOL>shutil.move(self.path[:-<NUM_LIT:6>] + '<STR_LIT>',  self.p.accnos)<EOL>if os.path.exists('<STR_LIT>'): os.remove('<STR_LIT>')<EOL>if os.path.exists('<STR_LIT>') and os.path.getsize('<STR_LIT>') == <NUM_LIT:0>: os.remove('<STR_LIT>')<EOL>for p in sh.glob('<STR_LIT>'): os.remove(p)<EOL>
We align the sequences in the fasta file with mothur and a template.