def template_align(self, ref_path):
        """We align the sequences in the fasta file with mothur and a template."""
        # Run it #
        sh.mothur("#align.seqs(candidate=%s, template=%s, search=blast, flip=false, processors=8);" % (self.path, ref_path))
        # Move things #
        shutil.move(self.path[:-6] + '.align',        self.p.aligned)
        shutil.move(self.path[:-6] + '.align.report', self.p.report)
        shutil.move(self.path[:-6] + '.flip.accnos',  self.p.accnos)
        # Clean up #
        if os.path.exists('formatdb.log'): os.remove('formatdb.log')
        if os.path.exists('error.log') and os.path.getsize('error.log') == 0: os.remove('error.log')
        for p in sh.glob('mothur.*.logfile'): os.remove(p)
def template_align ( self , ref_path ) : sh . mothur ( "#align.seqs(candidate=%s, template=%s, search=blast, flip=false, processors=8);" % ( self . path , ref_path ) ) shutil . move ( self . path [ : - 6 ] + '.align' , self . p . aligned ) shutil . move ( self . path [ : - 6 ] + '.align.report' , self . p . report ) shutil . move ( self . path [ : - 6 ] + '.flip.accnos' , self . p . accnos ) if os . path . exists ( 'formatdb.log' ) : os . remove ( 'formatdb.log' ) if os . path . exists ( 'error.log' ) and os . path . getsize ( 'error.log' ) == 0 : os . remove ( 'error.log' ) for p in sh . glob ( 'mothur.*.logfile' ) : os . remove ( p )
We align the sequences in the fasta file with mothur and a template.