def blat(args):
    """
    %prog blat ref.fasta query.fasta

    Calls blat and filters BLAST hits.
    """
    p = OptionParser(blat.__doc__)
    p.set_align(pctid=95, hitlen=30)
    p.set_cpus()
    opts, args = p.parse_args(args)

    if len(args) != 2:
        sys.exit(not p.print_help())

    reffasta, queryfasta = args
    blastfile = get_outfile(reffasta, queryfasta, suffix="blat")

    run_blat(infile=queryfasta, outfile=blastfile, db=reffasta,
             pctid=opts.pctid, hitlen=opts.hitlen, cpus=opts.cpus,
             overwrite=False)

    return blastfile
def blat ( args ) : p = OptionParser ( blat . __doc__ ) p . set_align ( pctid = 95 , hitlen = 30 ) p . set_cpus ( ) opts , args = p . parse_args ( args ) if len ( args ) != 2 : sys . exit ( not p . print_help ( ) ) reffasta , queryfasta = args blastfile = get_outfile ( reffasta , queryfasta , suffix = "blat" ) run_blat ( infile = queryfasta , outfile = blastfile , db = reffasta , pctid = opts . pctid , hitlen = opts . hitlen , cpus = opts . cpus , overwrite = False ) return blastfile
%prog blat ref.fasta query.fasta

    Calls blat and filters BLAST hits.