def mcscanx(args):
    """
    %prog mcscanx athaliana.athaliana.last athaliana.bed

    Wrap around MCScanX.
    """
    p = OptionParser(mcscanx.__doc__)
    opts, args = p.parse_args(args)

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

    blastfile = args[0]
    bedfiles = args[1:]
    prefix = "_".join(op.basename(x)[:2] for x in bedfiles)
    symlink(blastfile, prefix + ".blast")
    allbedfile = prefix + ".gff"
    fw = open(allbedfile, "w")
    for i, bedfile in enumerate(bedfiles):
        prefix = chr(ord('A') + i)
        make_gff(bedfile, prefix, fw)
    fw.close()
def mcscanx ( args ) : p = OptionParser ( mcscanx . __doc__ ) opts , args = p . parse_args ( args ) if len ( args ) < 2 : sys . exit ( not p . print_help ( ) ) blastfile = args [ 0 ] bedfiles = args [ 1 : ] prefix = "_" . join ( op . basename ( x ) [ : 2 ] for x in bedfiles ) symlink ( blastfile , prefix + ".blast" ) allbedfile = prefix + ".gff" fw = open ( allbedfile , "w" ) for i , bedfile in enumerate ( bedfiles ) : prefix = chr ( ord ( 'A' ) + i ) make_gff ( bedfile , prefix , fw ) fw . close ( )
%prog mcscanx athaliana.athaliana.last athaliana.bed

    Wrap around MCScanX.