def merge(args):
    p = OptionParser(merge.__doc__)
    p.add_option("--seq", default=False, action="store_true",
                 help="Print FASTA sequences at the end")
    p.set_outfile()

    opts, args = p.parse_args(args)

    nargs = len(args)
    if nargs < 1:
        sys.exit(not p.print_help())

    if nargs == 1:
        listfile, = args
        fp = open(listfile)
        gffiles = [x.strip() for x in fp]
    else:
        gffiles = args

    outfile = opts.outfile

    deflines = set()
    fw = must_open(outfile, "w")
    fastarecs = {}
    for gffile in natsorted(gffiles, key=lambda x: op.basename(x)):
        logging.debug(gffile)
        fp = open(gffile)
        for row in fp:
            row = row.rstrip()
            if not row or row[0] == '#':
                if row == FastaTag:
                    break
                if row in deflines:
                    continue
                else:
                    deflines.add(row)

            print >> fw, row

        if not opts.seq:
            continue

        f = Fasta(gffile, lazy=True)
        for key, rec in f.iteritems_ordered():
            if key in fastarecs:
                continue
            fastarecs[key] = rec

    if opts.seq:
        print >> fw, FastaTag
        SeqIO.write(fastarecs.values(), fw, "fasta")

    fw.close()
%prog merge gffiles
dataset/ETHPy150Open tanghaibao/jcvi/formats/gff.py/merge