def flanking(args):
    """
    %prog flanking bedfile [options]

    Get up to n features (upstream or downstream or both) flanking a given position.
    """
    from numpy import array, argsort

    p = OptionParser(flanking.__doc__)
    p.add_option("--chrom", default=None, type="string",
            help="chrom name of the position in query. Make sure it matches bedfile.")
    p.add_option("--coord", default=None, type="int",
            help="coordinate of the position in query.")
    p.add_option("-n", default=10, type="int",
            help="number of flanking features to get [default: %default]")
    p.add_option("--side", default="both", choices=("upstream", "downstream", "both"),
            help="which side to get flanking features [default: %default]")
    p.add_option("--max_d", default=None, type="int",
            help="features <= max_d away from position [default: %default]")
    p.set_outfile()

    opts, args = p.parse_args(args)

    if any([len(args) != 1, opts.chrom is None, opts.coord is None]):
        sys.exit(not p.print_help())

    bedfile, = args
    position = (opts.chrom, opts.coord)
    n, side, maxd = opts.n, opts.side, opts.max_d

    chrombed = Bed(bedfile).sub_bed(position[0])

    if side == "upstream":
        data = [(abs(f.start-position[1]), f) for f in chrombed \
            if f.start <= position[1]]
    elif side == "downstream":
        data = [(abs(f.start-position[1]), f) for f in chrombed \
            if f.start < position[1]]
    else:
        data = [(abs(f.start-position[1]), f) for f in chrombed]

    if maxd:
        data = [f for f in data if f[0]<=maxd]

    n += 1 # not counting self
    n = min(n, len(data))
    distances, subbed = zip(*data)
    distances = array(distances)
    idx = argsort(distances)[:n]
    flankingbed = [f for (i, f) in enumerate(subbed) if i in idx]

    fw = must_open(opts.outfile, "w")
    for atom in flankingbed:
        print >>fw, str(atom)

    return (position, flankingbed)
dataset/ETHPy150Open tanghaibao/jcvi/formats/bed.py/flanking/operator `>=` -> `<`