def distance(args):
    """
    %prog distance bedfile

    Calculate distance between bed features. The output file is a list of
    distances, which can be used to plot histogram, etc.
    """
    from jcvi.utils.iter import pairwise

    p = OptionParser(distance.__doc__)
    p.add_option("--distmode", default="ss", choices=("ss", "ee"),
            help="Distance mode between paired reads. ss is outer distance, " \
                 "ee is inner distance [default: %default]")
    opts, args = p.parse_args(args)

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

    bedfile, = args
    sortedbedfile = sort([bedfile])
    valid = total = 0
    fp = open(sortedbedfile)
    for a, b in pairwise(fp):
        a = BedLine(a)
        b = BedLine(b)
        ar = (a.seqid, a.start, a.end, "+")
        br = (b.seqid, b.start, b.end, "+")
        dist, oo = range_distance(ar, br, distmode=opts.distmode)
        total += 1
        if dist > 0:
            print dist
            valid += 1

    logging.debug("Total valid (> 0) distances: {0}.".\
                  format(percentage(valid, total)))
dataset/ETHPy150Open tanghaibao/jcvi/formats/bed.py/distance/original