def pile(args):
    """
    %prog pile abedfile bbedfile > piles

    Call intersectBed on two bedfiles.
    """
    from jcvi.utils.grouper import Grouper

    p = OptionParser(pile.__doc__)
    p.add_option("--minOverlap", default=0, type="int",
                 help="Minimum overlap required [default: %default]")
    opts, args = p.parse_args(args)

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

    abedfile, bbedfile = args
    iw = intersectBed_wao(abedfile, bbedfile, minOverlap=opts.minOverlap)
    groups = Grouper()
    for a, b in iw:
        groups.join(a.accn, b.accn)

    ngroups = 0
    for group in groups:
        if len(group) > 1:
            ngroups += 1
            print("|".join(group))

    logging.debug("A total of {0} piles (>= 2 members)".format(ngroups))
def pile ( args ) : from jcvi . utils . grouper import Grouper p = OptionParser ( pile . __doc__ ) p . add_option ( "--minOverlap" , default = 0 , type = "int" , help = "Minimum overlap required [default: %default]" ) opts , args = p . parse_args ( args ) if len ( args ) != 2 : sys . exit ( not p . print_help ( ) ) abedfile , bbedfile = args iw = intersectBed_wao ( abedfile , bbedfile , minOverlap = opts . minOverlap ) groups = Grouper ( ) for a , b in iw : groups . join ( a . accn , b . accn ) ngroups = 0 for group in groups : if len ( group ) > 1 : ngroups += 1 print ( "|" . join ( group ) ) logging . debug ( "A total of {0} piles (>= 2 members)" . format ( ngroups ) )
%prog pile abedfile bbedfile > piles

    Call intersectBed on two bedfiles.