def _combine_regions(all_regions, ref_regions):
    """Combine multiple BEDtools regions of regions into sorted final BEDtool.
    """
    chrom_order = {}
    for i, x in enumerate(ref_regions):
        chrom_order[x.chrom] = i
    def wchrom_key(x):
        chrom, start, end = x
        return (chrom_order[chrom], start, end)
    all_intervals = []
    for region_group in all_regions:
        for region in region_group:
            all_intervals.append((region.chrom, int(region.start), int(region.stop)))
    all_intervals.sort(key=wchrom_key)
    bed_lines = ["%s\t%s\t%s" % (c, s, e) for (c, s, e) in all_intervals]
    return pybedtools.BedTool("\n".join(bed_lines), from_string=True)
Combine multiple BEDtools regions of regions into sorted final BEDtool.