Subset a BED file to only have items from the specified chromosome.

def subset_bed_by_chrom(in_file, chrom, data, out_dir=None):
    """Subset a BED file to only have items from the specified chromosome.
    """
    if out_dir is None:
        out_dir = os.path.dirname(in_file)
    base, ext = os.path.splitext(os.path.basename(in_file))
    out_file = os.path.join(out_dir, "%s-%s%s" % (base, chrom, ext))
    if not utils.file_uptodate(out_file, in_file):
        with file_transaction(data, out_file) as tx_out_file:
            _rewrite_bed_with_chrom(in_file, tx_out_file, chrom)
    return out_file