def coverage(args):
    """
    %prog coverage coordsfile

    Report the coverage per query record, useful to see which query matches
    reference.  The coords file MUST be filtered with supermap::

    jcvi.algorithms.supermap --filter query
    """
    p = OptionParser(coverage.__doc__)
    p.add_option("-c", dest="cutoff", default=0.5, type="float",
            help="only report query with coverage greater than [default: %default]")

    opts, args = p.parse_args(args)

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

    coordsfile, = args
    fp = open(coordsfile)

    coords = []
    for row in fp:
        try:
            c = CoordsLine(row)
        except __HOLE__:
            continue
        coords.append(c)

    coords.sort(key=lambda x: x.query)

    coverages = []
    for query, lines in groupby(coords, key=lambda x: x.query):
        cumulative_cutoff = sum(x.querycov for x in lines)
        coverages.append((query, cumulative_cutoff))

    coverages.sort(key=lambda x: (-x[1], x[0]))
    for query, cumulative_cutoff in coverages:
        if cumulative_cutoff < opts.cutoff:
            break
        print "{0}\t{1:.2f}".format(query, cumulative_cutoff)
dataset/ETHPy150Open tanghaibao/jcvi/formats/coords.py/coverage