def A50(args):
    p = OptionParser(A50.__doc__)
    p.add_option("--overwrite", default=False, action="store_true",
            help="overwrite .rplot file if exists [default: %default]")
    p.add_option("--cutoff", default=0, type="int", dest="cutoff",
            help="use contigs above certain size [default: %default]")
    p.add_option("--stepsize", default=10, type="int", dest="stepsize",
            help="stepsize for the distribution [default: %default]")
    opts, args = p.parse_args(args)

    if not args:
        sys.exit(p.print_help())

    import numpy as np
    from jcvi.utils.table import loadtable

    stepsize = opts.stepsize  # use stepsize to speed up drawing
    rplot = "A50.rplot"
    if not op.exists(rplot) or opts.overwrite:
        fw = open(rplot, "w")
        header = "\t".join(("index", "cumsize", "fasta"))
        statsheader = ("Fasta", "L50", "N50", "Min", "Max", "Average", "Sum",
                "Counts")
        statsrows = []
        print >>fw, header
        for fastafile in args:
            f = Fasta(fastafile, index=False)
            ctgsizes = [length for k, length in f.itersizes()]
            ctgsizes = np.array(ctgsizes)

            a50, l50, n50 = calculate_A50(ctgsizes, cutoff=opts.cutoff)
            cmin, cmax, cmean = min(ctgsizes), max(ctgsizes), np.mean(ctgsizes)
            csum, counts = np.sum(ctgsizes), len(ctgsizes)
            cmean = int(round(cmean))
            statsrows.append((fastafile, l50, n50, cmin, cmax, cmean, csum,
                counts))

            logging.debug("`{0}` ctgsizes: {1}".format(fastafile, ctgsizes))

            tag = "{0} (L50={1})".format(\
                    op.basename(fastafile).rsplit(".", 1)[0], l50)
            logging.debug(tag)

            for i, s in zip(xrange(0, len(a50), stepsize), a50[::stepsize]):
                print >> fw, "\t".join((str(i), str(s / 1000000.), tag))
        fw.close()

        table = loadtable(statsheader, statsrows)
        print >> sys.stderr, table

    generate_plot(rplot)
%prog A50 contigs_A.fasta contigs_B.fasta ...
dataset/ETHPy150Open tanghaibao/jcvi/graphics/assembly.py/A50