def main():
    p = OptionParser(main.__doc__)
    p.add_option("--title", default="Medicago truncatula v3.5",
            help="title of the image [default: `%default`]")
    p.add_option("--gauge", default=False, action="store_true",
            help="draw a gauge with size label [default: %default]")
    p.add_option("--imagemap", default=False, action="store_true",
            help="generate an HTML image map associated with the image [default: %default]")
    p.add_option("--winsize", default=50000, type="int",
            help="if drawing an imagemap, specify the window size (bases) of each map element "
                 "[default: %default bp]")
    p.add_option("--empty", help="Write legend for unpainted region")
    opts, args, iopts = p.set_image_options(figsize="6x6", dpi=300)

    if len(args) not in (1, 2):
        sys.exit(p.print_help())

    bedfile = args[0]
    mappingfile = None
    if len(args) == 2:
        mappingfile = args[1]

    winsize = opts.winsize
    imagemap = opts.imagemap
    w, h = iopts.w, iopts.h
    dpi = iopts.dpi

    prefix = bedfile.rsplit(".", 1)[0]
    figname = prefix + "." + opts.format
    if imagemap:
        imgmapfile = prefix + '.map'
        mapfh = open(imgmapfile, "w")
        print >> mapfh, '<map id="' + prefix + '">'

    if mappingfile:
        mappings = DictFile(mappingfile, delimiter="\t")
        classes = sorted(set(mappings.values()))
        logging.debug("A total of {0} classes found: {1}".format(len(classes),
            ','.join(classes)))
    else:
        mappings = {}
        classes = []
        logging.debug("No classes registered (no id_mappings given).")

    mycolors = "rgbymc"
    class_colors = dict(zip(classes, mycolors))

    bed = Bed(bedfile)
    chr_lens = {}
    centromeres = {}
    for b, blines in groupby(bed, key=(lambda x: x.seqid)):
        blines = list(blines)
        maxlen = max(x.end for x in blines)
        chr_lens[b] = maxlen

    for b in bed:
        accn = b.accn
        if accn == "centromere":
            centromeres[b.seqid] = b.start
        if accn in mappings:
            b.accn = mappings[accn]
        else:
            b.accn = '-'

    chr_number = len(chr_lens)
    if centromeres:
        assert chr_number == len(centromeres)

    fig = plt.figure(1, (w, h))
    root = fig.add_axes([0, 0, 1, 1])

    r = .7  # width and height of the whole chromosome set
    xstart, ystart = .15, .85
    xinterval = r / chr_number
    xwidth = xinterval * .5  # chromosome width
    max_chr_len = max(chr_lens.values())
    ratio = r / max_chr_len  # canvas / base

    # first the chromosomes
    for a, (chr, clen) in enumerate(sorted(chr_lens.items())):
        xx = xstart + a * xinterval + .5 * xwidth
        root.text(xx, ystart + .01, chr, ha="center")
        if centromeres:
            yy = ystart - centromeres[chr] * ratio
            ChromosomeWithCentromere(root, xx, ystart, yy,
                    ystart - clen * ratio, width=xwidth)
        else:
            Chromosome(root, xx, ystart, ystart - clen * ratio, width=xwidth)

    chr_idxs = dict((a, i) for i, a in enumerate(sorted(chr_lens.keys())))

    alpha = .75
    # color the regions
    for chr in sorted(chr_lens.keys()):
        segment_size, excess = 0, 0
        bac_list = []
        for b in bed.sub_bed(chr):
            clen = chr_lens[chr]
            idx = chr_idxs[chr]
            klass = b.accn
            start = b.start
            end = b.end
            xx = xstart + idx * xinterval
            yystart = ystart - end * ratio
            yyend = ystart - start * ratio
            root.add_patch(Rectangle((xx, yystart), xwidth, yyend - yystart,
                fc=class_colors.get(klass, "w"), lw=0, alpha=alpha))

            if imagemap:
                """
                `segment` : size of current BAC being investigated + `excess`
                `excess`  : left-over bases from the previous BAC, as a result of
                            iterating over `winsize` regions of `segment`
                """
                if excess == 0:
                    segment_start = start
                segment = (end - start + 1) + excess
                while True:
                    if segment < winsize:
                        bac_list.append(b.accn)
                        excess = segment
                        break
                    segment_end = segment_start + winsize - 1
                    tlx, tly, brx, bry = xx, (1 - ystart) + segment_start * ratio, \
                                  xx + xwidth, (1 - ystart) + segment_end * ratio
                    print >> mapfh, '\t' + write_ImageMapLine(tlx, tly, brx, bry, \
                            w, h, dpi, chr+":"+",".join(bac_list), segment_start, segment_end)

                    segment_start += winsize
                    segment -= winsize
                    bac_list = []

        if imagemap and excess > 0:
            bac_list.append(b.accn)
            segment_end = end
            tlx, tly, brx, bry = xx, (1 - ystart) + segment_start * ratio, \
                          xx + xwidth, (1 - ystart) + segment_end * ratio
            print >> mapfh, '\t' + write_ImageMapLine(tlx, tly, brx, bry, \
                    w, h, dpi, chr+":"+",".join(bac_list), segment_start, segment_end)

    if imagemap:
        print >> mapfh, '</map>'
        mapfh.close()
        logging.debug("Image map written to `{0}`".format(mapfh.name))

    if opts.gauge:
        xstart, ystart = .9, .85
        Gauge(root, xstart, ystart - r, ystart, max_chr_len)

    # class legends, four in a row
    xstart = .1
    xinterval = .2
    xwidth = .04
    yy = .08
    for klass, cc in sorted(class_colors.items()):
        if klass == '-':
            continue
        root.add_patch(Rectangle((xstart, yy), xwidth, xwidth, fc=cc, lw=0,
            alpha=alpha))
        root.text(xstart + xwidth + .01, yy, klass, fontsize=10)
        xstart += xinterval

    empty = opts.empty
    if empty:
        root.add_patch(Rectangle((xstart, yy), xwidth, xwidth, fill=False, lw=1))
        root.text(xstart + xwidth + .01, yy, empty, fontsize=10)

    root.text(.5, .95, opts.title, fontstyle="italic", ha="center", va="center")

    root.set_xlim(0, 1)
    root.set_ylim(0, 1)
    root.set_axis_off()

    savefig(figname, dpi=dpi, iopts=iopts)
Test channels-dropping functionality
dataset/ETHPy150Open tanghaibao/jcvi/graphics/chromosome.py/main--crossover with--dataset/ETHPy150Open mne-tools/mne-python/mne/tests/test_evoked.py/test_drop_channels_mixin