Python Sizes.values方法代码示例

# 需要导入模块: from jcvi.formats.sizes import Sizes [as 别名]
# 或者: from jcvi.formats.sizes.Sizes import values [as 别名]
def ancestral(args):
    """
    %prog ancestral ancestral.txt assembly.fasta

    Karyotype evolution of pineapple. The figure is inspired by Amphioxus paper
    Figure 3 and Tetradon paper Figure 9.
    """
    p = OptionParser(ancestral.__doc__)
    opts, args, iopts = p.set_image_options(args, figsize="8x7")

    if len(args) != 2:
        sys.exit(not p.print_help())

    regionsfile, sizesfile = args
    regions = RegionsFile(regionsfile)
    sizes = Sizes(sizesfile).mapping
    sizes = dict((k, v) for (k, v) in sizes.iteritems() if k[:2] == "LG")
    maxsize = max(sizes.values())
    ratio = .5 / maxsize

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

    from jcvi.graphics.base import set2
    a, b, c, d, e, f, g = set2[:7]
    set2 = (c, g, b, e, d, a, f)

    # Upper panel is the evolution of segments
    # All segments belong to one of seven karyotypes 1 to 7
    karyotypes = regions.karyotypes
    xgap = 1. / (1 + len(karyotypes))
    ygap = .05
    mgap = xgap / 4.5
    gwidth = mgap * .75
    tip = .02
    coords = {}
    for i, k in enumerate(regions.karyotypes):
        x = (i + 1) * xgap
        y = .9
        root.text(x, y + tip, "Anc" + k, ha="center")
        root.plot((x, x), (y, y - ygap), "k-", lw=2)
        y -= 2 * ygap
        coords['a'] = (x - 1.5 * mgap , y)
        coords['b'] = (x - .5 * mgap , y)
        coords['c'] = (x + .5 * mgap , y)
        coords['d'] = (x + 1.5 * mgap , y)
        coords['ab'] = join_nodes_vertical(root, coords, 'a', 'b', y + ygap / 2)
        coords['cd'] = join_nodes_vertical(root, coords, 'c', 'd', y + ygap / 2)
        coords['abcd'] = join_nodes_vertical(root, coords, 'ab', 'cd', y + ygap)
        for n in 'abcd':
            nx, ny = coords[n]
            root.text(nx, ny - tip, n, ha="center")
            coords[n] = (nx, ny - ygap / 2)

        kdata = regions.get_karyotype(k)
        for kd in kdata:
            g = kd.group
            gx, gy = coords[g]
            gsize = ratio * kd.span
            gy -= gsize
            p = Rectangle((gx - gwidth / 2, gy),
                           gwidth, gsize, lw=0, color=set2[i])
            root.add_patch(p)
            root.text(gx, gy + gsize / 2, kd.chromosome,
                      ha="center", va="center", color='w')
            coords[g] = (gx, gy - tip)

    # Bottom panel shows the location of segments on chromosomes
    # TODO: redundant code, similar to graphics.chromosome
    ystart = .54
    chr_number = len(sizes)
    xstart, xend = xgap - 2 * mgap, 1 - xgap + 2 * mgap
    xinterval = (xend - xstart - gwidth) / (chr_number - 1)
    chrpos = {}
    for a, (chr, clen) in enumerate(sorted(sizes.items())):
        chr = get_number(chr)
        xx = xstart + a * xinterval + gwidth / 2
        chrpos[chr] = xx
        root.text(xx, ystart + .01, chr, ha="center")
        Chromosome(root, xx, ystart, ystart - clen * ratio, width=gwidth)

    # Start painting
    for r in regions:
        xx = chrpos[r.chromosome]
        yystart = ystart - r.start * ratio
        yyend = ystart - r.end * ratio
        p = Rectangle((xx - gwidth / 2, yystart), gwidth, yyend - yystart,
                      color=set2[int(r.karyotype) - 1], lw=0)
        root.add_patch(p)

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

    pf = "pineapple-karyotype"
    image_name = pf + "." + iopts.format
    savefig(image_name, dpi=iopts.dpi, iopts=iopts)