Пример #1
0
    def run(self):
        #name2obj = libcommon.load_pickledir_to_dict(self.indir)
        self.load_indir()
        name2obj = self.name2obj
        attrs = ['clones', 'reads'] 
        plotfmt = self.opts.plotformat
        if not self.avr and len(name2obj) >= 20:
            self.avr = True
        for attr in attrs:
            plotfile = os.path.join(self.outdir, "%s" % attr)
            #if len(name2obj) >= 20:
            if self.avr:
                ldplot.draw_lendist_avr(name2obj, attr, plotfile, plotfmt,
                                        self.opts.dpi, bar=True)
                                        #self.opts.dpi)
            else:
                ldplot.draw_lendist(name2obj, attr, plotfile, plotfmt,
                                    self.opts.dpi)
            # ttests
            g2n = self.opts.group2samples
            if g2n:
                ttestfile = os.path.join(self.outdir, "ttests_%s.txt" % attr)
                lendist_ttests(attr, ttestfile, g2n, name2obj,
                               self.opts.matched, self.opts.pval)

            # median len distribution
            meddist_file  = os.path.join(self.outdir, "median_lendist_%s.txt" % attr)
            lendist_median(name2obj, attr, meddist_file)
Пример #2
0
def draw_plots(name2obj, outdir):
    vfile = os.path.join(outdir, "v")
    vgenes = union_lists([obj.type2gene2clones['v'].keys() for obj in name2obj.values()])
    draw_gene_usage(name2obj, "clones", "v", vfile, vgenes)

    jfile = os.path.join(outdir, "j")
    jgenes = union_lists([obj.type2gene2clones['j'].keys() for obj in name2obj.values()])
    draw_gene_usage(name2obj, "clones", "j", jfile, jgenes)

    lfile = os.path.join(outdir, "lendist")
    draw_lendist(name2obj, "clones", lfile)