Beispiel #1
0
    def yield_karyotype(self, karyotype):
        assert self.level == 1, "Karyotype file can only be built for the top level." 
        line = ['chr','-','c_c','Cell_Communication','0','725', 'spectral-5-div-1']
        
        ### if there s only one chromosome create a hypothetical one
        ##### very unpythonic but it's too late to quench the root of the circular import evil.    
        from pacfm.controller import CircosConfigParser
        ccp= CircosConfigParser("conf")
        ccp.parse()
        chromosomes= []

        for chromosome in self.chromosomes:
            name= chromosome.name
            line[2] = karyotype[name]
            line[3] = name.replace(' ','_')
            line[5] = str(chromosome.get_end())
            chromosomes.append(karyotype[name])
            yield "\t".join(line)+ "\n"
       
        if len(self.chromosomes) == 1:
            name= "Hypothetical"
            abbr= "h"
            end= "2"
            line[2]= abbr
            line[3]= name
            line[5]= end
            chromosomes.append(abbr)
            yield "\t".join(line) +"\n"
   
        
        ccp.set("chromosomes", ";".join(chromosomes))
        ccp.write() 
Beispiel #2
0
 def dump(self):
     ### very unpythonic
     from pacfm.controller import CircosConfigParser
     
     pickle.dump(self.items, open(self.dmp_file,'w'))
     parser= CircosConfigParser('plots')
     parser.parse()
     for plot in self.items:    
         parser.set('type', plot.plot_type, 'plot', 'index', 'plot_%s'%plot.level)
         parser.set('color', plot.color_scheme, 'plot', 'index', 'plot_%s'%plot.level)
         color=plot.color
         if color is not None:
             color= list(color)
             if len(color) == 4:
                 color= list(color)
                 color[3] = 1- (color[3] / 255.0)
     
             color= ','.join(map(str, color))
     
         parser.set('fill_color',color, 'plot', 'index', 'plot_%s'%plot.level)
         parser.set('min', plot.min_value, 'plot', 'index', 'plot_%s'%plot.level)
         parser.set('max', plot.max_value, 'plot', 'index', 'plot_%s'%plot.level)