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()
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)