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()
