def run(self, number=0):
if number == 0:
number = hotspothist_mongo.get_next_number()
else:
if not hotspothist_mongo.is_hotspot_hist(number):
self.__log_not_hotspot_number()
sys.exit(1)
hotspothist_mongo.add_new_hist(number)
hotspot_dir = self.__ensure_directory(number)
if not hotspothist_mongo.has_loaded_hotspots(number):
if not self.__has_complete_hotspot_vcfs(hotspot_dir):
# CREATING HOTSPOT FILE
self.create_hotspot_file(hotspot_dir)
print "Perform hotspotting"
print "Load hotspot"
# ANNOTATING
annotate = Annotate()
annovar_input = self.create_annovar_input(hotspot_dir)
annovar_output = annotate.annotate_hotspot(annovar_input)
annotate.save_annotations(annovar_output)
