def create_hotspot_file(self, hotspot_dir):
hotspot_input = "%s/hotspot_orig.vcf" % hotspot_dir
final_hotspot = hotspot_input.split(".vcf")[0]+'_prepped.vcf'
if os.path.isfile(final_hotspot):
self.__log_hotspot_already_exists()
else:
with open(hotspot_input, "w") as out_file:
vcf_header = "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tsample\n"
out_file.write(vcf_header)
hotspots = hotspot_mongo.get_valid_hotspot_vars()
self.__process_hotspot_vars(hotspots, out_file)
ref_fasta = self.project_config['ref_fasta']
final_hotspot = hotspot_input.split(".vcf")[0]+'_prepped.vcf'
self.__log_preparing_hotpot()
hotspot_bash.prep_hotspot(hotspot_input, final_hotspot, ref_fasta)
self.reconcile_hotspot_and_database(final_hotspot)
def create_annovar_input(self, hotspot_dir):
annovar_input = "%s/annov_in.vcf" % hotspot_dir
final_annovar_input = annovar_input.split(".vcf")[0]+'_prepped.vcf'
if os.path.isfile(final_annovar_input):
self.__log_hotspot_already_exists()
else:
with open(annovar_input, "w") as out_file:
vcf_header = "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tsample\n"
out_file.write(vcf_header)
hotspots = hotspot_mongo.get_valid_hotspot_vars()
self.__get_unannotated_hotspots(hotspots, out_file)
ref_fasta = self.project_config['ref_fasta']
final_annovar_input = annovar_input.split(".vcf")[0]+'_prepped.vcf'
self.__log_preparing_hotpot()
hotspot_bash.prep_hotspot(annovar_input, final_annovar_input, ref_fasta)
return final_annovar_input