Beispiel #1
0
    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)
Beispiel #2
0
    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