def add_vcf_file_to_annotator(self, vcf_file_path, force_all=False): """ Add the variants in vcf_file_path to annotator Convenience wrapper around add_variants_to_annotator """ if not force_all and self.get_annotator_datastore().vcf_files.find_one( {'vcf_file_path': vcf_file_path}): print "VCF already annotated" return print "Scanning VCF file first..." variant_t_list = [] for variant_t in vcf_stuff.iterate_tuples( compressed_file(vcf_file_path)): variant_t_list.append(variant_t) if len(variant_t_list) == 100000: print "Adding another 100000 variants, through {}".format( variant_t_list[-1][0]) self.add_variants_to_annotator(variant_t_list, force_all) variant_t_list = [] self.add_variants_to_annotator(variant_t_list, force_all) self.get_annotator_datastore().vcf_files.insert({ 'vcf_file_path': vcf_file_path, 'date_added': datetime.datetime.utcnow() })
def add_vcf_file_to_annotator(self, vcf_file_path, force_all=False): """ Add the variants in vcf_file_path to annotator Convenience wrapper around add_variants_to_annotator """ print "Scanning VCF file first..." variant_t_list = [] for variant_t in vcf_stuff.iterate_tuples(compressed_file(vcf_file_path)): variant_t_list.append(variant_t) if len(variant_t_list) == 100000: print "Adding another 100000 variants, through {}".format(variant_t_list[-1][0]) self.add_variants_to_annotator(variant_t_list, force_all) variant_t_list = [] self.add_variants_to_annotator(variant_t_list, force_all)
def add_vcf_file_to_annotator(self, vcf_file_path, force_all=False): """ Add the variants in vcf_file_path to annotator Convenience wrapper around add_variants_to_annotator """ if not force_all and self._db.vcf_files.find_one({'vcf_file_path': vcf_file_path}): print "VCF already annotated" return print "Scanning VCF file first..." variant_t_list = [] for variant_t in vcf_stuff.iterate_tuples(compressed_file(vcf_file_path)): variant_t_list.append(variant_t) if len(variant_t_list) == 100000: print "Adding another 100000 variants, through {}".format(variant_t_list[-1][0]) self.add_variants_to_annotator(variant_t_list, force_all) variant_t_list = [] self.add_variants_to_annotator(variant_t_list, force_all) self._db.vcf_files.insert({'vcf_file_path': vcf_file_path, 'date_added': datetime.datetime.utcnow()})