def finish(args, loader=None): """ all things that are performed by single core, multi, ipython should be done here """ if loader is None: loader = GeminiLoader(args, prepare_db=False) print "storing version, header, etc." loader.store_resources() loader.store_version() loader.store_vcf_header() if not args.skip_gene_tables: print "storing gene-detailed" loader._get_gene_detailed() print "storing gene-summary" loader._get_gene_summary() if not args.test_mode: print "updating gene-table" loader.update_gene_table() if not args.test_mode: print "building indices" loader.build_indices_and_disconnect() else: import database database.close_and_commit(loader.c)
def load_singlecore(args): # create a new gemini loader and populate # the gemini db and files from the VCF gemini_loader = GeminiLoader(args) gemini_loader.store_resources() gemini_loader.store_version() gemini_loader.populate_from_vcf() gemini_loader.build_indices_and_disconnect() if not args.no_genotypes and not args.no_load_genotypes: gemini_loader.store_sample_gt_counts()
def load_singlecore(args): # create a new gemini loader and populate # the gemini db and files from the VCF gemini_loader = GeminiLoader(args) gemini_loader.store_resources() gemini_loader.store_version() gemini_loader.populate_from_vcf() if not args.skip_gene_tables and not args.test_mode: gemini_loader.update_gene_table() if not args.test_mode: gemini_loader.build_indices_and_disconnect() if not args.no_genotypes and not args.no_load_genotypes: gemini_loader.store_sample_gt_counts() gemini_annotate.add_extras(args.db, [args.db])