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])
def load_ipython(args): grabix_file = bgzip(args.vcf) with cluster_view(*get_ipython_args(args)) as view: chunks = load_chunks_ipython(grabix_file, args, view) merge_chunks_ipython(chunks, args.db, view) gemini_annotate.add_extras(args.db, chunks)
def load_multicore(args): grabix_file = bgzip(args.vcf) chunks = load_chunks_multicore(grabix_file, args) merge_chunks_multicore(chunks, args.db) gemini_annotate.add_extras(args.db, chunks)
def load_multicore(args): grabix_file = bgzip(args.vcf) chunks = load_chunks_multicore(grabix_file, args) merge_chunks_multicore(chunks, args) gemini_annotate.add_extras(args.db, chunks, region_only=False, tempdir=args.tempdir)