def load(parser, args): if (args.db is None or args.vcf is None): parser.print_help() exit("ERROR: load needs both a VCF file and a database file\n") annos = annotations.get_anno_files(args) # force skipping CADD and GERP if the data files have not been installed if args.skip_cadd is False: if 'cadd_score' not in annos: sys.stderr.write("\nCADD scores are not being loaded because the" " annotation file could not be found.\n" "`Run gemini update --dataonly --extra cadd_score`" " to install the annotation file.\n\n") args.skip_cadd = True else: sys.stderr.write("CADD scores are being loaded (to skip use:--skip-cadd).\n") if args.skip_gerp_bp is False: if 'gerp_bp' not in annos: sys.stderr.write("\nGERP per bp is not being loaded because the annotation file" " could not be found.\n Run `gemini update --dataonly --extra gerp_bp`" " to install the annotation file.\n\n") args.skip_gerp_bp = True else: sys.stderr.write("GERP per bp is being loaded (to skip use:--skip-gerp-bp).\n") # collect of the the add'l annotation files annotations.load_annos(args) if args.scheduler: load_ipython(args) elif args.cores > 1: load_multicore(args) else: load_singlecore(args) if not args.no_bcolz: from gemini.gemini_bcolz import create create(args.db)