示例#1
0
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)

    l = None
    if args.scheduler:
        load_ipython(args)
    elif args.cores > 1:
        load_multicore(args)
    else:
        l = load_singlecore(args)
    finish(args, l)
示例#2
0
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)

    l = None
    if args.scheduler:
        load_ipython(args)
    elif args.cores > 1:
        load_multicore(args)
    else:
        l = load_singlecore(args)
    finish(args, l)
示例#3
0
def get_gemini_files(data):
    """Enumerate available gemini data files in a standard installation.
    """
    try:
        from gemini import annotations, config
    except ImportError:
        return {}
    return {"base": config.read_gemini_config()["annotation_dir"], "files": annotations.get_anno_files().values()}
示例#4
0
def get_gemini_files(data):
    """Enumerate available gemini data files in a standard installation.
    """
    try:
        from gemini import annotations, config
    except ImportError:
        return {}
    return {"base": config.read_gemini_config()["annotation_dir"],
            "files": annotations.get_anno_files().values()}