How to use the refgenie._version.__version__ function in refgenie

To help you get started, we’ve selected a few refgenie examples, based on popular ways it is used in public projects.

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github databio / refgenie / refgenie / refgenie.py View on Github external
def main():
    """ Primary workflow """
    parser = logmuse.add_logging_options(build_argparser())
    args, remaining_args = parser.parse_known_args()
    global _LOGGER
    _LOGGER = logmuse.logger_via_cli(args, make_root=True)
    _LOGGER.debug("refgenie {}".format(__version__))
    _LOGGER.debug("Args: {}".format(args))

    if not args.command:
        parser.print_help()
        _LOGGER.error("No command given")
        sys.exit(1)

    gencfg = refgenconf.select_genome_config(filename=args.genome_config, check_exist=not args.command == INIT_CMD,
                                             on_missing=lambda fp: fp, strict_env=True)
    if gencfg is None:
        raise MissingGenomeConfigError(args.genome_config)
    _LOGGER.debug("Determined genome config: {}".format(gencfg))

    # From user input we want to construct a list of asset dicts, where each
    # asset has a genome name, asset name, and tag
github databio / refgenie / refgenie / refgenie.py View on Github external
def build_argparser():
    """
    Builds argument parser.

    :return argparse.ArgumentParser
    """

    banner = "%(prog)s - reference genome asset manager"
    additional_description = "\nhttps://refgenie.databio.org"

    parser = VersionInHelpParser(
        prog="refgenie",
        version=__version__,
        description=banner,
        epilog=additional_description)

    subparsers = parser.add_subparsers(dest="command")

    def add_subparser(cmd, description):
        return subparsers.add_parser(
            cmd, description=description, help=description)

    sps = {}
    for cmd, desc in SUBPARSER_MESSAGES.items():
        sps[cmd] = add_subparser(cmd, desc)
        # It's required for init
        sps[cmd].add_argument(
            '-c', '--genome-config', required=(cmd == INIT_CMD), dest="genome_config",
            help="Path to local genome configuration file. Optional if {} environment variable is set."

refgenie

Refgenie creates a standardized folder structure for reference genome files and indexes. You can download pre-built genomes or build your own for any fasta file

BSD-2-Clause
Latest version published 3 years ago

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