How to use the refgenconf.select_genome_config function in refgenconf

To help you get started, we’ve selected a few refgenconf 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

    if "asset_registry_paths" in args and args.asset_registry_paths:
        _LOGGER.debug("Found registry_path: {}".format(args.asset_registry_paths))
        asset_list = [parse_registry_path(x) for x in args.asset_registry_paths]

        for a in asset_list:
            # every asset must have a genome, either provided via registry path
            # or the args.genome arg.
            if not a["genome"]:
github databio / pepatac / pipelines / pepatac.py View on Github external
def _add_resources(args, res, asset_dict=None):
    """
    Add additional resources needed for pipeline.

    :param argparse.Namespace args: binding between option name and argument,
        e.g. from parsing command-line options
    :param pm.config.resources res: pipeline manager resources list
    :param asset_dict list: list of dictionary of assets to add
    """

    rgc = RGC(select_genome_config(res.get("genome_config")))

    key_errors = []
    exist_errors = []
    required_list = []

    # Check that bowtie2 indicies exist for specified prealignments
    for reference in args.prealignments:
        for asset in [BT2_IDX_KEY]:
            try:
                res[asset] = rgc.seek(reference, asset)
            except KeyError:
                err_msg = "{} for {} is missing from REFGENIE config file."
                pm.fail_pipeline(KeyError(err_msg.format(asset, reference)))
            except:
                err_msg = "{} for {} does not exist."
                pm.fail_pipeline(IOError(err_msg.format(asset, reference)))

refgenconf

A standardized configuration object for reference genome assemblies

BSD-2-Clause
Latest version published 3 years ago

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