How to use the refgenconf.MissingGenomeError function in refgenconf

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github databio / refgenie / refgenie / refgenie.py View on Github external
rgc = RefGenConf(filepath=gencfg)
        for a in asset_list:
            a["tag"] = a["tag"] or rgc.get_default_tag(a["genome"], a["asset"],
                                                       use_existing=False)
            _LOGGER.debug("Determined tag for removal: {}".format(a["tag"]))
            if a["seek_key"] is not None:
                raise NotImplementedError("You can't remove a specific seek_key.")
            bundle = [a["genome"], a["asset"], a["tag"]]
            try:
                if not rgc.is_asset_complete(*bundle):
                    with rgc as r:
                        r.cfg_remove_assets(*bundle)
                    _LOGGER.info("Removed an incomplete asset '{}/{}:{}'".
                                 format(*bundle))
                    return
            except (KeyError, MissingAssetError, MissingGenomeError):
                _LOGGER.info("Asset '{}/{}:{}' does not exist".format(*bundle))
                return
        if len(asset_list) > 1:
            if not query_yes_no("Are you sure you want to remove {} assets?".
                                        format(len(asset_list))):
                _LOGGER.info("Action aborted by the user")
                return
            force = True
        for a in asset_list:
            rgc.remove(genome=a["genome"], asset=a["asset"], tag=a["tag"],
                       force=force)

    elif args.command == TAG_CMD:
        rgc = RefGenConf(filepath=gencfg)
        if len(asset_list) > 1:
            raise NotImplementedError("Can only tag 1 asset at a time")

refgenconf

A standardized configuration object for reference genome assemblies

BSD-2-Clause
Latest version published 3 years ago

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