How to use the refgenie.refget.fasta_checksum function in refgenie

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github databio / refgenie / refgenie / refgenie.py View on Github external
if recipe_name == 'fasta' and genome in rgc.genomes_list() \
                    and 'fasta' in rgc.list_assets_by_genome(genome):
                _LOGGER.warning("'{g}' genome is already initialized with other fasta asset ({g}/{a}:{t}). "
                                "It will be re-initialized.".format(g=genome, a=asset_key, t=asset_tag))
            if not build_asset(genome, asset_key, asset_tag, asset_build_package, genome_outfolder,
                               specified_args, specified_params, **input_assets):
                log_path = os.path.abspath(os.path.join(genome_outfolder, asset_key, asset_tag,
                                                        BUILD_STATS_DIR, ORI_LOG_NAME))
                _LOGGER.info("'{}/{}:{}' was not added to the config, but directory has been left in place. "
                             "See the log file for details: {}".format(genome, asset_key, asset_tag, log_path))
                return
            # If the recipe was a fasta, we init the genome
            if recipe_name == 'fasta':
                _LOGGER.info("Computing initial genome digest...")
                collection_checksum, content_checksums = \
                    fasta_checksum(_seek(rgc, genome, asset_key, asset_tag, "fasta"))
                _LOGGER.info("Initializing genome...")
                refgenie_initg(rgc, genome, content_checksums)
            _LOGGER.info("Finished building '{}' asset".format(asset_key))
            with rgc as r:
                # update asset relationships
                r.update_relatives_assets(genome, asset_key, asset_tag, parent_assets)  # adds parents
                for i in parent_assets:
                    parsed_parent = parse_registry_path(i)
                    # adds child (currently built asset) to the parent
                    r.update_relatives_assets(parsed_parent["genome"], parsed_parent["asset"], parsed_parent["tag"],
                                                   ["{}/{}:{}".format(genome, asset_key, asset_tag)], True)
                if args.genome_description is not None:
                    _LOGGER.debug("adding genome ({}) description: '{}'".format(genome, args.genome_description))
                    r.update_genomes(genome, {CFG_GENOME_DESC_KEY: args.genome_description})
                if args.tag_description is not None:
                    _LOGGER.debug("adding tag ({}/{}:{}) description: '{}'".format(genome, asset_key, asset_tag,

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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