ASDB taxonomy handling

NCBI taxdump handling for ASDB

This package is designed to help the antiSMASH database to handle NCBI taxid lookups using NCBI taxdump data.

The package contains both a Rust library as well as a command line tool asdb-taxa to manage a local JSON-based cache of interesting taxa, allowing bulk database imports to speed up compared to parsing directly from the taxdump files.

Installation

cargo install asdb-taxa

Usage

In order to use it, grab the latest taxdump collection and extract it. You'll also need a directory of antiSMASH database result json files.

Then, you can run the command line tool like

asdb-taxa init --cache asdb_cache.json --datadir path/to/asdb/jsons/ --mergeddump path/to/merged.dmp --taxdump path/to/rankedlineage.dmp

to initialise the cache and

asdb-taxa list --cache asdb_cache.json

to list the contents of the provided cache.

For using the library, see the API documentation.

License

Licensed under the Apache License, Version 2.0 (LICENSE or http://www.apache.org/licenses/LICENSE-2.0)

Contribution

Unless you explicitly state otherwise, any contribution intentionally submitted for inclusion in the work by you, as defined in the Apache-2.0 license, shall be licensed as Apache-2.0, without any additional terms or conditions.