Ebedthan / xgt

Efficient and fast querying and parsing of GTDB's data

xgt

xgt is a Rust tool that enables efficient querying and parsing of the GTDB database. xgt consists of a collection of commands mirroring the GTDB API and providing additional parsing capability.

Installation

git clone https://github.com/Ebedthan/xgt.git
cd xgt

# If default rust install directory is ~/.cargo
cargo install --path . --root ~/.cargo
xgt -h

Quick start guide

# Search subcommand: search GTDB
## Search all Escherichia (genus) genomes
xgt search Escherichia

## Search all genomes with genus name containing escherichia
xgt search --partial escherichia

## Search from a list
xgt search -f list.txt

# Genome subcommand: information about a genome
## Get GTDB genome information
xgt genome GCA_001512625.1

## Get taxon history on GTDB
xgt genome --history GCA_001512625.1

## Get genome metadata
xgt genome --metadata GCA_001512625.1

# Taxon subcommand: information about a specific taxon
## Get direct descendant of a taxon
xgt taxon g__Escherichia

## Search for a taxon in GTDB's current release
xgt taxon --search g__Escherichia

## Search for a taxon in GTDB's current release with partial matching
xgt taxon --search --partial g__Escherichia

Full help is available from xgt --help.

Certificate verification

xgt through ureq performs peer SSL certificate verification by default. To tell xgt to not verify the peer, use the -k/--insecure option. Currently (as of Apr 28, 2024), you should add this option to your command to get the desired result as GTDB API's server has a certificate issue.

Minimum supported Rust version

xgt minimum Rust version is 1.70.0.

Semver

xgt is following Semantic Versioning 2.0.

Licence

xgt is distributed under the terms of both the MIT license and the Apache License (Version 2.0).

See LICENSE-APACHE and LICENSE-MIT for details.

Note

Unstable work is on dev branch.