https://github.com/ebedthan/xgt
Efficient and fast querying and parsing of GTDB's data
https://github.com/ebedthan/xgt
bioinformatics database rust
Last synced: 3 months ago
JSON representation
Efficient and fast querying and parsing of GTDB's data
- Host: GitHub
- URL: https://github.com/ebedthan/xgt
- Owner: Ebedthan
- License: apache-2.0
- Created: 2023-03-10T11:43:24.000Z (about 2 years ago)
- Default Branch: main
- Last Pushed: 2025-03-13T16:47:31.000Z (3 months ago)
- Last Synced: 2025-03-13T17:51:42.460Z (3 months ago)
- Topics: bioinformatics, database, rust
- Language: Rust
- Homepage: https://github.com/Ebedthan/xgt/wiki
- Size: 409 KB
- Stars: 28
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE-APACHE
Awesome Lists containing this project
README
# xgt
*Efficient querying and parsing of the GTDB database*
[](https://github.com/Ebedthan/xgt/actions/workflows/ci.yml)
[](https://codecov.io/gh/Ebedthan/xgt)
> [!WARNING]
> You should add the `-k/--insecure` option to all your current command as the GTDB API has currently SSL issue.
> We have not yet decided to switch it as a default configuration as disabling peer SSL certificate verification can be a critical issue.
## 🗺️ Overview
`xgt` is a [Rust](https://www.rust-lang.org/) 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.
## 📋 Features
### `search` subcommand
It offers both exact and partial matches, along with additional parsing capabilities. Additionally, it supports searching the GTDB using multiple names listed in a plain text file.
### `genome` subcommand
It can be used to retrieve information about a genome. The `--metadata` option provides concise genome metadata such as accession and surveillance data, while `--history` retrieves the genome taxon history in the GTDB. The default option fetches nucleotide, gene, and taxonomy metadata of the genome.
### `taxon` subcommand
This tool fetches information about a specific taxon. Users can search for
the direct descendants of a taxon and retrieve taxon genomes in the GTDB using partial or exact matches.
## 🔧 Installing
### From source
#### Download source using Git
```
git clone https://github.com/Ebedthan/xgt.git
```
#### Download source using packaged source
* [xgt-0.4.2.tar.gz](https://github.com/Ebedthan/xgt/archive/refs/tags/v0.4.2.tar.gz)
* [xgt-0.4.2.zip](https://github.com/Ebedthan/xgt/archive/refs/tags/v0.4.2.zip)
#### Installing
You can install using [cargo](https://doc.rust-lang.org/cargo/):
```
# Change "xgt" to correct folder name
cd xgt
# If default rust install directory is ~/.cargo
cargo install --path . --root ~/.cargo
xgt -h
```
### Using binaries
Please find the binaries for the latest release using the [release page](https://github.com/Ebedthan/xgt/releases) or using the direct link below:
* [Apple Silicon macOS](https://github.com/Ebedthan/xgt/releases/download/v0.4.2/xgt-aarch64-apple-darwin.tar.xz) with its [checksum](https://github.com/Ebedthan/xgt/releases/download/v0.4.2/xgt-aarch64-apple-darwin.tar.xz.sha256)
* [Intel macOS](https://github.com/Ebedthan/xgt/releases/download/v0.4.2/xgt-x86_64-apple-darwin.tar.xz) with its [checksum](https://github.com/Ebedthan/xgt/releases/download/v0.4.2/xgt-x86_64-apple-darwin.tar.xz.sha256)
* [x64 Windows](https://github.com/Ebedthan/xgt/releases/download/v0.4.2/xgt-x86_64-pc-windows-msvc.zip) with its [checksum](https://github.com/Ebedthan/xgt/releases/download/v0.4.2/xgt-x86_64-pc-windows-msvc.zip.sha256)
* [x64 Linux](https://github.com/Ebedthan/xgt/releases/download/v0.4.2/xgt-x86_64-unknown-linux-gnu.tar.xz) with its [checksum](https://github.com/Ebedthan/xgt/releases/download/v0.4.2/xgt-x86_64-unknown-linux-gnu.tar.xz.sha256)
## 💡 Examples
```
# Search subcommand: search GTDB
## Search all Escherichia (genus) genomes
xgt search -kw g__Escherichia
## Search all genomes with genus name containing Escherichia
xgt search -k -o output.csv g__Escherichia
## Search from a list
xgt search -k -f list.txt
# Genome subcommand: information about a genome
## Get GTDB genome information
xgt genome -k GCA_001512625.1
## Get taxon history on GTDB
xgt genome -k --history GCA_001512625.1
## Get genome metadata
xgt genome -k --metadata GCA_001512625.1
# Taxon subcommand: information about a specific taxon
## Get direct descendant of a taxon
xgt taxon -k g__Escherichia
## Search for a taxon in GTDB's current release
xgt taxon -k --search g__Escherichia
## Search for a taxon in GTDB's current release with partial matching
xgt taxon -k --search g__Escherichia
```
## ⚠️ Issue Tracker
Found a bug ? Have an enhancement request ? Head over to the [GitHub issue
tracker](https://github.com/Ebedthan/xgt/issues) if you need to report
or ask something. If you are filing in on a bug, please include as much
information as you can about the issue, and try to recreate the same bug
in a simple, easily reproducible situation.
## ⚖️ License
`xgt` is distributed under the terms of both the MIT license and the Apache License (Version 2.0).
See [LICENSE-APACHE](https://github.com/Ebedthan/xgt/blob/main/LICENSE-APACHE) and [LICENSE-MIT](https://github.com/Ebedthan/xgt/blob/main/LICENSE-MIT) for details.
Full help is available from `xgt --help`.
## Minimum supported Rust version
`xgt` minimum [Rust](https://www.rust-lang.org/) version is 1.70.0.
## Semver
`xgt` is following [Semantic Versioning 2.0](https://semver.org/).