{"id":16755304,"url":"https://github.com/ebedthan/xgt","last_synced_at":"2025-03-17T02:31:09.091Z","repository":{"id":153909398,"uuid":"612187610","full_name":"Ebedthan/xgt","owner":"Ebedthan","description":"Efficient and fast querying and parsing of GTDB's data","archived":false,"fork":false,"pushed_at":"2025-03-13T16:47:31.000Z","size":419,"stargazers_count":28,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-03-13T17:51:42.460Z","etag":null,"topics":["bioinformatics","database","rust"],"latest_commit_sha":null,"homepage":"https://github.com/Ebedthan/xgt/wiki","language":"Rust","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Ebedthan.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE-APACHE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2023-03-10T11:43:24.000Z","updated_at":"2025-03-13T16:47:34.000Z","dependencies_parsed_at":"2024-02-11T21:28:34.349Z","dependency_job_id":"716b0c13-1792-4d2a-8fc8-e9630f4e0ad0","html_url":"https://github.com/Ebedthan/xgt","commit_stats":null,"previous_names":[],"tags_count":5,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Ebedthan%2Fxgt","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Ebedthan%2Fxgt/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Ebedthan%2Fxgt/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Ebedthan%2Fxgt/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Ebedthan","download_url":"https://codeload.github.com/Ebedthan/xgt/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243837004,"owners_count":20355812,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioinformatics","database","rust"],"created_at":"2024-10-13T03:07:18.478Z","updated_at":"2025-03-17T02:31:09.085Z","avatar_url":"https://github.com/Ebedthan.png","language":"Rust","funding_links":[],"categories":[],"sub_categories":[],"readme":"# xgt\n\n*Efficient querying and parsing of the GTDB database*\n\n[![Continuous Integration](https://github.com/Ebedthan/xgt/actions/workflows/ci.yml/badge.svg)](https://github.com/Ebedthan/xgt/actions/workflows/ci.yml)\n[![codecov](https://codecov.io/gh/Ebedthan/xgt/branch/main/graph/badge.svg?token=OFAOB6K5KB)](https://codecov.io/gh/Ebedthan/xgt)\n\u003ca href=\"https://github.com/Ebedthan/xgt/blob/main/LICENSE-MIT\"\u003e\n    \u003cimg src=\"https://img.shields.io/badge/license-MIT-blue?style=flat\"\u003e\n\u003c/a\u003e\n\u003ca href=\"https://github.com/Ebedthan/xgt/blob/main/LICENSE-APACHE\"\u003e\n    \u003cimg src=\"https://img.shields.io/badge/license-APACHE-blue?style=flat\"\u003e\n\u003c/a\u003e\n\n\u003e [!WARNING]\n\u003e You should add the `-k/--insecure` option to all your current command as the GTDB API has currently SSL issue.\n\u003e We have not yet decided to switch it as a default configuration as disabling peer SSL certificate verification can be a critical issue.\n\n## 🗺️ Overview\n\n`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.\n\n## 📋 Features\n\n### `search` subcommand\nIt 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.\n\n### `genome` subcommand\nIt 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.\n\n### `taxon` subcommand\nThis tool fetches information about a specific taxon. Users can search for\nthe direct descendants of a taxon and retrieve taxon genomes in the GTDB using partial or exact matches.\n\n## 🔧 Installing\n\n### From source\n\n#### Download source using Git\n\n```\ngit clone https://github.com/Ebedthan/xgt.git\n```\n\n#### Download source using packaged source\n\n* [xgt-0.4.2.tar.gz](https://github.com/Ebedthan/xgt/archive/refs/tags/v0.4.2.tar.gz)\n* [xgt-0.4.2.zip](https://github.com/Ebedthan/xgt/archive/refs/tags/v0.4.2.zip)\n\n#### Installing\n\nYou can install using [cargo](https://doc.rust-lang.org/cargo/):\n\n```\n# Change \"xgt\" to correct folder name\ncd xgt\n\n# If default rust install directory is ~/.cargo\ncargo install --path . --root ~/.cargo\nxgt -h\n```\n\n### Using binaries\n\nPlease find the binaries for the latest release using the [release page](https://github.com/Ebedthan/xgt/releases) or using the direct link below:\n* [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)\n* [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)\n* [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)\n* [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)\n\n## 💡 Examples\n\n```\n# Search subcommand: search GTDB\n## Search all Escherichia (genus) genomes\nxgt search -kw g__Escherichia\n\n## Search all genomes with genus name containing Escherichia\nxgt search -k -o output.csv g__Escherichia\n\n## Search from a list\nxgt search -k -f list.txt\n\n# Genome subcommand: information about a genome\n## Get GTDB genome information\nxgt genome -k GCA_001512625.1\n\n## Get taxon history on GTDB\nxgt genome -k --history GCA_001512625.1\n\n## Get genome metadata\nxgt genome -k --metadata GCA_001512625.1\n\n# Taxon subcommand: information about a specific taxon\n## Get direct descendant of a taxon\nxgt taxon -k g__Escherichia\n\n## Search for a taxon in GTDB's current release\nxgt taxon -k --search g__Escherichia\n\n## Search for a taxon in GTDB's current release with partial matching\nxgt taxon -k --search g__Escherichia\n```\n\n## ⚠️ Issue Tracker\n\nFound a bug ? Have an enhancement request ? Head over to the [GitHub issue\ntracker](https://github.com/Ebedthan/xgt/issues) if you need to report\nor ask something. If you are filing in on a bug, please include as much\ninformation as you can about the issue, and try to recreate the same bug\nin a simple, easily reproducible situation.\n\n## ⚖️ License\n\n`xgt` is distributed under the terms of both the MIT license and the Apache License (Version 2.0).\n\nSee [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.\n\nFull help is available from `xgt --help`.\n\n## Minimum supported Rust version\n`xgt` minimum [Rust](https://www.rust-lang.org/) version is 1.70.0.\n\n## Semver\n`xgt` is following [Semantic Versioning 2.0](https://semver.org/).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Febedthan%2Fxgt","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Febedthan%2Fxgt","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Febedthan%2Fxgt/lists"}