{"id":13541140,"url":"https://github.com/Euphrasiologist/nu_plugin_bio","last_synced_at":"2025-04-02T08:30:57.645Z","repository":{"id":64024820,"uuid":"557410657","full_name":"Euphrasiologist/nu_plugin_bio","owner":"Euphrasiologist","description":"Bioinformatics plugin for nushell.","archived":false,"fork":false,"pushed_at":"2023-10-21T12:00:00.000Z","size":18160,"stargazers_count":28,"open_issues_count":5,"forks_count":3,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-03-30T04:23:10.471Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Rust","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Euphrasiologist.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2022-10-25T16:30:45.000Z","updated_at":"2025-03-24T23:11:02.000Z","dependencies_parsed_at":"2023-10-21T13:21:19.745Z","dependency_job_id":null,"html_url":"https://github.com/Euphrasiologist/nu_plugin_bio","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Euphrasiologist%2Fnu_plugin_bio","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Euphrasiologist%2Fnu_plugin_bio/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Euphrasiologist%2Fnu_plugin_bio/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Euphrasiologist%2Fnu_plugin_bio/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Euphrasiologist","download_url":"https://codeload.github.com/Euphrasiologist/nu_plugin_bio/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":246781925,"owners_count":20832934,"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":[],"created_at":"2024-08-01T10:00:39.464Z","updated_at":"2025-04-02T08:30:57.243Z","avatar_url":"https://github.com/Euphrasiologist.png","language":"Rust","funding_links":[],"categories":["Plugins"],"sub_categories":[],"readme":"# Nushell bio\n\nA bioinformatics plugin for nushell. This plugin parses most common bioinformatics formats into structured data so you can use them with nushell more effectively.\n\n# Quick setup\n\nGo and get nushell, it's great. I'm assuming you have the rust toolchain installed. Then come back!\n\n```nu\n# clone this repo\ngit clone https://github.com/Euphrasiologist/nu_plugin_bio\n# change into the repo directory\ncd nu_plugin_bio\n# build\n# it's quite a long compile time...\ncargo build --release\n# register the plugin\nregister nu_plugin_bio/target/release/nu_plugin_bio\n\n# see the current file formats currently supported below\n# now you can just use open, and the file extension will be auto-detected.\n\n# there are some test files in the tests/ dir.\nopen ./tests/test.fasta\n    | get id\n\n# if you want to add flags you have to explicitly use from \u003cx\u003e\n# e.g. if you want descriptions in fasta files to be parsed.\n\nopen --raw ./tests/test.fasta \n    | from fasta -d\n    | first\n```\n\nThe backend is a \u003ca href=\"https://github.com/zaeleus/noodles/\"\u003e`noodles`\u003c/a\u003e wrapper, an excellent, all-Rust bioinformatics I/O library.\n\n## Aims\n\nAim to support the following:\n- [x] BAM 1.6\n- [x] BCF 2.2\n  - [x] bcf.gz \n- [x] VCF 4.3\n  - [x] vcf.gz\n- [x] BED(3 only right now)\n- [x] CRAM 3.0\n- [x] FASTA\n  - [x] fa.gz \n- [x] FASTQ\n  - [x] fq.gz\n- [x] GFF3\n- [ ] GTF 2.2\n- [x] SAM 1.6\n- [x] GFA 1.0\n  - [x] gfa.gz\n\nNote that performance will not be optimal with the current state of `nu_plugin`, as we cannot access the engine state of nushell, and therefore need to load entire data structures into memory. Testing still needs to be done on large files.\n\n## More?\n\nIf there's a bioinformatics format you want to add, let me know, or add a PR.","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FEuphrasiologist%2Fnu_plugin_bio","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FEuphrasiologist%2Fnu_plugin_bio","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FEuphrasiologist%2Fnu_plugin_bio/lists"}