{"id":20386917,"url":"https://github.com/cmdcolin/gff-nostream","last_synced_at":"2025-04-12T09:54:09.677Z","repository":{"id":255445460,"uuid":"852300783","full_name":"cmdcolin/gff-nostream","owner":"cmdcolin","description":null,"archived":false,"fork":false,"pushed_at":"2025-02-09T20:40:56.000Z","size":3036,"stargazers_count":2,"open_issues_count":1,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-04-12T09:54:02.211Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"TypeScript","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/cmdcolin.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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":"2024-09-04T15:16:53.000Z","updated_at":"2025-02-25T10:25:37.000Z","dependencies_parsed_at":"2025-01-16T21:34:26.383Z","dependency_job_id":"e6b2d582-ad49-4754-a8ca-2ff650568c70","html_url":"https://github.com/cmdcolin/gff-nostream","commit_stats":null,"previous_names":["cmdcolin/gff-nostream","cmdcolin/nostream-gff-js"],"tags_count":11,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdcolin%2Fgff-nostream","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdcolin%2Fgff-nostream/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdcolin%2Fgff-nostream/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdcolin%2Fgff-nostream/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cmdcolin","download_url":"https://codeload.github.com/cmdcolin/gff-nostream/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248550634,"owners_count":21122932,"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":"2024-11-15T02:41:23.229Z","updated_at":"2025-04-12T09:54:09.656Z","avatar_url":"https://github.com/cmdcolin.png","language":"TypeScript","funding_links":[],"categories":[],"sub_categories":[],"readme":"# gff-nostream\n\n[![Build Status](https://img.shields.io/github/actions/workflow/status/cmdcolin/gff-nostream/push.yml?branch=master\u0026logo=github\u0026style=for-the-badge)](https://github.com/cmdcolin/gff-nostream/actions?query=branch%3Amaster+workflow%3APush+)\n\nParse GFF3 data. This is a simplified version of\n[@gmod/gff](https://github.com/GMOD/gff-js) with just basic parsing and no\nnode.js stream module usage\n\n## Install\n\n    $ npm install --save gff-nostream\n\n## Usage\n\n```js\nconst { parseStringSync } = require('gff-nostream')\n// or in ES6 (recommended)\nimport { parseStringSync } from 'gff-nostream'\n\nconst fs = require('fs')\n\n// parse a string of gff3 synchronously\nconst stringOfGFF3 = fs.readFileSync('my_annotations.gff3', 'utf8')\nconst arrayOfThings = gff.parseStringSync(stringOfGFF3)\n```\n\n## Object format\n\n### features\n\nIn GFF3, features can have more than one location. We parse features as\narrayrefs of all the lines that share that feature's ID. Values that are `.` in\nthe GFF3 are `null` in the output.\n\nA simple feature that's located in just one place:\n\n```json\n[\n  {\n    \"seq_id\": \"ctg123\",\n    \"source\": null,\n    \"type\": \"gene\",\n    \"start\": 1000,\n    \"end\": 9000,\n    \"score\": null,\n    \"strand\": \"+\",\n    \"phase\": null,\n    \"attributes\": {\n      \"ID\": [\"gene00001\"],\n      \"Name\": [\"EDEN\"]\n    },\n    \"child_features\": [],\n    \"derived_features\": []\n  }\n]\n```\n\nA CDS called `cds00001` located in two places:\n\n```json\n[\n  {\n    \"seq_id\": \"ctg123\",\n    \"source\": null,\n    \"type\": \"CDS\",\n    \"start\": 1201,\n    \"end\": 1500,\n    \"score\": null,\n    \"strand\": \"+\",\n    \"phase\": \"0\",\n    \"attributes\": {\n      \"ID\": [\"cds00001\"],\n      \"Parent\": [\"mRNA00001\"]\n    },\n    \"child_features\": [],\n    \"derived_features\": []\n  },\n  {\n    \"seq_id\": \"ctg123\",\n    \"source\": null,\n    \"type\": \"CDS\",\n    \"start\": 3000,\n    \"end\": 3902,\n    \"score\": null,\n    \"strand\": \"+\",\n    \"phase\": \"0\",\n    \"attributes\": {\n      \"ID\": [\"cds00001\"],\n      \"Parent\": [\"mRNA00001\"]\n    },\n    \"child_features\": [],\n    \"derived_features\": []\n  }\n]\n```\n\n## API\n\n\u003c!-- Generated by documentation.js. Update this documentation by updating the source code. --\u003e\n\n#### Table of Contents\n\n- [ParseOptions](#parseoptions)\n  - [disableDerivesFromReferences](#disablederivesfromreferences)\n  - [encoding](#encoding)\n  - [parseFeatures](#parsefeatures)\n  - [parseDirectives](#parsedirectives)\n  - [parseComments](#parsecomments)\n  - [parseSequences](#parsesequences)\n  - [parseAll](#parseall)\n\n### ParseOptions\n\nParser options\n\n#### disableDerivesFromReferences\n\nWhether to resolve references to derives from features\n\nType:\n[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)\n\n#### encoding\n\nText encoding of the input GFF3. default 'utf8'\n\nType: BufferEncoding\n\n#### parseFeatures\n\nWhether to parse features, default true\n\nType:\n[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)\n\n#### parseDirectives\n\nWhether to parse directives, default false\n\nType:\n[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)\n\n#### parseComments\n\nWhether to parse comments, default false\n\nType:\n[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)\n\n#### parseSequences\n\nWhether to parse sequences, default true\n\nType:\n[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)\n\n#### parseAll\n\nParse all features, directives, comments, and sequences. Overrides other parsing\noptions. Default false.\n\nType:\n[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcmdcolin%2Fgff-nostream","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcmdcolin%2Fgff-nostream","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcmdcolin%2Fgff-nostream/lists"}