├── index.js ├── .npmignore ├── .gitignore ├── docs ├── public │ ├── fonts │ │ ├── aller-bold.eot │ │ ├── aller-bold.ttf │ │ ├── aller-bold.woff │ │ ├── aller-light.eot │ │ ├── aller-light.ttf │ │ ├── aller-light.woff │ │ ├── novecento-bold.eot │ │ ├── novecento-bold.ttf │ │ └── novecento-bold.woff │ └── stylesheets │ │ └── normalize.css ├── bionode-logo.min.svg ├── docco.css └── bionode-seq.html ├── contributors.md ├── .travis.yml ├── .jshintrc ├── LICENSE ├── package.json ├── CODE_OF_CONDUCT.md ├── README.md ├── test └── bionode-seq.js ├── cli.js ├── bionode-seq.min.js └── lib └── bionode-seq.js /index.js: -------------------------------------------------------------------------------- 1 | module.exports = require('./lib/bionode-seq') 2 | -------------------------------------------------------------------------------- /.npmignore: -------------------------------------------------------------------------------- 1 | .DS_Store 2 | node_modules 3 | coverage 4 | *.log -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | .DS_Store 2 | node_modules 3 | coverage 4 | *.log 5 | .coveralls.yml 6 | -------------------------------------------------------------------------------- /docs/public/fonts/aller-bold.eot: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bionode/bionode-seq/master/docs/public/fonts/aller-bold.eot -------------------------------------------------------------------------------- /docs/public/fonts/aller-bold.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bionode/bionode-seq/master/docs/public/fonts/aller-bold.ttf -------------------------------------------------------------------------------- /docs/public/fonts/aller-bold.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bionode/bionode-seq/master/docs/public/fonts/aller-bold.woff -------------------------------------------------------------------------------- /docs/public/fonts/aller-light.eot: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bionode/bionode-seq/master/docs/public/fonts/aller-light.eot -------------------------------------------------------------------------------- /docs/public/fonts/aller-light.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bionode/bionode-seq/master/docs/public/fonts/aller-light.ttf -------------------------------------------------------------------------------- /docs/public/fonts/aller-light.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bionode/bionode-seq/master/docs/public/fonts/aller-light.woff -------------------------------------------------------------------------------- /docs/public/fonts/novecento-bold.eot: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bionode/bionode-seq/master/docs/public/fonts/novecento-bold.eot -------------------------------------------------------------------------------- /docs/public/fonts/novecento-bold.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bionode/bionode-seq/master/docs/public/fonts/novecento-bold.ttf -------------------------------------------------------------------------------- /docs/public/fonts/novecento-bold.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bionode/bionode-seq/master/docs/public/fonts/novecento-bold.woff -------------------------------------------------------------------------------- /contributors.md: -------------------------------------------------------------------------------- 1 | ## Contributors 2 | ##### [Generated](https://github.com/jakeleboeuf/contributor) on Wed May 21 2014 13:14:06 GMT+0100 (BST) 3 | - [Alan Rice](https://github.com/alanrice) 4 | - [Bruno Vieira](https://github.com/bmpvieira) 5 | -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- 1 | language: node_js 2 | node_js: 3 | - "0.10" 4 | after_script: 5 | - npm run coveralls 6 | notifications: 7 | irc: 8 | channels: 9 | - "chat.freenode.net#bionode" 10 | template: 11 | - "%{message}: %{repository}#%{build_number}: %{commit_message} (%{branch} - %{commit} : %{author})" 12 | -------------------------------------------------------------------------------- /.jshintrc: -------------------------------------------------------------------------------- 1 | { 2 | "asi": true, // Tolerate Automatic Semicolon Insertion (no semicolons). 3 | "browser": true, // Standard browser globals e.g. `window`, `document`. 4 | "dojo": true, // Enable globals exposed by Dojo Toolkit. 5 | "jquery": true, // Enable globals exposed by jQuery JavaScript library. 6 | "node": true, // Enable globals available when code is running inside of the NodeJS runtime environment. 7 | "shadow": true, // This option suppresses warnings about variable shadowing i.e. declaring a variable that had been already declared somewhere in the outer scope. 8 | "laxcomma": true, // This option suppresses warnings about comma-first coding style. 9 | "laxbreak": true // This option suppresses most of the warnings about possibly unsafe line breakings in your code. 10 | } -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | The MIT License (MIT) 2 | 3 | Copyright (c) 2014 Bruno Vieira 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in 13 | all copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN 21 | THE SOFTWARE. 22 | -------------------------------------------------------------------------------- /docs/bionode-logo.min.svg: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /package.json: -------------------------------------------------------------------------------- 1 | { 2 | "name": "bionode-seq", 3 | "description": "Module for DNA, RNA and protein sequences manipulation", 4 | "version": "0.1.1", 5 | "homepage": "http://bionode.io", 6 | "repository": { 7 | "type": "git", 8 | "url": "git://github.com/bionode/bionode-seq.git" 9 | }, 10 | "author": { 11 | "name": "Bruno Vieira", 12 | "email": "mail@bmpvieira.com" 13 | }, 14 | "license": "MIT", 15 | "dependencies": { 16 | "minimist": "^1.2.0", 17 | "ndjson": "^1.5.0", 18 | "through2": "^2.0.3" 19 | }, 20 | "devDependencies": { 21 | "browserify": "^5.11.0", 22 | "contributor": "^0.1.16", 23 | "coveralls": "~2.6.1", 24 | "docco": "~0.6.2", 25 | "istanbul": "~0.2.4", 26 | "tap-spec": "^0.2.1", 27 | "tape": "^2.14.0", 28 | "testling": "^1.7.0", 29 | "uglify-js": "^2.4.15" 30 | }, 31 | "keywords": [ 32 | "bioinformatics", 33 | "genomics", 34 | "genetics", 35 | "dna", 36 | "util", 37 | "server", 38 | "client", 39 | "browser" 40 | ], 41 | "main": "index.js", 42 | "bin": { 43 | "bionode-seq": "cli.js" 44 | }, 45 | "scripts": { 46 | "test": "node test/bionode-seq.js | tap-spec", 47 | "test-browser": "browserify test/bionode-seq.js | testling | tap-spec", 48 | "coverage": "istanbul cover test/bionode-seq.js --report lcovonly -- | tap-spec && rm -rf ./coverage", 49 | "coveralls": "istanbul cover test/bionode-seq.js --report lcovonly -- | tap-spec && cat ./coverage/lcov.info | ./node_modules/.bin/coveralls && rm -rf ./coverage", 50 | "build-browser": "browserify index.js -r ./index.js:bionode-seq | uglifyjs > bionode-seq.min.js", 51 | "build-docs": "docco ./lib/bionode-seq.js" 52 | }, 53 | "testling": { 54 | "files": "test/bionode-seq.js", 55 | "browsers": [ 56 | "ie/8..latest", 57 | "firefox/17..latest", 58 | "firefox/nightly", 59 | "chrome/22..latest", 60 | "chrome/canary", 61 | "opera/12..latest", 62 | "opera/next", 63 | "safari/5.1..latest", 64 | "ipad/6.0..latest", 65 | "iphone/6.0..latest", 66 | "android-browser/4.2..latest" 67 | ] 68 | }, 69 | "contributors": [ 70 | { 71 | "name": "Alan Rice", 72 | "email": "alanmrice@gmail.com", 73 | "url": "https://github.com/alanrice", 74 | "contributions": 2, 75 | "hireable": false 76 | }, 77 | { 78 | "name": "Bruno Vieira", 79 | "email": "mail@bmpvieira.com", 80 | "url": "https://github.com/bmpvieira", 81 | "contributions": 15, 82 | "hireable": false 83 | } 84 | ] 85 | } 86 | -------------------------------------------------------------------------------- /CODE_OF_CONDUCT.md: -------------------------------------------------------------------------------- 1 | # Contributor Covenant Code of Conduct 2 | 3 | ## Our Pledge 4 | 5 | In the interest of fostering an open and welcoming environment, we as 6 | contributors and maintainers pledge to making participation in our project and 7 | our community a harassment-free experience for everyone, regardless of age, body 8 | size, disability, ethnicity, gender identity and expression, level of experience, 9 | nationality, personal appearance, race, religion, or sexual identity and 10 | orientation. 11 | 12 | ## Our Standards 13 | 14 | Examples of behavior that contributes to creating a positive environment 15 | include: 16 | 17 | * Using welcoming and inclusive language 18 | * Being respectful of differing viewpoints and experiences 19 | * Gracefully accepting constructive criticism 20 | * Focusing on what is best for the community 21 | * Showing empathy towards other community members 22 | 23 | Examples of unacceptable behavior by participants include: 24 | 25 | * The use of sexualized language or imagery and unwelcome sexual attention or 26 | advances 27 | * Trolling, insulting/derogatory comments, and personal or political attacks 28 | * Public or private harassment 29 | * Publishing others' private information, such as a physical or electronic 30 | address, without explicit permission 31 | * Other conduct which could reasonably be considered inappropriate in a 32 | professional setting 33 | 34 | ## Our Responsibilities 35 | 36 | Project maintainers are responsible for clarifying the standards of acceptable 37 | behavior and are expected to take appropriate and fair corrective action in 38 | response to any instances of unacceptable behavior. 39 | 40 | Project maintainers have the right and responsibility to remove, edit, or 41 | reject comments, commits, code, wiki edits, issues, and other contributions 42 | that are not aligned to this Code of Conduct, or to ban temporarily or 43 | permanently any contributor for other behaviors that they deem inappropriate, 44 | threatening, offensive, or harmful. 45 | 46 | ## Scope 47 | 48 | This Code of Conduct applies both within project spaces and in public spaces 49 | when an individual is representing the project or its community. Examples of 50 | representing a project or community include using an official project e-mail 51 | address, posting via an official social media account, or acting as an appointed 52 | representative at an online or offline event. Representation of a project may be 53 | further defined and clarified by project maintainers. 54 | 55 | ## Enforcement 56 | 57 | Instances of abusive, harassing, or otherwise unacceptable behavior may be 58 | reported by contacting the project team at mail@bionode.io. All 59 | complaints will be reviewed and investigated and will result in a response that 60 | is deemed necessary and appropriate to the circumstances. The project team is 61 | obligated to maintain confidentiality with regard to the reporter of an incident. 62 | Further details of specific enforcement policies may be posted separately. 63 | 64 | Project maintainers who do not follow or enforce the Code of Conduct in good 65 | faith may face temporary or permanent repercussions as determined by other 66 | members of the project's leadership. 67 | 68 | ## Attribution 69 | 70 | This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, 71 | available at [http://contributor-covenant.org/version/1/4][version] 72 | 73 | [homepage]: http://contributor-covenant.org 74 | [version]: http://contributor-covenant.org/version/1/4/ 75 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 |

2 | 3 | bionode logo 4 | 5 |
6 | bionode.io 7 |

8 | # bionode-seq 9 | > Module for DNA, RNA and protein sequences manipulation. 10 | 11 | [![NPM version][npm-image]][npm-url] 12 | [![Build Status][travis-image]][travis-url] 13 | [![Coveralls Status][coveralls-image]][coveralls-url] 14 | [![Dependency Status][depstat-image]][depstat-url] 15 | [![Gitter chat][gitter-image]][gitter-url] 16 | 17 | Install 18 | ------- 19 | 20 | Install bionode-seq with [npm](//npmjs.org): 21 | 22 | ```sh 23 | $ npm install bionode 24 | ``` 25 | 26 | Alternatively, just include `bionode-seq.min.js` via a `