Buffer Stream parser from FASTA to JSON
npm install fasta-parser[![NPM version][npm-image]][npm-url]
[![Build Status][travis-image]][travis-url]
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[![Dependency Status][depstat-image]][depstat-url]
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[![DOI][doi-image]][doi-url]
[![Browser][browser-image]][browser-url]
Install
-------
Install ``fasta-parser` with npm:
`sh`
$ npm install fasta-parser
Alternatively, just include fasta-parser.min.js via a in your page.
Usage
-----
`js
var fasta = require('fasta-parser')
var fastaData = new Buffer ('>sequence1\n\
ATGCACGTCACGTCAGTACTCGTCAGTAC\n\
>sequence2\n\
CAGTCCTACTGCATGCATGCATGCATGCATCGATGCATGTCGACTGCATGCATGC\n')
var parser = fasta()
parser.on('data', function(data) { console.log(JSON.parse(data.toString())) })
parser.write(fastaData)
parser.end()
//=> { id: 'sequence1',
// seq: 'ATGCACGTCACGTCAGTACTCGTCAGTAC' }
// { id: 'sequence2',
// seq: 'CAGTCCTACTGCATGCATGCATGCATGCATCGATGCATGTCGACTGCATGCATGC' }
`
For a more useful API, check the dependent module bionode-fasta.
Contributing
------------
To contribute, clone this repo locally and commit your code on a separate branch.
Please write unit tests for your code, and check that everything works by running the following before opening a pull-request:
`sh`
$ npm test
To test on the browser:
`sh`
$ npm run test-browserif you get "No headless browser found" do:
$ npm install -g phantomjs
$ rm ~/.config/browser-launcher/config.json
Please also check for code coverage:
`sh`
$ npm run coverage
To rebuild and minify the module for the browser:
`sh`
$ npm run build-browser
To rebuild the documentation using the comments in the code:
`sh``
$ npm run build-docs
Check the issues for ways to contribute.
Contacts
--------
Bruno Vieira <mail@bmpvieira.com> @bmpvieira
License
--------
fasta-parser is licensed under the MIT license.
Check ChooseALicense.com for details.
[npm-url]: http://npmjs.org/package/fasta-parser
[npm-image]: http://img.shields.io/npm/v/fasta-parser.svg?style=flat
[travis-url]: http:////travis-ci.org/bionode/fasta-parser
[travis-image]: http://img.shields.io/travis/bionode/fasta-parser.svg?style=flat
[coveralls-url]: http:////coveralls.io/r/bionode/fasta-parser
[coveralls-image]: http://img.shields.io/coveralls/bionode/fasta-parser.svg?style=flat
[depstat-url]: http://david-dm.org/bionode/fasta-parser
[depstat-image]: http://img.shields.io/david/bionode/fasta-parser.svg?style=flat
[gitter-image]: http://img.shields.io/badge/gitter-bionode/fasta--parser-brightgreen.svg?style=flat
[gitter-url]: https://gitter.im/bionode/fasta-parser
[doi-url]: http://dx.doi.org/10.5281/zenodo.11306
[doi-image]: http://img.shields.io/badge/doi-10.5281/zenodo.11306-blue.svg?style=flat
[browser-url]: https://ci.testling.com/bionode/fasta-parser
[browser-image]: https://ci.testling.com/bionode/fasta-parser.png