npm install bionode-fasta
bionode-fasta
> Streamable FASTA parser.
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[![Build Status][travis-image]][travis-url]
[![Coveralls Status][coveralls-image]][coveralls-url]
[![Dependency Status][depstat-image]][depstat-url]
[![Gitter chat][gitter-image]][gitter-url]
[![DOI][doi-image]][doi-url]
Install
-------
Install ``bionode-fasta` with npm:
`sh`
$ npm install bionode-fasta
To use it as a command line tool, you can install it globally by adding -g` .
Alternatively, just include bionode-fasta.min.js via a in your page.
Usage
-----
If you are using `bionode-fasta` with Node.js, you can require the module:
`js
var fasta = require('bionode-fasta')
fasta('./input.fasta').pipe(process.stdout) // Returns Buffers
fasta.obj('./input.fasta').on('data', console.log) // Returns Objects
fs.createReadStream('./input.fasta').pipe(fasta()) // Parses streamed content
fs.createReadStream('./fasta-list.txt')
.pipe(split())
.pipe(fasta({filenameMode: true})) // Parses files from filename Strings
=> { id: 'sequence1',
seq: 'ATGCACGTCACGTCAGTACTCGTCAGTAC' }
{ id: 'sequence2',
seq: 'CAGTCCTACTGCATGCATGCATGCATGCATCGATGCATGTCGACTGCATGCATGC' }
fasta.obj({includePath: true}, './input.fasta').on('data', console.log) // Returns Objects
=> { id: 'sequence1',
seq: 'ATGCACGTCACGTCAGTACTCGTCAGTAC'
path: './input.fasta' }
`
Please read the documentation for the methods exposed by bionode-fasta.
$3
`
sh
$ bionode-fasta input.fasta output.json
`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
`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
--------
bionode-fasta is licensed under the MIT license.
Check ChooseALicense.com for details.
[npm-url]: http://npmjs.org/package/bionode-fasta
[npm-image]: http://img.shields.io/npm/v/bionode-fasta.svg?style=flat
[travis-url]: http:////travis-ci.org/bionode/bionode-fasta
[travis-image]: http://img.shields.io/travis/bionode/bionode-fasta.svg?style=flat
[coveralls-url]: http:////coveralls.io/r/bionode/bionode-fasta
[coveralls-image]: http://img.shields.io/coveralls/bionode/bionode-fasta.svg?style=flat
[depstat-url]: http://david-dm.org/bionode/bionode-fasta
[depstat-image]: http://img.shields.io/david/bionode/bionode-fasta.svg?style=flat
[gitter-image]: http://img.shields.io/badge/gitter-bionode/bionode--fasta-brightgreen.svg?style=flat
[gitter-url]: https://gitter.im/bionode/bionode-fasta
[doi-url]: http://dx.doi.org/10.5281/zenodo.11307
[doi-image]: http://img.shields.io/badge/doi-10.5281/zenodo.11307-blue.svg?style=flat
