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https://github.com/bionode/bionode-fasta
Streamable FASTA parser.
https://github.com/bionode/bionode-fasta
bioinformatics bionode nodejs parser tools
Last synced: 2 months ago
JSON representation
Streamable FASTA parser.
- Host: GitHub
- URL: https://github.com/bionode/bionode-fasta
- Owner: bionode
- License: mit
- Created: 2014-07-11T21:04:35.000Z (over 10 years ago)
- Default Branch: master
- Last Pushed: 2019-11-19T13:25:20.000Z (about 5 years ago)
- Last Synced: 2024-10-08T11:42:15.320Z (3 months ago)
- Topics: bioinformatics, bionode, nodejs, parser, tools
- Language: JavaScript
- Homepage: bionode.io
- Size: 403 KB
- Stars: 14
- Watchers: 23
- Forks: 9
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
Awesome Lists containing this project
README
# bionode-fasta
> Streamable FASTA parser.
[![NPM version][npm-image]][npm-url]
[![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](//npmjs.org):
```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](http://rawgit.com/bionode/bionode-fasta/master/docs/bionode-fasta.html) for the methods exposed by bionode-fasta.
### Command line example
```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](http://github.com/bionode/bionode-fasta/issues) for ways to contribute.
Contacts
--------
Bruno Vieira <[[email protected]](mailto:[email protected])> [@bmpvieira](//twitter.com/bmpvieira)
License
--------
bionode-fasta is licensed under the [MIT](https://raw.github.com/bionode/bionode-fasta/master/LICENSE) license.
Check [ChooseALicense.com](http://choosealicense.com/licenses/mit) 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]: https://doi.org/10.5281/zenodo.11307
[doi-image]: http://img.shields.io/badge/doi-10.5281/zenodo.11307-blue.svg?style=flat
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