bionode-fasta

bionode.io

# bionode-fasta [](https://travis-ci.org/bionode/bionode-fasta)

FASTA format parser for bionode

Install

Install bionode-fasta with npm:

$ 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 <script/> in your page.

Usage

If you are using bionode-fasta with Node.js, you can require the module:

var bionodeFasta = require('bionode-fasta')
//Sample FASTA file
console.log(sampleFASTA);
=> >SEQUENCE_1
   MTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAKKADRLAAEG
   LVSVKVSDDFTIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHK
   IPQFASRKQLSDAILKEAEEKIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTL
   MGQFYVMDDKKTVEQVIAEKEKEFGGKIKIVEFICFEVGEGLEKKTEDFAAEVAAQL
   >SEQUENCE_2
   SATVSEINSETDFVAKNDQFIALTKDTTAHIQSNSLQSVEELHSSTINGVKFEEYLKSQI
   ATIGENLVVRRFATLKAGANGVVNGYIHTNGRVGVVIAAACDSAEVASKSRDLLRQICMH

bionodeFasta.readFasta(sampleFASTA);
=> [ { name: 'SEQUENCE_1',
       seq: 'MTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAKKADRLAAEGLVSVKVSDDFTIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHKIPQFASRKQLSDAILKEAEEKIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTLMGQFYVMDDKKTVEQVIAEKEKEFGGKIKIVEFICFEVGEGLEKKTEDFAAEVAAQL' },
     { name: 'SEQUENCE_2',
       seq: 'SATVSEINSETDFVAKNDQFIALTKDTTAHIQSNSLQSVEELHSSTINGVKFEEYLKSQIATIGENLVVRRFATLKAGANGVVNGYIHTNGRVGVVIAAACDSAEVASKSRDLLRQICMH' } ]

Please read the documentation for the methods exposed by bionode-fasta.

Command line examples

$ bionode-fasta readFasta ~/sequences.fa

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:

$ npm test

Please also check for code coverage:

$ npm run coverage

To rebuild and minify the module for the browser:

$ npm run build-browser

To rebuild the documentation using the comments in the code:

$ npm run build-docs

Check the issues for ways to contribute.

Contacts

Alan Rice <[e-mail]> @alanmrice

License

bionode-fasta is licensed under the MIT license.
Check ChooseALicense.com for details.