bioutils

bioUtils

Work with Bioinformatics Files in JavaScript

Goals:

• support sequence alignments and phylogenetic trees in fasta, fna, nexus and newick formats
• simple, fast and light
• fully tested, comprehensively documented
• work in Node and in the browser
• standardize input, output and formatting so that you can focus on analyzing the data

Docs: https://rdvelazquez.github.io/bioUtils/

Install

npm install bioutils

or

yarn add bioutils

Use

const bioUtils = require("bioutils");

// Read data from a file into a json object.
const exampleBioData = bioUtils.readFileSync("./exampleData.fasta");

// Get info about the data.
/*TODO: not sure if this will be implemented
// Some info is available in the "metaData".
const numberOfSequences = exampleBioData['metaData']['numberOfSequences'];
*/
// Other info can be obtained with functions.
const containsStopCodons = bioUtils.containsStopCodons(exampleBioData);

// Perform simple manipulations on the data.
const exampleBioDataWithoutStopCodons = bioUtils.replaceStopCodons(exampleBioData, "-");
const exampleBioDataAminoAcids = bioUtils.translateToAminoAcid(exampleBioData);

// Write the data to any file format you want.
bioUtils.writeFileSync(exampleBioDataWithoutStops, 'nexus', 'exampleOutputFile.nexus')
biUtils.writeFileSync(exampleBioDataAminoAcis, 'fasta', 'exampleOutputFileAA.fasta')

Previous/Similar Work

• https://github.com/TeselaGen/ve-sequence-parsers (looks very nice but doesn't support nexus or newick)
• https://github.com/jalview/biojson (specifies a json schema for alignments but doesn't support trees and seems to be unmaintained since 2015)
• Everyone's own piecemeal modules, functions and scripts (These are often all you need but this package is designed to provide another option)

Development

Test yarn test
Lint yarn lint
Build Docs yarn document
Publish to NPM... just npm publish