nucleotidy/indexedfasta-js

Read FASTA files indexed with .fai indexes. Also supports BGZIP+.gzi

Install

$ npm install --save @gmod/indexedfasta

Usage

const { IndexedFasta, BgzipIndexedFasta } = require('@gmod/indexedfasta')

const t = new IndexedFasta({
  path: 'test.fa',
  faiPath: 'test.fa.fai',
});
// or
const t = new BgzipIndexedFasta({
  path: 'test.fa.gz',
  faiPath: 'test.fa.gz.fai',
  gziPath: 'test.fa.gz.gzi',
  chunkSizeLimit: 500000
});

// get the first 10 bases of a sequence from the file.
// coordinates are UCSC standard 0-based half-open
//
const chr1Region = await t.getSequence('chr1', 0, 10);
// chr1Region is now a string of bases, 'ACTG...'

// get a whole sequence from the file
const chr1Bases = await t.getSequence('chr1');

// get object with all seq lengths as { seqName => length, ... }
const allSequenceSizes = await t.getSequenceSizes();

// get the size of a single sequence
const chr1Size = await t.getSequenceSize('chr1');

// get an array of all sequence names in the file
const seqNames = await t.getSequenceNames();

Academic Use

This package was written with funding from the NHGRI as part of the JBrowse project. If you use it in an academic project that you publish, please cite the most recent JBrowse paper, which will be linked from jbrowse.org.

License

MIT © Colin Diesh