@gmod/indexedfasta

read indexed fasta and bgzipped fasta formats

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@gmod/indexedfasta
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Readme

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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();

If you are using in the browser, you may use the generic-filehandle package and initialize like this

import { IndexedFasta, BgzipIndexedFasta } from '@gmod/indexedfasta'
import { RemoteFile } from 'generic-filehandle'

const t = new IndexedFasta({
  filehandle: new RemoteFile("http://yourside.com/test.fa"),
  faiFilehandle: new RemoteFile("http://yourside.com/test.fa.fai"),
});
const t = new BgzipIndexedFasta({
  filehandle: new RemoteFile("http://yourside.com/test.fa.gz"),
  faiFilehandle: new RemoteFile("http://yourside.com/test.fa.gz.fai"),
  gziFilehandle: new RemoteFile("http://yourside.com/test.fa.gz.gzi"),
});

In node.js you can also access remote files with generic-filehandle, but you would supply a fetch function e.g.

import { IndexedFasta, BgzipIndexedFasta } from '@gmod/indexedfasta'
import { RemoteFile } from 'generic-filehandle'
import fetch from 'cross-fetch'

const t = new IndexedFasta({
  filehandle: new RemoteFile("http://yourside.com/test.fa", {fetch}),
  faiFilehandle: new RemoteFile("http://yourside.com/test.fa.fai",{fetch}),
});

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

If you find any bugs or have a feature request, please open an issue on github!

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