@gmod/twobit
v4.0.1
Published
Read .2bit files in node or webpack
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@gmod/twobit
Read .2bit sequence files using pure JavaScript, works in node or in the browser.
Install
$ npm install --save @gmod/twobit
Usage
const { TwoBitFile } = require('@gmod/twobit')
const t = new TwoBitFile({
path: require.resolve('./data/foo.2bit'),
})
// 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()
API
TwoBitFile
Table of Contents
constructor
Parameters
args
objectargs.filehandle
Filehandle? node fs.promises-like filehandle for the .2bit file. Only needs to supportfilehandle.read(buffer, offset, length, position)
args.path
string? filesystem path for the .2bit file to open
getSequenceNames
Returns any for an array of string sequence names that are found in the file
getSequenceSizes
Returns any object listing the lengths of all sequences like {seqName:
length, ...}
.note: this is a relatively slow operation especially if there are many
refseqs in the file, if you can get this information from a different file
e.g. a chrom.sizes file, it will be much faster
getSequenceSize
Parameters
seqName
string name of the sequence
Returns any sequence length, or undefined if it is not in the file
getSequence
Parameters
seqName
string name of the sequence you wantregionStart
optional 0-based half-open start of the sequence region to fetch. (optional, default0
)regionEnd
optional 0-based half-open end of the sequence region to fetch. defaults to end of the sequence (optional, defaultNumber.POSITIVE_INFINITY
)
Returns any for a string of sequence bases
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 © Robert Buels