trix-js

Read UCSC Trix indexes in pure JavaScript

Install

npm install @gmod/trix

Usage

import Trix from '@gmod/trix'
import { RemoteFile } from 'generic-filehandle2'

// generic-filehandle2 also has LocalFile for files on disk
const trix = new Trix(
  new RemoteFile('https://hgdownload.soe.ucsc.edu/gbdb/hg38/knownGene.ixx'),
  new RemoteFile('https://hgdownload.soe.ucsc.edu/gbdb/hg38/knownGene.ix'),
)

const results = await trix.search('oca')
// => [[term, record], ...]

API

new Trix(ixxFile, ixFile, maxResults?)

• ixxFile - filehandle for the .ixx file
• ixFile - filehandle for the .ix file
• maxResults - most results a search returns, default 20. Also settable afterwards as trix.maxResults

trix.search(searchString, opts?)

Prefix-searches the index and resolves to [term, record][], where term is the indexed word that matched and record is the key it points to. Records are deduplicated, so two terms hitting the same record yield one result.

• searchString - the query; only its first whitespace-separated word is used
• opts.signal - an AbortSignal to cancel the underlying reads

Reference

See the UCSC trix documentation for the concepts, and ixixx-js for a JavaScript implementation of the ixIxx command that builds these indexes.

See CONTRIBUTING.md for development and release steps.