README.md

trix-js

Read UCSC Trix indexes in pure JavaScript

Usage

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

// We use generic-filehandle2 here to demonstrate searching files on remote servers.
const ixxFile = new RemoteFile(
  'https://hgdownload.soe.ucsc.edu/gbdb/hg38/knownGene.ixx',
)
const ixFile = new RemoteFile(
  'https://hgdownload.soe.ucsc.edu/gbdb/hg38/knownGene.ix',
)

const trix = new Trix(ixxFile, ixFile)

async function doStuff() {
  const results = await trix.search('oca')
  console.log(results)
}
doStuff()

Documentation

Trix constructor

The Trix class constructor accepts arguments:

• ixxFile - a filehandle object for the trix .ixx file
• ixFile - a filehandle object for the trix .ix file
• maxResults = 20 - an optional number specifying the maximum number of results to return on trix.search()

Trix search

Searches the index files for a term and returns its keys. When searching with multiple words, trix.search() finds the intersection of the result sets.

The Trix search function accepts arguments:

• searchString - a string of space-separated words to search the index file for

The Trix search function returns:

• Promise<[string, string][]> - an array of [term, result] pairs where term is the left column in the trix and result is the matching key

Examples

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

const ixxFile = new LocalFile('out.ixx')
const ixFile = new LocalFile('out.ix')

// limit maxResults to 5
const trix = new Trix(ixxFile, ixFile, 5)

async function doStuff() {
  const results1 = await trix.search('herc')
  console.log(results1)

  // increase maxResults to 30
  trix.maxResults = 30

  const results2 = await trix.search('linc')
  console.log(results2)
}

doStuff()

Reference

See the UCSC trix documentation for basic concepts of trix and ixixx-js for a JavaScript implementation of the ixIxx command.