!Build Status

trix-js

Read UCSC Trix indexes in pure JavaScript

Usage

``js
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

$3

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()

$3

Search the index files for a term and find its keys.

In the case of searching with multiple words, trix.search() finds the intersection of the result sets.

The Trix search function accepts argument:

- searchString - a string of space-separated words for what to search the index file and find keys for


The Trix search function returns:


- Promise<[term,result][] as [string,string][]> - an array of [term, result] pairs where each term is the left column in the trix and the right column is the trix match

Examples

`js
import { LocalFile } from 'generic-filehandle'
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()
`

Development

$3

First, clone this repo and install npm packages.

Then, run npm test.


$3

First, clone this repo.
To run test searches on a track hub using the USCS TrixSearch, navigate to tests/testdata/test# and run bash test#script.sh where # is the test number.
To change search terms, edit searchterms.txt.

Wondering what to search for?

Open up tests/testdata/test#/input.txt.

How to test my own .gff.gz data?

Navigate to /test/rawGenomes and create a directory with your .gff.gz file in it. From within that directory, run bash ../../programs/gff3ToInput.sh <.gff3.gz FILE>

`.

Reference

See https://genome.ucsc.edu/goldenPath/help/trix.html for basic concepts of trix and https://github.com/GMOD/ixixx-js for a javascript implementation of the ixIxx command