hic-straw

Command line and web utilities for reading .hic contact matrix files

Installation

Requires Node (https://nodejs.org)

npm install hic-straw

API

getContactRecords

Return a collection of binned contact counts.

Arguments

• normalization - string indicating normalization scheme
• region 1 {chr, start, end} - genomic region in base pair or fragment units. Interval convention is zero based 1/2 open
• region 2 {chr, start, end}
• units -- "BP" for base pairs. Currently this is the only unit supported
• binSize -- size of each bin in base pair or fragment units. Bins are square

Examples

Browser usage

Script tag - see examples/straw.html

<script src="../dist/hic-straw.js"></script>

...

 const straw = new HicStraw({
            url: "https://s3.amazonaws.com/igv.broadinstitute.org/data/hic/intra_nofrag_30.hic"
        })

        straw.getContactRecords(
            "KR",
            {chr: "8",start: 50000000, end: 60000000},
            {chr: "8",start: 50000000, end: 60000000},
            "BP",
            1000000
        )
            .then(function (contactRecords) {...})

ES6 module - see examples/straw-es6.html

    import HicStraw from '../dist/hic-straw_es6.js'

    const straw = new HicStraw({
        url: "https://s3.amazonaws.com/igv.broadinstitute.org/data/hic/intra_nofrag_30.hic"
    })

    straw.getContactRecords(
        "KR",
        {chr: "8",start: 50000000, end: 60000000},
        {chr: "8",start: 50000000, end: 60000000},
        "BP",
        1000000
     )
        .then(function (contactRecords) {...})

`

Node

The hic-straw distributions are built for browser usagae, but can be used in Node with shims.

local file

To use hic-straw with a local file use the NodeLocalFile class as follows

import NodeLocalFile from "src/io/nodeLocalFile.mjs"
const path = "test/data/test_chr22.hic"
const nodeLocalFile = new NodeLocalFile({path})
const straw = new Straw({file: nodeLocalFile})

remote file

For remote file access define a global fetch function

global.fetch = require("node-fetch")
const url = "https://foo.bar/test.hic"
const straw = new Straw({url: url})

See examples/script-es6.js and examples/script-cjs.js for complete examples.

Command line

Note: "straw" is installed in node_modules/.bin/straw. This should be added to the path automatically upon installing hic-straw, however if you get the error straw: command not found try running straw explicitly as

node_modules/.bin/straw...

Extract file metadata (genome identifier, sequences, resolutions)

straw --meta test/data/test_chr22.hic 

Extract normalization options.

straw --norms test/data/test_chr22.hic 

Extract contact records from a local hic file

straw KR test/data/test_chr22.hic 22:40,000,000-50,000,000 22:40,000,000-50,000,000 BP 100,000

Extract contact records from a remote hic file

straw KR https://s3.amazonaws.com/igv.broadinstitute.org/data/hic/intra_nofrag_30.hic 8:48,700,000-48,900,000 8:48700000-48900000 BP 10,000
``