hic-straw

hic-straw

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

Installation

Requires Node (https://nodejs.org)

npm install hic-straw

Examples

Command line

• Extract file metadata.

  • genome identifier
  • sequences (chromosomes)
  • bin sizes (resolutions)

straw --meta test/data/test_chr22.hic 

• Extract normalization options.

  • Array of normalization options

straw --norms test/data/test_chr22.hic 

• Extract values from a local hic file between 40MB and 50MB on chromosome 22 at 100KB resolution with KR (balanced) normalization and print to stdout.

  • array of contact records {binX, binY, value}

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 values from a remote hic file by URL.

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

In a script

See examples/script.js

const Straw = require("../src/straw")

const straw = new Straw({path: "../test/data/test_chr22.hic"})

// Get  metadata 
straw.getMetaData()
    .then(function (metaData) {
        console.log(JSON.stringify(metaData, null, 2))
    })


// Get the normalization options as an array 
straw.getNormalizationOptions()
    .then(function (normOptions) {
        console.log(normOptions)
    })

// Get the contact records over a region
straw.getContactRecords(
    "KR",
    {chr: "22", start: 40000000, end: 50000000},
    {chr: "22", start: 40000000, end: 50000000},
    "BP",
    100000
    )
    .then(function (contactRecords) {
        for (let record of contactRecords) {
            console.log(record)
        }
    })
    .catch(function (error) {
        console.log(error)
    })
    

In a web page

See examples/straw.html

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

...

 const straw = new HicStraw({
            "path": "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) {...})