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 node script

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

** Usage (run from the examples directory)

• node -r esm examples/script-es6.js

• node examples/script-cjs.js

In a web page

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({
        "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) {...})