hic-straw
v2.1.2
Published
Utilities for reading .files (contact matrix files)
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Readme
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
``