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add ucsc browser support for hic #4265

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add ucsc browser support for hic #4265

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bf2780a
add ucsc browser support for hic
leepc12 Mar 15, 2022
69ef66e
use juicebox session for hic vis (instead of urlencoded parameters)
leepc12 Mar 23, 2022
bb3b48f
lint
leepc12 Mar 24, 2022
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4 changes: 4 additions & 0 deletions package-lock.json
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1 change: 1 addition & 0 deletions package.json
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Original file line number Diff line number Diff line change
Expand Up @@ -87,6 +87,7 @@
"genome-visualizer": "ENCODE-DCC/valis-hpgv#1.9.0",
"google-analytics": "file:node_shims/google-analytics",
"graphlib": "ENCODE-DCC/graphlib#v1.0.8",
"igv-utils": "github:igvteam/igv-utils#v1.2.10-jb",
"immutable": "^3.7.5",
"install": "^0.13.0",
"js-cookie": "^2.2.1",
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15 changes: 10 additions & 5 deletions src/encoded/static/components/vis_defines.js
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Expand Up @@ -5,6 +5,7 @@ import React from 'react';
import PropTypes from 'prop-types';
import _ from 'underscore';
import url from 'url';
import { StringUtils } from 'igv-utils';
import * as encoding from '../libs/query_encoding';
import { Modal, ModalHeader, ModalBody, ModalFooter } from '../libs/ui/modal';
import * as globals from './globals';
Expand Down Expand Up @@ -116,12 +117,16 @@ export const visOpenBrowser = (dataset, browser, assembly, files, datasetUrl) =>
delete parsedUrl.path;
delete parsedUrl.search;
delete parsedUrl.query;
const fileQueries = files.map((file) => {
parsedUrl.pathname = file.href;
const name = file.biological_replicates && file.biological_replicates.length > 0 ? `&name=${dataset.accession} / ${file.title}, Replicate ${file.biological_replicates.join(',')}` : '';
return encoding.encodedURIComponentOLD(`{hicUrl=${url.format(parsedUrl)}${name}}`, { encodeEquals: true });
const juiceboxSessionJsonString = JSON.stringify({
browsers: files.map((file) => {
parsedUrl.pathname = file.href;
return {
name: file.biological_replicates && file.biological_replicates.length > 0 ? `${dataset.accession} / ${file.title}, Replicate ${file.biological_replicates.join(',')}` : '',
url: url.format(parsedUrl),
};
}),
});
href = `http://aidenlab.org/juicebox/?juicebox=${fileQueries.join(',')}`;
href = `http://aidenlab.org/juicebox/?session=blob:${StringUtils.compressString(juiceboxSessionJsonString)}`;
break;
}
case 'Ensembl': {
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8 changes: 7 additions & 1 deletion src/encoded/static/vis_defs/HiC_vis_def.json
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Expand Up @@ -10,7 +10,7 @@
"sortOrder": [ "Biosample", "Targets", "Replicates", "Views" ],
"Views": {
"tag": "view",
"group_order": [ "Topologically associated domains", "Nested TADs", "Genome compartments" ],
"group_order": [ "Topologically associated domains", "Nested TADs", "Genome compartments", "HiC" ],
"groups": {
"Topologically associated domains": {
"tag": "aTADS",
Expand All @@ -34,6 +34,12 @@
"maxHeightPixels": "64:18:8",
"windowingFunction": "mean+whiskers",
"output_type": [ "genome compartments" ]
},
"HiC": {
"tag": "dHIC",
"visibility": "dense",
"type": "hic",
"output_type": [ "chromatin interactions" ]
}
}
},
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2 changes: 1 addition & 1 deletion src/encoded/vis_defines.py
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Expand Up @@ -125,7 +125,7 @@
}

BROWSER_FILE_TYPES = {
'ucsc': {'bigWig', 'bigBed', 'bigInteract'},
'ucsc': {'bigWig', 'bigBed', 'bigInteract', 'hic'},
'ensembl': {'bigWig', 'bigBed'},
'quickview': {'bigWig', 'bigBed'},
'hic': {'hic'},
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