Skip to content

Instantly share code, notes, and snippets.

@nathandunn

nathandunn/features.html

Last active January 31, 2017 18:14
Show Gist options
  • Save nathandunn/8449f35d59bdcb0d67e80b6db012b303 to your computer and use it in GitHub Desktop.
Save nathandunn/8449f35d59bdcb0d67e80b6db012b303 to your computer and use it in GitHub Desktop.
Download ZIP
Grabs nclist from remote and local server data
Raw
features.html
<!DOCTYPE html>
<html>
<head>
<title>JBrowse - Retrieve data outside of browser</title>
<meta content="text/html;charset=utf-8" http-equiv="Content-Type">
<link rel="stylesheet" type="text/css" href="css/genome.css">
<script type="text/javascript" src="src/dojo/dojo.js" data-dojo-config="async: 1, baseUrl: './src'"></script>
<script type="text/javascript" src="src/JBrowse/init.js"></script>
<style>
pre {
white-space: pre-wrap;
word-wrap: break-word;
}
</style>
<script>
// Require bare bones jbrowse components without using the main browser object
require([
'JBrowse/Browser',
'JBrowse/Store/SeqFeature/GFF3Tabix',
'JBrowse/Store/SeqFeature/NCList',
'JBrowse/Model/SimpleFeature',
'JBrowse/Store/Sequence/StaticChunked',
'JBrowse/View/Export',
'JBrowse/View/Export/GFF3',
'JBrowse/View/Export/FASTA'
],
function (Browser,
GFF3Tabix,
NCList,
SimpleFeature,
StaticChunkedSequence,
ExportMixin,
GFF3Mixin,
FastaMixin) {
var getGFF = function (conf, region, callback) {
var conf = dojo.mixin({
storeClass: 'JBrowse/Store/SeqFeature/NCList'
}, conf);
var store = new NCList(conf);
store.refSeq = {};
store.refSeq.name = region.refseq;
var exp = new dojo.declare([ExportMixin, GFF3Mixin])({store: store});
exp.exportRegion({ref: region.refseq, start: region.start, end: region.end}, callback);
};
var getNCList = function (conf, region, callback) {
var conf = dojo.mixin({
storeClass: 'JBrowse/Store/SeqFeature/NCList'
}, conf);
var store = new NCList(conf);
store.refSeq = {};
store.refSeq.name = region.refseq;
var query = {ref: region.refseq, start: region.start, end: region.end};
store.getFeatures(query, callback)
};
// Initialize jbrowse instance in unittestmode so that it doesn't actually draw the browser to screen
var browser = new Browser({unitTestMode: true});
// standard mode
// var region = {start: 110548, end: 113863, refseq: 'chrI'};
// var url = 'jbrowse/sample_data/json/yeast/tracks/Genes/{refseq}/trackData.json';
// CORS issues
// var region = {start: 724017, end: 726601, refseq: 'Group1.1'};
// var url = 'https://genome.monarchinitiative.org/apollo/Honeybee/jbrowse/data/tracks/Official%20Gene%20Set%20v3.2/{refseq}/trackData.json';
var region = {start: 6884146, end: 6889697, refseq: 'III'};
// var url = 'http://www.wormbase.org/tools/genome/jbrowse/data/c_elegans_PRJNA13758/tracks/Curated_Genes/{refseq}/trackData.jsonz';
var url = 'http://agrjbrowse.s3-website-us-east-1.amazonaws.com/WormBase/c_elegans_PRJNA13758/tracks/Curated_Genes/{refseq}/trackData.jsonz';
getGFF({
urlTemplate: url,
label: 'Genes',
browser: browser
}, region, function (features) {
document.getElementById('gff').innerHTML = features;
});
getNCList({
urlTemplate: url,
label: 'Genes',
browser: browser
}, region, function (features) {
document.getElementById('nclist').innerHTML += features;
});
});
</script>
</head>
<body>
<h1>JBrowse gff store access outside of browser</h1>
<pre id="gff"></pre>
<h1>JBrowse store nclist</h1>
<pre id="nclist"></pre>
</body>
</html>
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment