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| <!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 getSequence = function(conf, region, callback) { | |
| var conf = dojo.mixin({ | |
| storeClass: 'JBrowse/Store/Sequence/StaticChunked', | |
| chunkSize: 20000, | |
| }, conf); | |
| var store = new StaticChunkedSequence(conf); | |
| store.refSeq = { name: region.refseq }; | |
| var exp = new dojo.declare([ExportMixin, FastaMixin])({ store: store }); | |
| exp.refSeq = store.refSeq; | |
| exp.exportRegion({ ref: region.refseq, start: region.start, end: region.end }, callback); | |
| }; | |
| 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); | |
| }; | |
| // Initialize jbrowse instance in unittestmode so that it doesn't actually draw the browser to screen | |
| var browser = new Browser({unitTestMode: true}); | |
| var region = { start: 1, end: 3000, refseq: 'ctgA' }; | |
| getSequence({ | |
| urlTemplate: 'jbrowse/sample_data/json/volvox/seq/{refseq_dirpath}/{refseq}-', | |
| label: 'DNA', | |
| browser: browser | |
| }, region, function(seq) { | |
| document.getElementById('sequence').innerHTML = seq; | |
| }); | |
| getGFF({ | |
| urlTemplate: 'jbrowse/sample_data/json/volvox/tracks/Genes/{refseq}/trackData.json', | |
| label: 'Genes', | |
| browser: browser | |
| }, region, function(features) { | |
| document.getElementById('gff').innerHTML = features; | |
| }); | |
| }); | |
| </script> | |
| </head> | |
| <body> | |
| <h1>JBrowse sequence store access outside of browser</h1> | |
| <pre id="sequence"></pre> | |
| <h1>JBrowse gff store access outside of browser</h1> | |
| <pre id="gff"></pre> | |
| </body> | |
| </html> | |
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Note that the machinery to figure out where the data directory is sort of messed up so the urlTemplate argument should be specialized for this
Basically, the urlTemplate to the track should include even the jbrowse folder name and the data directory path, so this sample assumes jbrowse is running at 'http://localhost/jbrowse/' and that this HTML file is in the jbrowse folder.