@gmod/jbrowse/tests/js_tests/spec/BigBed.spec.js

JBrowse - client-side genome browser

require([
            'dojo/_base/array',
            'JBrowse/Browser',
            'JBrowse/Store/SeqFeature/BigBed',
            'JBrowse/Model/XHRBlob'
        ], function(
            array,
            Browser,
            BigBed,
            XHRBlob
        ) {

    var errorFunc = function(e) { console.error(e); };

    describe( 'BigBed with volvox eden genes', function() {
        var browser = new Browser({ unitTestMode: true });
        var b = new BigBed({
            browser: browser,
            blob: new XHRBlob('../../sample_data/raw/volvox/volvox.bb')
        });

        it('constructs', function(){ expect(b).toBeTruthy(); });

        it('accesses volvox bigbed', function(){
            const features = [];
            const expectedFeatureData = cjsRequire('../../data/volvox.bb.expected.json')
            deleteUniqueIDSerial(expectedFeatureData)

            b.getFeatures(
                { ref: 'ctgA', start: 1, end: 50000 },
                f => features.push(f),
                () => { features.done = true },
                e => { console.error(e.stack||''+e) }
            )

            waitsFor( function() { return features.done; } )
            runs( function() {
                deleteUniqueIDSerial(expectedFeatureData)
                // console.log(JSON.stringify(features,undefined,2))
                const featureData = JSON.parse(JSON.stringify(features))
                deleteUniqueIDSerial(featureData)
                expect(featureData).toEqual(expectedFeatureData)
            })
        })
    })

    describe( 'BigBed with human peaks', function() {
        var browser = new Browser({ unitTestMode: true });
        var b = new BigBed({
            browser: browser,
            blob: new XHRBlob('../data/human_bigbed/peaks.bb')
        });

        it('constructs', function(){ expect(b).toBeTruthy(); });

        it('accesses peaks bigbed', function(){
            var features = [];
            b.getFeatures(
                { ref: 'chr1', start: 18000000, end: 19000000 },
                function(f) { features.push(f); },
                function() { features.done = true },
                function(e) { console.error(e.stack||''+e); }
            );

            waitsFor( function() { return features.done; } );
            runs( function() {
                expect( features.length ).toEqual( 33 );
            });
        });
    });


    describe( 'malformed bigbed', function() {
        var browser = new Browser({ unitTestMode: true });
        var b = new BigBed({
            browser: browser,
            blob: new XHRBlob('../data/malformed.bb')
        });

        it('constructs', function(){ expect(b).toBeTruthy(); });

        it('calls the error callback', function(){
            const features = [];
            let error
            b.getFeatures(
                { ref: 'chr1', start: 18000000, end: 19000000 },
                f => features.push(f),
                () => { features.done = true },
                e => { error = e }
            );

            waitsFor( () => error || features.done );
            runs( function() {
                expect( features.length ).toEqual( 0 );
                expect(error).toContain('Not a BigWig or BigBed file')
            });
        });
    });


    describe( 'BigBed with less than bed12 and autosql', function() {
        var browser = new Browser({ unitTestMode: true });
        var b = new BigBed({
            browser: browser,
            blob: new XHRBlob('../data/human_bigbed/genes.bb')
        });

        it('constructs', function(){ expect(b).toBeTruthy(); });

        it('accesses gene bigbed', function(){
            var features = [];
            b.getFeatures(
                { ref: 'chr1', start: 18000000, end: 19000000 },
                function(f) { features.push(f); },
                function() { features.done = true },
                function(e) { console.error(e.stack||''+e); }
            );

            waitsFor( function() { return features.done; } );
            runs( function() {
                expect( features.length ).toEqual( 14 );
                expect(features[0].get('gene_symbol')).toEqual('PRPS1L1');
                expect(features[0].get('name')).toEqual('uc003stz.1');
                expect(features[0].get('strand')).toEqual(-1);
                expect(features[13].get('gene_symbol')).toEqual('HDAC9');
                expect(features[13].get('name')).toEqual('uc003suk.1');
                expect(features[13].get('strand')).toEqual(1);
            });
        });
    });

    describe( 'BigBed GENCODE bed12+4 and autosql', () => {
        const browser = new Browser({ unitTestMode: true });
        const b = new BigBed({
            browser: browser,
            blob: new XHRBlob('../data/human_bigbed/gencode.bb')
        });
        const expectedFeatureData = cjsRequire('../../data/human_bigbed/ENST00000610940.4.json')

        it('constructs', function(){ expect(b).toBeTruthy(); });

        it('accesses gencode bigbed', () => {
            const features = [];
            b.getFeatures(
                { ref: 'chr1', start: 18000000, end: 19000000 },
                f => features.push(f),
                () => { features.done = true },
                e => { console.error(e.stack||''+e); }
            );

            waitsFor( () => features.done );
            runs( () => {
                expect( features.length ).toEqual( 114 )
                let featureData = JSON.parse(JSON.stringify(features[88], undefined, 2))
                // console.log(JSON.stringify(features[88],undefined,2))
                deleteUniqueIDSerial(featureData)
                deleteUniqueIDSerial(expectedFeatureData)
                expect(featureData).toEqual(expectedFeatureData)
            });
        });
    });

});

// recursively delete the unique serial numbers in all the _uniqueID properties of an
// object containing feature data
function deleteUniqueIDSerial(featureData) {
    Object.entries(featureData).forEach(([name,val]) => {
        if (!val) return

        if (name === '_uniqueID') {
            featureData[name] = val.replace(/_\d+$/,'_(serial redacted)')
        } else if (Array.isArray(val)) {
            val.forEach(v => deleteUniqueIDSerial(v))
        } else if (typeof val === 'object') {
            deleteUniqueIDSerial(val)
        }
    })
}