testBigbed.js

import BWSource from "../js/bigwig/bwSource.js";
import {parseAutoSQL} from "../js/util/ucscUtils"

function runBigbedTests() {

    QUnit.test("bed9+2 features", async function (assert) {
        var url = "./data/bb/myBigBed2.bb",
            chr = "chr7",
            bpStart = 0,
            bpEnd = Number.MAX_SAFE_INTEGER;
        var bWSource = new BWSource({url: url});
        const features = await bWSource.getFeatures(chr, bpStart, bpEnd, 1);
        assert.ok(features);
        assert.equal(features.length, 3339);   // Verified in iPad app

        //chr7	773975	792642	uc003sjb.2	0	+	776710	791816	0,255,0	HEATR2	Q86Y56-3
        const f = features[20];
        assert.equal(f.start, 773975);
        assert.equal(f.geneSymbol, 'HEATR2');
        assert.equal(f.spID, 'Q86Y56-3')
    });

    QUnit.test("interact features", async function (assert) {
        var url = "./data/bb/interactExample3.inter.bb",
            chr = "chr3",
            bpStart = 63702628,
            bpEnd = 63880091;

        var bWSource = new BWSource({url: url});
        const features = await bWSource.getFeatures(chr, bpStart, bpEnd, 1);
        assert.ok(features);
        assert.equal(features.length, 18);

        //chr3	63702628	63705638	.	584	10	.	0	chr17	58878552	58880897	.	.	chr3	63702628	63705638	.	.
        const firstFeature = features[0];
        assert.ok(firstFeature.interchr);

        //chr3	63741418	63978511	.	350	6	.	0	chr3	63741418	63743120	.	.	chr3	63976338	63978511	.	.
        const secondFeature = features[1];
        assert.equal(secondFeature.m1, (63741418 + 63743120) / 2);
        assert.equal(secondFeature.m2, (63976338 + 63978511) / 2);
    });


    QUnit.test("Autosql", function (assert) {
        const autosql = `
table chromatinInteract
"Chromatin interaction between two regions"
    (
    string chrom;      "Chromosome (or contig, scaffold, etc.). For interchromosomal, use 2 records"
    uint chromStart;   "Start position of lower region. For interchromosomal, set to chromStart of this region"
    uint chromEnd;     "End position of upper region. For interchromosomal, set to chromEnd of this region"
    string name;       "Name of item, for display"
    uint score;        "Score from 0-1000"
    double value;      "Strength of interaction or other data value. Typically basis for score"
    string exp;        "Experiment name (metadata for filtering). Use . if not applicable"
    string color;      "Item color.  Specified as r,g,b or hexadecimal #RRGGBB or html color name, as in //www.w3.org/TR/css3-color/#html4."
    string region1Chrom;  "Chromosome of lower region. For non-directional interchromosomal, chrom of this region."
    uint region1Start;  "Start position of lower/this region"
    uint region1End;    "End position in chromosome of lower/this region"
    string region1Name;  "Identifier of lower/this region"
    string region1Strand; "Orientation of lower/this region: + or -.  Use . if not applicable"
    string region2Chrom; "Chromosome of upper region. For non-directional interchromosomal, chrom of other region"
    uint region2Start;  "Start position in chromosome of upper/this region"
    uint region2End;    "End position in chromosome of upper/this region"
    string region2Name; "Identifier of upper/this region"
    string region2Strand; "Orientation of upper/this region: + or -.  Use . if not applicable"
    )
`

        const autosqlObject = parseAutoSQL(autosql);
        assert.ok(autosqlObject);
        assert.equal('chromatinInteract', autosqlObject.table);
        assert.equal(autosqlObject.fields.length, 18);

        const r2s = autosqlObject.fields[17];
        assert.equal(r2s.type, 'string');
        assert.equal(r2s.name, 'region2Strand');
        assert.equal(r2s.description, 'Orientation of upper/this region: + or -.  Use . if not applicable');
    })
}

export default runBigbedTests;