BigBedDataSource-test

src/BigBedDataSource.js

@@ -54,8 +54,9 @@ type BigBedSource = {
 function parseBedFeature(f): Gene {
   var position = new ContigInterval(f.contig, f.start, f.stop),
       x = f.rest.split('\t'),
-      exonLengths = x[7].split(',').map(Number),
-      exonStarts = x[8].split(',').map(Number),
+      // exons arrays sometimes have trailing commas
+      exonLengths = x[7].replace(/,*$/, '').split(',').map(Number),
+      exonStarts = x[8].replace(/,*$/, '').split(',').map(Number),
       exons = _.zip(exonStarts, exonLengths)
                .map(function([start, length]) {
                  return new Interval(f.start + start, f.start + start + length);
@@ -76,7 +77,6 @@ function parseBedFeature(f): Gene {
 function createBigBedDataSource(remoteSource: BigBed): BigBedSource {
   // Collection of genes that have already been loaded.
   var genes: Array<Gene> = [];
-  window.genes = genes;
 
   // Ranges for which we have complete information -- no need to hit network.
   var coveredRanges: Array<ContigInterval<string>> = []

test/BigBedDataSource-test.js

@@ -0,0 +1,48 @@
+/* @flow */
+var chai = require('chai');
+var expect = chai.expect;
+var assert = chai.assert;
+
+var BigBed = require('../src/BigBed'),
+    createBigBedDataSource = require('../src/BigBedDataSource'),
+    ContigInterval = require('../src/ContigInterval');
+
+describe('BigBedDataSource', function() {
+  function getTestSource() {
+    // This file was created from Biodalliance's ensGene.bb via:
+    // bigBedToBed ensGene.bb ensGene.bed
+    // grep '^chr17   ' ensGene.bed > /tmp/ensGene17.bed
+    // bedToBigBed -type=bed12+2 /tmp/ensGene17.bed <(echo "chr17 78774742")
+    //             test/data/ensembl.chr17.bb
+    return createBigBedDataSource(new BigBed('/test/data/ensembl.chr17.bb'));
+  }
+
+  // Shorthand
+  function ci(contig, start, stop) {
+    return new ContigInterval(contig, start, stop);
+  }
+
+  it('should extract features in a range', function(done) {
+    this.timeout(5000);
+    console.time('extract');
+    var source = getTestSource();
+
+    // No genes fetched initially
+    var tp53range = new ContigInterval('chr17', 7512444, 7517300)
+    var tp53 = source.getGenesInRange(tp53range);
+    expect(tp53).to.deep.equal([]);
+
+    // Fetching that one gene should cache its entire block.
+    source.on('newdata', () => {
+      console.timeEnd('extract');
+      var tp53s = source.getGenesInRange(tp53range);
+      expect(tp53s).to.have.length(1);
+
+      var tp53 = tp53s[0];
+      expect(tp53.name).to.equal('TP53');
+      expect(tp53.exons).to.have.length(11);
+      done();
+    });
+    source.rangeChanged(tp53range);
+  });
+});