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Testing Test gwas Update bedtabix More conversion GWAS stuff Update version Working config Updates Updates Demo of gwas data Fix lint Update Update add test Fix config Add reexport for wiggle component Add xyplotrenderercomponent Remove gwas plugin from core
GMOD · Feb 17, 2021 · b1f6911 · b1f6911
1 parent 708bafa
commit b1f6911
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Showing 12 changed files with 292 additions and 1,539 deletions.
diff --git a/plugins/bed/src/BedTabixAdapter/BedTabixAdapter.test.ts b/plugins/bed/src/BedTabixAdapter/BedTabixAdapter.test.ts
@@ -27,7 +27,7 @@ test('adapter can fetch features from volvox-bed12.bed.gz', async () => {
 
   const featuresArray = await features.pipe(toArray()).toPromise()
   const featuresJsonArray = featuresArray.map(f => f.toJSON())
-  expect(featuresJsonArray).toMatchSnapshot()
+  expect(featuresJsonArray.slice(0, 10)).toMatchSnapshot()
 })
 
 test('adapter can fetch features from volvox.sort.bed.gz simple bed3', async () => {
@@ -55,7 +55,7 @@ test('adapter can fetch features from volvox.sort.bed.gz simple bed3', async ()
 
   const featuresArray = await features.pipe(toArray()).toPromise()
   const featuresJsonArray = featuresArray.map(f => f.toJSON())
-  expect(featuresJsonArray).toMatchSnapshot()
+  expect(featuresJsonArray.slice(0, 10)).toMatchSnapshot()
 })
 
 test('adapter can fetch features bed with autosql', async () => {
@@ -123,7 +123,7 @@ test('adapter can fetch features bed with autosql', async () => {
 
   const featuresArray = await features.pipe(toArray()).toPromise()
   const featuresJsonArray = featuresArray.map(f => f.toJSON())
-  expect(featuresJsonArray).toMatchSnapshot()
+  expect(featuresJsonArray.slice(0, 10)).toMatchSnapshot()
 })
 
 test('adapter can fetch bed with header', async () => {
@@ -155,5 +155,31 @@ test('adapter can fetch bed with header', async () => {
 
   const featuresArray = await features.pipe(toArray()).toPromise()
   const featuresJsonArray = featuresArray.map(f => f.toJSON())
-  expect(featuresJsonArray).toMatchSnapshot()
+  expect(featuresJsonArray.slice(0, 10)).toMatchSnapshot()
+})
+
+test('adapter can use gwas header', async () => {
+  const adapter = new BedTabixAdapter(
+    MyConfigSchema.create({
+      bedGzLocation: {
+        localPath: require.resolve('./test_data/gwas.bed.gz'),
+      },
+      index: {
+        location: {
+          localPath: require.resolve('./test_data/gwas.bed.gz.tbi'),
+        },
+      },
+    }),
+  )
+
+  const features = adapter.getFeatures({
+    refName: '1',
+    start: 0,
+    end: 100_000,
+    assemblyName: 'hg19',
+  })
+
+  const featuresArray = await features.pipe(toArray()).toPromise()
+  const featuresJsonArray = featuresArray.map(f => f.toJSON())
+  expect(featuresJsonArray.slice(0, 10)).toMatchSnapshot()
 })
diff --git a/plugins/bed/src/BedTabixAdapter/BedTabixAdapter.ts b/plugins/bed/src/BedTabixAdapter/BedTabixAdapter.ts
@@ -19,6 +19,10 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
 
   protected bed: TabixIndexedFile
 
+  protected columnNames: string[]
+
+  protected scoreColumn: string
+
   public static capabilities = ['getFeatures', 'getRefNames']
 
   public constructor(config: Instance<typeof MyConfigSchema>) {
@@ -40,7 +44,8 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
       tbiFilehandle: indexType !== 'CSI' ? openLocation(location) : undefined,
       chunkCacheSize: 50 * 2 ** 20,
     })
-
+    this.columnNames = readConfObject(config, 'columnNames')
+    this.scoreColumn = readConfObject(config, 'scoreColumn')
     this.parser = new BED({ autoSql })
   }
 
@@ -52,18 +57,41 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
     return this.bed.getHeader()
   }
 
+  defaultParser(fields: string[], line: string) {
+    return Object.fromEntries(line.split('\t').map((f, i) => [fields[i], f]))
+  }
+
+  async getNames() {
+    if (this.columnNames.length) {
+      return this.columnNames
+    }
+    const header = await this.bed.getHeader()
+    const defs = header.split('\n').filter(f => !!f)
+    const defline = defs[defs.length - 1]
+    return defline && defline.includes('\t')
+      ? defline
+          .slice(1)
+          .split('\t')
+          .map(field => field.trim())
+      : null
+  }
+
   public getFeatures(query: Region, opts: BaseOptions = {}) {
     return ObservableCreate<Feature>(async observer => {
+      const meta = await this.bed.getMetadata()
+      const names = await this.getNames()
       await this.bed.getLines(query.refName, query.start, query.end, {
         lineCallback: (line: string, fileOffset: number) => {
           const l = line.split('\t')
-          const refName = l[0]
-          const start = +l[1]
-          const end = +l[2]
-          const uniqueId = `bed-${fileOffset}`
-          const data = this.parser.parseLine(line, {
-            uniqueId,
-          })
+          const refName = l[meta.columnNumbers.ref - 1]
+          const start = +l[meta.columnNumbers.start - 1]
+          const end =
+            +l[meta.columnNumbers.end - 1] +
+            (meta.columnNumbers.end === meta.columnNumbers.start ? 1 : 0)
+          const uniqueId = `${this.id}-${fileOffset}`
+          const data = names
+            ? this.defaultParser(names, line)
+            : this.parser.parseLine(line, { uniqueId })
 
           const { blockCount, blockSizes, blockStarts, chromStarts } = data
 
@@ -84,6 +112,10 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
               })
             }
           }
+
+          if (this.scoreColumn) {
+            data.score = data[this.scoreColumn]
+          }
           delete data.chrom
           delete data.chromStart
           delete data.chromEnd
@@ -92,6 +124,7 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
             start,
             end,
             refName,
+            uniqueId,
           })
           const r = f.get('thickStart') ? ucscProcessedTranscript(f) : f
           observer.next(r)