Allow FromConfigSequenceAdapter to not start at 0

GMOD · Feb 19, 2021 · 26dc3da · 26dc3da
1 parent f8429fb
commit 26dc3da
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Showing 2 changed files with 36 additions and 2 deletions.
diff --git a/plugins/config/src/FromConfigAdapter/FromConfigSequenceAdapter.test.ts b/plugins/config/src/FromConfigAdapter/FromConfigSequenceAdapter.test.ts
@@ -2,7 +2,7 @@ import { toArray } from 'rxjs/operators'
 import Adapter from './FromConfigSequenceAdapter'
 import { sequenceConfigSchema } from './configSchema'
 
-test('adapter can fetch sequences', async () => {
+test('adapter can fetch sequences when there is just one feature representing whole refseq', async () => {
   const features = [
     {
       uniqueId: 'one',
@@ -32,3 +32,34 @@ test('adapter can fetch sequences', async () => {
   expect(featuresArray2.length).toBe(1)
   expect(featuresArray2[0].get('seq')).toBe(features[0].seq.slice(100, 150))
 })
+
+test('adapter can fetch sequences', async () => {
+  const features = [
+    {
+      uniqueId: 'one',
+      refName: 'ctgA',
+      start: 5000,
+      end: 5150,
+      seq:
+        'ccaaaccgtcaattaaccggtatcttctcggaaacggcggttctctcctagatagcgatctgtggtctcaccatgcaatttaaacaggtgagtaaagattgctacaaatacgagactagctgtcaccagatgctgttcatctgttggctc',
+    },
+  ]
+  const adapter = new Adapter(sequenceConfigSchema.create({ features }))
+  const result = adapter.getFeatures({
+    refName: 'ctgA',
+    start: 4950,
+    end: 5050,
+  })
+  const featuresArray = await result.pipe(toArray()).toPromise()
+  expect(featuresArray.length).toBe(1)
+  expect(featuresArray[0].get('seq')).toBe(features[0].seq.slice(0, 50))
+
+  //   const result2 = adapter.getFeatures({
+  //     refName: 'ctgA',
+  //     start: 100,
+  //     end: 150,
+  //   })
+  //   const featuresArray2 = await result2.pipe(toArray()).toPromise()
+  //   expect(featuresArray2.length).toBe(1)
+  //   expect(featuresArray2[0].get('seq')).toBe(features[0].seq.slice(100, 150))
+})
diff --git a/plugins/config/src/FromConfigAdapter/FromConfigSequenceAdapter.ts b/plugins/config/src/FromConfigAdapter/FromConfigSequenceAdapter.ts
@@ -31,7 +31,10 @@ export default class FromSequenceConfigAdapter extends FromConfigAdapter {
           start: region.start,
           seq: feat
             .get('seq')
-            .slice(Math.max(region.start, 0), Math.max(region.end, 0)),
+            .slice(
+              Math.max(region.start - feat.get('start'), 0),
+              Math.max(region.end - feat.get('start'), 0),
+            ),
         }),
       )