Test expanded

packages/apollo-shared/src/GFF3/annotationFeatureToGFF3.test.ts

@@ -1,34 +1,69 @@
+/* eslint-disable prefer-destructuring */
 /* eslint-disable @typescript-eslint/no-floating-promises */
-
 import { describe, it } from 'node:test'
 import { assert } from 'chai'
 import { readAnnotationFeatureSnapshot } from './gff3ToAnnotationFeature.test'
 import { annotationFeatureToGFF3 } from './annotationFeatureToGFF3'
 
 describe('annotationFeatureToGFF3', () => {
-  it('Convert one gene', () => {
+  it('Convert one gene test fields', () => {
     const annotationFeature = readAnnotationFeatureSnapshot(
       'test_data/gene.json',
     )
     const [gff3Feature] = annotationFeatureToGFF3(annotationFeature)
 
+    assert.deepEqual(gff3Feature.seq_id, 'chr1')
     assert.deepEqual(gff3Feature.type, 'gene')
     assert.deepEqual(gff3Feature.start, 1000)
     assert.deepEqual(gff3Feature.end, 9000)
     assert.deepEqual(gff3Feature.strand, '+')
     assert.deepEqual(gff3Feature.score, 123)
     assert.deepEqual(gff3Feature.source, 'test_data')
+  })
+  it.skip('Convert one gene test phase', () => {
+    const annotationFeature = readAnnotationFeatureSnapshot(
+      'test_data/gene.json',
+    )
+    const [gff3Feature] = annotationFeatureToGFF3(annotationFeature)
+    const cds = gff3Feature.child_features[0][0].child_features[2][0]
+    assert.deepEqual(cds.start, 1201)
+    assert.deepEqual(cds.phase, '0')
+  })
+  it('Convert one gene test attributes', () => {
+    const annotationFeature = readAnnotationFeatureSnapshot(
+      'test_data/gene.json',
+    )
+    const [gff3Feature] = annotationFeatureToGFF3(annotationFeature)
+
     assert.deepEqual(gff3Feature.attributes?.Name, ['EDEN'])
-    assert.deepEqual(gff3Feature.attributes?.testid, ['t003'])
+    assert.deepEqual(gff3Feature.attributes?.testid, ['t001', 't003'])
     assert.deepEqual(gff3Feature.attributes?.ID, ['gene10001'])
-
+    assert.deepEqual(gff3Feature.attributes?.Ontology_term, [
+      'GO1234',
+      'GO4567',
+      'SO1234',
+    ])
+    assert.deepEqual(gff3Feature.attributes?.Alias, ['myalias'])
+    assert.deepEqual(gff3Feature.attributes?.Target, ['mytarget'])
+    assert.deepEqual(gff3Feature.attributes?.Gap, ['mygap'])
+    assert.deepEqual(gff3Feature.attributes?.Derives_from, ['myderives'])
+    assert.deepEqual(gff3Feature.attributes?.Note, ['mynote'])
+    assert.deepEqual(gff3Feature.attributes?.Dbxref, ['mydbxref'])
+    assert.deepEqual(gff3Feature.attributes?.Is_circular, ['true'])
+  })
+  it('Convert one gene test children', () => {
+    const annotationFeature = readAnnotationFeatureSnapshot(
+      'test_data/gene.json',
+    )
+    const [gff3Feature] = annotationFeatureToGFF3(annotationFeature)
     const [children] = gff3Feature.child_features
     const [mrna] = children
     assert.deepEqual(mrna.type, 'mRNA')
     assert.deepEqual(mrna.attributes?.Parent, ['gene10001'])
 
-    // Sanity check the annotationFeature does have a score, etc.
-    // assert.deepEqual(annotationFeature.attributes?.gff_score, ['123'])
-    // assert.deepEqual(annotationFeature.attributes?.gff_source, ['test_data'])
+    const [cds] = mrna.child_features[2]
+    assert.deepEqual(cds.type, 'CDS')
+    assert.deepEqual(cds.attributes?.ID, ['cds10001'])
+    assert.deepEqual(cds.attributes?.Parent, ['mRNA10001'])
   })
 })

packages/apollo-shared/test_data/gene.json

@@ -10,7 +10,17 @@
     "gff_name": ["EDEN"],
     "gff_score": ["123"],
     "gff_source": ["test_data"],
-    "testid": ["t003"]
+    "testid": ["t001", "t003"],
+    "gff_ontology_term": ["GO1234"],
+    "Gene Ontology": ["GO4567"],
+    "Sequence Ontology": ["SO1234"],
+    "gff_alias": ["myalias"],
+    "gff_target": ["mytarget"],
+    "gff_gap": ["mygap"],
+    "gff_derives_from": ["myderives"],
+    "gff_note": ["mynote"],
+    "gff_dbxref": ["mydbxref"],
+    "gff_is_circular": ["true"]
   },
   "children": {
     "66d70e4ccc30b55b65e5f618": {
@@ -20,6 +30,11 @@
       "min": 1049,
       "max": 9000,
       "strand": 1,
+      "attributes": {
+        "gff_id": ["mRNA10001"],
+        "gff_name": ["EDEN.1"],
+        "testid": ["t004", "t001", "t004"]
+      },
       "children": {
         "66d70e4ccc30b55b65e5f615": {
           "_id": "66d70e4ccc30b55b65e5f615",
@@ -58,11 +73,6 @@
             "testid": ["t012", "t013", "t014", "t015"]
           }
         }
-      },
-      "attributes": {
-        "gff_id": ["mRNA10001"],
-        "gff_name": ["EDEN.1"],
-        "testid": ["t004", "t001", "t004"]
       }
     }
   }