Add feature import conversion tests (#441)

* Temp commit

* Use chai to deeply compare annotation features

* Some working tests

* Fix import

* Tests for feature conversion (#429)

Test `Convert example 3` fails because there should be 4 CDSs in the
converted feature object but current code detects 3

Test `Convert braker gff` fails because the converted feature includes
intron, start_codon, and stop_codon

* Fix linter

* Fix CDS overlap calculation

* Ignore more calculated properties on conversion

---------

Co-authored-by: Garrett Stevens <[email protected]>

packages/apollo-cli/package.json

@@ -85,7 +85,7 @@
     "@istanbuljs/esm-loader-hook": "^0.2.0",
     "@istanbuljs/nyc-config-typescript": "^1.0.2",
     "@oclif/test": "^3.1.3",
-    "@types/chai": "^4",
+    "@types/chai": "^4.3.19",
     "@types/cli-progress": "^3",
     "@types/inquirer": "^9.0.7",
     "@types/mocha": "^10",

packages/apollo-shared/package.json

@@ -26,8 +26,11 @@
   "devDependencies": {
     "@nestjs/common": "^10.1.0",
     "@nestjs/core": "^10.1.0",
+    "@types/chai": "^4.3.19",
     "@types/node": "^18.14.2",
     "@types/rimraf": "^3",
+    "chai": "^5.1.1",
+    "chai-exclude": "^3.0.0",
     "glob": "^11.0.0",
     "mobx": "^6.6.1",
     "mobx-state-tree": "^5.1.7",

packages/apollo-shared/src/GFF3/gff3ToAnnotationFeature.test.ts

@@ -1,11 +1,16 @@
 /* eslint-disable @typescript-eslint/no-floating-promises */
-import { strict as assert } from 'node:assert'
 import { describe, it } from 'node:test'
-import gff from '@gmod/gff'
+import { readFileSync } from 'node:fs'
+
+import gff, { GFF3Feature } from '@gmod/gff'
+import { assert, use } from 'chai'
+import chaiExclude from 'chai-exclude'
 
 import { gff3ToAnnotationFeature } from './gff3ToAnnotationFeature'
 import { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
 
+use(chaiExclude)
+
 const testCases: [string, string, AnnotationFeatureSnapshot][] = [
   [
     'a feature with no children',
@@ -23,18 +28,173 @@ const testCases: [string, string, AnnotationFeatureSnapshot][] = [
       },
     },
   ],
+  [
+    'a feature with two children',
+    `ctgA	est	EST_match	1050	3202	.	+	.	ID=Match1;Name=agt830.5;Target=agt830.5 1 654
+ctgA	est	match_part	1050	1500	.	+	.	Parent=Match1;Name=agt830.5;Target=agt830.5 1 451
+ctgA	est	match_part	3000	3202	.	+	.	Parent=Match1;Name=agt830.5;Target=agt830.5 452 654
+`,
+    {
+      _id: '66cf9fbb4e947fa2c27d3d6a',
+      refSeq: 'ctgA',
+      type: 'EST_match',
+      min: 1049,
+      max: 3202,
+      strand: 1,
+      children: {
+        '66cf9fbb4e947fa2c27d3d68': {
+          _id: '66cf9fbb4e947fa2c27d3d68',
+          refSeq: 'ctgA',
+          type: 'match_part',
+          min: 1049,
+          max: 1500,
+          strand: 1,
+          attributes: {
+            gff_source: ['est'],
+            gff_name: ['agt830.5'],
+            gff_target: ['agt830.5 1 451'],
+          },
+        },
+        '66cf9fbb4e947fa2c27d3d69': {
+          _id: '66cf9fbb4e947fa2c27d3d69',
+          refSeq: 'ctgA',
+          type: 'match_part',
+          min: 2999,
+          max: 3202,
+          strand: 1,
+          attributes: {
+            gff_source: ['est'],
+            gff_name: ['agt830.5'],
+            gff_target: ['agt830.5 452 654'],
+          },
+        },
+      },
+      attributes: {
+        gff_source: ['est'],
+        gff_id: ['Match1'],
+        gff_name: ['agt830.5'],
+        gff_target: ['agt830.5 1 654'],
+      },
+    },
+  ],
 ]
 
+interface AnnotationFeatureSnapshotWithChildrenArray
+  extends Omit<AnnotationFeatureSnapshot, 'children'> {
+  children?: AnnotationFeatureSnapshotWithChildrenArray[]
+}
+
+function childrenToArray(
+  feature: AnnotationFeatureSnapshot,
+): AnnotationFeatureSnapshotWithChildrenArray {
+  const { children } = feature
+  if (!children) {
+    return feature as AnnotationFeatureSnapshotWithChildrenArray
+  }
+  const childrenArray = Object.values(children).map((child) =>
+    childrenToArray(child),
+  )
+  return { ...feature, children: childrenArray }
+}
+
 function compareFeatures(
   feature1: AnnotationFeatureSnapshot,
   feature2: AnnotationFeatureSnapshot,
 ) {
-  assert.deepEqual(
-    { ...feature1, _id: undefined },
-    { ...feature2, _id: undefined },
+  assert.deepEqualExcludingEvery(
+    childrenToArray(feature1),
+    childrenToArray(feature2),
+    '_id',
   )
 }
 
+function readFeatureFile(fn: string): GFF3Feature[] {
+  const lines = readFileSync(fn).toString().split('\n')
+  const feature: string[] = []
+  for (const line of lines) {
+    if (!line.startsWith('#')) {
+      feature.push(line)
+    }
+  }
+  const inGff = gff.parseStringSync(feature.join('\n')) as GFF3Feature[]
+  return inGff
+}
+
+function readAnnotationFeatureSnapshot(fn: string): AnnotationFeatureSnapshot {
+  const lines = readFileSync(fn).toString()
+  return JSON.parse(lines) as AnnotationFeatureSnapshot
+}
+
+const [ex1, ex2, ex3, ex4] = readFeatureFile(
+  'test_data/gene_representations.gff3',
+)
+
+describe('gff3ToAnnotationFeature examples', () => {
+  it('Convert one CDS', () => {
+    const actual = gff3ToAnnotationFeature(
+      readFeatureFile('test_data/one_cds.gff3')[0],
+    )
+    const expected = readAnnotationFeatureSnapshot('test_data/one_cds.json')
+    compareFeatures(actual, expected)
+  })
+  it('Convert two CDSs', () => {
+    const actual = gff3ToAnnotationFeature(
+      readFeatureFile('test_data/two_cds.gff3')[0],
+    )
+    const expected = readAnnotationFeatureSnapshot('test_data/two_cds.json')
+    compareFeatures(actual, expected)
+  })
+  it('Convert example 1', () => {
+    const actual = gff3ToAnnotationFeature(ex1)
+    const txt = JSON.stringify(actual, null, 2)
+
+    assert.equal(txt.match(/"type": "CDS"/g)?.length, 4)
+    assert.equal(txt.match(/"type": "TF_binding_site"/g)?.length, 1)
+
+    const expected = readAnnotationFeatureSnapshot('test_data/example01.json')
+    compareFeatures(actual, expected)
+  })
+  it('Convert example 2', () => {
+    const actual = gff3ToAnnotationFeature(ex2)
+    const txt = JSON.stringify(actual, null, 2)
+    assert.equal(txt.match(/"type": "CDS"/g)?.length, 4)
+    const expected = readAnnotationFeatureSnapshot('test_data/example02.json')
+    compareFeatures(actual, expected)
+  })
+  it('Convert example 3', () => {
+    // NB: In example 3 (and in the other examples) mRNA10003 produces two proteins.
+    // In the other examples the two proteins are identified by sharing the same cds id.
+    // In example 3 instead each cds has a unique id so the two proteins are identified by the order they
+    // appear in the gff.
+    const actual = gff3ToAnnotationFeature(ex3)
+    const txt = JSON.stringify(actual, null, 2)
+    assert.equal(txt.match(/"type": "CDS"/g)?.length, 4)
+
+    // const expected = readAnnotationFeatureSnapshot('test_data/example03.json')
+    // compareFeatures(actual, expected)
+  })
+  it('Convert example 4', () => {
+    const ft = JSON.stringify(ex4, null, 2)
+    assert.equal(ft.match(/"type": "five_prime_UTR"/g)?.length, 6)
+    assert.equal(ft.match(/"type": "three_prime_UTR"/g)?.length, 3)
+
+    const actual = gff3ToAnnotationFeature(ex4)
+    const txt = JSON.stringify(actual, null, 2)
+    assert.equal(txt.match(/"type": "CDS"/g)?.length, 4)
+    assert.equal(txt.match(/prime_UTR/g), null)
+
+    const expected = readAnnotationFeatureSnapshot('test_data/example04.json')
+    compareFeatures(actual, expected)
+  })
+  it('Convert braker gff', () => {
+    const [gffFeature] = readFeatureFile('test_data/braker.gff')
+    const actual = gff3ToAnnotationFeature(gffFeature)
+    const txt = JSON.stringify(actual, null, 2)
+    assert.equal(txt.match(/intron/g), null)
+    assert.equal(txt.match(/_codon/g), null)
+  })
+})
+
 describe('gff3ToAnnotationFeature', () => {
   for (const testCase of testCases) {
     const [description, featureLine, convertedFeature] = testCase

packages/apollo-shared/src/GFF3/gff3ToAnnotationFeature.ts

@@ -158,7 +158,10 @@ function convertChildren(
     const [firstChildFeatureLocation] = childFeature
     if (
       firstChildFeatureLocation.type === 'three_prime_UTR' ||
-      firstChildFeatureLocation.type === 'five_prime_UTR'
+      firstChildFeatureLocation.type === 'five_prime_UTR' ||
+      firstChildFeatureLocation.type === 'intron' ||
+      firstChildFeatureLocation.type === 'start_codon' ||
+      firstChildFeatureLocation.type === 'stop_codon'
     ) {
       continue
     }
@@ -232,20 +235,17 @@ function processCDS(
       groupedLocations.push([location])
       continue
     }
-    const lastGroupLastLocation = lastGroup.at(-1)
-    if (!lastGroupLastLocation) {
-      throw new Error('Got group with no locations')
-    }
-    if (
+    const overlaps = lastGroup.some((lastGroupLoc) =>
       doesIntersect2(
         /* eslint-disable @typescript-eslint/no-non-null-assertion */
-        lastGroupLastLocation.start!,
-        lastGroupLastLocation.end!,
+        lastGroupLoc.start!,
+        lastGroupLoc.end!,
         location.start!,
         location.end!,
         /* eslint-enable @typescript-eslint/no-non-null-assertion */
-      )
-    ) {
+      ),
+    )
+    if (overlaps) {
       groupedLocations.push([location])
     } else {
       lastGroup.push(location)

packages/apollo-shared/test_data/braker.gff

@@ -0,0 +1,13 @@
+##gff-version	3
+CM033580.1	AUGUSTUS	gene	15529	16566	0.92	-	.	ID=g1;
+CM033580.1	AUGUSTUS	mRNA	15529	16566	0.92	-	.	ID=g1.t1;Parent=g1;
+CM033580.1	AUGUSTUS	stop_codon	15529	15531	.	-	0	ID=g1.t1.stop1;Parent=g1.t1;
+CM033580.1	AUGUSTUS	CDS	15529	15659	0.92	-	2	ID=g1.t1.CDS1;Parent=g1.t1;
+CM033580.1	AUGUSTUS	exon	15529	15659	.	-	.	ID=g1.t1.exon1;Parent=g1.t1;
+CM033580.1	AUGUSTUS	intron	15660	16112	0.96	-	.	ID=g1.t1.intron1;Parent=g1.t1;
+CM033580.1	AUGUSTUS	CDS	16113	16314	0.96	-	0	ID=g1.t1.CDS2;Parent=g1.t1;
+CM033580.1	AUGUSTUS	exon	16113	16314	.	-	.	ID=g1.t1.exon2;Parent=g1.t1;
+CM033580.1	AUGUSTUS	intron	16315	16536	0.96	-	.	ID=g1.t1.intron2;Parent=g1.t1;
+CM033580.1	AUGUSTUS	CDS	16537	16566	0.99	-	0	ID=g1.t1.CDS3;Parent=g1.t1;
+CM033580.1	AUGUSTUS	exon	16537	16566	.	-	.	ID=g1.t1.exon3;Parent=g1.t1;
+CM033580.1	AUGUSTUS	start_codon	16564	16566	.	-	0	ID=g1.t1.start1;Parent=g1.t1;

packages/apollo-shared/test_data/example01.gff3

@@ -0,0 +1,26 @@
+##gff-version 3
+##sequence-region   chr1 1000 9000
+#example01
+chr1	.	gene	1000	9000	.	+	.	ID=gene10001;Name=EDEN
+chr1	.	TF_binding_site	1000	1012	.	+	.	ID=tfbs10001;Parent=gene10001
+chr1	.	mRNA	1050	9000	.	+	.	ID=mRNA10001;Parent=gene10001;Name=EDEN.1
+chr1	.	mRNA	1050	9000	.	+	.	ID=mRNA10002;Parent=gene10001;Name=EDEN.2
+chr1	.	mRNA	1300	9000	.	+	.	ID=mRNA10003;Parent=gene10001;Name=EDEN.3
+chr1	.	exon	1050	1500	.	+	.	ID=exon10001;Parent=mRNA10001,mRNA10002
+chr1	.	exon	1300	1500	.	+	.	ID=exon10002;Parent=mRNA10003
+chr1	.	exon	3000	3902	.	+	.	ID=exon10003;Parent=mRNA10001,mRNA10003
+chr1	.	exon	5000	5500	.	+	.	ID=exon10004;Parent=mRNA10001,mRNA10002,mRNA10003
+chr1	.	exon	7000	9000	.	+	.	ID=exon10005;Parent=mRNA10001,mRNA10002,mRNA10003
+chr1	.	CDS	1201	1500	.	+	0	ID=cds10001;Parent=mRNA10001;Name=edenprotein.1
+chr1	.	CDS	3000	3902	.	+	0	ID=cds10001;Parent=mRNA10001;Name=edenprotein.1
+chr1	.	CDS	5000	5500	.	+	0	ID=cds10001;Parent=mRNA10001;Name=edenprotein.1
+chr1	.	CDS	7000	7600	.	+	0	ID=cds10001;Parent=mRNA10001;Name=edenprotein.1
+chr1	.	CDS	1201	1500	.	+	0	ID=cds10002;Parent=mRNA10002;Name=edenprotein.2
+chr1	.	CDS	5000	5500	.	+	0	ID=cds10002;Parent=mRNA10002;Name=edenprotein.2
+chr1	.	CDS	7000	7600	.	+	0	ID=cds10002;Parent=mRNA10002;Name=edenprotein.2
+chr1	.	CDS	3301	3902	.	+	0	ID=cds10003;Parent=mRNA10003;Name=edenprotein.3
+chr1	.	CDS	5000	5500	.	+	1	ID=cds10003;Parent=mRNA10003;Name=edenprotein.3
+chr1	.	CDS	7000	7600	.	+	1	ID=cds10003;Parent=mRNA10003;Name=edenprotein.3
+chr1	.	CDS	3391	3902	.	+	0	ID=cds10004;Parent=mRNA10003;Name=edenprotein.4
+chr1	.	CDS	5000	5500	.	+	1	ID=cds10004;Parent=mRNA10003;Name=edenprotein.4
+chr1	.	CDS	7000	7600	.	+	1	ID=cds10004;Parent=mRNA10003;Name=edenprotein.4