@apollo-annotation/shared 0.3.1 → 0.3.2

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/shared",
-  "version": "0.3.1",
+  "version": "0.3.2",
   "main": "./dist/index.js",
   "scripts": {
     "build": "yarn clean && tsc --build",
@@ -10,12 +10,12 @@
     "test:ci": "NODE_V8_COVERAGE=./coverage glob -c \"tsx --test --test-reporter spec --experimental-test-coverage \" \"**/*.test.ts\""
   },
   "dependencies": {
-    "@apollo-annotation/common": "^0.3.1",
-    "@apollo-annotation/mst": "^0.3.1",
-    "@apollo-annotation/schemas": "^0.3.1",
+    "@apollo-annotation/common": "^0.3.2",
+    "@apollo-annotation/mst": "^0.3.2",
+    "@apollo-annotation/schemas": "^0.3.2",
     "@gmod/gff": "1.2.0",
     "@gmod/indexedfasta": "^2.0.4",
-    "@jbrowse/core": "^2.13.1",
+    "@jbrowse/core": "^3.0.1",
     "bson-objectid": "^2.0.4",
     "generic-filehandle": "^3.0.0",
     "jwt-decode": "^3.1.2",
@@ -39,7 +39,7 @@
     "typescript": "^5.5.3"
   },
   "peerDependencies": {
-    "@mui/material": "^5.11.14",
+    "@mui/material": "^6.0.0",
     "@mui/x-data-grid": "^7.0.0",
     "mobx": "^6.6.1",
     "mobx-react": "^7.2.1",

package/src/GFF3/annotationFeatureToGFF3.ts

@@ -14,7 +14,7 @@ export function annotationFeatureToGFF3(
   refSeqNames?: Record<string, string | undefined>,
 ): GFF3Feature {
   const attributes: Record<string, string[] | undefined> = JSON.parse(
-    JSON.stringify(feature.attributes),
+    JSON.stringify(feature.attributes ?? {}),
   )
   const ontologyTerms: string[] = []
   const source = feature.attributes?.gff_source?.[0] ?? null

package/src/GFF3/gff3ToAnnotationFeature.test.ts

@@ -197,6 +197,37 @@ describe('gff3ToAnnotationFeature examples', () => {
   })
 })
 
+describe('CDS without exons', () => {
+  it('Convert mRNA with CDS but without exon', () => {
+    const [gffFeature] = readFeatureFile('test_data/cds_without_exon.gff')
+    const actual = gff3ToAnnotationFeature(gffFeature)
+    const expected = readAnnotationFeatureSnapshot(
+      'test_data/cds_without_exon.json',
+    )
+    compareFeatures(actual, expected)
+  })
+  it('Convert mRNA with CDS but without exon and spliced UTR', () => {
+    const [gffFeature] = readFeatureFile(
+      'test_data/cds_without_exon_spliced_utr.gff',
+    )
+    const actual = gff3ToAnnotationFeature(gffFeature)
+    const expected = readAnnotationFeatureSnapshot(
+      'test_data/cds_without_exon_spliced_utr.json',
+    )
+    compareFeatures(actual, expected)
+  })
+  it('Convert mRNA with one CDS, without exons non-adjacent UTR', () => {
+    const [gffFeature] = readFeatureFile(
+      'test_data/onecds_without_exon_spliced_utr.gff',
+    )
+    const actual = gff3ToAnnotationFeature(gffFeature)
+    const expected = readAnnotationFeatureSnapshot(
+      'test_data/onecds_without_exon_spliced_utr.json',
+    )
+    compareFeatures(actual, expected)
+  })
+})
+
 describe('gff3ToAnnotationFeature', () => {
   for (const testCase of testCases) {
     const [description, featureLine, convertedFeature] = testCase
@@ -209,3 +240,30 @@ describe('gff3ToAnnotationFeature', () => {
     })
   }
 })
+
+describe('Source and score', () => {
+  it('Convert score and source', () => {
+    const gffFeature: GFF3Feature = [
+      {
+        seq_id: 'chr1',
+        source: 'mySource',
+        type: 'gene',
+        start: 1000,
+        end: 9000,
+        score: 0,
+        strand: '+',
+        phase: null,
+        attributes: {
+          ID: ['gene10001'],
+          Name: ['EDEN'],
+          testid: ['t003'],
+        },
+        child_features: [],
+        derived_features: [],
+      },
+    ]
+    const actual = gff3ToAnnotationFeature(gffFeature)
+    assert.deepStrictEqual(actual.attributes?.gff_source?.at(0), 'mySource')
+    assert.deepStrictEqual(actual.attributes?.gff_score?.at(0), '0')
+  })
+})

package/src/GFF3/gff3ToAnnotationFeature.ts

@@ -121,6 +121,9 @@ function convertFeatureAttributes(
         const newKey = isGFFReservedAttribute(key) ? gffToInternal[key] : key
         const existingVal = convertedAttributes[newKey]
         if (existingVal) {
+          // if (JSON.stringify(existingVal) === JSON.stringify(val)) {
+          //   continue
+          // }
           const valSet = new Set([...existingVal, ...val])
           convertedAttributes[newKey] = [...valSet]
         } else {
@@ -154,8 +157,19 @@ function convertChildren(
   const { child_features: childFeatures } = firstFeature
 
   const cdsFeatures: GFF3Feature[] = []
+  const exonFeatures: GFF3Feature[] = []
+  const utrFeatures: GFF3Feature[] = []
   for (const childFeature of childFeatures) {
     const [firstChildFeatureLocation] = childFeature
+    if (firstChildFeatureLocation.type === 'exon') {
+      exonFeatures.push(childFeature)
+    }
+    if (
+      firstChildFeatureLocation.type === 'three_prime_UTR' ||
+      firstChildFeatureLocation.type === 'five_prime_UTR'
+    ) {
+      utrFeatures.push(childFeature)
+    }
     if (
       firstChildFeatureLocation.type === 'three_prime_UTR' ||
       firstChildFeatureLocation.type === 'five_prime_UTR' ||
@@ -172,10 +186,23 @@ function convertChildren(
       convertedChildren[child._id] = child
     }
   }
-  const processedCDS =
-    cdsFeatures.length > 0 ? processCDS(cdsFeatures, refSeq, featureIds) : []
-  for (const cds of processedCDS) {
-    convertedChildren[cds._id] = cds
+
+  if (cdsFeatures.length > 0) {
+    const processedCDS = processCDS(cdsFeatures, refSeq, featureIds)
+
+    for (const cds of processedCDS) {
+      convertedChildren[cds._id] = cds
+    }
+
+    const missingExons = inferMissingExons(
+      cdsFeatures,
+      exonFeatures,
+      utrFeatures,
+      processedCDS[0].refSeq,
+    )
+    for (const exon of missingExons) {
+      convertedChildren[exon._id] = exon
+    }
   }
 
   if (Object.keys(convertedChildren).length > 0) {
@@ -184,6 +211,149 @@ function convertChildren(
   return
 }
 
+function inferMissingExons(
+  cdsFeatures: GFF3Feature[],
+  existingExons: GFF3Feature[],
+  utrFeatures: GFF3Feature[],
+  refSeq: string,
+): AnnotationFeatureSnapshot[] {
+  // Convert utrFeatures from GFF3Feature to AnnotationFeatureSnapshot
+  const utrExons: AnnotationFeatureSnapshot[] = []
+  for (const utrs of utrFeatures) {
+    for (const utr of utrs) {
+      if (!utr.start || !utr.end) {
+        throw new Error(
+          `UTR has undefined start and/or end\n: ${JSON.stringify(utr, null, 2)}`,
+        )
+      }
+      let strand: 1 | -1 | undefined = undefined
+      if (utr.strand === '+') {
+        strand = 1
+      } else if (utr.strand === '-') {
+        strand = -1
+      }
+      utrExons.push({
+        _id: new ObjectID().toHexString(),
+        refSeq,
+        type: 'exon',
+        min: utr.start - 1,
+        max: utr.end,
+        strand,
+      })
+    }
+  }
+  utrExons.sort((a, b) => a.min - b.min)
+
+  const missingExons: AnnotationFeatureSnapshot[] = []
+  for (const protein of cdsFeatures) {
+    protein.sort((a, b) => {
+      if (!a.start || !b.start) {
+        throw new Error('CDS has undefined start')
+      }
+      return a.start - b.start
+    })
+    for (let cdsIdx = 0; cdsIdx < protein.length; cdsIdx++) {
+      const cds = protein[cdsIdx]
+      // For CDS check if there is an exon containing it. If not, create an exon with same coords as the CDS.
+      let exonFound = false
+      for (const x of existingExons) {
+        if (x.length != 1) {
+          throw new Error('Unexpected number of exons')
+        }
+        const [exon] = x
+        if (
+          exon.start &&
+          exon.end &&
+          cds.start &&
+          cds.end &&
+          exon.start <= cds.start &&
+          exon.end >= cds.end
+        ) {
+          exonFound = true
+          break
+        }
+      }
+      if (!exonFound) {
+        if (!cds.start || !cds.end) {
+          throw new Error(
+            `CDS has undefined start and/or end: ${JSON.stringify(cds, null, 2)}`,
+          )
+        }
+        let strand: 1 | -1 | undefined = undefined
+        if (cds.strand === '+') {
+          strand = 1
+        } else if (cds.strand === '-') {
+          strand = -1
+        }
+        const newExon: AnnotationFeatureSnapshot = {
+          _id: new ObjectID().toHexString(),
+          refSeq,
+          type: 'exon',
+          min: cds.start - 1,
+          max: cds.end,
+          strand,
+        }
+        if (cdsIdx === 0) {
+          // If this CDS is the leftmost (or the only CDS in this protein), check if we need to add UTRs before it
+          for (const utr of utrExons) {
+            if (utr.max > newExon.min) {
+              break
+            }
+            if (utr.max === newExon.min) {
+              // UTR ends where exon begins: Extend the exon to include this UTR
+              newExon.min = utr.min
+            } else {
+              missingExons.push(utr)
+            }
+          }
+        }
+        if (cdsIdx === protein.length - 1) {
+          // If this CDS is the rightmost (or the only CDS in this protein), check if we need to add UTRs after it
+          for (const utr of utrExons) {
+            if (utr.min < newExon.max) {
+              continue
+            }
+            if (utr.min === newExon.max) {
+              // UTR begins where exon end: Extend the exon to include this UTR
+              newExon.max = utr.max
+            } else {
+              missingExons.push(utr)
+            }
+          }
+        }
+        missingExons.push(newExon)
+      }
+    }
+  }
+  const mergedExons = mergeAnnotationFeatures(missingExons)
+  return mergedExons
+}
+
+function mergeAnnotationFeatures(
+  features: AnnotationFeatureSnapshot[],
+): AnnotationFeatureSnapshot[] {
+  if (features.length === 0) {
+    return []
+  }
+  features.sort((a, b) => a.min - b.min)
+
+  const res = []
+  res.push(features[0])
+
+  for (let i = 1; i < features.length; i++) {
+    const last = res.at(-1)
+    const curr = features[i]
+
+    // If current interval overlaps with the last merged interval, merge them
+    if (last && curr.min <= last.max) {
+      last.max = Math.max(last.max, curr.max)
+    } else {
+      res.push(curr)
+    }
+  }
+  return res
+}
+
 /**
  * If a GFF3 file has CDS features that either (1) don't have an ID or (2) have
  * different IDs for each CDS, we have to do a bit of guessing about how they

package/test_data/cds_without_exon.gff

@@ -0,0 +1,12 @@
+##gff-version 3
+##sequence-region	53cb6b9b4f4ddef1ad47f943	1050	9000
+ctgA	example	gene	1050	9000	.	+	.	ID=eden
+ctgA	example	mRNA	1050	9000	.	+	.	ID=eden.1;Parent=eden
+ctgA	example	five_prime_UTR	1050	1210	.	+	0	ID=five1;Parent=eden.1
+ctgA	example	CDS	1211	1510	.	+	0	ID=cds2;Parent=eden.1
+ctgA	example	CDS	1611	1710	.	+	0	ID=cds2;Parent=eden.1
+ctgA	example	three_prime_UTR	1711	1800	.	+	0	ID=three1;Parent=eden.1
+ctgA	example	exon	1201	1500	.	+	0	ID=exon1;Parent=eden.1
+ctgA	example	CDS	1601	1700	.	+	0	ID=cds1;Parent=eden.1
+ctgA	example	CDS	1201	1500	.	+	0	ID=cds1;Parent=eden.1
+ctgA	example	TF_binding_site	1050	1100	.	+	.	Parent=eden

package/test_data/cds_without_exon.json

@@ -0,0 +1,74 @@
+{
+  "_id": "67581b7d5890a8eb1bedab6e",
+  "refSeq": "ctgA",
+  "type": "gene",
+  "min": 1049,
+  "max": 9000,
+  "strand": 1,
+  "children": {
+    "67581b7d5890a8eb1bedab6c": {
+      "_id": "67581b7d5890a8eb1bedab6c",
+      "refSeq": "ctgA",
+      "type": "mRNA",
+      "min": 1049,
+      "max": 9000,
+      "strand": 1,
+      "children": {
+        "67581b7d5890a8eb1bedab66": {
+          "_id": "67581b7d5890a8eb1bedab66",
+          "refSeq": "ctgA",
+          "type": "exon",
+          "min": 1200,
+          "max": 1500,
+          "strand": 1,
+          "attributes": { "gff_source": ["example"], "gff_id": ["exon1"] }
+        },
+        "67581b7d5890a8eb1bedab67": {
+          "_id": "67581b7d5890a8eb1bedab67",
+          "refSeq": "ctgA",
+          "type": "CDS",
+          "min": 1210,
+          "max": 1710,
+          "strand": 1,
+          "attributes": { "gff_source": ["example"], "gff_id": ["cds2"] }
+        },
+        "67581b7d5890a8eb1bedab68": {
+          "_id": "67581b7d5890a8eb1bedab68",
+          "refSeq": "ctgA",
+          "type": "CDS",
+          "min": 1200,
+          "max": 1700,
+          "strand": 1,
+          "attributes": { "gff_source": ["example"], "gff_id": ["cds1"] }
+        },
+        "67581b7d5890a8eb1bedab69": {
+          "_id": "67581b7d5890a8eb1bedab69",
+          "refSeq": "ctgA",
+          "type": "exon",
+          "min": 1049,
+          "max": 1510,
+          "strand": 1
+        },
+        "67581b7d5890a8eb1bedab6b": {
+          "_id": "67581b7d5890a8eb1bedab6b",
+          "refSeq": "ctgA",
+          "type": "exon",
+          "min": 1600,
+          "max": 1800,
+          "strand": 1
+        }
+      },
+      "attributes": { "gff_source": ["example"], "gff_id": ["eden.1"] }
+    },
+    "67581b7d5890a8eb1bedab6d": {
+      "_id": "67581b7d5890a8eb1bedab6d",
+      "refSeq": "ctgA",
+      "type": "TF_binding_site",
+      "min": 1049,
+      "max": 1100,
+      "strand": 1,
+      "attributes": { "gff_source": ["example"] }
+    }
+  },
+  "attributes": { "gff_source": ["example"], "gff_id": ["eden"] }
+}

package/test_data/cds_without_exon_spliced_utr.gff

@@ -0,0 +1,14 @@
+##gff-version 3
+chr1	.	gene	1000	9000	.	+	.	ID=gene00001
+#chr1	.	mRNA	1300	9000	.	+	.	ID=mRNA00001;Parent=gene00001
+#chr1	.	five_prime_UTR	3000	3300	.	+	.	Parent=mRNA00001
+#chr1	.	CDS	5000	5500	.	+	1	ID=cds00001;Parent=mRNA00001
+#chr1	.	three_prime_UTR	7601	8000	.	+	.	Parent=mRNA00001
+chr1	.	mRNA	1300	9000	.	+	.	ID=mRNA00003;Parent=gene00001
+chr1	.	five_prime_UTR	1300	1500	.	+	.	Parent=mRNA00003
+chr1	.	five_prime_UTR	3000	3300	.	+	.	Parent=mRNA00003
+chr1	.	CDS	3301	3902	.	+	0	ID=cds00003;Parent=mRNA00003
+chr1	.	CDS	5000	5500	.	+	1	ID=cds00003;Parent=mRNA00003
+chr1	.	CDS	7000	7600	.	+	2	ID=cds00003;Parent=mRNA00003
+chr1	.	three_prime_UTR	7601	8000	.	+	.	Parent=mRNA00003
+chr1	.	three_prime_UTR	8501	8900	.	+	.	Parent=mRNA00003

package/test_data/cds_without_exon_spliced_utr.json

@@ -0,0 +1,73 @@
+{
+  "_id": "675ad4e6a5abb3a5087c0652",
+  "refSeq": "chr1",
+  "type": "gene",
+  "min": 999,
+  "max": 9000,
+  "strand": 1,
+  "children": {
+    "675ad4e6a5abb3a5087c0651": {
+      "_id": "675ad4e6a5abb3a5087c0651",
+      "refSeq": "chr1",
+      "type": "mRNA",
+      "min": 1299,
+      "max": 9000,
+      "strand": 1,
+      "children": {
+        "675ad4e6a5abb3a5087c0649": {
+          "_id": "675ad4e6a5abb3a5087c0649",
+          "refSeq": "chr1",
+          "type": "CDS",
+          "min": 3300,
+          "max": 7600,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["cds00003"]
+          }
+        },
+        "675ad4e6a5abb3a5087c064a": {
+          "_id": "675ad4e6a5abb3a5087c064a",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 1299,
+          "max": 1500,
+          "strand": 1
+        },
+        "675ad4e6a5abb3a5087c064e": {
+          "_id": "675ad4e6a5abb3a5087c064e",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 2999,
+          "max": 3902,
+          "strand": 1
+        },
+        "675ad4e6a5abb3a5087c064f": {
+          "_id": "675ad4e6a5abb3a5087c064f",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 4999,
+          "max": 5500,
+          "strand": 1
+        },
+        "675ad4e6a5abb3a5087c0650": {
+          "_id": "675ad4e6a5abb3a5087c0650",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 6999,
+          "max": 8000,
+          "strand": 1
+        },
+        "675ad4e6a5abb3a5087c064d": {
+          "_id": "675ad4e6a5abb3a5087c064d",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 8500,
+          "max": 8900,
+          "strand": 1
+        }
+      },
+      "attributes": { "gff_id": ["mRNA00003"] }
+    }
+  },
+  "attributes": { "gff_id": ["gene00001"] }
+}

package/test_data/gene_representations.gff3

@@ -1,4 +1,5 @@
 ##gff-version 3
+##sequence-region   chr1 1000 39000
 # example 1
 chr1	.	gene	1000	9000	.	+	.	ID=gene10001;Name=EDEN
 chr1	.	TF_binding_site	1000	1012	.	+	.	ID=tfbs10001;Parent=gene10001
@@ -76,10 +77,10 @@ chr1	.	CDS	21201	21500	.	+	0	ID=cds30005;Parent=mRNA30002;Name=edenprotein.2
 chr1	.	CDS	25000	25500	.	+	0	ID=cds30006;Parent=mRNA30002;Name=edenprotein.2
 chr1	.	CDS	27000	27600	.	+	0	ID=cds30007;Parent=mRNA30002;Name=edenprotein.2
 chr1	.	CDS	23301	23902	.	+	0	ID=cds30008;Parent=mRNA30003;Name=edenprotein.3
-chr1	.	CDS	25000	25500	.	+	1	ID=cds30009;Parent=mRNA30003;Name=edenprotein.3
-chr1	.	CDS	27000	27600	.	+	1	ID=cds30010;Parent=mRNA30003;Name=edenprotein.3
-chr1	.	CDS	23391	23902	.	+	0	ID=cds30011;Parent=mRNA30003;Name=edenprotein.4
-chr1	.	CDS	25000	25500	.	+	1	ID=cds30012;Parent=mRNA30003;Name=edenprotein.4
+chr1	.	CDS	25000	25500	.	+	2	ID=cds30009;Parent=mRNA30003;Name=edenprotein.3
+chr1	.	CDS	27000	27600	.	+	2	ID=cds30010;Parent=mRNA30003;Name=edenprotein.3
+chr1	.	CDS	23391	23902	.	+	1	ID=cds30011;Parent=mRNA30003;Name=edenprotein.4
+chr1	.	CDS	25000	25500	.	+	2	ID=cds30012;Parent=mRNA30003;Name=edenprotein.4
 chr1	.	CDS	27000	27600	.	+	1	ID=cds30013;Parent=mRNA30003;Name=edenprotein.4
 # example 4
 chr1	.	gene	31000	39000	.	+	.	ID=gene40001;Name=EDEN

package/test_data/onecds_without_exon_spliced_utr.gff

@@ -0,0 +1,6 @@
+##gff-version 3
+chr1	.	gene	1000	9000	.	+	.	ID=gene00001
+chr1	.	mRNA	1300	9000	.	+	.	ID=mRNA00001;Parent=gene00001
+chr1	.	five_prime_UTR	3000	3300	.	+	.	Parent=mRNA00001
+chr1	.	CDS	5000	5500	.	+	1	ID=cds00001;Parent=mRNA00001
+chr1	.	three_prime_UTR	7601	8000	.	+	.	Parent=mRNA00001

package/test_data/onecds_without_exon_spliced_utr.json

@@ -0,0 +1,55 @@
+{
+  "_id": "675af35f5758c90ab1d55838",
+  "refSeq": "chr1",
+  "type": "gene",
+  "min": 999,
+  "max": 9000,
+  "strand": 1,
+  "children": {
+    "675af35f5758c90ab1d55837": {
+      "_id": "675af35f5758c90ab1d55837",
+      "refSeq": "chr1",
+      "type": "mRNA",
+      "min": 1299,
+      "max": 9000,
+      "strand": 1,
+      "children": {
+        "675af35f5758c90ab1d55833": {
+          "_id": "675af35f5758c90ab1d55833",
+          "refSeq": "chr1",
+          "type": "CDS",
+          "min": 4999,
+          "max": 5500,
+          "strand": 1,
+          "attributes": { "gff_id": ["cds00001"] }
+        },
+        "675af35f5758c90ab1d55834": {
+          "_id": "675af35f5758c90ab1d55834",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 2999,
+          "max": 3300,
+          "strand": 1
+        },
+        "675af35f5758c90ab1d55836": {
+          "_id": "675af35f5758c90ab1d55836",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 4999,
+          "max": 5500,
+          "strand": 1
+        },
+        "675af35f5758c90ab1d55835": {
+          "_id": "675af35f5758c90ab1d55835",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 7600,
+          "max": 8000,
+          "strand": 1
+        }
+      },
+      "attributes": { "gff_id": ["mRNA00001"] }
+    }
+  },
+  "attributes": { "gff_id": ["gene00001"] }
+}