@apollo-annotation/shared 1.1.1 → 1.1.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/GFF3/gff3ToAnnotationFeature.js +5 -0
- package/dist/GFF3/gff3ToAnnotationFeature.js.map +1 -1
- package/dist/GFF3/gff3ToAnnotationFeature.test.js +6 -0
- package/dist/GFF3/gff3ToAnnotationFeature.test.js.map +1 -1
- package/dist/tsconfig.tsbuildinfo +1 -1
- package/package.json +4 -4
- package/src/GFF3/gff3ToAnnotationFeature.test.ts +6 -0
- package/src/GFF3/gff3ToAnnotationFeature.ts +5 -0
- package/test_data/mixed_order.gff3 +13 -0
- package/test_data/mixed_order.json +87 -0
package/package.json
CHANGED
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@@ -1,6 +1,6 @@
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{
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"name": "@apollo-annotation/shared",
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-
"version": "1.1.
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"version": "1.1.2",
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"repository": {
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"type": "git",
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"url": "https://github.com/GMOD/Apollo3.git",
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@@ -17,9 +17,9 @@
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"test:ci": "NODE_V8_COVERAGE=./coverage glob -c \"tsx --test --test-reporter spec --experimental-test-coverage \" \"**/*.test.ts\""
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},
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"dependencies": {
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-
"@apollo-annotation/common": "^1.1.
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"@apollo-annotation/mst": "^1.1.
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"@apollo-annotation/schemas": "^1.1.
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"@apollo-annotation/common": "^1.1.2",
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"@apollo-annotation/mst": "^1.1.2",
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"@apollo-annotation/schemas": "^1.1.2",
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"@gmod/gff": "^2.1.0",
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"@gmod/indexedfasta": "^5.0.2",
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"@jbrowse/core": "^4.3.0",
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@@ -137,6 +137,12 @@ describe('gff3ToAnnotationFeature examples', () => {
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assert.equal(txt.match(/intron/g), null)
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assert.equal(txt.match(/_codon/g), null)
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})
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it('Convert noncontiguous CDS lines', () => {
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const [gffFeature] = readFeatureFile('test_data/mixed_order.gff3')
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const actual = gff3ToAnnotationFeature(gffFeature)
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const expected = readAnnotationFeatureSnapshot('test_data/mixed_order.json')
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compareFeatures(actual, expected)
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})
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})
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describe('CDS without exons', () => {
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@@ -171,7 +171,12 @@ function convertChildren(
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const cdsFeatures: GFF3Feature[] = []
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const exonFeatures: GFF3Feature[] = []
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const utrFeatures: GFF3Feature[] = []
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const seenChildFeatures = new Set<GFF3Feature>()
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for (const childFeature of childFeatures) {
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if (seenChildFeatures.has(childFeature)) {
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continue
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}
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seenChildFeatures.add(childFeature)
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const [firstChildFeatureLocation] = childFeature
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if (firstChildFeatureLocation.type === 'exon') {
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exonFeatures.push(childFeature)
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@@ -0,0 +1,13 @@
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OVOC_OM2 WormBase CDS 23840223 23840282 . - 0 ID=CDS:OVOC7322;Parent=Transcript:OVOC7322.1;Name=OVOC7322;prediction_status=Predicted;wormpep=OVP06434
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OVOC_OM2 WormBase exon 23840223 23840282 . - . Parent=Transcript:OVOC7322.1
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OVOC_OM2 WormBase gene 23840223 23842130 . - . ID=Gene:WBGene00244131;Name=WBGene00244131;sequence_name=OVOC7322;biotype=protein_coding;so_term_name=protein_coding_gene;curie=WB:WBGene00244131;Alias=OVOC7322
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OVOC_OM2 WormBase mRNA 23840223 23842130 . - . ID=Transcript:OVOC7322.1;Parent=Gene:WBGene00244131;Name=OVOC7322.1;wormpep=OVP06434
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OVOC_OM2 WormBase intron 23840283 23840606 . - . Parent=Transcript:OVOC7322.1
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OVOC_OM2 WormBase CDS 23840607 23840698 . - 2 ID=CDS:OVOC7322;Parent=Transcript:OVOC7322.1;Name=OVOC7322;prediction_status=Predicted;wormpep=OVP06434
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OVOC_OM2 WormBase exon 23840607 23840698 . - . Parent=Transcript:OVOC7322.1
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OVOC_OM2 WormBase intron 23840699 23840940 . - . Parent=Transcript:OVOC7322.1
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OVOC_OM2 WormBase CDS 23840941 23841057 . - 2 ID=CDS:OVOC7322;Parent=Transcript:OVOC7322.1;Name=OVOC7322;prediction_status=Predicted;wormpep=OVP06434
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OVOC_OM2 WormBase exon 23840941 23841057 . - . Parent=Transcript:OVOC7322.1
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OVOC_OM2 WormBase intron 23841058 23842123 . - . Parent=Transcript:OVOC7322.1
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OVOC_OM2 WormBase CDS 23842124 23842130 . - 0 ID=CDS:OVOC7322;Parent=Transcript:OVOC7322.1;Name=OVOC7322;prediction_status=Predicted;wormpep=OVP06434
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OVOC_OM2 WormBase exon 23842124 23842130 . - . Parent=Transcript:OVOC7322.1
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@@ -0,0 +1,87 @@
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{
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"_id": "6a9b52bb29ee0a50a460744a",
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"refSeq": "OVOC_OM2",
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"type": "gene",
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"min": 23840222,
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"max": 23842130,
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"strand": -1,
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"children": {
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"6a9b52bb29ee0a50a4607449": {
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"_id": "6a9b52bb29ee0a50a4607449",
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"refSeq": "OVOC_OM2",
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"type": "mRNA",
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"min": 23840222,
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"max": 23842130,
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"strand": -1,
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"children": {
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"6a9b52bb29ee0a50a4607443": {
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"_id": "6a9b52bb29ee0a50a4607443",
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"refSeq": "OVOC_OM2",
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"type": "exon",
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"min": 23840222,
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"max": 23840282,
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"strand": -1,
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"attributes": { "gff_source": ["WormBase"] }
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},
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"6a9b52bb29ee0a50a4607444": {
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"_id": "6a9b52bb29ee0a50a4607444",
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"refSeq": "OVOC_OM2",
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"type": "exon",
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"min": 23840606,
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"max": 23840698,
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"strand": -1,
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"attributes": { "gff_source": ["WormBase"] }
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},
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"6a9b52bb29ee0a50a4607445": {
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"_id": "6a9b52bb29ee0a50a4607445",
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"refSeq": "OVOC_OM2",
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"type": "exon",
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"min": 23840940,
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"max": 23841057,
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"strand": -1,
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"attributes": { "gff_source": ["WormBase"] }
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},
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"6a9b52bb29ee0a50a4607446": {
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"_id": "6a9b52bb29ee0a50a4607446",
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"refSeq": "OVOC_OM2",
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"type": "exon",
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"min": 23842123,
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"max": 23842130,
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"strand": -1,
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"attributes": { "gff_source": ["WormBase"] }
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},
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"6a9b52bb29ee0a50a4607447": {
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"_id": "6a9b52bb29ee0a50a4607447",
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"refSeq": "OVOC_OM2",
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"type": "CDS",
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"min": 23840222,
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"max": 23842130,
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"strand": -1,
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"attributes": {
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"gff_source": ["WormBase"],
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"gff_id": ["CDS:OVOC7322"],
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"gff_name": ["OVOC7322"],
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"prediction_status": ["Predicted"],
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"wormpep": ["OVP06434"]
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}
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}
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},
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"attributes": {
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"gff_source": ["WormBase"],
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"gff_id": ["Transcript:OVOC7322.1"],
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"gff_name": ["OVOC7322.1"],
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"wormpep": ["OVP06434"]
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}
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}
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},
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"attributes": {
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"gff_source": ["WormBase"],
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"gff_id": ["Gene:WBGene00244131"],
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"gff_name": ["WBGene00244131"],
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"sequence_name": ["OVOC7322"],
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"biotype": ["protein_coding"],
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"so_term_name": ["protein_coding_gene"],
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"curie": ["WB:WBGene00244131"],
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"gff_alias": ["OVOC7322"]
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}
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}
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