@apollo-annotation/shared 0.2.1 → 0.3.0

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Files changed (26) hide show
  1. package/dist/Checks/CDSCheck.js +1 -1
  2. package/dist/Checks/CDSCheck.js.map +1 -1
  3. package/dist/GFF3/annotationFeatureToGFF3.d.ts +3 -0
  4. package/dist/GFF3/annotationFeatureToGFF3.js +209 -0
  5. package/dist/GFF3/annotationFeatureToGFF3.js.map +1 -0
  6. package/dist/GFF3/annotationFeatureToGFF3.test.d.ts +1 -0
  7. package/dist/GFF3/annotationFeatureToGFF3.test.js +156 -0
  8. package/dist/GFF3/annotationFeatureToGFF3.test.js.map +1 -0
  9. package/dist/GFF3/gff3ToAnnotationFeature.test.d.ts +2 -1
  10. package/dist/GFF3/gff3ToAnnotationFeature.test.js +1 -0
  11. package/dist/GFF3/gff3ToAnnotationFeature.test.js.map +1 -1
  12. package/dist/GFF3/index.d.ts +1 -0
  13. package/dist/GFF3/index.js +1 -0
  14. package/dist/GFF3/index.js.map +1 -1
  15. package/dist/tsconfig.tsbuildinfo +1 -1
  16. package/dist/util.d.ts +0 -3
  17. package/dist/util.js +0 -90
  18. package/dist/util.js.map +1 -1
  19. package/package.json +6 -6
  20. package/src/Checks/CDSCheck.ts +1 -1
  21. package/src/GFF3/annotationFeatureToGFF3.test.ts +170 -0
  22. package/src/GFF3/annotationFeatureToGFF3.ts +257 -0
  23. package/src/GFF3/gff3ToAnnotationFeature.test.ts +3 -1
  24. package/src/GFF3/index.ts +1 -0
  25. package/src/util.ts +0 -102
  26. package/test_data/gene.json +117 -0
package/src/util.ts CHANGED
@@ -1,105 +1,3 @@
1
- /* eslint-disable @typescript-eslint/no-unsafe-assignment */
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-
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- import { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
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- import { GFF3Feature } from '@gmod/gff'
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-
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- export function makeGFF3Feature(
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- feature: AnnotationFeatureSnapshot,
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- parentId?: string,
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- refSeqNames?: Record<string, string | undefined>,
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- ): GFF3Feature {
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- const locations = [{ start: feature.min, end: feature.max }]
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- // const locations = feature.discontinuousLocations?.length
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- // ? feature.discontinuousLocations
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- // : [{ start: feature.start, end: feature.end, phase: feature.phase }]
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- const attributes: Record<string, string[] | undefined> = JSON.parse(
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- JSON.stringify(feature.attributes),
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- )
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- const ontologyTerms: string[] = []
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- const source = feature.attributes?.source?.[0] ?? null
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- delete attributes.source
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- if (parentId) {
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- attributes.Parent = [parentId]
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- }
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- if (attributes._id) {
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- attributes.ID = attributes._id
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- delete attributes._id
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- }
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- if (attributes.gff_name) {
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- attributes.Name = attributes.gff_name
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- delete attributes.gff_name
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- }
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- if (attributes.gff_alias) {
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- attributes.Alias = attributes.gff_alias
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- delete attributes.gff_alias
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- }
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- if (attributes.gff_target) {
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- attributes.Target = attributes.gff_target
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- delete attributes.gff_target
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- }
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- if (attributes.gff_gap) {
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- attributes.Gap = attributes.gff_gap
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- delete attributes.gff_gap
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- }
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- if (attributes.gff_derives_from) {
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- attributes.Derives_from = attributes.gff_derives_from
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- delete attributes.gff_derives_from
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- }
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- if (attributes.gff_note) {
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- attributes.Note = attributes.gff_note
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- delete attributes.gff_note
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- }
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- if (attributes.gff_dbxref) {
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- attributes.Dbxref = attributes.gff_dbxref
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- delete attributes.gff_dbxref
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- }
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- if (attributes.gff_is_circular) {
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- attributes.Is_circular = attributes.gff_is_circular
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- delete attributes.gff_is_circular
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- }
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- if (attributes.gff_ontology_term) {
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- ontologyTerms.push(...attributes.gff_ontology_term)
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- delete attributes.gff_ontology_term
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- }
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- if (attributes['Gene Ontology']) {
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- ontologyTerms.push(...attributes['Gene Ontology'])
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- delete attributes['Gene Ontology']
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- }
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- if (attributes['Sequence Ontology']) {
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- ontologyTerms.push(...attributes['Sequence Ontology'])
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- delete attributes['Sequence Ontology']
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- }
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- if (ontologyTerms.length > 0) {
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- attributes.Ontology_term = ontologyTerms
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- }
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- return locations.map((location) => ({
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- start: location.start + 1,
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- end: location.end,
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- seq_id: refSeqNames ? refSeqNames[feature.refSeq] ?? null : feature.refSeq,
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- source,
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- type: feature.type,
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- score: null,
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- // score: feature.score ?? null,
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- strand: feature.strand ? (feature.strand === 1 ? '+' : '-') : null,
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- phase: null,
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- // phase:
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- // location.phase === 0
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- // ? '0'
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- // : location.phase === 1
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- // ? '1'
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- // : location.phase === 2
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- // ? '2'
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- // : null,
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- attributes: Object.keys(attributes).length > 0 ? attributes : null,
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- derived_features: [],
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- child_features: feature.children
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- ? Object.values(feature.children).map((child) =>
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- makeGFF3Feature(child, attributes.ID?.[0], refSeqNames),
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- )
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- : [],
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- }))
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- }
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-
103
1
  export function splitStringIntoChunks(
104
2
  input: string,
105
3
  chunkSize: number,
package/test_data/gene.json ADDED
@@ -0,0 +1,117 @@
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+ {
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+ "_id": "66d70e4ccc30b55b65e5f619",
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+ "refSeq": "chr1",
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+ "type": "gene",
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+ "min": 999,
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+ "max": 9000,
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+ "strand": 1,
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+ "attributes": {
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+ "gff_id": ["gene10001"],
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+ "gff_name": ["EDEN"],
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+ "gff_score": ["123"],
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+ "gff_source": ["test_data"],
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+ "testid": ["t001", "t003"],
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+ "gff_ontology_term": ["GO1234"],
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+ "Gene Ontology": ["GO4567"],
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+ "Sequence Ontology": ["SO1234"],
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+ "gff_alias": ["myalias"],
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+ "gff_target": ["mytarget"],
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+ "gff_gap": ["mygap"],
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+ "gff_derives_from": ["myderives"],
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+ "gff_note": ["mynote"],
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+ "gff_dbxref": ["mydbxref"],
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+ "gff_is_circular": ["true"]
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+ },
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+ "children": {
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+ "66d70e4ccc30b55b65e5f618": {
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+ "_id": "66d70e4ccc30b55b65e5f618",
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+ "refSeq": "chr1",
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+ "type": "mRNA",
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+ "min": 1049,
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+ "max": 9000,
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+ "strand": 1,
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+ "attributes": {
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+ "gff_id": ["mRNA10001"],
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+ "gff_name": ["EDEN.1"],
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+ "testid": ["t004", "t001", "t004"]
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+ },
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+ "children": {
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+ "66d70e4ccc30b55b65e5f615": {
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+ "_id": "66d70e4ccc30b55b65e5f615",
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+ "refSeq": "chr1",
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+ "type": "exon",
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+ "min": 1049,
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+ "max": 1500,
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+ "strand": 1,
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+ "attributes": {
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+ "gff_id": ["exon10001"],
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+ "testid": ["t007"]
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+ }
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+ },
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+ "66d70e4ccc30b55b65e5f616": {
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+ "_id": "66d70e4ccc30b55b65e5f616",
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+ "refSeq": "chr1",
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+ "type": "exon",
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+ "min": 4999,
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+ "max": 5500,
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+ "strand": 1,
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+ "attributes": {
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+ "gff_id": ["exon10004"],
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+ "testid": ["t010"]
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+ },
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+ "children": {
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+ "xyz": {
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+ "_id": "xyz",
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+ "refSeq": "chr1",
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+ "type": "exon_region",
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+ "min": 5300,
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+ "max": 5400,
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+ "strand": 1,
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+ "attributes": {
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+ "gff_id": ["exon_region10001"]
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+ }
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+ }
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+ }
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+ },
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+ "66d70e4ccc30b55b65e5f617": {
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+ "_id": "66d70e4ccc30b55b65e5f617",
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+ "refSeq": "chr1",
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+ "type": "CDS",
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+ "min": 1200,
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+ "max": 5100,
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+ "strand": 1,
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+ "attributes": {
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+ "gff_id": ["cds10001"],
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+ "gff_name": ["edenprotein.1"],
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+ "testid": ["t012", "t013", "t014", "t015"]
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+ },
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+ "children": {
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+ "abc": {
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+ "id": "abc",
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+ "refSeq": "chr1",
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+ "type": "CDS_region",
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+ "min": "1350",
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+ "max": "1400",
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+ "strand": 1,
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+ "attributes": {
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+ "gff_id": ["cds_region10001"]
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+ }
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+ }
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+ }
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+ },
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+ "66e049f17b9cedae9ad89106": {
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+ "_id": "66e049f17b9cedae9ad89106",
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+ "refSeq": "chr1",
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+ "type": "CDS",
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+ "min": 1300,
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+ "max": 5200,
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+ "strand": 1,
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+ "attributes": {
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+ "gff_id": ["cds10004"],
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+ "gff_name": ["edenprotein.4"]
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+ }
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+ }
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+ }
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+ }
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+ }
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+ }