@apollo-annotation/shared 0.1.11

package/src/index.ts

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+export * from './Changes'
+export * from './Operations'
+export * from './Validations'
+export * from './Common'
+export * from './Checks'
+export * from './util'
+export * from './Messages'

package/src/util.ts

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+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
+import { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
+import { GFF3Feature } from '@gmod/gff'
+
+export function makeGFF3Feature(
+  feature: AnnotationFeatureSnapshot,
+  parentId?: string,
+  refSeqNames?: Record<string, string | undefined>,
+): GFF3Feature {
+  const locations = feature.discontinuousLocations?.length
+    ? feature.discontinuousLocations
+    : [{ start: feature.start, end: feature.end, phase: feature.phase }]
+  const attributes: Record<string, string[] | undefined> = JSON.parse(
+    JSON.stringify(feature.attributes),
+  )
+  const ontologyTerms: string[] = []
+  const source = feature.attributes?.source?.[0] ?? null
+  delete attributes.source
+  if (parentId) {
+    attributes.Parent = [parentId]
+  }
+  if (attributes._id) {
+    attributes.ID = attributes._id
+    delete attributes._id
+  }
+  if (attributes.gff_name) {
+    attributes.Name = attributes.gff_name
+    delete attributes.gff_name
+  }
+  if (attributes.gff_alias) {
+    attributes.Alias = attributes.gff_alias
+    delete attributes.gff_alias
+  }
+  if (attributes.gff_target) {
+    attributes.Target = attributes.gff_target
+    delete attributes.gff_target
+  }
+  if (attributes.gff_gap) {
+    attributes.Gap = attributes.gff_gap
+    delete attributes.gff_gap
+  }
+  if (attributes.gff_derives_from) {
+    attributes.Derives_from = attributes.gff_derives_from
+    delete attributes.gff_derives_from
+  }
+  if (attributes.gff_note) {
+    attributes.Note = attributes.gff_note
+    delete attributes.gff_note
+  }
+  if (attributes.gff_dbxref) {
+    attributes.Dbxref = attributes.gff_dbxref
+    delete attributes.gff_dbxref
+  }
+  if (attributes.gff_is_circular) {
+    attributes.Is_circular = attributes.gff_is_circular
+    delete attributes.gff_is_circular
+  }
+  if (attributes.gff_ontology_term) {
+    ontologyTerms.push(...attributes.gff_ontology_term)
+    delete attributes.gff_ontology_term
+  }
+  if (attributes['Gene Ontology']) {
+    ontologyTerms.push(...attributes['Gene Ontology'])
+    delete attributes['Gene Ontology']
+  }
+  if (attributes['Sequence Ontology']) {
+    ontologyTerms.push(...attributes['Sequence Ontology'])
+    delete attributes['Sequence Ontology']
+  }
+  if (ontologyTerms.length > 0) {
+    attributes.Ontology_term = ontologyTerms
+  }
+  return locations.map((location) => ({
+    start: location.start + 1,
+    end: location.end,
+    seq_id: refSeqNames ? refSeqNames[feature.refSeq] ?? null : feature.refSeq,
+    source,
+    type: feature.type,
+    score: feature.score ?? null,
+    strand: feature.strand ? (feature.strand === 1 ? '+' : '-') : null,
+    phase:
+      location.phase === 0
+        ? '0'
+        : location.phase === 1
+          ? '1'
+          : location.phase === 2
+            ? '2'
+            : null,
+    attributes: Object.keys(attributes).length > 0 ? attributes : null,
+    derived_features: [],
+    child_features: feature.children
+      ? Object.values(feature.children).map((child) =>
+          makeGFF3Feature(child, attributes.ID?.[0], refSeqNames),
+        )
+      : [],
+  }))
+}
+
+export function splitStringIntoChunks(
+  input: string,
+  chunkSize: number,
+): string[] {
+  const chunks: string[] = []
+  for (let i = 0; i < input.length; i += chunkSize) {
+    const chunk = input.slice(i, i + chunkSize)
+    chunks.push(chunk)
+  }
+  return chunks
+}

package/tsconfig.json

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+{
+  "extends": "../../tsconfig.json",
+  "compilerOptions": {
+    "composite": true,
+    "incremental": true,
+    "outDir": "./dist",
+    "rootDir": "./src",
+    "target": "ES2022",
+    "lib": ["ES2022", "DOM"],
+    "module": "CommonJS",
+    "tsBuildInfoFile": "./dist/tsconfig.tsbuildinfo",
+  },
+  "include": ["./src"],
+  "references": [
+    { "path": "../apollo-mst"},
+    { "path": "../apollo-schemas"},
+    { "path": "../apollo-common"},
+  ]
+}