@apollo-annotation/shared 0.3.7 → 0.3.8
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/Changes/AddAssemblyAndFeaturesFromFileChange.js +1 -1
- package/dist/Changes/AddAssemblyAndFeaturesFromFileChange.js.map +1 -1
- package/dist/Changes/AddAssemblyFromFileChange.js +1 -1
- package/dist/Changes/AddAssemblyFromFileChange.js.map +1 -1
- package/dist/Changes/AddRefSeqAliasesChange.js +2 -4
- package/dist/Changes/AddRefSeqAliasesChange.js.map +1 -1
- package/dist/Changes/ImportJBrowseConfigChange.js +1 -1
- package/dist/Changes/ImportJBrowseConfigChange.js.map +1 -1
- package/dist/Changes/MergeExonsChange.d.ts +0 -1
- package/dist/Changes/MergeExonsChange.js +14 -30
- package/dist/Changes/MergeExonsChange.js.map +1 -1
- package/dist/Changes/MergeTranscriptsChange.d.ts +1 -3
- package/dist/Changes/MergeTranscriptsChange.js +55 -56
- package/dist/Changes/MergeTranscriptsChange.js.map +1 -1
- package/dist/Checks/CDSCheck.d.ts +1 -1
- package/dist/Checks/CDSCheck.js +8 -9
- package/dist/Checks/CDSCheck.js.map +1 -1
- package/dist/Checks/TranscriptCheck.d.ts +9 -0
- package/dist/Checks/TranscriptCheck.js +109 -0
- package/dist/Checks/TranscriptCheck.js.map +1 -0
- package/dist/Checks/index.d.ts +1 -0
- package/dist/Checks/index.js +1 -0
- package/dist/Checks/index.js.map +1 -1
- package/dist/GFF3/gff3ToAnnotationFeature.test.js +1 -1
- package/dist/GFF3/gff3ToAnnotationFeature.test.js.map +1 -1
- package/dist/tsconfig.tsbuildinfo +1 -1
- package/dist/util.d.ts +3 -0
- package/dist/util.js +33 -0
- package/dist/util.js.map +1 -1
- package/package.json +7 -7
- package/src/Changes/AddAssemblyAndFeaturesFromFileChange.ts +2 -1
- package/src/Changes/AddAssemblyFromFileChange.ts +1 -1
- package/src/Changes/AddRefSeqAliasesChange.ts +2 -4
- package/src/Changes/ImportJBrowseConfigChange.ts +1 -1
- package/src/Changes/MergeExonsChange.ts +52 -36
- package/src/Changes/MergeTranscriptsChange.ts +82 -67
- package/src/Checks/CDSCheck.ts +10 -10
- package/src/Checks/TranscriptCheck.ts +139 -0
- package/src/Checks/index.ts +1 -0
- package/src/GFF3/gff3ToAnnotationFeature.test.ts +1 -1
- package/src/util.ts +37 -0
- package/test_data/example01.json +20 -20
- package/test_data/example02.json +38 -38
- package/test_data/example04.json +57 -57
- package/test_data/gene_representations.gff3 +1054 -276
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@@ -0,0 +1,139 @@
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import { Check } from '@apollo-annotation/common'
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import {
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type AnnotationFeatureSnapshot,
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type CheckResultSnapshot,
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} from '@apollo-annotation/mst'
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import { revcom } from '@jbrowse/core/util'
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import ObjectID from 'bson-objectid'
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interface SpliceSequence {
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fivePrimeSeq: string
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fivePrimeMin: number
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threePrimeSeq: string
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threePrimeMin: number
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}
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enum CAUSES {
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'NonCanonicalSpliceSiteAtFivePrime',
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'NonCanonicalSpliceSiteAtThreePrime',
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}
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const CHECK_NAME = 'TranscriptCheck'
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async function getSpliceSequences(
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transcript: AnnotationFeatureSnapshot,
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getSequence: (start: number, end: number) => Promise<string>,
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): Promise<SpliceSequence[]> {
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if (!transcript.children) {
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return []
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}
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const exons: AnnotationFeatureSnapshot[] = []
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for (const [, child] of Object.entries(transcript.children)) {
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if (child.type === 'exon') {
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exons.push(child)
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}
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}
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if (exons.length < 2) {
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return []
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}
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const spliceSeq: SpliceSequence[] = []
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for (let i = 0; i < exons.length - 1; i++) {
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let fivePrimeMin = exons[i].max
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let threePrimeMin = exons[i + 1].min - 2
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if (transcript.strand === -1) {
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const _fivePrimeMin = fivePrimeMin
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fivePrimeMin = threePrimeMin
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threePrimeMin = _fivePrimeMin
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}
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let fivePrimeSeq = await getSequence(fivePrimeMin, fivePrimeMin + 2)
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let threePrimeSeq = await getSequence(threePrimeMin, threePrimeMin + 2)
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if (transcript.strand === -1) {
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threePrimeSeq = revcom(threePrimeSeq)
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fivePrimeSeq = revcom(fivePrimeSeq)
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}
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spliceSeq.push({
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fivePrimeSeq,
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fivePrimeMin,
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threePrimeSeq,
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threePrimeMin,
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})
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}
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return spliceSeq
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}
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async function checkTranscript(
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feature: AnnotationFeatureSnapshot,
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getSequence: (start: number, end: number) => Promise<string>,
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): Promise<CheckResultSnapshot[]> {
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const checkResults: CheckResultSnapshot[] = []
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const VALID_FIVE_PRIME_SEQ = new Set(['GT'])
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const VALID_THREE_PRIME_SEQ = new Set(['AG'])
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const spliceSequences = await getSpliceSequences(feature, getSequence)
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for (const spliceSequence of spliceSequences) {
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if (!VALID_FIVE_PRIME_SEQ.has(spliceSequence.fivePrimeSeq.toUpperCase())) {
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checkResults.push({
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_id: new ObjectID().toHexString(),
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name: CHECK_NAME,
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cause: CAUSES[CAUSES.NonCanonicalSpliceSiteAtFivePrime],
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ids: [feature._id],
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refSeq: feature.refSeq.toString(),
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start: spliceSequence.fivePrimeMin,
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end: spliceSequence.fivePrimeMin + 2,
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message: `Unexpected 5' splice site in "${feature._id}". Expected: ${[...VALID_FIVE_PRIME_SEQ].join('|')}, got: ${spliceSequence.fivePrimeSeq}`,
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})
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}
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if (
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!VALID_THREE_PRIME_SEQ.has(spliceSequence.threePrimeSeq.toUpperCase())
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) {
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checkResults.push({
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_id: new ObjectID().toHexString(),
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name: CHECK_NAME,
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cause: CAUSES[CAUSES.NonCanonicalSpliceSiteAtThreePrime],
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ids: [feature._id],
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refSeq: feature.refSeq.toString(),
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start: spliceSequence.threePrimeMin,
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end: spliceSequence.threePrimeMin + 2,
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message: `Unexpected 3' splice site in "${feature._id}". Expected: ${[...VALID_THREE_PRIME_SEQ].join('|')}, got: ${spliceSequence.threePrimeSeq}`,
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})
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}
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}
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return checkResults
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}
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function getCauses(): string[] {
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return Object.values(CAUSES).filter((x) =>
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Number.isNaN(Number(x)),
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) as string[]
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}
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export class TranscriptCheck extends Check {
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name = 'TranscriptCheck'
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causes = getCauses()
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version = 1
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isDefault = true
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async checkFeature(
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feature: AnnotationFeatureSnapshot,
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getSequence: (start: number, end: number) => Promise<string>,
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): Promise<CheckResultSnapshot[]> {
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if (
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feature.type === 'mRNA' ||
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feature.type === 'transcript' ||
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feature.type === 'pseudogenic_transcript'
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) {
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return checkTranscript(feature, getSequence)
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}
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if (!feature.children) {
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return []
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}
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const checkResults: CheckResultSnapshot[] = []
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for (const child of Object.values(feature.children)) {
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checkResults.push(...(await this.checkFeature(child, getSequence)))
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}
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return checkResults
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}
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}
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package/src/Checks/index.ts
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return JSON.parse(lines) as AnnotationFeatureSnapshot
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}
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const [ex1, ex2, ex3, ex4] = readFeatureFile(
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const [ex1, , ex2, , ex3, , ex4] = readFeatureFile(
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'test_data/gene_representations.gff3',
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)
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package/src/util.ts
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import { type AnnotationFeature } from '@apollo-annotation/mst'
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import { type Feature } from '@apollo-annotation/schemas'
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import { type IKeyValueMap } from 'mobx'
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export function splitStringIntoChunks(
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input: string,
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@@ -25,3 +26,39 @@ export function getPrintableId(feature: Feature): string {
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}
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return `_id: ${feature._id.toString()}`
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}
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export function attributesToRecords(
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attributes: IKeyValueMap<readonly string[] | undefined> | undefined,
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): Record<string, string[] | undefined> {
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const records: Record<string, string[] | undefined> = {}
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if (!attributes) {
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return records
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}
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for (const [key, value] of Object.entries(attributes)) {
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records[key] = value?.slice()
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}
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return records
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}
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export function stringifyAttributes(
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attributes: Record<string, string[] | undefined> | undefined,
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): string {
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if (!attributes) {
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return ''
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}
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const str = []
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for (const [key, value] of Object.entries(attributes)) {
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let attributeName = key
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if (attributeName.startsWith('gff_')) {
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attributeName = attributeName.slice(4)
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attributeName =
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attributeName.charAt(0).toUpperCase() + attributeName.slice(1)
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}
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if (value) {
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str.push(`${attributeName}=${value.join(',')}`)
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} else {
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str.push(attributeName)
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}
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}
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return encodeURIComponent(str.join(';'))
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}
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package/test_data/example01.json
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"max": 1012,
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"strand": 1,
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"attributes": {
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"gff_id": ["
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"gff_id": ["tfbs00001"]
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}
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},
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"66e049f17b9cedae9ad890fb": {
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"max": 1499,
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"strand": 1,
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"attributes": {
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"gff_id": ["
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"gff_id": ["exon00002"]
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}
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},
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"66e049f17b9cedae9ad890f7": {
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"max": 3902,
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"strand": 1,
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"attributes": {
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"gff_id": ["
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"gff_id": ["exon00003"]
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}
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},
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"66e049f17b9cedae9ad890f8": {
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"max": 5500,
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"strand": 1,
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"attributes": {
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"gff_id": ["
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"gff_id": ["exon00004"]
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}
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},
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"66e049f17b9cedae9ad890f9": {
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"max": 9000,
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"strand": 1,
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"attributes": {
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"gff_id": ["
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"gff_id": ["exon00005"]
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}
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},
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"66e049f17b9cedae9ad890fa": {
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"max": 7600,
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"strand": 1,
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"attributes": {
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"gff_id": ["
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"gff_id": ["cds00001"],
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"gff_name": ["edenprotein.1"]
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}
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}
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},
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"attributes": {
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"gff_id": ["
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"gff_id": ["mRNA00001"],
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"gff_name": ["EDEN.1"]
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}
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},
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"max": 1499,
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"strand": 1,
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"attributes": {
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"gff_id": ["
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"gff_id": ["exon00002"]
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}
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},
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"66e049f17b9cedae9ad890fd": {
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"max": 5500,
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"strand": 1,
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"attributes": {
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"gff_id": ["
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"gff_id": ["exon00004"]
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}
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},
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"66e049f17b9cedae9ad890fe": {
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"max": 9000,
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"strand": 1,
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"attributes": {
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"gff_id": ["
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"gff_id": ["exon00005"]
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}
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},
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"66e049f17b9cedae9ad890ff": {
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"max": 7600,
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"strand": 1,
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"attributes": {
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"gff_id": ["
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"gff_id": ["cds00002"],
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"gff_name": ["edenprotein.2"]
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}
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}
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},
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"attributes": {
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"gff_id": ["
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"gff_id": ["mRNA00002"],
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"gff_name": ["EDEN.2"]
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}
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},
|
|
@@ -162,7 +162,7 @@
|
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"max": 1499,
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"strand": 1,
|
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|
"attributes": {
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-
"gff_id": ["
|
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+
"gff_id": ["exon00001"]
|
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|
}
|
|
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167
|
},
|
|
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|
"66e049f17b9cedae9ad89102": {
|
|
@@ -173,7 +173,7 @@
|
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|
"max": 3902,
|
|
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"strand": 1,
|
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|
"attributes": {
|
|
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-
"gff_id": ["
|
|
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+
"gff_id": ["exon00003"]
|
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|
}
|
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|
},
|
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|
"66e049f17b9cedae9ad89103": {
|
|
@@ -184,7 +184,7 @@
|
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"max": 5500,
|
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"strand": 1,
|
|
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|
"attributes": {
|
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-
"gff_id": ["
|
|
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|
+
"gff_id": ["exon00004"]
|
|
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188
|
}
|
|
189
189
|
},
|
|
190
190
|
"66e049f17b9cedae9ad89104": {
|
|
@@ -195,7 +195,7 @@
|
|
|
195
195
|
"max": 9000,
|
|
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|
"strand": 1,
|
|
197
197
|
"attributes": {
|
|
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|
-
"gff_id": ["
|
|
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|
+
"gff_id": ["exon00005"]
|
|
199
199
|
}
|
|
200
200
|
},
|
|
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201
|
"66e049f17b9cedae9ad89105": {
|
|
@@ -206,7 +206,7 @@
|
|
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206
206
|
"max": 7600,
|
|
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|
"strand": 1,
|
|
208
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|
"attributes": {
|
|
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|
-
"gff_id": ["
|
|
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|
+
"gff_id": ["cds00003"],
|
|
210
210
|
"gff_name": ["edenprotein.3"]
|
|
211
211
|
}
|
|
212
212
|
},
|
|
@@ -218,19 +218,19 @@
|
|
|
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|
"max": 7600,
|
|
219
219
|
"strand": 1,
|
|
220
220
|
"attributes": {
|
|
221
|
-
"gff_id": ["
|
|
221
|
+
"gff_id": ["cds00004"],
|
|
222
222
|
"gff_name": ["edenprotein.4"]
|
|
223
223
|
}
|
|
224
224
|
}
|
|
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225
|
},
|
|
226
226
|
"attributes": {
|
|
227
|
-
"gff_id": ["
|
|
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|
+
"gff_id": ["mRNA00003"],
|
|
228
228
|
"gff_name": ["EDEN.3"]
|
|
229
229
|
}
|
|
230
230
|
}
|
|
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231
|
},
|
|
232
232
|
"attributes": {
|
|
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|
-
"gff_id": ["
|
|
233
|
+
"gff_id": ["gene00001"],
|
|
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234
|
"gff_name": ["EDEN"]
|
|
235
235
|
}
|
|
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|
}
|
package/test_data/example02.json
CHANGED
|
@@ -2,24 +2,24 @@
|
|
|
2
2
|
"_id": "66e049609048deab4117a33e",
|
|
3
3
|
"refSeq": "chr1",
|
|
4
4
|
"type": "gene",
|
|
5
|
-
"min":
|
|
6
|
-
"max":
|
|
5
|
+
"min": 20999,
|
|
6
|
+
"max": 29000,
|
|
7
7
|
"strand": 1,
|
|
8
8
|
"children": {
|
|
9
9
|
"66e049609048deab4117a331": {
|
|
10
10
|
"_id": "66e049609048deab4117a331",
|
|
11
11
|
"refSeq": "chr1",
|
|
12
12
|
"type": "mRNA",
|
|
13
|
-
"min":
|
|
14
|
-
"max":
|
|
13
|
+
"min": 21049,
|
|
14
|
+
"max": 29000,
|
|
15
15
|
"strand": 1,
|
|
16
16
|
"children": {
|
|
17
17
|
"66e049609048deab4117a32c": {
|
|
18
18
|
"_id": "66e049609048deab4117a32c",
|
|
19
19
|
"refSeq": "chr1",
|
|
20
20
|
"type": "exon",
|
|
21
|
-
"min":
|
|
22
|
-
"max":
|
|
21
|
+
"min": 21049,
|
|
22
|
+
"max": 21499,
|
|
23
23
|
"strand": 1,
|
|
24
24
|
"attributes": {
|
|
25
25
|
"gff_id": ["exon20001"]
|
|
@@ -29,8 +29,8 @@
|
|
|
29
29
|
"_id": "66e049609048deab4117a32d",
|
|
30
30
|
"refSeq": "chr1",
|
|
31
31
|
"type": "exon",
|
|
32
|
-
"min":
|
|
33
|
-
"max":
|
|
32
|
+
"min": 22999,
|
|
33
|
+
"max": 23902,
|
|
34
34
|
"strand": 1,
|
|
35
35
|
"attributes": {
|
|
36
36
|
"gff_id": ["exon20004"]
|
|
@@ -40,8 +40,8 @@
|
|
|
40
40
|
"_id": "66e049609048deab4117a32e",
|
|
41
41
|
"refSeq": "chr1",
|
|
42
42
|
"type": "exon",
|
|
43
|
-
"min":
|
|
44
|
-
"max":
|
|
43
|
+
"min": 24999,
|
|
44
|
+
"max": 25500,
|
|
45
45
|
"strand": 1,
|
|
46
46
|
"attributes": {
|
|
47
47
|
"gff_id": ["exon20006"]
|
|
@@ -51,8 +51,8 @@
|
|
|
51
51
|
"_id": "66e049609048deab4117a32f",
|
|
52
52
|
"refSeq": "chr1",
|
|
53
53
|
"type": "exon",
|
|
54
|
-
"min":
|
|
55
|
-
"max":
|
|
54
|
+
"min": 26999,
|
|
55
|
+
"max": 29000,
|
|
56
56
|
"strand": 1,
|
|
57
57
|
"attributes": {
|
|
58
58
|
"gff_id": ["exon20009"]
|
|
@@ -62,8 +62,8 @@
|
|
|
62
62
|
"_id": "66e049609048deab4117a330",
|
|
63
63
|
"refSeq": "chr1",
|
|
64
64
|
"type": "CDS",
|
|
65
|
-
"min":
|
|
66
|
-
"max":
|
|
65
|
+
"min": 21200,
|
|
66
|
+
"max": 27600,
|
|
67
67
|
"strand": 1,
|
|
68
68
|
"attributes": {
|
|
69
69
|
"gff_id": ["cds20001"],
|
|
@@ -80,16 +80,16 @@
|
|
|
80
80
|
"_id": "66e049609048deab4117a336",
|
|
81
81
|
"refSeq": "chr1",
|
|
82
82
|
"type": "mRNA",
|
|
83
|
-
"min":
|
|
84
|
-
"max":
|
|
83
|
+
"min": 21049,
|
|
84
|
+
"max": 29000,
|
|
85
85
|
"strand": 1,
|
|
86
86
|
"children": {
|
|
87
87
|
"66e049609048deab4117a332": {
|
|
88
88
|
"_id": "66e049609048deab4117a332",
|
|
89
89
|
"refSeq": "chr1",
|
|
90
90
|
"type": "exon",
|
|
91
|
-
"min":
|
|
92
|
-
"max":
|
|
91
|
+
"min": 21049,
|
|
92
|
+
"max": 21499,
|
|
93
93
|
"strand": 1,
|
|
94
94
|
"attributes": {
|
|
95
95
|
"gff_id": ["exon20002"]
|
|
@@ -99,8 +99,8 @@
|
|
|
99
99
|
"_id": "66e049609048deab4117a333",
|
|
100
100
|
"refSeq": "chr1",
|
|
101
101
|
"type": "exon",
|
|
102
|
-
"min":
|
|
103
|
-
"max":
|
|
102
|
+
"min": 24999,
|
|
103
|
+
"max": 25500,
|
|
104
104
|
"strand": 1,
|
|
105
105
|
"attributes": {
|
|
106
106
|
"gff_id": ["exon20007"]
|
|
@@ -110,8 +110,8 @@
|
|
|
110
110
|
"_id": "66e049609048deab4117a334",
|
|
111
111
|
"refSeq": "chr1",
|
|
112
112
|
"type": "exon",
|
|
113
|
-
"min":
|
|
114
|
-
"max":
|
|
113
|
+
"min": 26999,
|
|
114
|
+
"max": 29000,
|
|
115
115
|
"strand": 1,
|
|
116
116
|
"attributes": {
|
|
117
117
|
"gff_id": ["exon20010"]
|
|
@@ -121,8 +121,8 @@
|
|
|
121
121
|
"_id": "66e049609048deab4117a335",
|
|
122
122
|
"refSeq": "chr1",
|
|
123
123
|
"type": "CDS",
|
|
124
|
-
"min":
|
|
125
|
-
"max":
|
|
124
|
+
"min": 21200,
|
|
125
|
+
"max": 27600,
|
|
126
126
|
"strand": 1,
|
|
127
127
|
"attributes": {
|
|
128
128
|
"gff_id": ["cds20002"],
|
|
@@ -139,16 +139,16 @@
|
|
|
139
139
|
"_id": "66e049609048deab4117a33d",
|
|
140
140
|
"refSeq": "chr1",
|
|
141
141
|
"type": "mRNA",
|
|
142
|
-
"min":
|
|
143
|
-
"max":
|
|
142
|
+
"min": 21299,
|
|
143
|
+
"max": 29000,
|
|
144
144
|
"strand": 1,
|
|
145
145
|
"children": {
|
|
146
146
|
"66e049609048deab4117a337": {
|
|
147
147
|
"_id": "66e049609048deab4117a337",
|
|
148
148
|
"refSeq": "chr1",
|
|
149
149
|
"type": "exon",
|
|
150
|
-
"min":
|
|
151
|
-
"max":
|
|
150
|
+
"min": 21299,
|
|
151
|
+
"max": 21499,
|
|
152
152
|
"strand": 1,
|
|
153
153
|
"attributes": {
|
|
154
154
|
"gff_id": ["exon20003"]
|
|
@@ -158,8 +158,8 @@
|
|
|
158
158
|
"_id": "66e049609048deab4117a338",
|
|
159
159
|
"refSeq": "chr1",
|
|
160
160
|
"type": "exon",
|
|
161
|
-
"min":
|
|
162
|
-
"max":
|
|
161
|
+
"min": 22999,
|
|
162
|
+
"max": 23902,
|
|
163
163
|
"strand": 1,
|
|
164
164
|
"attributes": {
|
|
165
165
|
"gff_id": ["exon20005"]
|
|
@@ -169,8 +169,8 @@
|
|
|
169
169
|
"_id": "66e049609048deab4117a339",
|
|
170
170
|
"refSeq": "chr1",
|
|
171
171
|
"type": "exon",
|
|
172
|
-
"min":
|
|
173
|
-
"max":
|
|
172
|
+
"min": 24999,
|
|
173
|
+
"max": 25500,
|
|
174
174
|
"strand": 1,
|
|
175
175
|
"attributes": {
|
|
176
176
|
"gff_id": ["exon20008"]
|
|
@@ -180,8 +180,8 @@
|
|
|
180
180
|
"_id": "66e049609048deab4117a33a",
|
|
181
181
|
"refSeq": "chr1",
|
|
182
182
|
"type": "exon",
|
|
183
|
-
"min":
|
|
184
|
-
"max":
|
|
183
|
+
"min": 26999,
|
|
184
|
+
"max": 29000,
|
|
185
185
|
"strand": 1,
|
|
186
186
|
"attributes": {
|
|
187
187
|
"gff_id": ["exon20011"]
|
|
@@ -191,8 +191,8 @@
|
|
|
191
191
|
"_id": "66e049609048deab4117a33b",
|
|
192
192
|
"refSeq": "chr1",
|
|
193
193
|
"type": "CDS",
|
|
194
|
-
"min":
|
|
195
|
-
"max":
|
|
194
|
+
"min": 23300,
|
|
195
|
+
"max": 27600,
|
|
196
196
|
"strand": 1,
|
|
197
197
|
"attributes": {
|
|
198
198
|
"gff_id": ["cds20003"],
|
|
@@ -203,8 +203,8 @@
|
|
|
203
203
|
"_id": "66e049609048deab4117a33c",
|
|
204
204
|
"refSeq": "chr1",
|
|
205
205
|
"type": "CDS",
|
|
206
|
-
"min":
|
|
207
|
-
"max":
|
|
206
|
+
"min": 23390,
|
|
207
|
+
"max": 27600,
|
|
208
208
|
"strand": 1,
|
|
209
209
|
"attributes": {
|
|
210
210
|
"gff_id": ["cds20004"],
|