jbrowse-plugin-protein3d 0.0.3 → 0.0.5

package/src/ProteinView/util.ts

@@ -5,7 +5,10 @@ import { proteinAbbreviationMapping } from './proteinAbbreviationMapping'
 
 export function checkHovered(hovered: unknown): hovered is {
   hoverFeature: Feature
-  hoverPosition: { coord: number; refName: string }
+  hoverPosition: {
+    coord: number
+    refName: string
+  }
 } {
   return (
     !!hovered &&
@@ -35,22 +38,30 @@ export function getMolstarStructureSelection({
   )
 }
 
-export function toStr(r: {
-  structureSeqPos: number
+export function toStr({
+  chain,
+  code,
+  structureSeqPos,
+}: {
+  structureSeqPos?: number
   code?: string
   chain?: string
 }) {
   return [
-    `Position: ${r.structureSeqPos}`,
-    r.code
-      ? `Letter: ${r.code} (${proteinAbbreviationMapping[r.code]?.singleLetterCode})`
+    structureSeqPos === undefined ? '' : `Position: ${structureSeqPos}`,
+    code
+      ? `Letter: ${code} (${proteinAbbreviationMapping[code]?.singleLetterCode})`
       : '',
-    r.chain ? `Chain: ${r.chain}` : '',
+    chain ? `Chain: ${chain}` : '',
   ]
     .filter(f => !!f)
     .join(', ')
 }
 
-export function invertMap(arg: Record<number, number | undefined>) {
-  return Object.fromEntries(Object.entries(arg).map(([a, b]) => [b, a]))
+export function invertMap(arg: Record<number, number>): Record<number, number> {
+  return Object.fromEntries(
+    Object.entries(arg)
+      .map(([a, b]) => [b, +a])
+      .filter(f => f[0] !== undefined),
+  )
 }

package/src/UniProtVariationAdapter/UniProtVariationAdapter.ts

@@ -0,0 +1,99 @@
+import {
+  BaseFeatureDataAdapter,
+  BaseOptions,
+} from '@jbrowse/core/data_adapters/BaseAdapter'
+import { openLocation } from '@jbrowse/core/util/io'
+import { ObservableCreate } from '@jbrowse/core/util/rxjs'
+import {
+  Region,
+  Feature,
+  doesIntersect2,
+  SimpleFeature,
+} from '@jbrowse/core/util'
+
+interface UniProtVariantFeature {
+  begin: string
+  end: string
+  wildType: string
+  mutatedType: string
+  xrefs: {
+    name: string
+    id: string
+    url: string
+    alternativeUrl: string
+  }[]
+  predictions?: {
+    score: number
+  }[]
+  descriptions?: {
+    value: string
+  }[]
+  populationFrequencies?: {
+    frequency?: number
+  }[]
+}
+
+export default class UniProtVariationAdapter extends BaseFeatureDataAdapter {
+  public static capabilities = ['getFeatures', 'getRefNames']
+
+  public feats:
+    | Promise<{ uniqueId: string; start: number; end: number }[]>
+    | undefined
+
+  private async loadDataP() {
+    const { features } = JSON.parse(
+      await openLocation(this.getConf('location')).readFile('utf8'),
+    ) as { features: UniProtVariantFeature[] }
+
+    const scoreField = this.getConf('scoreField')
+
+    return features.map(({ begin, end, ...rest }, idx) => ({
+      ...rest,
+      uniqueId: `feat-${idx}`,
+      start: +begin,
+      end: +end + 1,
+      score:
+        scoreField === 'population_frequency'
+          ? rest.populationFrequencies?.[0]?.frequency
+          : scoreField === 'variant_impact_score'
+            ? rest.predictions?.[0]?.score
+            : undefined,
+      description: rest.descriptions?.map(d => d.value).join(','),
+      name: [
+        rest.mutatedType
+          ? `${rest.wildType}->${rest.mutatedType}`
+          : `${rest.wildType}->del`,
+      ],
+    }))
+  }
+
+  private async loadData(_opts: BaseOptions = {}) {
+    if (!this.feats) {
+      this.feats = this.loadDataP().catch((e: unknown) => {
+        this.feats = undefined
+        throw e
+      })
+    }
+
+    return this.feats
+  }
+
+  public async getRefNames(_opts: BaseOptions = {}) {
+    return []
+  }
+
+  public getFeatures(query: Region, opts: BaseOptions = {}) {
+    return ObservableCreate<Feature>(async observer => {
+      const { start, end, refName } = query
+      const data = await this.loadData()
+      for (const f of data) {
+        if (doesIntersect2(f.start, f.end, start, end)) {
+          observer.next(new SimpleFeature({ ...f, refName }))
+        }
+      }
+      observer.complete()
+    }, opts.signal)
+  }
+
+  public freeResources(): void {}
+}

package/src/UniProtVariationAdapter/configSchema.ts

@@ -0,0 +1,25 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+
+/**
+ * #config UniProtVariationAdapter
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const UniProtVariationAdapter = ConfigurationSchema(
+  'UniProtVariationAdapter',
+  {
+    /**
+     * #slot
+     */
+    location: {
+      type: 'fileLocation',
+      defaultValue: { uri: '/path/to/my.bed.gz', locationType: 'UriLocation' },
+    },
+    scoreField: {
+      type: 'string',
+      defaultValue: '',
+    },
+  },
+  { explicitlyTyped: true },
+)
+export default UniProtVariationAdapter

package/src/UniProtVariationAdapter/index.ts

@@ -0,0 +1,17 @@
+import PluginManager from '@jbrowse/core/PluginManager'
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
+
+import configSchema from './configSchema'
+
+export default function UniProtVariationAdapterF(pluginManager: PluginManager) {
+  pluginManager.addAdapterType(
+    () =>
+      new AdapterType({
+        name: 'UniProtVariationAdapter',
+        displayName: 'UniProtVariation adapter',
+        configSchema,
+        getAdapterClass: () =>
+          import('./UniProtVariationAdapter').then(r => r.default),
+      }),
+  )
+}

package/src/__snapshots__/mappings.test.ts.snap

@@ -1,4 +1,4 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
+// Vitest Snapshot v1, https://vitest.dev/guide/snapshot.html
 
 exports[`mapping 1`] = `
 {
@@ -902,229 +902,6 @@ exports[`mapping 1`] = `
 exports[`test 1`] = `
 {
   "structureSeqToTranscriptSeqPosition": {
-    "392": 0,
-    "393": 1,
-    "394": 2,
-    "395": 3,
-    "396": 4,
-    "397": 5,
-    "398": 6,
-    "399": 7,
-    "400": 8,
-    "401": 9,
-    "402": 10,
-    "403": 11,
-    "404": 12,
-    "405": 13,
-    "406": 14,
-    "407": 15,
-    "408": 16,
-    "409": 17,
-    "410": 18,
-    "411": 19,
-    "412": 20,
-    "413": 21,
-    "414": 22,
-    "415": 23,
-    "416": 24,
-    "417": 25,
-    "418": 26,
-    "419": 27,
-    "420": 28,
-    "421": 29,
-    "422": 30,
-    "423": 31,
-    "424": 32,
-    "425": 33,
-    "426": 34,
-    "427": 35,
-    "428": 36,
-    "429": 37,
-    "430": 38,
-    "431": 39,
-    "432": 40,
-    "433": 41,
-    "434": 42,
-    "435": 43,
-    "436": 44,
-    "437": 45,
-    "438": 46,
-    "439": 47,
-    "440": 48,
-    "441": 49,
-    "442": 50,
-    "443": 51,
-    "444": 52,
-    "445": 53,
-    "446": 54,
-    "447": 55,
-    "448": 56,
-    "449": 57,
-    "450": 58,
-    "451": 59,
-    "452": 60,
-    "453": 61,
-    "454": 62,
-    "455": 63,
-    "456": 64,
-    "457": 65,
-    "458": 66,
-    "459": 67,
-    "460": 68,
-    "461": 69,
-    "462": 70,
-    "463": 71,
-    "464": 72,
-    "465": 73,
-    "466": 74,
-    "467": 75,
-    "468": 76,
-    "469": 77,
-    "470": 78,
-    "471": 79,
-    "472": 80,
-    "473": 81,
-    "474": 82,
-    "475": 83,
-    "476": 84,
-    "477": 85,
-    "478": 86,
-    "479": 87,
-    "480": 88,
-    "481": 89,
-    "482": 90,
-    "483": 91,
-    "484": 92,
-    "485": 93,
-    "486": 94,
-    "487": 95,
-    "488": 96,
-    "489": 97,
-    "490": 98,
-    "491": 99,
-    "492": 100,
-    "493": 101,
-    "494": 102,
-    "495": 103,
-    "496": 104,
-    "497": 105,
-    "498": 106,
-    "499": 107,
-    "500": 108,
-    "501": 109,
-    "502": 110,
-    "503": 111,
-    "504": 112,
-    "505": 113,
-    "506": 114,
-    "507": 115,
-    "508": 116,
-    "509": 117,
-    "510": 118,
-    "511": 119,
-    "512": 120,
-    "513": 121,
-    "514": 122,
-    "515": 123,
-    "516": 124,
-    "517": 125,
-    "518": 126,
-    "519": 127,
-    "520": 128,
-    "521": 129,
-    "522": 130,
-    "523": 131,
-    "524": 132,
-    "525": 133,
-    "526": 134,
-    "527": 135,
-    "528": 136,
-    "529": 137,
-    "530": 138,
-    "531": 139,
-    "532": 140,
-    "533": 141,
-    "534": 142,
-    "535": 143,
-    "536": 144,
-    "537": 145,
-    "538": 146,
-    "539": 147,
-    "540": 148,
-    "541": 149,
-    "542": 150,
-    "543": 151,
-    "544": 152,
-    "545": 153,
-    "546": 154,
-    "547": 155,
-    "548": 156,
-    "549": 157,
-    "550": 158,
-    "551": 159,
-    "552": 160,
-    "553": 161,
-    "554": 162,
-    "555": 163,
-    "556": 164,
-    "557": 165,
-    "558": 166,
-    "559": 167,
-    "560": 168,
-    "561": 169,
-    "562": 170,
-    "563": 171,
-    "564": 172,
-    "565": 173,
-    "566": 174,
-    "567": 175,
-    "568": 176,
-    "569": 177,
-    "570": 178,
-    "571": 179,
-    "572": 180,
-    "573": 181,
-    "574": 182,
-    "575": 183,
-    "576": 184,
-    "577": 185,
-    "578": 186,
-    "579": 187,
-    "580": 188,
-    "581": 189,
-    "582": 190,
-    "583": 191,
-    "584": 192,
-    "585": 193,
-    "586": 194,
-    "587": 195,
-    "588": 196,
-    "589": 197,
-    "590": 198,
-    "591": 199,
-    "592": 200,
-    "593": 201,
-    "594": 202,
-    "595": 203,
-    "596": 204,
-    "597": 205,
-    "598": 206,
-    "599": 207,
-    "600": 208,
-    "601": 209,
-    "602": 210,
-    "603": 211,
-    "604": 212,
-    "605": 213,
-    "606": 214,
-    "607": 215,
-    "608": 216,
-    "609": 217,
-    "610": 218,
-    "611": 219,
-    "612": 220,
-  },
-  "transcriptSeqToStructureSeqPosition": {
     "0": 392,
     "1": 393,
     "10": 402,
@@ -1347,5 +1124,228 @@ exports[`test 1`] = `
     "98": 490,
     "99": 491,
   },
+  "transcriptSeqToStructureSeqPosition": {
+    "392": 0,
+    "393": 1,
+    "394": 2,
+    "395": 3,
+    "396": 4,
+    "397": 5,
+    "398": 6,
+    "399": 7,
+    "400": 8,
+    "401": 9,
+    "402": 10,
+    "403": 11,
+    "404": 12,
+    "405": 13,
+    "406": 14,
+    "407": 15,
+    "408": 16,
+    "409": 17,
+    "410": 18,
+    "411": 19,
+    "412": 20,
+    "413": 21,
+    "414": 22,
+    "415": 23,
+    "416": 24,
+    "417": 25,
+    "418": 26,
+    "419": 27,
+    "420": 28,
+    "421": 29,
+    "422": 30,
+    "423": 31,
+    "424": 32,
+    "425": 33,
+    "426": 34,
+    "427": 35,
+    "428": 36,
+    "429": 37,
+    "430": 38,
+    "431": 39,
+    "432": 40,
+    "433": 41,
+    "434": 42,
+    "435": 43,
+    "436": 44,
+    "437": 45,
+    "438": 46,
+    "439": 47,
+    "440": 48,
+    "441": 49,
+    "442": 50,
+    "443": 51,
+    "444": 52,
+    "445": 53,
+    "446": 54,
+    "447": 55,
+    "448": 56,
+    "449": 57,
+    "450": 58,
+    "451": 59,
+    "452": 60,
+    "453": 61,
+    "454": 62,
+    "455": 63,
+    "456": 64,
+    "457": 65,
+    "458": 66,
+    "459": 67,
+    "460": 68,
+    "461": 69,
+    "462": 70,
+    "463": 71,
+    "464": 72,
+    "465": 73,
+    "466": 74,
+    "467": 75,
+    "468": 76,
+    "469": 77,
+    "470": 78,
+    "471": 79,
+    "472": 80,
+    "473": 81,
+    "474": 82,
+    "475": 83,
+    "476": 84,
+    "477": 85,
+    "478": 86,
+    "479": 87,
+    "480": 88,
+    "481": 89,
+    "482": 90,
+    "483": 91,
+    "484": 92,
+    "485": 93,
+    "486": 94,
+    "487": 95,
+    "488": 96,
+    "489": 97,
+    "490": 98,
+    "491": 99,
+    "492": 100,
+    "493": 101,
+    "494": 102,
+    "495": 103,
+    "496": 104,
+    "497": 105,
+    "498": 106,
+    "499": 107,
+    "500": 108,
+    "501": 109,
+    "502": 110,
+    "503": 111,
+    "504": 112,
+    "505": 113,
+    "506": 114,
+    "507": 115,
+    "508": 116,
+    "509": 117,
+    "510": 118,
+    "511": 119,
+    "512": 120,
+    "513": 121,
+    "514": 122,
+    "515": 123,
+    "516": 124,
+    "517": 125,
+    "518": 126,
+    "519": 127,
+    "520": 128,
+    "521": 129,
+    "522": 130,
+    "523": 131,
+    "524": 132,
+    "525": 133,
+    "526": 134,
+    "527": 135,
+    "528": 136,
+    "529": 137,
+    "530": 138,
+    "531": 139,
+    "532": 140,
+    "533": 141,
+    "534": 142,
+    "535": 143,
+    "536": 144,
+    "537": 145,
+    "538": 146,
+    "539": 147,
+    "540": 148,
+    "541": 149,
+    "542": 150,
+    "543": 151,
+    "544": 152,
+    "545": 153,
+    "546": 154,
+    "547": 155,
+    "548": 156,
+    "549": 157,
+    "550": 158,
+    "551": 159,
+    "552": 160,
+    "553": 161,
+    "554": 162,
+    "555": 163,
+    "556": 164,
+    "557": 165,
+    "558": 166,
+    "559": 167,
+    "560": 168,
+    "561": 169,
+    "562": 170,
+    "563": 171,
+    "564": 172,
+    "565": 173,
+    "566": 174,
+    "567": 175,
+    "568": 176,
+    "569": 177,
+    "570": 178,
+    "571": 179,
+    "572": 180,
+    "573": 181,
+    "574": 182,
+    "575": 183,
+    "576": 184,
+    "577": 185,
+    "578": 186,
+    "579": 187,
+    "580": 188,
+    "581": 189,
+    "582": 190,
+    "583": 191,
+    "584": 192,
+    "585": 193,
+    "586": 194,
+    "587": 195,
+    "588": 196,
+    "589": 197,
+    "590": 198,
+    "591": 199,
+    "592": 200,
+    "593": 201,
+    "594": 202,
+    "595": 203,
+    "596": 204,
+    "597": 205,
+    "598": 206,
+    "599": 207,
+    "600": 208,
+    "601": 209,
+    "602": 210,
+    "603": 211,
+    "604": 212,
+    "605": 213,
+    "606": 214,
+    "607": 215,
+    "608": 216,
+    "609": 217,
+    "610": 218,
+    "611": 219,
+    "612": 220,
+  },
 }
 `;

package/src/genomeToTranscriptMapping.ts

@@ -8,16 +8,16 @@ export function genomeToTranscriptMapping(feature: Feature) {
   const cds = subs
     .filter(f => f.get('type') === 'CDS')
     .sort((a, b) => strand * (a.get('start') - b.get('start')))
-  const g2p = {} as Record<number, number | undefined>
-  const p2g = {} as Record<number, number | undefined>
+  const g2p = {} as Record<number, number>
+  const p2g = {} as Record<number, number>
 
   let proteinCounter = 0
-  if (strand !== -1) {
+  if (strand === -1) {
     for (const f of cds) {
       for (
-        let genomePos = f.get('start');
-        genomePos < f.get('end');
-        genomePos++
+        let genomePos = f.get('end');
+        genomePos > f.get('start');
+        genomePos--
       ) {
         const proteinPos = Math.floor(proteinCounter++ / 3)
         g2p[genomePos] = proteinPos
@@ -29,9 +29,9 @@ export function genomeToTranscriptMapping(feature: Feature) {
   } else {
     for (const f of cds) {
       for (
-        let genomePos = f.get('end');
-        genomePos > f.get('start');
-        genomePos--
+        let genomePos = f.get('start');
+        genomePos < f.get('end');
+        genomePos++
       ) {
         const proteinPos = Math.floor(proteinCounter++ / 3)
         g2p[genomePos] = proteinPos

package/src/index.ts

@@ -6,6 +6,9 @@ import { version } from '../package.json'
 import ProteinViewF from './ProteinView'
 import LaunchProteinViewF from './LaunchProteinView'
 import AddHighlightModelF from './AddHighlightModel'
+import AlphaFoldConfidenceAdapterF from './AlphaFoldConfidenceAdapter'
+import UniProtVariationAdapterF from './UniProtVariationAdapter'
+import AlphaMissensePathogenicityAdapterF from './AlphaMissensePathogenicityAdapter'
 
 export default class ProteinViewer extends Plugin {
   name = 'ProteinViewer'
@@ -15,6 +18,9 @@ export default class ProteinViewer extends Plugin {
     ProteinViewF(pluginManager)
     LaunchProteinViewF(pluginManager)
     AddHighlightModelF(pluginManager)
+    AlphaFoldConfidenceAdapterF(pluginManager)
+    AlphaMissensePathogenicityAdapterF(pluginManager)
+    UniProtVariationAdapterF(pluginManager)
   }
 
   configure(_pluginManager: PluginManager) {}