Add some adapters for uniprot alphafold data (#14)

eslint.config.mjs

@@ -61,7 +61,7 @@ export default tseslint.config(
           markers: ['/'],
         },
       ],
-
+      '@typescript-eslint/require-await': 'off',
       '@typescript-eslint/no-unsafe-argument': 'off',
       '@typescript-eslint/no-unsafe-return': 'off',
       '@typescript-eslint/no-unsafe-call': 'off',

src/AlphaFoldConfidenceAdapter/AlphaFoldConfidenceAdapter.ts

@@ -0,0 +1,63 @@
+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'
+
+export default class AlphaFoldConfidenceAdapter extends BaseFeatureDataAdapter {
+  public static capabilities = ['getFeatures', 'getRefNames']
+
+  public feats:
+    | Promise<{ uniqueId: string; start: number; end: number; score: number }[]>
+    | undefined
+
+  private async loadDataP() {
+    const scores = JSON.parse(
+      await openLocation(this.getConf('location')).readFile('utf8'),
+    ) as { residueNumber: number[]; confidenceScore: number[] }
+
+    return scores.residueNumber.map((value, idx) => ({
+      uniqueId: `feat-${idx}`,
+      start: value,
+      end: value + 1,
+      score: scores.confidenceScore[idx]!,
+    }))
+  }
+
+  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 {}
+}

src/AlphaFoldConfidenceAdapter/configSchema.ts

@@ -0,0 +1,21 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+
+/**
+ * #config AlphaFoldConfidenceAdapter
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const AlphaFoldConfidenceAdapter = ConfigurationSchema(
+  'AlphaFoldConfidenceAdapter',
+  {
+    /**
+     * #slot
+     */
+    location: {
+      type: 'fileLocation',
+      defaultValue: { uri: '/path/to/my.bed.gz', locationType: 'UriLocation' },
+    },
+  },
+  { explicitlyTyped: true },
+)
+export default AlphaFoldConfidenceAdapter

src/AlphaFoldConfidenceAdapter/index.ts

@@ -0,0 +1,19 @@
+import PluginManager from '@jbrowse/core/PluginManager'
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
+
+import configSchema from './configSchema'
+
+export default function AlphaFoldConfidenceAdapterF(
+  pluginManager: PluginManager,
+) {
+  pluginManager.addAdapterType(
+    () =>
+      new AdapterType({
+        name: 'AlphaFoldConfidenceAdapter',
+        displayName: 'AlphaFoldConfidence adapter',
+        configSchema,
+        getAdapterClass: () =>
+          import('./AlphaFoldConfidenceAdapter').then(r => r.default),
+      }),
+  )
+}

src/AlphaMissensePathogenicityAdapter/AlphaMissensePathogenicityAdapter.ts

@@ -0,0 +1,109 @@
+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,
+  max,
+  min,
+} from '@jbrowse/core/util'
+
+export default class AlphaMissensePathogenicityAdapter extends BaseFeatureDataAdapter {
+  public static capabilities = ['getFeatures', 'getRefNames']
+
+  public feats:
+    | Promise<
+        {
+          uniqueId: string
+          start: number
+          end: number
+          score: number
+          ref: string
+          variant: string
+          am_class: string
+        }[]
+      >
+    | undefined
+
+  private async loadDataP() {
+    const scores = await openLocation(this.getConf('location')).readFile('utf8')
+    return scores
+      .split('\n')
+      .slice(1)
+      .map(f => f.trim())
+      .filter(f => !!f)
+      .map((row, idx) => {
+        const [protein_variant, score, am_class] = row.split(',')
+        const ref = protein_variant![0]
+        const variant = protein_variant!.at(-1)
+        const coord = protein_variant!.slice(1, -1)
+        return {
+          uniqueId: `feat-${idx}`,
+          ref: ref!,
+          variant: variant!,
+          start: +coord,
+          end: +coord + 1,
+          score: +score!,
+          am_class: am_class!,
+        }
+      })
+  }
+
+  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 getGlobalStats(_opts?: BaseOptions) {
+    const data = await this.loadData()
+    const scoreMin = min(data.map(s => s.score))
+    const scoreMax = max(data.map(s => s.score))
+    return { scoreMin, scoreMax }
+  }
+
+  // always render bigwig instead of calculating a feature density for it
+  async getMultiRegionFeatureDensityStats(_regions: Region[]) {
+    return { featureDensity: 0 }
+  }
+  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, source: f.variant }))
+        }
+      }
+      observer.complete()
+    }, opts.signal)
+  }
+
+  public async getSources() {
+    const sources = new Set<string>()
+    const data = await this.loadData()
+    for (const f of data) {
+      sources.add(f.variant)
+    }
+    return [...sources].map(s => ({
+      name: s,
+      __name: s,
+    }))
+  }
+
+  public freeResources(): void {}
+}

src/AlphaMissensePathogenicityAdapter/configSchema.ts

@@ -0,0 +1,21 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+
+/**
+ * #config AlphaMissensePathogenicityAdapter
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const AlphaMissensePathogenicityAdapter = ConfigurationSchema(
+  'AlphaMissensePathogenicityAdapter',
+  {
+    /**
+     * #slot
+     */
+    location: {
+      type: 'fileLocation',
+      defaultValue: { uri: '/path/to/my.bed.gz', locationType: 'UriLocation' },
+    },
+  },
+  { explicitlyTyped: true },
+)
+export default AlphaMissensePathogenicityAdapter

src/AlphaMissensePathogenicityAdapter/index.ts

@@ -0,0 +1,19 @@
+import PluginManager from '@jbrowse/core/PluginManager'
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
+
+import configSchema from './configSchema'
+
+export default function AlphaMissensePathogenicityAdapterF(
+  pluginManager: PluginManager,
+) {
+  pluginManager.addAdapterType(
+    () =>
+      new AdapterType({
+        name: 'AlphaMissensePathogenicityAdapter',
+        displayName: 'AlphaMissensePathogenicity adapter',
+        configSchema,
+        getAdapterClass: () =>
+          import('./AlphaMissensePathogenicityAdapter').then(r => r.default),
+      }),
+  )
+}

src/index.ts

@@ -6,6 +6,8 @@ import { version } from '../package.json'
 import ProteinViewF from './ProteinView'
 import LaunchProteinViewF from './LaunchProteinView'
 import AddHighlightModelF from './AddHighlightModel'
+import AlphaFoldConfidenceAdapterF from './AlphaFoldConfidenceAdapter'
+import AlphaMissensePathogenicityAdapterF from './AlphaMissensePathogenicityAdapter'
 
 export default class ProteinViewer extends Plugin {
   name = 'ProteinViewer'
@@ -15,6 +17,8 @@ export default class ProteinViewer extends Plugin {
     ProteinViewF(pluginManager)
     LaunchProteinViewF(pluginManager)
     AddHighlightModelF(pluginManager)
+    AlphaFoldConfidenceAdapterF(pluginManager)
+    AlphaMissensePathogenicityAdapterF(pluginManager)
   }
 
   configure(_pluginManager: PluginManager) {}