Merge pull request #1624 from GMOD/gccontent_adapter

GCContent adapter

plugins/sequence/package.json

@@ -44,6 +44,7 @@
   "peerDependencies": {
     "@jbrowse/core": "^1.0.0",
     "@jbrowse/plugin-linear-genome-view": "^1.0.0",
+    "@jbrowse/plugin-wiggle": "^1.0.0",
     "@material-ui/core": "^4.9.13",
     "mobx-react": "^6.0.0",
     "mobx-state-tree": "3.14.1",

plugins/sequence/src/GCContentAdapter/GCContentAdapter.ts

@@ -0,0 +1,174 @@
+import {
+  BaseFeatureDataAdapter,
+  RegionsAdapter,
+  BaseOptions,
+} from '@jbrowse/core/data_adapters/BaseAdapter'
+import { Region, NoAssemblyRegion } from '@jbrowse/core/util/types'
+import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
+import { ObservableCreate } from '@jbrowse/core/util/rxjs'
+import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'
+import { readConfObject } from '@jbrowse/core/configuration'
+import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema'
+import { toArray } from 'rxjs/operators'
+
+import { blankStats, rectifyStats, scoresToStats } from '@jbrowse/plugin-wiggle'
+
+export default class extends BaseFeatureDataAdapter implements RegionsAdapter {
+  private sequenceAdapter: BaseFeatureDataAdapter
+
+  private windowSize = 1000
+
+  private windowDelta = 1000
+
+  private gcMode = 'content'
+
+  public static capabilities = ['hasLocalStats']
+
+  public constructor(
+    config: AnyConfigurationModel,
+    getSubAdapter?: getSubAdapterType,
+  ) {
+    super(config)
+    // instantiate the sequence adapter
+    const sequenceAdapterType = readConfObject(config, [
+      'sequenceAdapter',
+      'type',
+    ])
+
+    const dataAdapter = getSubAdapter?.(
+      readConfObject(config, 'sequenceAdapter'),
+    ).dataAdapter
+    if (dataAdapter instanceof BaseFeatureDataAdapter) {
+      this.sequenceAdapter = dataAdapter
+    } else {
+      throw new Error(
+        `Feature adapters cannot use sequence adapters of type '${sequenceAdapterType}'`,
+      )
+    }
+  }
+
+  public getRefNames() {
+    return this.sequenceAdapter.getRefNames()
+  }
+
+  public async getRegions(): Promise<NoAssemblyRegion[]> {
+    // @ts-ignore
+    return this.sequenceAdapter.getRegions()
+  }
+
+  // Taken from bigwigadapter
+  public getRegionStats(region: Region, opts: BaseOptions) {
+    const feats = this.getFeatures(region, opts)
+    return scoresToStats(region, feats)
+  }
+
+  // Taken from bigwigadapter
+  public async getMultiRegionStats(regions: Region[] = [], opts: BaseOptions) {
+    if (!regions.length) {
+      return blankStats()
+    }
+    const feats = await Promise.all(
+      regions.map(region => this.getRegionStats(region, opts)),
+    )
+
+    const scoreMax = feats
+      .map(s => s.scoreMax)
+      .reduce((acc, curr) => Math.max(acc, curr))
+    const scoreMin = feats
+      .map(s => s.scoreMin)
+      .reduce((acc, curr) => Math.min(acc, curr))
+    const scoreSum = feats.map(s => s.scoreSum).reduce((a, b) => a + b, 0)
+    const scoreSumSquares = feats
+      .map(s => s.scoreSumSquares)
+      .reduce((a, b) => a + b, 0)
+    const featureCount = feats
+      .map(s => s.featureCount)
+      .reduce((a, b) => a + b, 0)
+    const basesCovered = feats
+      .map(s => s.basesCovered)
+      .reduce((a, b) => a + b, 0)
+
+    return rectifyStats({
+      scoreMin,
+      scoreMax,
+      featureCount,
+      basesCovered,
+      scoreSumSquares,
+      scoreSum,
+    })
+  }
+
+  /**
+   * Fetch features for a certain region
+   * @param param -
+   * @returns Observable of Feature objects in the region
+   */
+  public getFeatures(query: Region, opts: BaseOptions) {
+    this.windowSize = 1000
+    this.windowDelta = 1000
+    this.gcMode = 'content'
+    return ObservableCreate<Feature>(async observer => {
+      const hw = this.windowSize === 1 ? 1 : this.windowSize / 2 // Half the window size
+      const f = this.windowSize === 1
+
+      let { start: queryStart, end: queryEnd } = query
+      queryStart = Math.max(0, queryStart - hw)
+      queryEnd += hw
+
+      if (queryEnd < 0 || queryStart > queryEnd) {
+        observer.complete()
+        return
+      }
+
+      const ret = this.sequenceAdapter.getFeatures(
+        { ...query, start: queryStart, end: queryEnd },
+        opts,
+      )
+      const [feat] = await ret.pipe(toArray()).toPromise()
+      const residues = feat.get('seq')
+
+      for (let i = hw; i < residues.length - hw; i += this.windowDelta) {
+        const r = f ? residues[i] : residues.slice(i - hw, i + hw)
+        let nc = 0
+        let ng = 0
+        let len = 0
+        for (let j = 0; j < r.length; j++) {
+          if (r[j] === 'c' || r[j] === 'C') {
+            nc++
+          } else if (r[j] === 'g' || r[j] === 'G') {
+            ng++
+          }
+          if (r[j] !== 'N') {
+            len++
+          }
+        }
+        const pos = queryStart
+        let score
+        if (this.gcMode === 'content') {
+          score = (ng + nc) / (len || 1)
+        } else if (this.gcMode === 'skew') {
+          score = (ng - nc) / (ng + nc || 1)
+        }
+
+        // if (r[Math.floor(r.length / 2)] !== 'N') {
+        observer.next(
+          new SimpleFeature({
+            uniqueId: `${this.id}_${pos + i}`,
+            start: pos + i,
+            end: pos + i + this.windowDelta,
+            score,
+          }),
+        )
+        // }
+      }
+      observer.complete()
+    })
+  }
+
+  /**
+   * called to provide a hint that data tied to a certain region
+   * will not be needed for the forseeable future and can be purged
+   * from caches, etc
+   */
+  public freeResources(/* { region } */): void {}
+}

plugins/sequence/src/GCContentAdapter/configSchema.ts

@@ -0,0 +1,12 @@
+import PluginManager from '@jbrowse/core/PluginManager'
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+
+export default (pluginManager: PluginManager) => {
+  return ConfigurationSchema(
+    'GCContentAdapter',
+    {
+      sequenceAdapter: pluginManager.pluggableConfigSchemaType('adapter'),
+    },
+    { explicitlyTyped: true },
+  )
+}

plugins/sequence/src/GCContentAdapter/index.ts

@@ -0,0 +1,10 @@
+import PluginManager from '@jbrowse/core/PluginManager'
+import configSchemaF from './configSchema'
+import AdapterClass from './GCContentAdapter'
+
+export default (pluginManager: PluginManager) => {
+  return {
+    configSchema: pluginManager.load(configSchemaF),
+    AdapterClass,
+  }
+}

plugins/sequence/src/index.ts

@@ -30,6 +30,7 @@ import {
   AdapterClass as TwoBitAdapterClass,
   configSchema as twoBitAdapterConfigSchema,
 } from './TwoBitAdapter'
+import GCContentAdapterF from './GCContentAdapter'
 import { createReferenceSeqTrackConfig } from './referenceSeqTrackConfig'
 
 /* adjust in both directions */
@@ -83,6 +84,13 @@ export default class SequencePlugin extends Plugin {
         }),
     )
 
+    pluginManager.addAdapterType(
+      () =>
+        new AdapterType({
+          name: 'GCContentAdapter',
+          ...pluginManager.load(GCContentAdapterF),
+        }),
+    )
     pluginManager.addTrackType(() => {
       const configSchema = createReferenceSeqTrackConfig(pluginManager)
 

plugins/wiggle/src/LinearWiggleDisplay/models/model.ts

@@ -401,6 +401,7 @@ const stateModelFactory = (
             },
           )) as FeatureStats
           const { scoreMin, scoreMean, scoreStdDev } = results
+
           // localsd uses heuristic to avoid unnecessary scoreMin<0
           // if the scoreMin is never less than 0
           // helps with most coverage bigwigs just being >0

test_data/config_demo.json

@@ -742,6 +742,28 @@
         }
       }
     },
+    {
+      "type": "QuantitativeTrack",
+      "trackId": "gccontent_hg19",
+      "name": "GCContent",
+      "assemblyNames": ["hg19"],
+      "adapter": {
+        "type": "GCContentAdapter",
+        "sequenceAdapter": {
+          "type": "BgzipFastaAdapter",
+          "fastaLocation": {
+            "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz"
+          },
+          "faiLocation": {
+            "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.fai"
+          },
+          "gziLocation": {
+            "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.gzi"
+          }
+        }
+      }
+    },
+
     {
       "type": "AlignmentsTrack",
       "trackId": "illumina_hg002",