@jbrowse/plugin-data-management 2.3.1 → 2.3.2

package/src/ucsc-trackhub/ucscTrackHub.ts

@@ -0,0 +1,326 @@
+/* eslint-disable @typescript-eslint/no-explicit-any */
+import { RaStanza, TrackDbFile } from '@gmod/ucsc-hub'
+import { FileLocation, isUriLocation, objectHash } from '@jbrowse/core/util'
+import { openLocation } from '@jbrowse/core/util/io'
+import {
+  generateUnsupportedTrackConf,
+  generateUnknownTrackConf,
+} from '@jbrowse/core/util/tracks'
+import ucscAssemblies from './ucscAssemblies'
+
+export { ucscAssemblies }
+
+export async function fetchHubFile(hubLocation: FileLocation) {
+  try {
+    const hubFileText = await openLocation(hubLocation).readFile('utf8')
+    const { HubFile } = await import('@gmod/ucsc-hub')
+    return new HubFile(hubFileText)
+  } catch (error) {
+    throw new Error(`Not a valid hub.txt file, got error: '${error}'`)
+  }
+}
+
+export async function fetchGenomesFile(genomesLoc: FileLocation) {
+  const genomesFileText = await openLocation(genomesLoc).readFile('utf8')
+  const { GenomesFile } = await import('@gmod/ucsc-hub')
+  return new GenomesFile(genomesFileText)
+}
+
+export async function fetchTrackDbFile(trackDbLoc: FileLocation) {
+  const text = await openLocation(trackDbLoc).readFile('utf8')
+  const { TrackDbFile } = await import('@gmod/ucsc-hub')
+  return new TrackDbFile(text)
+}
+
+export function makeLoc(first: string, base: { uri: string }) {
+  return {
+    uri: new URL(first, base.uri).href,
+    locationType: 'UriLocation',
+  }
+}
+
+export function makeLocAlt(first: string, alt: string, base: { uri: string }) {
+  return first ? makeLoc(first, base) : makeLoc(alt, base)
+}
+
+export function makeLoc2(first: string, alt?: string) {
+  return first
+    ? {
+        uri: first,
+        locationType: 'LocalPath',
+      }
+    : {
+        uri: alt,
+        locationType: 'UriLocation',
+      }
+}
+
+export function generateTracks(
+  trackDb: TrackDbFile,
+  trackDbLoc: FileLocation,
+  assemblyName: string,
+  sequenceAdapter: any,
+) {
+  const tracks: any = []
+
+  trackDb.forEach((track, trackName) => {
+    const trackKeys = Array.from(track.keys()) as string[]
+    const parentTrackKeys = [
+      'superTrack',
+      'compositeTrack',
+      'container',
+      'view',
+    ]
+    if (trackKeys.some(key => parentTrackKeys.includes(key))) {
+      return
+    }
+    const parentTracks = []
+    let currentTrackName = trackName
+    do {
+      currentTrackName = trackDb.get(currentTrackName)?.get('parent') || ''
+      if (currentTrackName) {
+        ;[currentTrackName] = currentTrackName.split(' ')
+        parentTracks.push(trackDb.get(currentTrackName))
+      }
+    } while (currentTrackName)
+    parentTracks.reverse()
+    const categories = parentTracks
+      .map(p => p?.get('shortLabel'))
+      .filter((f): f is string => !!f)
+    const res = makeTrackConfig(
+      track,
+      categories,
+      trackDbLoc,
+      trackDb,
+      sequenceAdapter,
+    )
+    tracks.push({
+      ...res,
+      trackId: `ucsc-trackhub-${objectHash(res)}`,
+      assemblyNames: [assemblyName],
+    })
+  })
+
+  return tracks
+}
+
+function makeTrackConfig(
+  track: RaStanza,
+  categories: string[],
+  trackDbLoc: FileLocation,
+  trackDb: TrackDbFile,
+  sequenceAdapter: any,
+) {
+  let trackType = track.get('type')
+  const name = track.get('shortLabel') || ''
+  const bigDataUrl = track.get('bigDataUrl') || ''
+  const bigDataIdx = track.get('bigDataIndex') || ''
+  const isUri = isUriLocation(trackDbLoc)
+  if (!trackType) {
+    trackType = trackDb.get(track.get('parent') || '')?.get('type')
+  }
+  let baseTrackType = trackType?.split(' ')[0] || ''
+  if (baseTrackType === 'bam' && bigDataUrl.toLowerCase().endsWith('cram')) {
+    baseTrackType = 'cram'
+  }
+  const bigDataLocation = isUri
+    ? makeLoc(bigDataUrl, trackDbLoc)
+    : makeLoc2(bigDataUrl)
+
+  switch (baseTrackType) {
+    case 'bam':
+      return {
+        type: 'AlignmentsTrack',
+        name: track.get('shortLabel'),
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'BamAdapter',
+          bamLocation: bigDataLocation,
+          index: {
+            location: isUri
+              ? makeLocAlt(bigDataIdx, bigDataUrl + '.bai', trackDbLoc)
+              : makeLoc2(bigDataIdx, bigDataUrl + '.bai'),
+          },
+        },
+      }
+
+    case 'bigBarChart':
+      return {
+        type: 'FeatureTrack',
+        name,
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'BigBedAdapter',
+          bigBedLocation: bigDataLocation,
+        },
+        renderer: {
+          type: 'SvgFeatureRenderer',
+        },
+      }
+    case 'bigBed':
+      return {
+        type: 'FeatureTrack',
+        name,
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'BigBedAdapter',
+          bigBedLocation: bigDataLocation,
+        },
+      }
+    case 'bigGenePred':
+      return {
+        type: 'FeatureTrack',
+        name,
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'BigBedAdapter',
+          bigBedLocation: bigDataLocation,
+        },
+      }
+    case 'bigChain':
+      return {
+        type: 'FeatureTrack',
+        name,
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'BigBedAdapter',
+          bigBedLocation: bigDataLocation,
+        },
+        renderer: {
+          type: 'SvgFeatureRenderer',
+        },
+      }
+    case 'bigInteract':
+      return {
+        type: 'FeatureTrack',
+        name,
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'BigBedAdapter',
+          bigBedLocation: bigDataLocation,
+        },
+        renderer: {
+          type: 'SvgFeatureRenderer',
+        },
+      }
+    case 'bigMaf':
+      return {
+        type: 'FeatureTrack',
+        name,
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'BigBedAdapter',
+          bigBedLocation: bigDataLocation,
+        },
+        renderer: {
+          type: 'SvgFeatureRenderer',
+        },
+      }
+    case 'bigPsl':
+      return {
+        type: 'FeatureTrack',
+        name,
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'BigBedAdapter',
+          bigBedLocation: bigDataLocation,
+        },
+        renderer: {
+          type: 'SvgFeatureRenderer',
+        },
+      }
+    case 'bigWig':
+      return {
+        type: 'QuantitativeTrack',
+        name,
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'BigWigAdapter',
+          bigWigLocation: bigDataLocation,
+        },
+      }
+
+    case 'cram':
+      return {
+        type: 'AlignmentsTrack',
+        name,
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'CramAdapter',
+          cramLocation: bigDataLocation,
+          craiLocation: isUri
+            ? makeLocAlt(bigDataIdx, bigDataUrl + '.crai', trackDbLoc)
+            : makeLoc2(bigDataIdx, bigDataUrl + '.crai'),
+          sequenceAdapter,
+        },
+      }
+
+    case 'bigNarrowPeak':
+      return {
+        type: 'FeatureTrack',
+        name,
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'BigBedAdapter',
+          bigBedLocation: bigDataLocation,
+        },
+      }
+    case 'peptideMapping':
+      return generateUnsupportedTrackConf(name, baseTrackType, categories)
+    case 'vcfTabix':
+      return {
+        type: 'VariantTrack',
+        name,
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'VcfTabixAdapter',
+          vcfGzLocation: bigDataLocation,
+          index: {
+            location: isUri
+              ? makeLocAlt(bigDataIdx, bigDataUrl + '.tbi', trackDbLoc)
+              : makeLoc2(bigDataIdx, bigDataUrl + '.tbi'),
+          },
+        },
+      }
+
+    case 'hic':
+      return {
+        type: 'HicTrack',
+        name,
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'HicAdapter',
+          hicLocation: bigDataLocation,
+        },
+      }
+
+    // unsupported types
+    //     case 'gvf':
+    //     case 'ld2':
+    //     case 'narrowPeak':
+    //     case 'wig':
+    //     case 'wigMaf':
+    //     case 'halSnake':
+    //     case 'bed':
+    //     case 'bed5FloatScore':
+    //     case 'bedGraph':
+    //     case 'bedRnaElements':
+    //     case 'broadPeak':
+    //     case 'coloredExon':
+    default:
+      return generateUnknownTrackConf(name, baseTrackType, categories)
+  }
+}