@jbrowse/plugin-gff3 1.5.0 → 1.5.4

package/src/Gff3Adapter/Gff3Adapter.ts

@@ -1,100 +1,102 @@
-import { Instance } from 'mobx-state-tree'
 import {
   BaseFeatureDataAdapter,
   BaseOptions,
 } from '@jbrowse/core/data_adapters/BaseAdapter'
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { readConfObject } from '@jbrowse/core/configuration'
 import { NoAssemblyRegion } from '@jbrowse/core/util/types'
+import { readConfObject } from '@jbrowse/core/configuration'
 import { openLocation } from '@jbrowse/core/util/io'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
 import IntervalTree from '@flatten-js/interval-tree'
 import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'
+import { unzip } from '@gmod/bgzf-filehandle'
 
-import gff from '@gmod/gff'
-import { GenericFilehandle } from 'generic-filehandle'
+import gff, { GFF3FeatureLineWithRefs } from '@gmod/gff'
 
-import MyConfigSchema from './configSchema'
-import { FeatureLoc } from '../util'
+function isGzip(buf: Buffer) {
+  return buf[0] === 31 && buf[1] === 139 && buf[2] === 8
+}
 
 export default class extends BaseFeatureDataAdapter {
-  protected gffFeatures?: Promise<Record<string, IntervalTree>>
-
-  protected uri: string
-
-  protected filehandle: GenericFilehandle
-
-  public constructor(
-    config: Instance<typeof MyConfigSchema>,
-    getSubAdapter?: getSubAdapterType,
-    pluginManager?: PluginManager,
-  ) {
-    super(config, getSubAdapter, pluginManager)
-    const gffLocation = readConfObject(config, 'gffLocation')
-    const { uri } = gffLocation
-    this.uri = uri
-    this.filehandle = openLocation(gffLocation, this.pluginManager)
+  protected gffFeatures?: Promise<{
+    header: string
+    intervalTree: Record<string, IntervalTree>
+  }>
+
+  private async loadDataP() {
+    const buffer = await openLocation(
+      readConfObject(this.config, 'gffLocation'),
+      this.pluginManager,
+    ).readFile()
+    const buf = isGzip(buffer) ? await unzip(buffer) : buffer
+    // 512MB  max chrome string length is 512MB
+    if (buf.length > 536_870_888) {
+      throw new Error('Data exceeds maximum string length (512MB)')
+    }
+    const data = new TextDecoder('utf8', { fatal: true }).decode(buf)
+    const lines = data.split('\n')
+    const headerLines = []
+    for (let i = 0; i < lines.length && lines[i].startsWith('#'); i++) {
+      headerLines.push(lines[i])
+    }
+    const header = headerLines.join('\n')
+
+    const feats = gff.parseStringSync(data, {
+      parseFeatures: true,
+      parseComments: false,
+      parseDirectives: false,
+      parseSequences: false,
+    })
+
+    const intervalTree = feats
+      .flat()
+      .map(
+        (f, i) =>
+          new SimpleFeature({
+            data: this.featureData(f),
+            id: `${this.id}-offset-${i}`,
+          }),
+      )
+      .reduce((acc, obj) => {
+        const key = obj.get('refName')
+        if (!acc[key]) {
+          acc[key] = new IntervalTree()
+        }
+        acc[key].insert([obj.get('start'), obj.get('end')], obj)
+        return acc
+      }, {} as Record<string, IntervalTree>)
+
+    return { header, intervalTree }
   }
 
   private async loadData() {
-    const { size } = await this.filehandle.stat()
-    // Add a warning to avoid crashing the browser, recommend indexing
-    if (size > 500_000_000) {
-      throw new Error('This file is too large. Consider using Gff3TabixAdapter')
-    }
     if (!this.gffFeatures) {
-      this.gffFeatures = this.filehandle
-        .readFile('utf8')
-        .then(data => {
-          const gffFeatures = gff.parseStringSync(data, {
-            parseFeatures: true,
-            parseComments: false,
-            parseDirectives: false,
-            parseSequences: false,
-          }) as FeatureLoc[][]
-
-          return gffFeatures
-            .flat()
-            .map(
-              (f, i) =>
-                new SimpleFeature({
-                  data: this.featureData(f),
-                  id: `${this.id}-offset-${i}`,
-                }),
-            )
-            .reduce((acc: Record<string, IntervalTree>, obj: SimpleFeature) => {
-              const key = obj.get('refName')
-              if (!acc[key]) {
-                acc[key] = new IntervalTree()
-              }
-              acc[key].insert([obj.get('start'), obj.get('end')], obj)
-              return acc
-            }, {})
-        })
-        .catch(e => {
-          this.gffFeatures = undefined
-          throw e
-        })
+      this.gffFeatures = this.loadDataP().catch(e => {
+        this.gffFeatures = undefined
+        throw e
+      })
     }
 
     return this.gffFeatures
   }
 
   public async getRefNames(opts: BaseOptions = {}) {
-    const gffFeatures = await this.loadData()
-    return Object.keys(gffFeatures)
+    const { intervalTree } = await this.loadData()
+    return Object.keys(intervalTree)
   }
+
+  public async getHeader() {
+    const { header } = await this.loadData()
+    return header
+  }
+
   public getFeatures(query: NoAssemblyRegion, opts: BaseOptions = {}) {
     return ObservableCreate<Feature>(async observer => {
       try {
         const { start, end, refName } = query
-        const gffFeatures = await this.loadData()
-        const tree = gffFeatures[refName]
-        const feats = tree.search([start, end])
-        feats.forEach(f => {
-          observer.next(f)
-        })
+        const { intervalTree } = await this.loadData()
+        intervalTree[refName]
+          ?.search([start, end])
+          .forEach(f => observer.next(f))
         observer.complete()
       } catch (e) {
         observer.error(e)
@@ -102,10 +104,18 @@ export default class extends BaseFeatureDataAdapter {
     }, opts.signal)
   }
 
-  private featureData(data: FeatureLoc) {
+  private featureData(data: GFF3FeatureLineWithRefs) {
     const f: Record<string, unknown> = { ...data }
     ;(f.start as number) -= 1 // convert to interbase
-    f.strand = { '+': 1, '-': -1, '.': 0, '?': undefined }[data.strand] // convert strand
+    if (data.strand === '+') {
+      f.strand = 1
+    } else if (data.strand === '-') {
+      f.strand = -1
+    } else if (data.strand === '.') {
+      f.strand = 0
+    } else {
+      f.strand = undefined
+    }
     f.phase = Number(data.phase)
     f.refName = data.seq_id
     if (data.score === null) {
@@ -124,15 +134,16 @@ export default class extends BaseFeatureDataAdapter {
       'phase',
       'strand',
     ]
-    Object.keys(data.attributes).forEach(a => {
+    const dataAttributes = data.attributes || {}
+    Object.keys(dataAttributes).forEach(a => {
       let b = a.toLowerCase()
       if (defaultFields.includes(b)) {
         // add "suffix" to tag name if it already exists
         // reproduces behavior of NCList
         b += '2'
       }
-      if (data.attributes[a] !== null) {
-        let attr = data.attributes[a]
+      if (dataAttributes[a] !== null) {
+        let attr: string | string[] | undefined = dataAttributes[a]
         if (Array.isArray(attr) && attr.length === 1) {
           ;[attr] = attr
         }

package/src/Gff3TabixAdapter/Gff3TabixAdapter.ts

@@ -9,7 +9,7 @@ import { openLocation } from '@jbrowse/core/util/io'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
 import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'
 import { TabixIndexedFile } from '@gmod/tabix'
-import gff from '@gmod/gff'
+import gff, { GFF3Feature, GFF3FeatureLineWithRefs } from '@gmod/gff'
 import { Observer } from 'rxjs'
 
 import { Instance } from 'mobx-state-tree'
@@ -17,7 +17,6 @@ import { readConfObject } from '@jbrowse/core/configuration'
 import MyConfigSchema from './configSchema'
 import PluginManager from '@jbrowse/core/PluginManager'
 import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
-import { FeatureLoc } from '../util'
 
 interface LineFeature {
   start: number
@@ -110,12 +109,8 @@ export default class extends BaseFeatureDataAdapter {
           }
         })
         if (maxEnd > query.end || minStart < query.start) {
-          // console.log(
-          //   `redispatching ${query.start}-${query.end} => ${minStart}-${maxEnd}`,
-          // )
           // make a new feature callback to only return top-level features
           // in the original query range
-
           this.getFeaturesHelper(
             { ...query, start: minStart, end: maxEnd },
             opts,
@@ -146,7 +141,7 @@ export default class extends BaseFeatureDataAdapter {
         parseComments: false,
         parseDirectives: false,
         parseSequences: false,
-      }) as FeatureLoc[][]
+      })
 
       features.forEach(featureLocs =>
         this.formatFeatures(featureLocs).forEach(f => {
@@ -184,20 +179,29 @@ export default class extends BaseFeatureDataAdapter {
     }
   }
 
-  private formatFeatures(featureLocs: FeatureLoc[]) {
+  private formatFeatures(featureLocs: GFF3Feature) {
     return featureLocs.map(
       featureLoc =>
         new SimpleFeature({
           data: this.featureData(featureLoc),
-          id: `${this.id}-offset-${featureLoc.attributes._lineHash[0]}`,
+          // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
+          id: `${this.id}-offset-${featureLoc.attributes!._lineHash![0]}`,
         }),
     )
   }
 
-  private featureData(data: FeatureLoc) {
+  private featureData(data: GFF3FeatureLineWithRefs) {
     const f: Record<string, unknown> = { ...data }
     ;(f.start as number) -= 1 // convert to interbase
-    f.strand = { '+': 1, '-': -1, '.': 0, '?': undefined }[data.strand] // convert strand
+    if (data.strand === '+') {
+      f.strand = 1
+    } else if (data.strand === '-') {
+      f.strand = -1
+    } else if (data.strand === '.') {
+      f.strand = 0
+    } else {
+      f.strand = undefined
+    }
     f.phase = Number(data.phase)
     f.refName = data.seq_id
     if (data.score === null) {
@@ -216,15 +220,16 @@ export default class extends BaseFeatureDataAdapter {
       'phase',
       'strand',
     ]
-    Object.keys(data.attributes).forEach(a => {
+    const dataAttributes = data.attributes || {}
+    Object.keys(dataAttributes).forEach(a => {
       let b = a.toLowerCase()
       if (defaultFields.includes(b)) {
         // add "suffix" to tag name if it already exists
         // reproduces behavior of NCList
         b += '2'
       }
-      if (data.attributes[a] !== null) {
-        let attr = data.attributes[a]
+      if (dataAttributes[a] !== null) {
+        let attr: string | string[] | undefined = dataAttributes[a]
         if (Array.isArray(attr) && attr.length === 1) {
           ;[attr] = attr
         }

package/src/index.ts

@@ -2,6 +2,13 @@ import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
 import PluginManager from '@jbrowse/core/PluginManager'
 import Plugin from '@jbrowse/core/Plugin'
 import { configSchema as gff3TabixAdapterConfigSchema } from './Gff3TabixAdapter'
+import { FileLocation } from '@jbrowse/core/util/types'
+import {
+  makeIndex,
+  makeIndexType,
+  AdapterGuesser,
+  getFileName,
+} from '@jbrowse/core/util/tracks'
 import { configSchema as gff3AdapterConfigSchema } from './Gff3Adapter'
 
 export default class extends Plugin {
@@ -17,7 +24,33 @@ export default class extends Plugin {
             import('./Gff3TabixAdapter/Gff3TabixAdapter').then(r => r.default),
         }),
     )
-
+    pluginManager.addToExtensionPoint(
+      'Core-guessAdapterForLocation',
+      (adapterGuesser: AdapterGuesser) => {
+        return (
+          file: FileLocation,
+          index?: FileLocation,
+          adapterHint?: string,
+        ) => {
+          const regexGuess = /\.gff3?\.b?gz$/i
+          const adapterName = 'Gff3TabixAdapter'
+          const fileName = getFileName(file)
+          const indexName = index && getFileName(index)
+          if (regexGuess.test(fileName) || adapterHint === adapterName) {
+            return {
+              type: adapterName,
+              bamLocation: file,
+              gffGzLocation: file,
+              index: {
+                location: index || makeIndex(file, '.tbi'),
+                indexType: makeIndexType(indexName, 'CSI', 'TBI'),
+              },
+            }
+          }
+          return adapterGuesser(file, index, adapterHint)
+        }
+      },
+    )
     pluginManager.addAdapterType(
       () =>
         new AdapterType({
@@ -27,5 +60,26 @@ export default class extends Plugin {
             import('./Gff3Adapter/Gff3Adapter').then(r => r.default),
         }),
     )
+    pluginManager.addToExtensionPoint(
+      'Core-guessAdapterForLocation',
+      (adapterGuesser: AdapterGuesser) => {
+        return (
+          file: FileLocation,
+          index?: FileLocation,
+          adapterHint?: string,
+        ) => {
+          const regexGuess = /\.gff3?$/i
+          const adapterName = 'Gff3Adapter'
+          const fileName = getFileName(file)
+          if (regexGuess.test(fileName) || adapterHint === adapterName) {
+            return {
+              type: adapterName,
+              gffLocation: file,
+            }
+          }
+          return adapterGuesser(file, index, adapterHint)
+        }
+      },
+    )
   }
 }

package/dist/util.d.ts

@@ -1,14 +0,0 @@
-export declare type Strand = '+' | '-' | '.' | '?';
-export interface FeatureLoc {
-    [key: string]: unknown;
-    start: number;
-    end: number;
-    strand: Strand;
-    seq_id: string;
-    child_features: FeatureLoc[][];
-    data: unknown;
-    derived_features: unknown;
-    attributes: {
-        [key: string]: unknown[];
-    };
-}

package/src/declare.d.ts

@@ -1 +0,0 @@
-declare module '@gmod/gff'

package/src/util.ts

@@ -1,12 +0,0 @@
-export type Strand = '+' | '-' | '.' | '?'
-export interface FeatureLoc {
-  [key: string]: unknown
-  start: number
-  end: number
-  strand: Strand
-  seq_id: string
-  child_features: FeatureLoc[][]
-  data: unknown
-  derived_features: unknown
-  attributes: { [key: string]: unknown[] }
-}