@jbrowse/plugin-gff3 2.6.1 → 2.6.2

package/src/Gff3TabixAdapter/Gff3TabixAdapter.ts

@@ -1,260 +0,0 @@
-/* eslint-disable no-underscore-dangle */
-import {
-  BaseFeatureDataAdapter,
-  BaseOptions,
-} from '@jbrowse/core/data_adapters/BaseAdapter'
-import { doesIntersect2 } from '@jbrowse/core/util/range'
-import { Region } from '@jbrowse/core/util/types'
-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, { GFF3Feature, GFF3FeatureLineWithRefs } from '@gmod/gff'
-import { Observer } from 'rxjs'
-import {
-  readConfObject,
-  AnyConfigurationModel,
-} from '@jbrowse/core/configuration'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
-
-interface LineFeature {
-  start: number
-  end: number
-  lineHash: number
-  fields: string[]
-}
-
-export default class extends BaseFeatureDataAdapter {
-  protected gff: TabixIndexedFile
-
-  protected dontRedispatch: string[]
-
-  public constructor(
-    config: AnyConfigurationModel,
-    getSubAdapter?: getSubAdapterType,
-    pluginManager?: PluginManager,
-  ) {
-    super(config, getSubAdapter, pluginManager)
-    const gffGzLocation = readConfObject(config, 'gffGzLocation')
-    const indexType = readConfObject(config, ['index', 'indexType'])
-    const location = readConfObject(config, ['index', 'location'])
-    const dontRedispatch = readConfObject(config, 'dontRedispatch')
-
-    this.dontRedispatch = dontRedispatch || ['chromosome', 'contig', 'region']
-    this.gff = new TabixIndexedFile({
-      filehandle: openLocation(gffGzLocation, this.pluginManager),
-      csiFilehandle:
-        indexType === 'CSI'
-          ? openLocation(location, this.pluginManager)
-          : undefined,
-      tbiFilehandle:
-        indexType !== 'CSI'
-          ? openLocation(location, this.pluginManager)
-          : undefined,
-      chunkCacheSize: 50 * 2 ** 20,
-      renameRefSeqs: (n: string) => n,
-    })
-  }
-
-  public async getRefNames(opts: BaseOptions = {}) {
-    return this.gff.getReferenceSequenceNames(opts)
-  }
-
-  public async getHeader() {
-    return this.gff.getHeader()
-  }
-
-  public getFeatures(query: Region, opts: BaseOptions = {}) {
-    return ObservableCreate<Feature>(async observer => {
-      const metadata = await this.gff.getMetadata()
-      await this.getFeaturesHelper(query, opts, metadata, observer, true)
-    }, opts.signal)
-  }
-
-  private async getFeaturesHelper(
-    query: Region,
-    opts: BaseOptions = {},
-    metadata: { columnNumbers: { start: number; end: number } },
-    observer: Observer<Feature>,
-    allowRedispatch: boolean,
-    originalQuery = query,
-  ) {
-    try {
-      const lines: LineFeature[] = []
-
-      await this.gff.getLines(
-        query.refName,
-        query.start,
-        query.end,
-        (line: string, fileOffset: number) => {
-          lines.push(this.parseLine(metadata.columnNumbers, line, fileOffset))
-        },
-      )
-      if (allowRedispatch && lines.length) {
-        let minStart = Infinity
-        let maxEnd = -Infinity
-        lines.forEach(line => {
-          const featureType = line.fields[2]
-          // only expand redispatch range if feature is not a "dontRedispatch" type
-          // skips large regions like chromosome,region
-          if (!this.dontRedispatch.includes(featureType)) {
-            const start = line.start - 1 // gff is 1-based
-            if (start < minStart) {
-              minStart = start
-            }
-            if (line.end > maxEnd) {
-              maxEnd = line.end
-            }
-          }
-        })
-        if (maxEnd > query.end || minStart < query.start) {
-          // make a new feature callback to only return top-level features
-          // in the original query range
-          await this.getFeaturesHelper(
-            { ...query, start: minStart, end: maxEnd },
-            opts,
-            metadata,
-            observer,
-            false,
-            query,
-          )
-          return
-        }
-      }
-
-      const gff3 = lines
-        .map((lineRecord: LineFeature) => {
-          if (lineRecord.fields[8] && lineRecord.fields[8] !== '.') {
-            if (!lineRecord.fields[8].includes('_lineHash')) {
-              lineRecord.fields[8] += `;_lineHash=${lineRecord.lineHash}`
-            }
-          } else {
-            lineRecord.fields[8] = `_lineHash=${lineRecord.lineHash}`
-          }
-          return lineRecord.fields.join('\t')
-        })
-        .join('\n')
-
-      const features = gff.parseStringSync(gff3, {
-        parseFeatures: true,
-        parseComments: false,
-        parseDirectives: false,
-        parseSequences: false,
-        disableDerivesFromReferences: true,
-      })
-
-      features.forEach(featureLocs =>
-        this.formatFeatures(featureLocs).forEach(f => {
-          if (
-            doesIntersect2(
-              f.get('start'),
-              f.get('end'),
-              originalQuery.start,
-              originalQuery.end,
-            )
-          ) {
-            observer.next(f)
-          }
-        }),
-      )
-      observer.complete()
-    } catch (e) {
-      observer.error(e)
-    }
-  }
-
-  private parseLine(
-    columnNumbers: { start: number; end: number },
-    line: string,
-    fileOffset: number,
-  ) {
-    const fields = line.split('\t')
-
-    // note: index column numbers are 1-based
-    return {
-      start: +fields[columnNumbers.start - 1],
-      end: +fields[columnNumbers.end - 1],
-      lineHash: fileOffset,
-      fields,
-    }
-  }
-
-  private formatFeatures(featureLocs: GFF3Feature) {
-    return featureLocs.map(
-      featureLoc =>
-        new SimpleFeature({
-          data: this.featureData(featureLoc),
-          // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
-          id: `${this.id}-offset-${featureLoc.attributes!._lineHash![0]}`,
-        }),
-    )
-  }
-
-  private featureData(data: GFF3FeatureLineWithRefs) {
-    const f: Record<string, unknown> = { ...data }
-    ;(f.start as number) -= 1 // convert to interbase
-    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) {
-      delete f.score
-    }
-    if (data.phase === null) {
-      delete f.score
-    }
-    const defaultFields = new Set([
-      'start',
-      'end',
-      'seq_id',
-      'score',
-      'type',
-      'source',
-      'phase',
-      'strand',
-    ])
-    const dataAttributes = data.attributes || {}
-    for (const a of Object.keys(dataAttributes)) {
-      let b = a.toLowerCase()
-      if (defaultFields.has(b)) {
-        // add "suffix" to tag name if it already exists
-        // reproduces behavior of NCList
-        b += '2'
-      }
-      if (dataAttributes[a] !== null) {
-        let attr: string | string[] | undefined = dataAttributes[a]
-        if (Array.isArray(attr) && attr.length === 1) {
-          ;[attr] = attr
-        }
-        f[b] = attr
-      }
-    }
-    f.refName = f.seq_id
-
-    // the SimpleFeature constructor takes care of recursively inflating subfeatures
-    if (data.child_features && data.child_features.length > 0) {
-      f.subfeatures = data.child_features.flatMap(childLocs =>
-        childLocs.map(childLoc => this.featureData(childLoc)),
-      )
-    }
-
-    delete f.child_features
-    delete f.data
-    // delete f.derived_features
-    delete f._linehash
-    delete f.attributes
-    delete f.seq_id
-
-    return f
-  }
-
-  public freeResources(/* { region } */) {}
-}

package/src/Gff3TabixAdapter/__snapshots__/Gff3TabixAdapter.test.ts.snap

@@ -1,57 +0,0 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
-
-exports[`adapter can fetch features from volvox.gff3 test getfeatures on gff plain text adapter 1`] = `
-[
-  {
-    "derived_features": [],
-    "end": 6079,
-    "name": "ctgB",
-    "phase": 0,
-    "refName": "ctgB",
-    "source": "example",
-    "start": 0,
-    "strand": undefined,
-    "type": "contig",
-    "uniqueId": "test-offset-794328",
-  },
-  {
-    "derived_features": [],
-    "end": 1984,
-    "name": "f07",
-    "note": "This is an example",
-    "phase": 0,
-    "refName": "ctgB",
-    "source": "example",
-    "start": 1658,
-    "strand": 1,
-    "type": "remark",
-    "uniqueId": "test-offset-794371",
-  },
-  {
-    "derived_features": [],
-    "end": 6130,
-    "name": "f06",
-    "note": "This is another example",
-    "phase": 0,
-    "refName": "ctgB",
-    "source": "example",
-    "start": 3013,
-    "strand": 1,
-    "type": "remark",
-    "uniqueId": "test-offset-794440",
-  },
-  {
-    "derived_features": [],
-    "end": 5968,
-    "name": "f05",
-    "note": "ああ、この機能は、世界中を旅しています！",
-    "phase": 0,
-    "refName": "ctgB",
-    "source": "example",
-    "start": 4714,
-    "strand": -1,
-    "type": "remark",
-    "uniqueId": "test-offset-794514",
-  },
-]
-`;

package/src/Gff3TabixAdapter/configSchema.ts

@@ -1,56 +0,0 @@
-import { types } from 'mobx-state-tree'
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-
-/**
- * #config Gff3TabixAdapter
- * #category adapter
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const Gff3TabixAdapter = ConfigurationSchema(
-  'Gff3TabixAdapter',
-  {
-    /**
-     * #slot
-     */
-    gffGzLocation: {
-      type: 'fileLocation',
-      defaultValue: { uri: '/path/to/my.gff.gz', locationType: 'UriLocation' },
-    },
-
-    index: ConfigurationSchema('Gff3TabixIndex', {
-      /**
-       * #slot index.indexType
-       */
-      indexType: {
-        model: types.enumeration('IndexType', ['TBI', 'CSI']),
-        type: 'stringEnum',
-        defaultValue: 'TBI',
-      },
-      /**
-       * #slot index.indexType
-       */
-      location: {
-        type: 'fileLocation',
-        defaultValue: {
-          uri: '/path/to/my.gff.gz.tbi',
-          locationType: 'UriLocation',
-        },
-      },
-    }),
-    /**
-     * #slot
-     * the Gff3TabixAdapter has to "redispatch" if it fetches a region and
-     * features it finds inside that region extend outside the region we requested.
-     * you can disable this for certain feature types to avoid fetching e.g. the
-     * entire chromosome
-     */
-    dontRedispatch: {
-      type: 'stringArray',
-      defaultValue: ['chromosome', 'region'],
-    },
-  },
-  { explicitlyTyped: true },
-)
-
-export default Gff3TabixAdapter

package/src/Gff3TabixAdapter/index.ts

@@ -1,16 +0,0 @@
-import { AdapterType } from '@jbrowse/core/pluggableElementTypes'
-import PluginManager from '@jbrowse/core/PluginManager'
-import configSchema from './configSchema'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addAdapterType(
-    () =>
-      new AdapterType({
-        name: 'Gff3TabixAdapter',
-        displayName: 'GFF3 tabix adapter',
-        configSchema,
-        getAdapterClass: () =>
-          import('./Gff3TabixAdapter').then(r => r.default),
-      }),
-  )
-}

package/src/GuessGff3/index.ts

@@ -1,63 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import { FileLocation } from '@jbrowse/core/util/types'
-import {
-  makeIndex,
-  makeIndexType,
-  getFileName,
-  AdapterGuesser,
-} from '@jbrowse/core/util/tracks'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addToExtensionPoint(
-    'Core-guessAdapterForLocation',
-    (adapterGuesser: AdapterGuesser) => {
-      return (
-        file: FileLocation,
-        index?: FileLocation,
-        adapterHint?: string,
-      ) => {
-        const regexGuess = /\.gff3?\.b?gz$/i
-        const adapterName = 'Gff3TabixAdapter'
-        const fileName = getFileName(file)
-        const indexName = index && getFileName(index)
-        if (regexGuess.test(fileName) || adapterHint === adapterName) {
-          return {
-            type: adapterName,
-            bamLocation: file,
-            gffGzLocation: file,
-            index: {
-              location: index || makeIndex(file, '.tbi'),
-              indexType: makeIndexType(indexName, 'CSI', 'TBI'),
-            },
-          }
-        }
-        return adapterGuesser(file, index, adapterHint)
-      }
-    },
-  )
-
-  pluginManager.addToExtensionPoint(
-    'Core-guessAdapterForLocation',
-    (adapterGuesser: AdapterGuesser) => {
-      return (
-        file: FileLocation,
-        index?: FileLocation,
-        adapterHint?: string,
-      ) => {
-        const regexGuess = /\.gff3?$/i
-        const adapterName = 'Gff3Adapter'
-        const fileName = getFileName(file)
-        const obj = {
-          type: adapterName,
-          gffLocation: file,
-        }
-        if (regexGuess.test(fileName) && !adapterHint) {
-          return obj
-        } else if (adapterHint === adapterName) {
-          return obj
-        }
-        return adapterGuesser(file, index, adapterHint)
-      }
-    },
-  )
-}

package/src/index.ts

@@ -1,16 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import Plugin from '@jbrowse/core/Plugin'
-
-import Gff3TabixAdapterF from './Gff3TabixAdapter'
-import Gff3AdapterF from './Gff3Adapter'
-import GuessGff3F from './GuessGff3'
-
-export default class extends Plugin {
-  name = 'GFF3Plugin'
-
-  install(pluginManager: PluginManager) {
-    Gff3TabixAdapterF(pluginManager)
-    Gff3AdapterF(pluginManager)
-    GuessGff3F(pluginManager)
-  }
-}