@jbrowse/plugin-comparative-adapters 2.6.1 → 2.6.3

package/src/MCScanAnchorsAdapter/MCScanAnchorsAdapter.ts

@@ -1,134 +0,0 @@
-import {
-  BaseFeatureDataAdapter,
-  BaseOptions,
-} from '@jbrowse/core/data_adapters/BaseAdapter'
-import { openLocation } from '@jbrowse/core/util/io'
-import {
-  doesIntersect2,
-  SimpleFeature,
-  Feature,
-  Region,
-} from '@jbrowse/core/util'
-import { ObservableCreate } from '@jbrowse/core/util/rxjs'
-import { readFile, parseBed } from '../util'
-
-interface BareFeature {
-  strand: number
-  refName: string
-  start: number
-  end: number
-  score: number
-  name: string
-}
-
-type Row = [BareFeature, BareFeature, number, number]
-
-export default class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
-  private setupP?: Promise<{
-    assemblyNames: string[]
-    feats: Row[]
-  }>
-
-  public static capabilities = ['getFeatures', 'getRefNames']
-
-  async setup(opts: BaseOptions) {
-    if (!this.setupP) {
-      this.setupP = this.setupPre(opts).catch(e => {
-        this.setupP = undefined
-        throw e
-      })
-    }
-    return this.setupP
-  }
-  async setupPre(opts: BaseOptions) {
-    const assemblyNames = this.getConf('assemblyNames') as string[]
-
-    const pm = this.pluginManager
-    const bed1 = openLocation(this.getConf('bed1Location'), pm)
-    const bed2 = openLocation(this.getConf('bed2Location'), pm)
-    const mcscan = openLocation(this.getConf('mcscanAnchorsLocation'), pm)
-    const [bed1text, bed2text, mcscantext] = await Promise.all(
-      [bed1, bed2, mcscan].map(r => readFile(r, opts)),
-    )
-
-    const bed1Map = parseBed(bed1text)
-    const bed2Map = parseBed(bed2text)
-    const feats = mcscantext
-      .split(/\n|\r\n|\r/)
-      .filter(f => !!f && f !== '###')
-      .map((line, index) => {
-        const [name1, name2, score] = line.split('\t')
-        const r1 = bed1Map.get(name1)
-        const r2 = bed2Map.get(name2)
-        if (!r1 || !r2) {
-          throw new Error(`feature not found, ${name1} ${name2} ${r1} ${r2}`)
-        }
-        return [r1, r2, +score, index] as Row
-      })
-
-    return {
-      assemblyNames,
-      feats,
-    }
-  }
-
-  async hasDataForRefName() {
-    // determining this properly is basically a call to getFeatures
-    // so is not really that important, and has to be true or else
-    // getFeatures is never called (BaseFeatureDataAdapter filters it out)
-    return true
-  }
-
-  async getRefNames() {
-    // we cannot determine this accurately
-    return []
-  }
-
-  getFeatures(region: Region, opts: BaseOptions = {}) {
-    return ObservableCreate<Feature>(async observer => {
-      const { assemblyNames, feats } = await this.setup(opts)
-
-      // The index of the assembly name in the region list corresponds to
-      // the adapter in the subadapters list
-      const index = assemblyNames.indexOf(region.assemblyName)
-      if (index !== -1) {
-        const flip = index === 0
-        feats.forEach(f => {
-          const [r1, r2, score, rowNum] = f
-          const [f1, f2] = !flip ? [r2, r1] : [r1, r2]
-          if (
-            f1.refName === region.refName &&
-            doesIntersect2(region.start, region.end, f1.start, f1.end)
-          ) {
-            observer.next(
-              new SimpleFeature({
-                ...f1,
-                uniqueId: `${index}-${rowNum}`,
-                syntenyId: rowNum,
-
-                // note: strand would be -1 if the two features are on opposite
-                // strands, indicating inverted alignment
-                strand: f1.strand * f2.strand,
-                assemblyName: assemblyNames[+!flip],
-                score,
-                mate: {
-                  ...f2,
-                  assemblyName: assemblyNames[+flip],
-                },
-              }),
-            )
-          }
-        })
-      }
-
-      observer.complete()
-    })
-  }
-
-  /**
-   * called to provide a hint that data tied to a certain region
-   * will not be needed for the foreseeable future and can be purged
-   * from caches, etc
-   */
-  freeResources(/* { region } */): void {}
-}

package/src/MCScanAnchorsAdapter/configSchema.ts

@@ -1,52 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-
-/**
- * #config MCScanAnchorsAdapter
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const MCScanAnchorsAdapter = ConfigurationSchema(
-  'MCScanAnchorsAdapter',
-  {
-    /**
-     * #slot
-     */
-    mcscanAnchorsLocation: {
-      type: 'fileLocation',
-      defaultValue: {
-        uri: '/path/to/mcscan.anchors',
-        locationType: 'UriLocation',
-      },
-    },
-    /**
-     * #slot
-     */
-    bed1Location: {
-      type: 'fileLocation',
-      defaultValue: {
-        uri: '/path/to/file.bed',
-        locationType: 'UriLocation',
-      },
-    },
-    /**
-     * #slot
-     */
-    bed2Location: {
-      type: 'fileLocation',
-      defaultValue: {
-        uri: '/path/to/file.bed',
-        locationType: 'UriLocation',
-      },
-    },
-    /**
-     * #slot
-     */
-    assemblyNames: {
-      type: 'stringArray',
-      defaultValue: [],
-    },
-  },
-  { explicitlyTyped: true },
-)
-
-export default MCScanAnchorsAdapter

package/src/MCScanAnchorsAdapter/index.ts

@@ -1,20 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
-import configSchema from './configSchema'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addAdapterType(
-    () =>
-      new AdapterType({
-        name: 'MCScanAnchorsAdapter',
-        displayName: 'MCScan anchors adapter',
-        configSchema,
-        adapterMetadata: {
-          hiddenFromGUI: true,
-        },
-
-        getAdapterClass: () =>
-          import('./MCScanAnchorsAdapter').then(r => r.default),
-      }),
-  )
-}

package/src/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.ts

@@ -1,157 +0,0 @@
-import {
-  BaseFeatureDataAdapter,
-  BaseOptions,
-} from '@jbrowse/core/data_adapters/BaseAdapter'
-import { Region } from '@jbrowse/core/util/types'
-import { openLocation } from '@jbrowse/core/util/io'
-import { doesIntersect2 } from '@jbrowse/core/util'
-import { ObservableCreate } from '@jbrowse/core/util/rxjs'
-import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'
-import { readFile, parseBed } from '../util'
-
-interface BareFeature {
-  refName: string
-  start: number
-  end: number
-  score: number
-  name: string
-}
-
-type Row = [
-  BareFeature,
-  BareFeature,
-  BareFeature,
-  BareFeature,
-  number,
-  number,
-  number,
-]
-
-export default class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
-  private setupP?: Promise<{
-    assemblyNames: string[]
-    feats: Row[]
-  }>
-
-  public static capabilities = ['getFeatures', 'getRefNames']
-
-  async setup(opts: BaseOptions) {
-    if (!this.setupP) {
-      this.setupP = this.setupPre(opts).catch(e => {
-        this.setupP = undefined
-        throw e
-      })
-    }
-    return this.setupP
-  }
-  async setupPre(opts: BaseOptions) {
-    const assemblyNames = this.getConf('assemblyNames') as string[]
-    const pm = this.pluginManager
-    const bed1 = openLocation(this.getConf('bed1Location'), pm)
-    const bed2 = openLocation(this.getConf('bed2Location'), pm)
-    const mcscan = openLocation(this.getConf('mcscanSimpleAnchorsLocation'), pm)
-    const [bed1text, bed2text, mcscantext] = await Promise.all(
-      [bed1, bed2, mcscan].map(r => readFile(r, opts)),
-    )
-    const bed1Map = parseBed(bed1text)
-    const bed2Map = parseBed(bed2text)
-    const feats = mcscantext
-      .split(/\n|\r\n|\r/)
-      .filter(f => !!f && f !== '###')
-      .map((line, index) => {
-        const [n11, n12, n21, n22, score, strand] = line.split('\t')
-        const r11 = bed1Map.get(n11)
-        const r12 = bed1Map.get(n12)
-        const r21 = bed2Map.get(n21)
-        const r22 = bed2Map.get(n22)
-        if (!r11 || !r12 || !r21 || !r22) {
-          throw new Error(
-            `feature not found, ${n11} ${n12} ${n21} ${n22} ${r11} ${r12} ${r21} ${r22}`,
-          )
-        }
-        return [
-          r11,
-          r12,
-          r21,
-          r22,
-          +score,
-          strand === '-' ? -1 : 1,
-          index,
-        ] as Row
-      })
-
-    return {
-      assemblyNames,
-      feats,
-    }
-  }
-
-  async hasDataForRefName() {
-    // determining this properly is basically a call to getFeatures
-    // so is not really that important, and has to be true or else
-    // getFeatures is never called (BaseFeatureDataAdapter filters it out)
-    return true
-  }
-
-  async getRefNames() {
-    // we cannot determine this accurately
-    return []
-  }
-
-  getFeatures(region: Region, opts: BaseOptions = {}) {
-    return ObservableCreate<Feature>(async observer => {
-      const { assemblyNames, feats } = await this.setup(opts)
-
-      // The index of the assembly name in the region list corresponds to
-      // the adapter in the subadapters list
-      const index = assemblyNames.indexOf(region.assemblyName)
-      if (index !== -1) {
-        const flip = index === 0
-        feats.forEach(f => {
-          const [f11, f12, f21, f22, score, strand, rowNum] = f
-          let r1 = {
-            refName: f11.refName,
-            start: Math.min(f11.start, f12.start),
-            end: Math.max(f11.end, f12.end),
-          }
-          let r2 = {
-            refName: f21.refName,
-            start: Math.min(f21.start, f22.start),
-            end: Math.max(f21.end, f22.end),
-          }
-          if (!flip) {
-            ;[r2, r1] = [r1, r2]
-          }
-          if (
-            r1.refName === region.refName &&
-            doesIntersect2(r1.start, r1.end, region.start, region.end)
-          ) {
-            observer.next(
-              new SimpleFeature({
-                ...r1,
-                uniqueId: `${rowNum}`,
-                syntenyId: rowNum,
-                assemblyName: assemblyNames[+!flip],
-                score,
-                strand,
-                mate: {
-                  ...r2,
-                  assemblyName: assemblyNames[+flip],
-                },
-              }),
-            )
-          }
-        })
-      }
-
-      observer.complete()
-    })
-  }
-
-  /**
-   * called to provide a hint that data tied to a certain region
-   * will not be needed for the foreseeable future and can be purged
-   * from caches, etc
-   */
-  freeResources(/* { region } */): void {}
-}

package/src/MCScanSimpleAnchorsAdapter/configSchema.ts

@@ -1,52 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-
-/**
- * #config MCScanSimpleAnchorsAdapter
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const MCScanSimpleAnchorsAdapter = ConfigurationSchema(
-  'MCScanSimpleAnchorsAdapter',
-  {
-    /**
-     * #slot
-     */
-    mcscanSimpleAnchorsLocation: {
-      type: 'fileLocation',
-      defaultValue: {
-        uri: '/path/to/mcscan.anchors.simple',
-        locationType: 'UriLocation',
-      },
-    },
-    /**
-     * #slot
-     */
-    bed1Location: {
-      type: 'fileLocation',
-      defaultValue: {
-        uri: '/path/to/file.bed',
-        locationType: 'UriLocation',
-      },
-    },
-    /**
-     * #slot
-     */
-    bed2Location: {
-      type: 'fileLocation',
-      defaultValue: {
-        uri: '/path/to/file.bed',
-        locationType: 'UriLocation',
-      },
-    },
-
-    /**
-     * #slot
-     */
-    assemblyNames: {
-      type: 'stringArray',
-      defaultValue: [],
-    },
-  },
-  { explicitlyTyped: true },
-)
-export default MCScanSimpleAnchorsAdapter

package/src/MCScanSimpleAnchorsAdapter/index.ts

@@ -1,19 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
-import configSchema from './configSchema'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addAdapterType(
-    () =>
-      new AdapterType({
-        name: 'MCScanSimpleAnchorsAdapter',
-        displayName: 'MCScan anchors.simple adapter',
-        configSchema,
-        adapterMetadata: {
-          hiddenFromGUI: true,
-        },
-        getAdapterClass: () =>
-          import('./MCScanSimpleAnchorsAdapter').then(r => r.default),
-      }),
-  )
-}

package/src/MashMapAdapter/MashMapAdapter.ts

@@ -1,40 +0,0 @@
-import { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'
-import { openLocation } from '@jbrowse/core/util/io'
-import { unzip } from '@gmod/bgzf-filehandle'
-import PAFAdapter from '../PAFAdapter/PAFAdapter'
-import { parseLineByLine } from '../util'
-
-function isGzip(buf: Buffer) {
-  return buf[0] === 31 && buf[1] === 139 && buf[2] === 8
-}
-
-export default class MashMapAdapter extends PAFAdapter {
-  async setupPre(opts?: BaseOptions) {
-    const outLoc = openLocation(this.getConf('outLocation'), this.pluginManager)
-    const buffer = (await outLoc.readFile(opts)) as Buffer
-    const buf = isGzip(buffer) ? await unzip(buffer) : buffer
-    return parseLineByLine(buf, parseMashMapLine)
-  }
-}
-
-function parseMashMapLine(line: string) {
-  const fields = line.split(' ')
-  if (fields.length < 9) {
-    // xref https://github.com/marbl/MashMap/issues/38
-    throw new Error('improperly formatted line: ' + line)
-  }
-  const [qname, , qstart, qend, strand, tname, , tstart, tend, mq] = fields
-
-  return {
-    tname,
-    tstart: +tstart,
-    tend: +tend,
-    qname,
-    qstart: +qstart,
-    qend: +qend,
-    strand: strand === '-' ? -1 : 1,
-    extra: {
-      mappingQual: +mq,
-    },
-  }
-}

package/src/MashMapAdapter/configSchema.ts

@@ -1,51 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-
-/**
- * #config MashMapAdapter
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const MashMapAdapter = ConfigurationSchema(
-  'MashMapAdapter',
-  {
-    /**
-     * #slot
-     */
-    assemblyNames: {
-      type: 'stringArray',
-      defaultValue: [],
-      description:
-        'Target is the first value in the array, query is the second',
-    },
-
-    /**
-     * #slot
-     */
-    targetAssembly: {
-      type: 'string',
-      defaultValue: '',
-      description: 'Alternative to assemblyNames array: the target assembly',
-    },
-    /**
-     * #slot
-     */
-    queryAssembly: {
-      type: 'string',
-      defaultValue: '',
-      description: 'Alternative to assemblyNames array: the query assembly',
-    },
-    /**
-     * #slot
-     */
-    outLocation: {
-      type: 'fileLocation',
-      defaultValue: {
-        uri: '/path/to/mashmap.out',
-        locationType: 'UriLocation',
-      },
-    },
-  },
-  { explicitlyTyped: true },
-)
-
-export default MashMapAdapter

package/src/MashMapAdapter/index.ts

@@ -1,18 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
-import configSchema from './configSchema'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addAdapterType(
-    () =>
-      new AdapterType({
-        name: 'MashMapAdapter',
-        displayName: 'MashMap adapter',
-        configSchema,
-        adapterMetadata: {
-          hiddenFromGUI: true,
-        },
-        getAdapterClass: () => import('./MashMapAdapter').then(r => r.default),
-      }),
-  )
-}

package/src/PAFAdapter/PAFAdapter.test.ts

@@ -1,37 +0,0 @@
-import { toArray } from 'rxjs/operators'
-import { firstValueFrom } from 'rxjs'
-import Adapter from './PAFAdapter'
-import MyConfigSchema from './configSchema'
-
-test('adapter can fetch features from peach_grape.paf', async () => {
-  const adapter = new Adapter(
-    MyConfigSchema.create({
-      pafLocation: {
-        localPath: require.resolve('./test_data/peach_grape.paf'),
-        locationType: 'LocalPathLocation',
-      },
-      assemblyNames: ['peach', 'grape'],
-    }),
-  )
-
-  const features1 = adapter.getFeatures({
-    refName: 'Pp01',
-    start: 0,
-    end: 200000,
-    assemblyName: 'peach',
-  })
-
-  const features2 = adapter.getFeatures({
-    refName: 'chr1',
-    start: 0,
-    end: 200000,
-    assemblyName: 'grape',
-  })
-
-  const fa1 = await firstValueFrom(features1.pipe(toArray()))
-  const fa2 = await firstValueFrom(features2.pipe(toArray()))
-  expect(fa1.length).toBe(11)
-  expect(fa2.length).toBe(5)
-  expect(fa1[0].get('refName')).toBe('Pp01')
-  expect(fa2[0].get('refName')).toBe('chr1')
-})