jbrowse-plugin-protein3d 0.0.2

package/src/declare.d.ts

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+declare module '*.json'

package/src/fetchUtils.ts

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+export async function myfetch(url: string, args?: RequestInit) {
+  const response = await fetch(url, args)
+
+  if (!response.ok) {
+    throw new Error(
+      `HTTP ${response.status} fetching ${url} ${await response.text()}`,
+    )
+  }
+
+  return response
+}
+
+export async function textfetch(url: string, args?: RequestInit) {
+  const response = await myfetch(url, args)
+  return response.text()
+}
+
+export async function jsonfetch(url: string, args?: RequestInit) {
+  const response = await myfetch(url, args)
+  return response.json()
+}
+
+export async function abfetch(url: string) {
+  const res = await myfetch(url)
+  return res.arrayBuffer()
+}
+
+export function timeout(time: number) {
+  return new Promise(res => setTimeout(res, time))
+}

package/src/genomeToTranscriptMapping.ts

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+import { Feature } from '@jbrowse/core/util'
+
+// see similar function in msaview plugin
+export function genomeToTranscriptMapping(feature: Feature) {
+  const strand = feature.get('strand') as number
+  const refName = feature.get('refName')
+  const subs = feature.children() ?? []
+  const cds = subs
+    .filter(f => f.get('type') === 'CDS')
+    .sort((a, b) => strand * (a.get('start') - b.get('start')))
+  const g2p = {} as Record<number, number | undefined>
+  const p2g = {} as Record<number, number | undefined>
+
+  let proteinCounter = 0
+  if (strand !== -1) {
+    for (const f of cds) {
+      for (
+        let genomePos = f.get('start');
+        genomePos < f.get('end');
+        genomePos++
+      ) {
+        const proteinPos = Math.floor(proteinCounter++ / 3)
+        g2p[genomePos] = proteinPos
+        if (!p2g[proteinPos]) {
+          p2g[proteinPos] = genomePos
+        }
+      }
+    }
+  } else {
+    for (const f of cds) {
+      for (
+        let genomePos = f.get('end');
+        genomePos > f.get('start');
+        genomePos--
+      ) {
+        const proteinPos = Math.floor(proteinCounter++ / 3)
+        g2p[genomePos] = proteinPos
+        if (!p2g[proteinPos]) {
+          p2g[proteinPos] = genomePos
+        }
+      }
+    }
+  }
+
+  return { g2p, p2g, refName, strand }
+}

package/src/index.ts

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+import Plugin from '@jbrowse/core/Plugin'
+import PluginManager from '@jbrowse/core/PluginManager'
+import { types } from 'mobx-state-tree'
+// locals
+import { version } from '../package.json'
+import ProteinViewF from './ProteinView'
+import LaunchProteinViewF from './LaunchProteinView'
+import AddHighlightModelF from './AddHighlightModel'
+import ProteinModelSessionExtension from './ProteinModelSessionExtension'
+
+export default class ProteinViewer extends Plugin {
+  name = 'ProteinViewer'
+  version = version
+
+  install(pluginManager: PluginManager) {
+    ProteinViewF(pluginManager)
+    LaunchProteinViewF(pluginManager)
+    AddHighlightModelF(pluginManager)
+
+    pluginManager.addToExtensionPoint('Core-extendSession', session => {
+      return types.compose(
+        types.model({
+          proteinModel: types.optional(ProteinModelSessionExtension, {}),
+        }),
+        // @ts-expect-error
+        session,
+      )
+    })
+  }
+
+  configure(_pluginManager: PluginManager) {}
+}

package/src/mappings.test.ts

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+import {
+  genomeToTranscriptSeqMapping,
+  structureSeqVsTranscriptSeqMap,
+} from './mappings'
+import { SimpleFeature } from '@jbrowse/core/util'
+import { feature, alignment } from './test_data/gene'
+
+test('test', () => {
+  const ret = structureSeqVsTranscriptSeqMap(alignment)
+  expect(ret).toMatchSnapshot()
+})
+
+test('mapping', () => {
+  const res = genomeToTranscriptSeqMapping(new SimpleFeature(feature))
+  const { p2g } = res
+  const aln = structureSeqVsTranscriptSeqMap(alignment)
+
+  // expected position in sequence
+  const s2 = alignment.alns[1].seq
+  expect(s2[392]).toBe('M')
+  expect(s2[393]).toBe('K')
+  expect(s2[394]).toBe('A')
+  expect(s2[395]).toBe('A')
+  // maps the 392 position in the "pdb version of the protein" to the 0th
+  // position in the genome version of the protein, and then maps that back to
+  // the genome
+  const p0 = aln.structureSeqToTranscriptSeqPosition[392]!
+  const g0 = p2g[p0]
+  expect(p0).toBe(0)
+  expect(g0).toBe(51_296_155)
+  expect(res).toMatchSnapshot()
+})

package/src/mappings.ts

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+import { Feature } from '@jbrowse/core/util'
+import { genomeToTranscriptSeqMapping as g2p } from 'g2p_mapper'
+
+export interface Alignment {
+  alns: {
+    id: string
+    seq: string
+  }[]
+}
+
+export function structureSeqVsTranscriptSeqMap(alignment: Alignment) {
+  const structureSeq = alignment.alns[0].seq
+  const transcriptSeq = alignment.alns[1].seq
+  if (structureSeq.length !== transcriptSeq.length) {
+    throw new Error('mismatched length')
+  }
+
+  let j = 0
+  let k = 0
+  const structureSeqToTranscriptSeqPosition = {} as Record<
+    string,
+    number | undefined
+  >
+  const transcriptSeqToStructureSeqPosition = {} as Record<
+    string,
+    number | undefined
+  >
+
+  // eslint-disable-next-line unicorn/no-for-loop
+  for (let i = 0; i < structureSeq.length; i++) {
+    const c1 = structureSeq[i]
+    const c2 = transcriptSeq[i]
+
+    if (c1 === c2) {
+      structureSeqToTranscriptSeqPosition[j] = k
+      transcriptSeqToStructureSeqPosition[k] = j
+      k++
+      j++
+    } else if (c2 === '-') {
+      j++
+    } else if (c1 === '-') {
+      k++
+    } else {
+      structureSeqToTranscriptSeqPosition[j] = k
+      transcriptSeqToStructureSeqPosition[k] = j
+
+      k++
+      j++
+    }
+  }
+  return {
+    structureSeqToTranscriptSeqPosition,
+    transcriptSeqToStructureSeqPosition,
+  }
+}
+
+export function structurePositionToAlignmentMap(alignment: Alignment) {
+  const structureSeq = alignment.alns[0].seq
+  const structurePositionToAlignment = {} as Record<string, number | undefined>
+
+  for (let i = 0, j = 0; i < structureSeq.length; i++) {
+    if (structureSeq[i] !== '-') {
+      structurePositionToAlignment[j] = i
+      j++
+    }
+  }
+
+  return structurePositionToAlignment
+}
+
+export function transcriptPositionToAlignmentMap(alignment: Alignment) {
+  const transcriptSeq = alignment.alns[1].seq
+  const transcriptPositionToAlignment = {} as Record<string, number | undefined>
+
+  for (let i = 0, j = 0; i < transcriptSeq.length; i++) {
+    if (transcriptSeq[i] !== '-') {
+      transcriptPositionToAlignment[j] = i
+      j++
+    }
+  }
+
+  return transcriptPositionToAlignment
+}
+
+// see similar function in msaview plugin
+export function genomeToTranscriptSeqMapping(feature: Feature) {
+  // @ts-expect-error
+  return g2p(feature.toJSON())
+}