jbrowse-plugin-msaview 2.5.2 → 2.6.0

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "2.5.2";
+export declare const version = "2.6.0";

package/dist/version.js

@@ -1 +1 @@
-export const version = '2.5.2';
+export const version = '2.6.0';

package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "2.5.2",
+  "version": "2.6.0",
   "license": "MIT",
   "name": "jbrowse-plugin-msaview",
   "repository": {
@@ -17,6 +17,7 @@
   ],
   "dependencies": {
     "@emotion/styled": "^11.14.1",
+    "@gmod/tabix": "^3.0.1",
     "g2p_mapper": "^2.1.5",
     "idb": "^8.0.3",
     "pako-esm2": "^2.0.2",

package/src/LaunchMsaViewExtensionPoint/index.ts

@@ -11,6 +11,9 @@ export default function LaunchMsaViewExtensionPointF(
       session,
       data,
       msaFileLocation,
+      msaTabixLocation,
+      msaIndexLocation,
+      msaId,
       treeFileLocation,
       connectedViewId,
       connectedFeature,
@@ -29,6 +32,9 @@ export default function LaunchMsaViewExtensionPointF(
       session: AbstractSessionModel
       data?: { msa: string; tree?: string }
       msaFileLocation?: { uri: string }
+      msaTabixLocation?: { uri: string }
+      msaIndexLocation?: { uri: string }
+      msaId?: string
       treeFileLocation?: { uri: string }
       connectedViewId?: string
       connectedFeature?: Record<string, unknown>
@@ -44,7 +50,7 @@ export default function LaunchMsaViewExtensionPointF(
       querySeqName?: string
       highlightColumns?: number[]
     }) => {
-      if (!data && !msaFileLocation) {
+      if (!data && !msaFileLocation && !msaTabixLocation) {
         throw new Error(
           'No MSA data or file location provided when launching MSA view',
         )
@@ -68,6 +74,9 @@ export default function LaunchMsaViewExtensionPointF(
           msaData: data?.msa,
           treeData: data?.tree,
           msaUrl: msaFileLocation?.uri,
+          msaTabixLocation,
+          msaIndexLocation,
+          msaId,
           treeUrl: treeFileLocation?.uri,
           querySeqName,
         },

package/src/MsaViewPanel/afterCreateAutoruns.ts

@@ -1,6 +1,7 @@
 import { getSession } from '@jbrowse/core/util'
 
 import { doLaunchBlast } from './doLaunchBlast'
+import { fetchTabixMsa } from './fetchTabixMsa'
 import { genomeToMSA } from './genomeToMSA'
 import { loadProteinDomains } from './loadProteinDomains'
 import {
@@ -133,7 +134,16 @@ export function processInit(self: JBrowsePluginMsaViewModel) {
     void (async () => {
       try {
         self.setError(undefined)
-        const { msaData, msaUrl, treeData, treeUrl, querySeqName } = init
+        const {
+          msaData,
+          msaUrl,
+          msaTabixLocation,
+          msaIndexLocation,
+          msaId,
+          treeData,
+          treeUrl,
+          querySeqName,
+        } = init
 
         if (msaUrl) {
           const id = getUniprotIdFromAlphaFoldUrl(msaUrl)
@@ -156,6 +166,25 @@ export function processInit(self: JBrowsePluginMsaViewModel) {
           }
           const data = await response.text()
           self.setMSA(data)
+        } else if (msaTabixLocation) {
+          const feature = self.connectedFeature
+          if (feature) {
+            const fasta = await fetchTabixMsa({
+              location: msaTabixLocation,
+              indexLocation: msaIndexLocation,
+              msaId: msaId ?? String(feature.name),
+              refName: String(feature.refName),
+              start: Number(feature.start),
+              end: Number(feature.end),
+            })
+            if (fasta) {
+              self.setMSA(fasta)
+            } else {
+              throw new Error(
+                `No alignment for ${msaId ?? String(feature.name)} in ${msaTabixLocation.uri}`,
+              )
+            }
+          }
         }
 
         if (treeData) {

package/src/MsaViewPanel/fetchTabixMsa.ts

@@ -0,0 +1,50 @@
+import { TabixIndexedFile } from '@gmod/tabix'
+import { openLocation } from '@jbrowse/core/util/io'
+
+// Pull one transcript's whole multiple-alignment out of a locus-keyed tabix
+// file. Each line is `refName<TAB>start<TAB>end<TAB>msaId<TAB>packed`, where
+// `packed` is `name:SEQ;name:SEQ;...` — no newlines, so the alignment survives
+// as a single tabix column. We query the transcript's genomic locus, then pick
+// the line whose msaId matches, and rebuild a FASTA string.
+export async function fetchTabixMsa({
+  location,
+  indexLocation,
+  msaId,
+  refName,
+  start,
+  end,
+}: {
+  location: { uri: string }
+  indexLocation?: { uri: string }
+  msaId: string
+  refName: string
+  start: number
+  end: number
+}) {
+  const uri = (loc: { uri: string }) =>
+    openLocation({ uri: loc.uri, locationType: 'UriLocation' as const })
+  const file = new TabixIndexedFile({
+    filehandle: uri(location),
+    csiFilehandle: uri(indexLocation ?? { uri: `${location.uri}.csi` }),
+  })
+  const lines: string[] = []
+  await file.getLines(refName, start, end, {
+    lineCallback: line => {
+      lines.push(line)
+    },
+  })
+  const line = lines.find(l => l.split('\t')[3] === msaId)
+  return line ? unpack(line) : undefined
+}
+
+function unpack(line: string) {
+  const packed = line.split('\t')[4] ?? ''
+  return packed
+    .split(';')
+    .filter(Boolean)
+    .map(pair => {
+      const colon = pair.indexOf(':')
+      return `>${pair.slice(0, colon)}\n${pair.slice(colon + 1)}`
+    })
+    .join('\n')
+}

package/src/MsaViewPanel/types.ts

@@ -1,6 +1,14 @@
 export interface MsaViewInitState {
   msaData?: string
   msaUrl?: string
+  // a tabix file keyed by genomic locus, where each line packs one transcript's
+  // whole multiple-alignment (`name:SEQ;name:SEQ;...`). The transcript's locus
+  // comes from the view's connectedFeature, and `msaId` (default the feature's
+  // name) selects its line. Lets one genome-scale alignment serve any gene
+  // without per-gene files. See react-msaview's gene-explorer.
+  msaTabixLocation?: { uri: string }
+  msaIndexLocation?: { uri: string }
+  msaId?: string
   treeData?: string
   treeUrl?: string
   querySeqName?: string

package/src/version.ts

@@ -1 +1 @@
-export const version = '2.5.2'
+export const version = '2.6.0'