jbrowse-plugin-msaview 2.5.2 → 2.6.0

package/dist/LaunchMsaViewExtensionPoint/index.js

@@ -1,8 +1,8 @@
 export default function LaunchMsaViewExtensionPointF(pluginManager) {
     pluginManager.addToExtensionPoint('LaunchView-MsaView', 
     // @ts-expect-error
-    ({ session, data, msaFileLocation, treeFileLocation, connectedViewId, connectedFeature, displayName, colorSchemeName, colWidth, rowHeight, treeAreaWidth, treeWidth, drawNodeBubbles, labelsAlignRight, showBranchLen, querySeqName, highlightColumns, }) => {
-        if (!data && !msaFileLocation) {
+    ({ session, data, msaFileLocation, msaTabixLocation, msaIndexLocation, msaId, treeFileLocation, connectedViewId, connectedFeature, displayName, colorSchemeName, colWidth, rowHeight, treeAreaWidth, treeWidth, drawNodeBubbles, labelsAlignRight, showBranchLen, querySeqName, highlightColumns, }) => {
+        if (!data && !msaFileLocation && !msaTabixLocation) {
             throw new Error('No MSA data or file location provided when launching MSA view');
         }
         session.addView('MsaView', {
@@ -23,6 +23,9 @@ export default function LaunchMsaViewExtensionPointF(pluginManager) {
                 msaData: data?.msa,
                 treeData: data?.tree,
                 msaUrl: msaFileLocation?.uri,
+                msaTabixLocation,
+                msaIndexLocation,
+                msaId,
                 treeUrl: treeFileLocation?.uri,
                 querySeqName,
             },

package/dist/MsaViewPanel/afterCreateAutoruns.js

@@ -1,5 +1,6 @@
 import { getSession } from '@jbrowse/core/util';
 import { doLaunchBlast } from './doLaunchBlast';
+import { fetchTabixMsa } from './fetchTabixMsa';
 import { genomeToMSA } from './genomeToMSA';
 import { loadProteinDomains } from './loadProteinDomains';
 import { cleanupOldData, generateDataStoreId, retrieveMsaData, storeMsaData, } from './msaDataStore';
@@ -121,7 +122,7 @@ export function processInit(self) {
         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);
                     if (id) {
@@ -143,6 +144,25 @@ export function processInit(self) {
                     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) {
                     self.setTree(treeData);
                 }

package/dist/MsaViewPanel/fetchTabixMsa.d.ts

@@ -0,0 +1,12 @@
+export declare function fetchTabixMsa({ location, indexLocation, msaId, refName, start, end, }: {
+    location: {
+        uri: string;
+    };
+    indexLocation?: {
+        uri: string;
+    };
+    msaId: string;
+    refName: string;
+    start: number;
+    end: number;
+}): Promise<string | undefined>;

package/dist/MsaViewPanel/fetchTabixMsa.js

@@ -0,0 +1,33 @@
+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, }) {
+    const uri = (loc) => openLocation({ uri: loc.uri, locationType: 'UriLocation' });
+    const file = new TabixIndexedFile({
+        filehandle: uri(location),
+        csiFilehandle: uri(indexLocation ?? { uri: `${location.uri}.csi` }),
+    });
+    const lines = [];
+    await file.getLines(refName, start, end, {
+        lineCallback: line => {
+            lines.push(line);
+        },
+    });
+    const line = lines.find(l => l.split('\t')[3] === msaId);
+    return line ? unpack(line) : undefined;
+}
+function unpack(line) {
+    const packed = line.split('\t')[4] ?? '';
+    return packed
+        .split(';')
+        .filter(Boolean)
+        .map(pair => {
+        const colon = pair.indexOf(':');
+        return `>${pair.slice(0, colon)}\n${pair.slice(colon + 1)}`;
+    })
+        .join('\n');
+}

package/dist/MsaViewPanel/types.d.ts

@@ -1,6 +1,13 @@
 export interface MsaViewInitState {
     msaData?: string;
     msaUrl?: string;
+    msaTabixLocation?: {
+        uri: string;
+    };
+    msaIndexLocation?: {
+        uri: string;
+    };
+    msaId?: string;
     treeData?: string;
     treeUrl?: string;
     querySeqName?: string;