gramene-search 2.26.0 → 2.28.0

package/dist/index.js

@@ -11485,6 +11485,110 @@ var $527ebc19dc92444d$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.conn
 
 
 
+/**
+ * Gene models for the primer designer's variant browser.
+ *
+ * `/primers` has no genes-in-region endpoint — it can only fetch a gene by id —
+ * so the designer takes this from its host. Ensembl REST's `overlap/region`
+ * returns genes, transcripts, exons and CDS for a window in one request, all in
+ * genomic coordinates, which is exactly what the browser draws.
+ *
+ * Read from `config.ensemblRest`, which must be the same Ensembl release the
+ * primers API reads variants from (release 115 for sorghum_v11). A different
+ * release would draw gene models that do not line up with the variants beside
+ * them.
+ */ /**
+ * Beyond this the response runs to thousands of features and the models would
+ * be too small to read, so the track is simply left empty.
+ */ const $31284fcdc45a1688$var$MAX_SPAN = 1000000;
+function $31284fcdc45a1688$export$3a249e9030170bda(ensemblRest) {
+    if (!ensemblRest) return undefined;
+    return async ({ system_name: system_name, region: region, start: start, end: end }, options)=>{
+        if (!system_name || !region || end - start + 1 > $31284fcdc45a1688$var$MAX_SPAN) return [];
+        const signal = options && options.signal;
+        const url = `${ensemblRest}/overlap/region/${encodeURIComponent(system_name)}/${encodeURIComponent(region)}:${start}-${end}` + `?feature=gene;feature=transcript;feature=exon;feature=cds;content-type=application/json`;
+        const res = await fetch(url, {
+            headers: {
+                Accept: 'application/json'
+            },
+            signal: signal
+        });
+        if (!res.ok) throw new Error(`HTTP ${res.status}`);
+        const features = await res.json();
+        if (!Array.isArray(features)) return [];
+        const of = (type)=>features.filter((f)=>f && f.feature_type === type);
+        const transcripts = of('transcript');
+        const exons = of('exon');
+        const cds = of('cds');
+        return of('gene').map((gene)=>{
+            // One transcript per gene: the canonical one when Ensembl marks it.
+            const mine = transcripts.filter((t)=>t.Parent === gene.id);
+            const transcript = mine.find((t)=>t.is_canonical) || mine[0];
+            const myExons = transcript ? exons.filter((e)=>e.Parent === transcript.id) : [];
+            const myCds = transcript ? cds.filter((c)=>c.Parent === transcript.id) : [];
+            return {
+                id: gene.id,
+                label: gene.external_name || gene.id,
+                start: gene.start,
+                end: gene.end,
+                strand: gene.strand === -1 ? -1 : 1,
+                // Ensembl returns only the exons overlapping the window, which is all
+                // the browser can show anyway.
+                exons: myExons.map((e)=>({
+                        start: e.start,
+                        end: e.end
+                    })),
+                cds: myCds.length ? {
+                    start: Math.min(...myCds.map((c)=>c.start)),
+                    end: Math.max(...myCds.map((c)=>c.end))
+                } : null,
+                biotype: gene.biotype
+            };
+        });
+    };
+}
+
+
+/**
+ * Reference sequence for the primer designer's CAPS annotation.
+ *
+ * A variant listing from `/primers` carries coordinates and alleles but no
+ * bases, and restriction sites cannot be found without them, so the designer
+ * takes sequence from its host. Ensembl REST's `sequence/region` returns the
+ * plus strand of a window as `{molecule, seq, id, query}`.
+ *
+ * Read from `config.ensemblRest`, which must be the same Ensembl release the
+ * primers API reads variants from (release 115 for sorghum_v11). This matters
+ * more here than it does for the gene track: a gene model from the wrong
+ * release is visibly out of place, whereas sequence from the wrong release
+ * produces a confident and wrong enzyme call. The designer checks every window
+ * against the reference alleles the API reports and shows nothing if they
+ * disagree, but the right release is still the actual fix.
+ */ /**
+ * Beyond this the annotation is not worth the transfer; the variant listing is
+ * already capped well below it, so this only guards against a stray query.
+ */ const $f49aa8a0cf25aef4$var$MAX_SPAN = 200000;
+function $f49aa8a0cf25aef4$export$30e3f6c97d3f3a29(ensemblRest) {
+    if (!ensemblRest) return undefined;
+    return async ({ system_name: system_name, region: region, start: start, end: end }, options)=>{
+        if (!system_name || !region || start < 1 || end < start || end - start + 1 > $f49aa8a0cf25aef4$var$MAX_SPAN) return null;
+        const signal = options && options.signal;
+        const url = `${ensemblRest}/sequence/region/${encodeURIComponent(system_name)}/${encodeURIComponent(region)}:${start}-${end}` + `?content-type=application/json`;
+        const res = await fetch(url, {
+            headers: {
+                Accept: 'application/json'
+            },
+            signal: signal
+        });
+        if (!res.ok) throw new Error(`HTTP ${res.status}`);
+        const body = await res.json();
+        // A short or absent read would be indexed with genomic offsets and give
+        // wrong answers quietly; the designer discards it, and so does this.
+        return body && typeof body.seq === 'string' ? body.seq.toUpperCase() : null;
+    };
+}
+
+
 // Primers detail: PCR/qPCR primer design, genome specificity and pan-genome
 // coverage checks (gramene-primers <PrimerDesigner>, backed by the
 // gramene-swagger /primers endpoints).
@@ -11519,6 +11623,15 @@ const $88d24ae9beb83d5d$var$Primers = (props)=>{
     const conf = props.config.details.primers // true | { apiBase?, pangenome?, genotyping? }
     ;
     const apiBase = conf && typeof conf === 'object' && conf.apiBase || props.grameneAPI;
+    // Gene models for the variant browser come from Ensembl REST, which must be
+    // the same release the primers API reads variants from.
+    const ensemblRest = props.config && props.config.ensemblRest;
+    const genesInRegion = (0, $gXNCa$react.useMemo)(()=>(0, $31284fcdc45a1688$export$3a249e9030170bda)(ensemblRest), [
+        ensemblRest
+    ]);
+    const sequenceForRegion = (0, $gXNCa$react.useMemo)(()=>(0, $f49aa8a0cf25aef4$export$30e3f6c97d3f3a29)(ensemblRest), [
+        ensemblRest
+    ]);
     const byGene = props.uiViewState && props.uiViewState.byGene && props.uiViewState.byGene[geneId];
     const saved = byGene && byGene.primers;
     const { doSetPrimersState: doSetPrimersState } = props;
@@ -11539,6 +11652,8 @@ const $88d24ae9beb83d5d$var$Primers = (props)=>{
         gene: gene,
         systemName: gene.system_name,
         modes: $88d24ae9beb83d5d$var$MODES,
+        genesInRegion: genesInRegion,
+        sequenceForRegion: sequenceForRegion,
         defaultMode: "gene",
         // an empty slice (never visited, or a snapshot without primers) leaves
         // the designer uncontrolled until its first change is stored