gramene-search 2.32.1 → 2.34.0

package/dist/index.js

@@ -11589,6 +11589,64 @@ function $f49aa8a0cf25aef4$export$30e3f6c97d3f3a29(ensemblRest) {
 }
 
 
+/**
+ * Allele frequencies for the primer designer's variant picker.
+ *
+ * A variant listing from `/primers` says which alleles exist but not how common
+ * they are, and how common an allele is decides whether a variant is worth
+ * genotyping at all: a marker near fixation in the panel you mean to screen
+ * tells you nothing. Ensembl REST's `variation` endpoint carries the figures,
+ * and its POST form answers about many ids in one request — ids beyond a couple
+ * of hundred are the difference between one call and hundreds.
+ *
+ * Read from `config.ensemblRest`, which must be the same Ensembl release the
+ * primers API reads variants from (release 115 for sorghum_v11), for the same
+ * reason the gene track and the sequence must: a frequency read against another
+ * release could be attached to the wrong variant entirely.
+ *
+ * Two things about the upstream shape are dealt with here. The tally is spelled
+ * `allele_count`, which is mapped to `count` so a host with some other
+ * frequency source is not made to speak Ensembl; and rows arrive repeated, the
+ * same population and allele several times over, which the designer collapses.
+ */ /** Ids per request. The designer sends batches; this is a guard, not the policy. */ const $24c27aa5d34bb08e$var$MAX_IDS = 500;
+function $24c27aa5d34bb08e$export$849a7b5b35ad4649(ensemblRest) {
+    if (!ensemblRest) return undefined;
+    return async ({ system_name: system_name, ids: ids }, options)=>{
+        if (!system_name || !Array.isArray(ids) || !ids.length) return {};
+        const signal = options && options.signal;
+        const wanted = ids.filter((id)=>typeof id === 'string' && id).slice(0, $24c27aa5d34bb08e$var$MAX_IDS);
+        if (!wanted.length) return {};
+        const res = await fetch(`${ensemblRest}/variation/${encodeURIComponent(system_name)}?pops=1`, {
+            method: 'POST',
+            headers: {
+                'Content-Type': 'application/json',
+                Accept: 'application/json'
+            },
+            body: JSON.stringify({
+                ids: wanted
+            }),
+            signal: signal
+        });
+        if (!res.ok) throw new Error(`HTTP ${res.status}`);
+        const body = await res.json();
+        if (!body || typeof body !== 'object') return {};
+        const out = {};
+        for (const id of wanted){
+            const rows = body[id] && body[id].populations;
+            if (!Array.isArray(rows)) continue;
+            out[id] = rows.filter((r)=>r && typeof r.population === 'string' && typeof r.allele === 'string' && Number.isFinite(Number(r.frequency))).map((r)=>({
+                    population: r.population,
+                    allele: r.allele,
+                    frequency: Number(r.frequency),
+                    // Absent is not nought: a missing tally must stay unknown.
+                    count: r.allele_count === undefined || r.allele_count === null ? null : Number(r.allele_count)
+                }));
+        }
+        return out;
+    };
+}
+
+
 // Primers detail: PCR/qPCR primer design, genome specificity and pan-genome
 // coverage checks (gramene-primers <PrimerDesigner>, backed by the
 // gramene-swagger /primers endpoints).
@@ -11632,6 +11690,9 @@ const $88d24ae9beb83d5d$var$Primers = (props)=>{
     const sequenceForRegion = (0, $gXNCa$react.useMemo)(()=>(0, $f49aa8a0cf25aef4$export$30e3f6c97d3f3a29)(ensemblRest), [
         ensemblRest
     ]);
+    const alleleFrequencies = (0, $gXNCa$react.useMemo)(()=>(0, $24c27aa5d34bb08e$export$849a7b5b35ad4649)(ensemblRest), [
+        ensemblRest
+    ]);
     const byGene = props.uiViewState && props.uiViewState.byGene && props.uiViewState.byGene[geneId];
     const saved = byGene && byGene.primers;
     const { doSetPrimersState: doSetPrimersState } = props;
@@ -11654,6 +11715,7 @@ const $88d24ae9beb83d5d$var$Primers = (props)=>{
         modes: $88d24ae9beb83d5d$var$MODES,
         genesInRegion: genesInRegion,
         sequenceForRegion: sequenceForRegion,
+        alleleFrequencies: alleleFrequencies,
         defaultMode: "gene",
         // an empty slice (never visited, or a snapshot without primers) leaves
         // the designer uncontrolled until its first change is stored