gramene-search 1.2.86 → 1.2.87

package/.parcel-cache/2126881b633272fa.txt

@@ -1,2 +1,2 @@
-248900716
-1704819222968880000
+256893153
+1704849569404690000

package/.parcel-cache/bbfc6fab41a92806.txt

@@ -0,0 +1,2 @@
+256886579
+1704849461051869000

package/dist/index.js

@@ -1208,6 +1208,8 @@ const $671312b287158a8a$var$grameneDocs = {
             pathways: {},
             expression: {},
             sequences: {},
+            rnaSequences: {},
+            pepSequences: {},
             studies: {}
         };
         return (state = initialState, { type: type , payload: payload  })=>{
@@ -1269,11 +1271,35 @@ const $671312b287158a8a$var$grameneDocs = {
                         return newState;
                     }
                     break;
+                case "RNA_SEQUENCE_REQUESTED":
+                    if (!state.rnaSequences.hasOwnProperty(payload)) {
+                        newState = Object.assign({}, state);
+                        newState.rnaSequences[payload] = {};
+                        return newState;
+                    }
+                    break;
+                case "PEP_SEQUENCE_REQUESTED":
+                    if (!state.rnaSequences.hasOwnProperty(payload)) {
+                        newState = Object.assign({}, state);
+                        newState.pepSequences[payload] = {};
+                        return newState;
+                    }
+                    break;
                 case "GENE_SEQUENCE_RECEIVED":
                     newState = Object.assign({}, state);
                     newState.sequences = Object.assign({}, state.sequences);
                     newState.sequences[payload.id] = payload.geneSeq;
                     return newState;
+                case "RNA_SEQUENCE_RECEIVED":
+                    newState = Object.assign({}, state);
+                    newState.rnaSequences = Object.assign({}, state.rnaSequences);
+                    newState.rnaSequences[payload.id] = payload.RnaSeq;
+                    return newState;
+                case "PEP_SEQUENCE_RECEIVED":
+                    newState = Object.assign({}, state);
+                    newState.pepSequences = Object.assign({}, state.pepSequences);
+                    newState.pepSequences[payload.id] = payload.PepSeq;
+                    return newState;
                 case "PARALOG_EXPRESSION_REQUESTED":
                     if (!state.expression.hasOwnProperty(payload)) {
                         newState = Object.assign({}, state);
@@ -1418,6 +1444,44 @@ const $671312b287158a8a$var$grameneDocs = {
                 });
             }
         },
+    doRequestRnaSequence: (id)=>({ dispatch: dispatch , store: store  })=>{
+            const maps = store.selectGrameneMaps();
+            const seqs = store.selectRnaSequences();
+            if (!seqs.hasOwnProperty(id)) {
+                dispatch({
+                    type: "RNA_SEQUENCE_REQUESTED",
+                    payload: id
+                });
+                fetch(`${store.selectEnsemblAPI()}/sequence/id/${id}?type=cdna&content-type=application/json`).then((res)=>res.json()).then((RnaSeq)=>{
+                    dispatch({
+                        type: "RNA_SEQUENCE_RECEIVED",
+                        payload: {
+                            id: id,
+                            RnaSeq: RnaSeq
+                        }
+                    });
+                });
+            }
+        },
+    doRequestPepSequence: (id)=>({ dispatch: dispatch , store: store  })=>{
+            const maps = store.selectGrameneMaps();
+            const seqs = store.selectPepSequences();
+            if (!seqs.hasOwnProperty(id)) {
+                dispatch({
+                    type: "PEP_SEQUENCE_REQUESTED",
+                    payload: id
+                });
+                fetch(`${store.selectEnsemblAPI()}/sequence/id/${id}?type=protein&content-type=application/json`).then((res)=>res.json()).then((PepSeq)=>{
+                    dispatch({
+                        type: "PEP_SEQUENCE_RECEIVED",
+                        payload: {
+                            id: id,
+                            PepSeq: PepSeq
+                        }
+                    });
+                });
+            }
+        },
     doRequestParalogExpression: (id)=>({ dispatch: dispatch , store: store  })=>{
             const expr = store.selectParalogExpression();
             if (!expr.hasOwnProperty(id)) {
@@ -1471,6 +1535,8 @@ const $671312b287158a8a$var$grameneDocs = {
     selectGramenePathways: (state)=>state.grameneDocs.pathways,
     selectParalogExpression: (state)=>state.grameneDocs.expression,
     selectGeneSequences: (state)=>state.grameneDocs.sequences,
+    selectRnaSequences: (state)=>state.grameneDocs.rnaSequences,
+    selectPepSequences: (state)=>state.grameneDocs.pepSequences,
     selectAtlasStudies: (state)=>state.grameneDocs.studies
 };
 var $671312b287158a8a$export$2e2bcd8739ae039 = $671312b287158a8a$var$grameneDocs;
@@ -3312,7 +3378,7 @@ const $527ebc19dc92444d$var$CodeBlock = (props)=>{
     return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
         className: "fasta-container",
         children: [
-            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("code", {
+            props.mode === "dna" && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("code", {
                 className: "fasta",
                 children: [
                     /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("b", {
@@ -3350,6 +3416,40 @@ const $527ebc19dc92444d$var$CodeBlock = (props)=>{
                     /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("br", {})
                 ]
             }),
+            props.mode === "rna" && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("code", {
+                className: "fasta",
+                children: [
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("b", {
+                        children: "Key:"
+                    }),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                        className: "utr5",
+                        children: "--5'UTR exon 1--"
+                    }),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                        className: "utr5-other",
+                        children: "--5'UTR exon 2--"
+                    }),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                        className: "cds",
+                        children: "--Coding exon 1--"
+                    }),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                        className: "cds-other",
+                        children: "--Coding exon 2--"
+                    }),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                        className: "utr3",
+                        children: "--3'UTR exon 1--"
+                    }),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                        className: "utr3-other",
+                        children: "--3'UTR exon 2--"
+                    }),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("br", {}),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("br", {})
+                ]
+            }),
             /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("code", {
                 className: "fasta",
                 children: [
@@ -3379,7 +3479,7 @@ const $527ebc19dc92444d$var$CodeBlock = (props)=>{
         ]
     });
 };
-const $527ebc19dc92444d$var$decorateDNA = (geneSeq, gene, up, down, tid)=>{
+const $527ebc19dc92444d$var$decorateSeq = (geneSeq, gene, up, down, tid, mode)=>{
     // return a list of blocks with kind and seq properties
     let blocks = [];
     const transcript = gene.gene_structure.transcripts.find((tr)=>tr.id === tid);
@@ -3395,23 +3495,24 @@ const $527ebc19dc92444d$var$decorateDNA = (geneSeq, gene, up, down, tid)=>{
     let pos_in_transcript = 0;
     let pos_in_gene = 0;
     let blockType = "utr5";
+    let extra = "";
     transcript.exons.forEach((eid, e_idx)=>{
         const exon = gene.gene_structure.exons.find((exon)=>exon.id === eid);
-        if (exon.start > 1) {
-            let intronBlock = {
+        if (e_idx > 0 && mode === "dna") {
+            blocks.push({
                 kind: "intron",
                 seq: geneSeq.seq.substring(offset + pos_in_gene, offset + exon.start - 1).toLowerCase()
-            };
-            // actually, don't do this blocks.push(intronBlock);
+            });
             pos_in_gene = exon.start - 1;
         }
+        if (mode === "rna") extra = e_idx % 2 === 1 ? "-other" : "";
         let exon_length = exon.end - exon.start + 1;
         if (transcript.cds && pos_in_transcript < transcript.cds.start && pos_in_transcript + exon_length >= transcript.cds.start) {
             // CDS starts in this exon
             const utr5_len = transcript.cds.start - pos_in_transcript - 1;
             if (utr5_len > 0) {
                 blocks.push({
-                    kind: blockType,
+                    kind: blockType + extra,
                     seq: geneSeq.seq.substring(offset + pos_in_gene, offset + pos_in_gene + utr5_len)
                 });
                 exon_length -= utr5_len;
@@ -3425,7 +3526,7 @@ const $527ebc19dc92444d$var$decorateDNA = (geneSeq, gene, up, down, tid)=>{
             const cds_len = transcript.cds.end - pos_in_transcript;
             if (cds_len > 0) {
                 blocks.push({
-                    kind: blockType,
+                    kind: blockType + extra,
                     seq: geneSeq.seq.substring(offset + pos_in_gene, offset + pos_in_gene + cds_len)
                 });
                 exon_length -= cds_len;
@@ -3435,7 +3536,7 @@ const $527ebc19dc92444d$var$decorateDNA = (geneSeq, gene, up, down, tid)=>{
             blockType = "utr3";
         }
         if (exon_length > 0) blocks.push({
-            kind: blockType,
+            kind: blockType + extra,
             seq: geneSeq.seq.substring(offset + pos_in_gene, offset + pos_in_gene + exon_length)
         });
         pos_in_gene = exon.end;
@@ -3460,7 +3561,13 @@ const $527ebc19dc92444d$var$buildId = (gene, geneSeq, up, down)=>{
 };
 const $527ebc19dc92444d$var$Detail = (props)=>{
     const gene = props.geneDocs[props.searchResult.id];
+    const [tab, setTab] = (0, $gXNCa$react.useState)("dna");
+    const [upstream, setUpstream] = (0, $gXNCa$react.useState)(0);
+    const [downstream, setDownstream] = (0, $gXNCa$react.useState)(0);
+    const [tid, setTid] = (0, $gXNCa$react.useState)(gene.gene_structure.canonical_transcript);
     let geneSeq;
+    let rnaSeq;
+    let pepSeq;
     if (props.geneSequences && props.geneSequences[gene._id]) geneSeq = props.geneSequences[gene._id];
     else {
         props.doRequestGeneSequence(gene);
@@ -3468,12 +3575,30 @@ const $527ebc19dc92444d$var$Detail = (props)=>{
             children: "loading"
         });
     }
+    if (props.rnaSequences && props.rnaSequences[tid]) rnaSeq = props.rnaSequences[tid];
+    else {
+        props.doRequestRnaSequence(tid);
+        return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("pre", {
+            children: "loading"
+        });
+    }
     const maxUp = gene.location.strand === 1 ? gene.location.start - geneSeq.start : geneSeq.end - gene.location.end;
     const maxDown = gene.location.strand === -1 ? gene.location.start - geneSeq.start : geneSeq.end - gene.location.end;
-    const [upstream, setUpstream] = (0, $gXNCa$react.useState)(0);
-    const [downstream, setDownstream] = (0, $gXNCa$react.useState)(0);
-    const [tid, setTid] = (0, $gXNCa$react.useState)(gene.gene_structure.canonical_transcript);
+    const transcript = gene.gene_structure.transcripts.find((tr)=>tr.id === tid);
+    let tl_id;
+    if (transcript.translation) {
+        tl_id = transcript.translation.id;
+        if (props.pepSequences && props.pepSequences[tl_id]) pepSeq = props.pepSequences[tl_id];
+        else {
+            props.doRequestPepSequence(tl_id);
+            return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("pre", {
+                children: "loading"
+            });
+        }
+    }
     return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Tabs), {
+        activeKey: tab,
+        onSelect: (k)=>setTab(k),
         children: [
             /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Tab), {
                 tabClassName: "dna",
@@ -3610,26 +3735,116 @@ const $527ebc19dc92444d$var$Detail = (props)=>{
                         ]
                     }),
                     geneSeq && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($527ebc19dc92444d$var$CodeBlock, {
+                        mode: "dna",
                         id: $527ebc19dc92444d$var$buildId(gene, geneSeq, +upstream, +downstream),
                         seq: geneSeq.seq.substring(maxUp - +upstream, maxUp + gene.location.end - gene.location.start + 1 + +downstream),
-                        blocks: $527ebc19dc92444d$var$decorateDNA(geneSeq, gene, +upstream, +downstream, tid)
+                        blocks: $527ebc19dc92444d$var$decorateSeq(geneSeq, gene, +upstream, +downstream, tid, "dna")
                     })
                 ]
             }),
-            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Tab), {
-                tabClassName: "cdna",
-                eventKey: "cdna",
-                title: "Transcript sequence"
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Tab), {
+                tabClassName: "rna",
+                eventKey: "rna",
+                title: "Transcript sequence",
+                children: [
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Container), {
+                        style: {
+                            width: "100ch",
+                            marginLeft: 0
+                        },
+                        children: gene.gene_structure.transcripts.length > 1 && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Row), {
+                            children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Col), {
+                                children: [
+                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("b", {
+                                        children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("i", {
+                                            children: "Select transcript"
+                                        })
+                                    }),
+                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("br", {}),
+                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.ButtonGroup), {
+                                        children: gene.gene_structure.transcripts.sort((a, b)=>a.id.localeCompare(b.id)).map((tr, idx)=>{
+                                            let v = tr.id === gene.gene_structure.canonical_transcript ? "primary" : "secondary";
+                                            if (tr.id !== tid) v = `outline-${v}`;
+                                            return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.ToggleButton), {
+                                                variant: v,
+                                                id: `radio-${idx}`,
+                                                type: "radio",
+                                                name: tr.id,
+                                                value: tr.id,
+                                                checked: tr.id === tid,
+                                                onChange: (e)=>setTid(e.currentTarget.value),
+                                                children: tr.id
+                                            }, idx);
+                                        })
+                                    })
+                                ]
+                            })
+                        })
+                    }),
+                    geneSeq && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($527ebc19dc92444d$var$CodeBlock, {
+                        mode: "rna",
+                        id: tid,
+                        seq: rnaSeq.seq,
+                        blocks: $527ebc19dc92444d$var$decorateSeq(geneSeq, gene, 0, 0, tid, "rna")
+                    })
+                ]
             }),
-            gene.biotype === "protein_coding" && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Tab), {
+            gene.biotype === "protein_coding" && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Tab), {
                 tabClassName: "pep",
                 eventKey: "pep",
-                title: "Peptide sequence"
+                title: "Peptide sequence",
+                children: [
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Container), {
+                        style: {
+                            width: "100ch",
+                            marginLeft: 0
+                        },
+                        children: gene.gene_structure.transcripts.length > 1 && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Row), {
+                            children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Col), {
+                                children: [
+                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("b", {
+                                        children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("i", {
+                                            children: "Select transcript"
+                                        })
+                                    }),
+                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("br", {}),
+                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.ButtonGroup), {
+                                        children: gene.gene_structure.transcripts.sort((a, b)=>a.id.localeCompare(b.id)).map((tr, idx)=>{
+                                            let v = tr.id === gene.gene_structure.canonical_transcript ? "primary" : "secondary";
+                                            if (tr.id !== tid) v = `outline-${v}`;
+                                            return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.ToggleButton), {
+                                                variant: v,
+                                                id: `radio-${idx}`,
+                                                type: "radio",
+                                                name: tr.id,
+                                                value: tr.id,
+                                                checked: tr.id === tid,
+                                                onChange: (e)=>setTid(e.currentTarget.value),
+                                                children: tr.id
+                                            }, idx);
+                                        })
+                                    })
+                                ]
+                            })
+                        })
+                    }),
+                    geneSeq && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($527ebc19dc92444d$var$CodeBlock, {
+                        mode: "pep",
+                        id: tl_id,
+                        seq: pepSeq.seq,
+                        blocks: [
+                            {
+                                type: "pep",
+                                seq: pepSeq.seq
+                            }
+                        ]
+                    })
+                ]
             })
         ]
     });
 };
-var $527ebc19dc92444d$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.connect)("selectConfiguration", "selectGeneSequences", "doRequestGeneSequence", $527ebc19dc92444d$var$Detail);
+var $527ebc19dc92444d$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.connect)("selectConfiguration", "selectGeneSequences", "selectRnaSequences", "selectPepSequences", "doRequestGeneSequence", "doRequestRnaSequence", "doRequestPepSequence", $527ebc19dc92444d$var$Detail);