feat: add transcript lookup for genes

cancervariants · Nov 15, 2023 · 005823a · 005823a
1 parent 047cc77
commit 005823a
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Showing 6 changed files with 84 additions and 41 deletions.
diff --git a/client/src/components/Utilities/GetCoordinates/GetCoordinates.tsx b/client/src/components/Utilities/GetCoordinates/GetCoordinates.tsx
@@ -9,6 +9,8 @@ import {
   makeStyles,
   Box,
   Link,
+  InputLabel,
+  FormControl,
 } from "@material-ui/core";
 import React, { useEffect, useState } from "react";
 import { GeneAutocomplete } from "../../main/shared/GeneAutocomplete/GeneAutocomplete";
@@ -97,6 +99,7 @@ const GetCoordinates: React.FC = () => {
 
   const [geneTranscripts, setGeneTranscripts] = useState([]);
   const [geneTxWarnings, setGeneTxWarnings] = useState<string[]>();
+  const [selectedTranscript, setSelectedTranscript] = useState("");
 
   const [results, setResults] = useState<GenomicData | null>(null);
   const [error, setError] = useState<string>("");
@@ -122,8 +125,8 @@ const GetCoordinates: React.FC = () => {
     !exonEndText;
 
   useEffect(() => {
+    console.log(inputComplete)
     if (inputComplete) {
-      handleGetTranscripts();
       fetchResults();
     }
   }, [
@@ -184,16 +187,9 @@ const GetCoordinates: React.FC = () => {
     }
   };
 
-  const handleGetTranscripts = () => {
-    getTranscriptsForGene(gene).then((transcriptsResponse: GetGeneTranscriptsResponse) => {
-      if (transcriptsResponse.warnings) {
-        setGeneTxWarnings(transcriptsResponse.warnings);
-        setGeneTranscripts([]);
-      } else {
-        setGeneTxWarnings([]);
-        setGeneTranscripts(transcriptsResponse.transcripts);
-      }
-    });
+  const handleTranscriptSelect = (event: any) => {
+    setSelectedTranscript(event.target.value as string);
+    setTxAc(event.target.value as string);
   };
 
   const fetchResults = () => {
@@ -207,11 +203,7 @@ const GetCoordinates: React.FC = () => {
         exonEndOffset
       ).then((coordsResponse) => handleResponse(coordsResponse));
     } else if (inputType == "genomic_coords") {
-      getExonCoords(chromosome, start, end, strand, gene).then(
-        (coordsResponse) => handleResponse(coordsResponse)
-      );
-    } else if (inputType == "genomic_coords_tx") {
-      getExonCoords(chromosome, start, end, strand, "", txAc).then(
+      getExonCoords(chromosome, start, end, strand, gene, txAc).then(
         (coordsResponse) => handleResponse(coordsResponse)
       );
     }
@@ -269,7 +261,7 @@ const GetCoordinates: React.FC = () => {
           errorText={chromosomeText}
         />
         <Box mt="18px">
-          <Box className={classes.strand} width="125px">
+          <Box className={classes.strand}>
             <StrandSwitch
               setStrand={setStrand}
               selectedStrand={strand}
@@ -296,12 +288,27 @@ const GetCoordinates: React.FC = () => {
                 setGeneText={setGeneText}
                 setChromosome={setChromosome}
                 setStrand={setStrand}
+                setTranscripts={setGeneTranscripts}
+                setDefaultTranscript={setSelectedTranscript}
               />
-              <TranscriptField
-                fieldValue={txAc}
-                valueSetter={setTxAc}
-                errorText={txAcText}
-              />
+              <FormControl>
+              <InputLabel>Transcript</InputLabel>
+              <Select
+                labelId="transcript-select-label"
+                id="transcript-select"
+                value={selectedTranscript}
+                label="Transcript"
+                onChange={handleTranscriptSelect}
+                placeholder="Transcript"
+                style={{minWidth: "150px"}}
+              >
+                {geneTranscripts.map((tx, index) => (
+                  <MenuItem key={index} value={tx}>
+                    {tx}
+                  </MenuItem>
+                ))}
+              </Select>
+              </FormControl>
             </Box>
             {genomicCoordinateInfo}
             <Box className={classes.fieldsPair}>
@@ -333,7 +340,7 @@ const GetCoordinates: React.FC = () => {
             <Box className={classes.fieldsPair}>
               <TextField
                 margin="dense"
-                style={{ width: 125 }}
+                style={{ minWidth: 125 }}
                 label="Starting Exon"
                 value={exonStart}
                 onChange={(event) => setExonStart(event.target.value)}
@@ -342,7 +349,7 @@ const GetCoordinates: React.FC = () => {
               />
               <TextField
                 margin="dense"
-                style={{ width: 125 }}
+                style={{ minWidth: 125 }}
                 label="Starting Offset"
                 value={exonStartOffset}
                 onChange={(event) => setExonStartOffset(event.target.value)}
@@ -351,7 +358,7 @@ const GetCoordinates: React.FC = () => {
             <Box className={classes.fieldsPair}>
               <TextField
                 margin="dense"
-                style={{ width: 125 }}
+                style={{ minWidth: 125 }}
                 label="Ending Exon"
                 value={exonEnd}
                 onChange={(event) => setExonEnd(event.target.value)}
@@ -360,7 +367,7 @@ const GetCoordinates: React.FC = () => {
               />
               <TextField
                 margin="dense"
-                style={{ width: 125 }}
+                style={{ minWidth: 125 }}
                 label="Ending Offset"
                 value={exonEndOffset}
                 onChange={(event) => setExonEndOffset(event.target.value)}

diff --git a/client/src/components/main/shared/GeneAutocomplete/GeneAutocomplete.tsx b/client/src/components/main/shared/GeneAutocomplete/GeneAutocomplete.tsx
@@ -3,8 +3,8 @@ import { TextField, Typography, makeStyles } from "@material-ui/core";
 import Autocomplete, {
   AutocompleteRenderGroupParams,
 } from "@material-ui/lab/Autocomplete";
-import { getGeneSuggestions } from "../../../../services/main";
-import { SuggestGeneResponse } from "../../../../services/ResponseModels";
+import { getGeneSuggestions, getTranscriptsForGene } from "../../../../services/main";
+import { GetGeneTranscriptsResponse, SuggestGeneResponse } from "../../../../services/ResponseModels";
 import HelpTooltip from "../HelpTooltip/HelpTooltip";
 import { useColorTheme } from "../../../../global/contexts/Theme/ColorThemeContext";
 
@@ -50,6 +50,8 @@ interface Props {
   promptText?: string | undefined;
   setChromosome?: CallableFunction;
   setStrand?: CallableFunction;
+  setTranscripts?: CallableFunction;
+  setDefaultTranscript?: CallableFunction;
 }
 
 export const GeneAutocomplete: React.FC<Props> = ({
@@ -61,6 +63,8 @@ export const GeneAutocomplete: React.FC<Props> = ({
   promptText,
   setChromosome,
   setStrand,
+  setTranscripts,
+  setDefaultTranscript,
 }) => {
   const existingGeneOption = gene
     ? { value: gene, type: GeneSuggestionType.symbol }
@@ -95,6 +99,15 @@ export const GeneAutocomplete: React.FC<Props> = ({
     if (setStrand) {
       setStrand(selection.strand);
     }
+    if (setTranscripts) {
+      getTranscriptsForGene(selection.value).then((transcriptsResponse: GetGeneTranscriptsResponse) => {
+        const transcripts = transcriptsResponse.transcripts
+        setTranscripts(transcripts);
+        if (setDefaultTranscript) {
+          setDefaultTranscript(transcripts[0])
+        }
+      });
+    }
   };
 
   // Update options

diff --git a/client/src/components/main/shared/TranscriptField/TranscriptDropdown.tsx b/client/src/components/main/shared/TranscriptField/TranscriptDropdown.tsx
@@ -0,0 +1,27 @@
+import { makeStyles, TextField, Typography } from "@material-ui/core";
+import React, { KeyboardEventHandler } from "react";
+import HelpTooltip from "../HelpTooltip/HelpTooltip";
+
+interface Props {
+  fieldValue: string;
+  valueSetter: CallableFunction;
+  errorText: string;
+}
+
+const TranscriptDropdown: React.FC<Props> = ({
+  fieldValue,
+  valueSetter,
+  errorText,
+}) => {
+  const useStyles = makeStyles(() => ({
+    textField: {
+    },
+  }));
+  const classes = useStyles();
+
+  return (
+    <></>
+  );
+};
+
+export default TranscriptDropdown;
diff --git a/client/src/components/main/shared/TranscriptField/TranscriptField.tsx b/client/src/components/main/shared/TranscriptField/TranscriptField.tsx
@@ -6,7 +6,7 @@ interface Props {
   fieldValue: string;
   valueSetter: CallableFunction;
   errorText: string;
-  keyHandler: KeyboardEventHandler<HTMLDivElement> | undefined;
+  keyHandler?: KeyboardEventHandler<HTMLDivElement> | undefined;
   width?: number | undefined;
 }
 

diff --git a/server/curfu/routers/utilities.py b/server/curfu/routers/utilities.py
@@ -66,16 +66,12 @@ async def get_transcripts_for_gene(request: Request, gene: str) -> Dict:
     """
     normalized = request.app.state.fusor.gene_normalizer.normalize(gene)
     symbol = normalized.gene_descriptor.label
-    print(symbol)
-    print(request.app.state.fusor.cool_seq_tool.uta_db)
-    transcripts = await request.app.state.fusor.cool_seq_tool.uta_db.get_transcripts(symbol)
-    transcripts_dict = transcripts.to_dict()
-    tx_for_gene = transcripts_dict["tx_ac"]
-    print(transcripts.glimpse())
+    transcripts = await request.app.state.fusor.cool_seq_tool.uta_db.get_transcripts(gene=symbol)
+    tx_for_gene = list(transcripts.rows_by_key("tx_ac"))
     if transcripts.is_empty():
         return {"warnings": [f"No matching transcripts: {gene}"], "transcripts": []}
     else:
-        return {"transcripts": transcripts}
+        return {"transcripts": tx_for_gene}
 
 @router.get(
     "/api/utilities/get_genomic",
@@ -133,7 +129,7 @@ async def get_genome_coords(
     if exon_end is not None and exon_end_offset is None:
         exon_end_offset = 0
 
-    response = await request.app.state.fusor.cool_seq_tool.transcript_to_genomic_coordinates(  # noqa: E501
+    response = await request.app.state.fusor.cool_seq_tool.ex_g_coords_mapper.transcript_to_genomic_coordinates(  # noqa: E501
         gene=gene,
         transcript=transcript,
         exon_start=exon_start,
@@ -281,7 +277,7 @@ async def get_sequence(
     """
     _, path = tempfile.mkstemp(suffix=".fasta")
     try:
-        request.app.state.fusor.cool_seq_tool.get_fasta_file(sequence_id, Path(path))
+        request.app.state.fusor.cool_seq_tool.seqrepo_access.get_fasta_file(sequence_id, Path(path))
     except KeyError:
         resp = request.app.state.fusor.cool_seq_tool.seqrepo_access.translate_identifier(  # noqa: E501
             sequence_id, "refseq"
@@ -293,7 +289,7 @@ async def get_sequence(
         else:
             try:
                 new_seq_id = resp[0][0].split(":")[1]
-                request.app.state.fusor.cool_seq_tool.get_fasta_file(
+                request.app.state.fusor.cool_seq_tool.seqrepo_access.get_fasta_file(
                     new_seq_id, Path(path)
                 )
             except KeyError:

diff --git a/server/curfu/schemas.py b/server/curfu/schemas.py
@@ -251,12 +251,12 @@ class ManeGeneTranscript(BaseModel):
 class GetTranscriptsResponse(Response):
     """Response model for MANE transcript retrieval endpoint."""
 
-    transcripts: Optional[List[ManeGeneTranscript]]
+    transcripts: Optional[List[ManeGeneTranscript]] = None
 
 class GetGeneTranscriptsResponse(Response):
     """Response model for MANE transcript retrieval endpoint."""
 
-    transcripts: Optional[Dict]
+    transcripts: Optional[List[str]] = None
 
 
 class ServiceInfoResponse(Response):