feat: add transcript lookup for genes

cancervariants · Nov 10, 2023 · 047cc77 · 047cc77
1 parent c11b094
commit 047cc77
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Showing 2 changed files with 9 additions and 2 deletions.
diff --git a/server/curfu/routers/utilities.py b/server/curfu/routers/utilities.py
@@ -64,7 +64,14 @@ async def get_transcripts_for_gene(request: Request, gene: str) -> Dict:
     :param str gene: gene term provided by user
     :return: Dict containing transcripts if lookup succeeds, or warnings upon failure
     """
-    transcripts = await request.app.state.fusor.cool_seq_tool.uta_db.get_transcripts(gene)
+    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())
     if transcripts.is_empty():
         return {"warnings": [f"No matching transcripts: {gene}"], "transcripts": []}
     else:

diff --git a/server/curfu/schemas.py b/server/curfu/schemas.py
@@ -256,7 +256,7 @@ class GetTranscriptsResponse(Response):
 class GetGeneTranscriptsResponse(Response):
     """Response model for MANE transcript retrieval endpoint."""
 
-    transcripts: Optional[pl.DataFrame]
+    transcripts: Optional[Dict]
 
 
 class ServiceInfoResponse(Response):