Add popEVE links to variant page

CHANGELOG.md

@@ -18,6 +18,7 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
 - Display inheritance models on structural variantS pages (#6015)
 - Analysis types wgs-lr and panel-lr (#6029)
 - Option to specify database name for the loqusdb API in the scout config file (#6028)
+- popEVE link on variant page, RefSeq transcripts table (#6016)
 ### Changed
 - Institutes are now ordered alphabetically by display name on gene panels search (#5965)
 - Display all available individual/sample IDs for a case (display_name, individual_id and subject_id) directly on cases page (#5966)

scout/server/blueprints/variant/controllers.py

@@ -128,6 +128,7 @@ def tx_overview(variant_obj: dict, genome_build: str):
                 "cbioportal_link",
                 "mutalyzer_link",
                 "mycancergenome_link",
+                "popeve_link",
                 "tp53_link",
                 "varsome_link",
                 "vutr_link",

scout/server/blueprints/variant/templates/variant/tx_overview.html

@@ -113,6 +113,10 @@
                   <a href="{{ tx.mycancergenome_link }}" class="badge bg-secondary text-white" target="_blank" rel="noopener"
                     data-bs-toggle="tooltip" title="MyCancerGenome">MCG</a>
                 {% endif %}
+                {% if tx.popeve_link %}
+                  <a href="{{ tx.popeve_link }}" class="badge bg-secondary text-white" target="_blank" rel="noopener"
+                    data-bs-toggle="tooltip" title="popEVE mutation portal">pE</a>
+                {% endif %}
               </td> <!-- end of links col -->
             </tr>
           {% endfor %} <!-- end of for tx in variant.overview_transcripts -->

scout/server/links.py

@@ -356,6 +356,8 @@ def add_tx_links(tx_obj, build=37, hgnc_symbol=None):
     if build == 38:
         tx_obj["ensembl_link"] = ensembl_38_link
 
+    tx_obj["popeve_link"] = popeve(tx_obj)
+
     refseq_links = []
     refseq_id = tx_obj.get("refseq_id") or (
         tx_obj.get("transcript_id")
@@ -403,6 +405,16 @@ def refseq(refseq_id):
     return link.format(refseq_id)
 
 
+def popeve(tx_obj: dict) -> Optional[str]:
+    """Generates a PopEVE link for a transcript by extracting the RefSeq protein_id, if present."""
+    protein_id = tx_obj.get("protein_id")
+    if not protein_id or not protein_id.startswith("NP_"):
+        return None
+
+    protein_id = protein_id.replace(".", "-")  # Format RefSeq protein ID for PopEVE URL
+    return f"https://pop.evemodel.org/protein/{protein_id}"
+
+
 def ensembl_tx(ens_tx_id, build=37):
     link = "http://grch37.ensembl.org/Homo_sapiens/" "Gene/Summary?t={}"