An improvement for gsea/gmt converter (try/match hgnc.symbol first)

BioPAX · Apr 29, 2024 · 3ec3dc4 · 3ec3dc4
1 parent 12edd01
commit 3ec3dc4
Showing 1 changed file with 3 additions and 1 deletion.
diff --git a/gsea-converter/src/main/java/org/biopax/paxtools/io/gsea/GMTConverter.java b/gsea-converter/src/main/java/org/biopax/paxtools/io/gsea/GMTConverter.java
@@ -47,7 +47,9 @@ final class GMTConverter {
 	public GMTConverter()
 	{
 		idFetcher = new IdFetcher().chemDbStartsWithOrEquals("chebi")
-			.seqDbStartsWithOrEquals("hgnc symbol").seqDbStartsWithOrEquals("hgnc");
+			.seqDbStartsWithOrEquals("hgnc.symbol") //the order in the list does matter
+			.seqDbStartsWithOrEquals("hgnc symbol")
+			.seqDbStartsWithOrEquals("hgnc");
 		skipSubPathways = true;
 		minNumIdsPerEntry = 1;
 		skipOutsidePathways = false;