From 3ec3dc4f1275baa7b325ab84016226faa12737e6 Mon Sep 17 00:00:00 2001
From: IgorRodchenkov <rodche@gmail.com>
Date: Mon, 29 Apr 2024 00:00:19 -0400
Subject: [PATCH] An improvement for gsea/gmt converter (try/match hgnc.symbol
 first)

---
 .../main/java/org/biopax/paxtools/io/gsea/GMTConverter.java   | 4 +++-
 1 file changed, 3 insertions(+), 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
index 0254d7efe..d92c89068 100644
--- 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;