# HG changeset patch
# User davidvanzessen
# Date 1512572137 18000
# Node ID dc06e94bc1e34b4ef32df6872d6345c09bf83355
# Parent  c6dd3215ebe01a21ee4e8f2b670f2de7a5328a0c
Uploaded

diff -r c6dd3215ebe0 -r dc06e94bc1e3 new_imgt.r
--- a/new_imgt.r	Wed Dec 06 08:52:00 2017 -0500
+++ b/new_imgt.r	Wed Dec 06 09:55:37 2017 -0500
@@ -4,7 +4,12 @@
 merged.file = args[2]
 gene = args[3]
 
-merged = read.table(merged.file, header=T, sep="\t", fill=T, stringsAsFactors=F, comment.char="")
+merged = read.table(merged.file, header=T, sep="\t", fill=T, stringsAsFactors=F, comment.char="", quote="")
+
+if(!("Sequence.ID" %in% names(merged))){ #change-o db
+	print("Change-O DB changing 'SEQUENCE_ID' to 'Sequence.ID'")
+	names(merged)[which(names[merged] == "SEQUENCE_ID")] = "Sequence.ID"
+}
 
 if(gene != "-"){
 	merged = merged[grepl(paste("^", gene, sep=""), merged$best_match),]