--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/igat.r	Wed Jun 08 03:54:49 2016 -0400
@@ -0,0 +1,20 @@
+args <- commandArgs(trailingOnly = TRUE)
+
+imgt.dir = args[1]
+merged.file = args[2]
+
+merged = read.table(merged.file, header=T, sep="\t", fill=T, stringsAsFactors=F)
+
+for(f in list.files(imgt.dir, pattern="*.txt$")){
+	print(paste("filtering", f))
+	path = paste(imgt.dir, f, sep="")
+	dat = read.table(path, header=T, sep="\t", fill=T, quote="", stringsAsFactors=F)
+	
+	dat = dat[dat$Sequence.ID %in% merged$Sequence.ID,]
+	
+	if("FR1.IMGT" %in% colnames(dat)){
+		dat$FR1.IMGT = ""
+	}
+	
+	write.table(dat, path, quote=F, sep="\t", row.names=F, col.names=T)
+}