--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter.r	Mon Aug 18 04:04:37 2014 -0400
@@ -0,0 +1,13 @@
+args <- commandArgs(trailingOnly = TRUE)
+
+input = args[1]
+filterf = args[2]
+output = args[3]
+
+
+dat = read.table(input, header=T, sep="\t", fill=T, stringsAsFactors=F)
+filterdat = read.table(filterf, header=T, sep="\t", fill=T, stringsAsFactors=F)
+
+dat = dat[dat$Sequence.ID %in% filterdat$ID,]
+
+write.table(x=dat, file=output, sep="\t",quote=F,row.names=F,col.names=T)