--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ChoosePatterns.R	Mon Jun 16 16:21:33 2014 -0400
@@ -0,0 +1,30 @@
+sink(file="/tmp/none")
+sink("/dev/null")
+options(warn=-1)
+options(echo=F) 
+
+#invisible("EBSeq")
+#suppressMessages(library("EBSeq"))  ##cms - changed on 11/11/13. Don't need EBSeq package.
+
+args <- commandArgs(trailingOnly = T)
+inputfile <- args[1]
+Idx <- args[2]
+outputfile <- args[3]
+
+print(args)
+
+ReadIn=read.table(inputfile,stringsAsFactors=F,header=T, sep="\t")
+
+IndexIn=strsplit(Idx,split=",")[[1]]
+Index=as.numeric(IndexIn)
+
+#Mat=data.matrix(ReadIn)
+Mat=data.matrix(ReadIn[,-1])  ##cms - changed on 11/11/13. Otherwise pattern IDs are replaced with NA.
+rownames(Mat)=ReadIn[,1]  ##cms - also added on 11/11/13 to add pattern IDs back in.
+
+Out=Mat[Index,]
+
+
+#write.table(Out,file=outputfile,quote=F,col.names=T,row.names=T,sep = "\t")
+write.table(Out,file=outputfile,quote=F,col.names=NA,row.names=T,sep = "\t")  ##cms - changed on 11/11/13
+