--- a/aa_histogram.r	Wed Jul 13 08:04:13 2016 -0400
+++ b/aa_histogram.r	Wed Jul 13 09:04:15 2016 -0400
@@ -26,7 +26,9 @@
 	if(nrow(mutations.by.id.gene) == 0){
 		next
 	}
-
+	
+	print(paste("nrow", gene, nrow(absent.aa.by.id.gene)))
+	
 	mutations.at.position = colSums(mutations.by.id.gene[,-c(1,2)])
 	aa.at.position = colSums(absent.aa.by.id.gene[,-c(1,2,3,4)])
 
@@ -45,7 +47,12 @@
 	m = m + expand_limits(y=c(-0.1,1)) + xlab("AA position") + ylab("Frequency") + ggtitle(paste(gene, "AA mutation frequency"))
 
 	print("---------------- write/print ----------------")
-
+	
+	dat.sums = data.frame(index=1:length(mutations.at.position), mutations.at.position=mutations.at.position, aa.at.position=aa.at.position)	
+	
+	write.table(dat.sums, paste(outdir, "/aa_histogram_sum_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T)
+	write.table(mutations.by.id.gene, paste(outdir, "/aa_histogram_count_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T)
+	write.table(absent.aa.by.id.gene, paste(outdir, "/aa_histogram_absent_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T)
 	write.table(dat_dt, paste(outdir, "/aa_histogram_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T)
 	png(filename=paste(outdir, "/aa_histogram_", gene, ".png", sep=""), width=1280, height=720)
 	print(m)