# HG changeset patch
# User davidvanzessen
# Date 1428406363 14400
# Node ID 58a62d2c03774adf051e977a28e6c98ec8c75149
# Parent  31eee1b3d7df6fd138dde0c7cfdef25915819e0f
Uploaded

diff -r 31eee1b3d7df -r 58a62d2c0377 mutation_analysis.r
--- a/mutation_analysis.r	Tue Apr 07 05:57:47 2015 -0400
+++ b/mutation_analysis.r	Tue Apr 07 07:32:43 2015 -0400
@@ -176,12 +176,12 @@
   matrx[5,x] = sum(tmp$totalMutationsAtGC)
   matrx[5,y] = sum(tmp$VRegionMutations)
   matrx[5,z] = round(matrx[5,x] / matrx[5,y] * 100, digits=1)
-  matrx[6,x] = sum(tmp$silentMutationsFR)
-  matrx[6,y] = sum(tmp$nonSilentMutationsFR)
-  matrx[6,z] = round(matrx[6,x] / matrx[6,y] * 100, digits=1)
-  matrx[7,x] = sum(tmp$silentMutationsCDR)
-  matrx[7,y] = sum(tmp$nonSilentMutationsCDR)
-  matrx[7,z] = round(matrx[7,x] / matrx[7,y] * 100, digits=1)
+  matrx[6,x] = sum(tmp$nonSilentMutationsFR)
+  matrx[6,y] = sum(tmp$silentMutationsFR)
+  matrx[6,z] = round(matrx[6,x] / matrx[6,y], digits=1)
+  matrx[7,x] = sum(tmp$nonSilentMutationsCDR)
+  matrx[7,y] = sum(tmp$silentMutationsCDR)
+  matrx[7,z] = round(matrx[7,x] / matrx[7,y], digits=1)
   
   
   transitionTable = data.frame(A=zeros,C=zeros,G=zeros,T=zeros)
@@ -242,12 +242,12 @@
 matrx[5,x] = sum(tmp$totalMutationsAtGC)
 matrx[5,y] = sum(tmp$VRegionMutations)
 matrx[5,z] = round(matrx[5,x] / matrx[5,y] * 100, digits=1)
-matrx[6,x] = sum(tmp$silentMutationsFR)
-matrx[6,y] = sum(tmp$nonSilentMutationsFR)
-matrx[6,z] = round(matrx[6,x] / matrx[6,y] * 100, digits=1)
-matrx[7,x] = sum(tmp$silentMutationsCDR)
-matrx[7,y] = sum(tmp$nonSilentMutationsCDR)
-matrx[7,z] = round(matrx[7,x] / matrx[7,y] * 100, digits=1)
+matrx[6,x] = sum(tmp$nonSilentMutationsFR)
+matrx[6,y] = sum(tmp$silentMutationsFR)
+matrx[6,z] = round(matrx[6,x] / matrx[6,y], digits=1)
+matrx[7,x] = sum(tmp$nonSilentMutationsCDR)
+matrx[7,y] = sum(tmp$silentMutationsCDR)
+matrx[7,z] = round(matrx[7,x] / matrx[7,y], digits=1)
 
 transitionTable = data.frame(A=1:4,C=1:4,G=1:4,T=1:4)
 row.names(transitionTable) = c("A", "C", "G", "T")
@@ -284,7 +284,7 @@
 
 
 result = data.frame(matrx)
-row.names(result) = c("Number of Mutations (%)", "Transition (%)", "Transversions (%)", "Transitions at G C (%)", "Targeting of C.G (%)", "FR S/R (%)", "CDR S/R (%)")
+row.names(result) = c("Number of Mutations (%)", "Transition (%)", "Transversions (%)", "Transitions at G C (%)", "Targeting of C.G (%)", "FR S/R (ratio)", "CDR S/R (ratio)")
 
 write.table(x=result, file="mutations.txt", sep=",",quote=F,row.names=T,col.names=F)
 
diff -r 31eee1b3d7df -r 58a62d2c0377 wrapper.sh
--- a/wrapper.sh	Tue Apr 07 05:57:47 2015 -0400
+++ b/wrapper.sh	Tue Apr 07 07:32:43 2015 -0400
@@ -67,8 +67,12 @@
 echo "<th><a href='matched_all.txt'>all (N = $tmp)</a></th>" >> $output
 
 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz allx ally allz
-	do
+do
+	if [ "$name" == "FR S/R (ratio)" ] || [ "$name" == "CDR S/R (ratio)" ] ; then #meh
+		echo "<tr><td>$name</td><td>${cax}/${cay} (${caz})</td><td>${ca1x}/${ca1y} (${ca1z})</td><td>${ca2x}/${ca2y} (${ca2z})</td><td>${cgx}/${cgy} (${cgz})</td><td>${cg1x}/${cg1y} (${cg1z})</td><td>${cg2x}/${cg2y} (${cg2z})</td><td>${cg3x}/${cg3y} (${cg3z})</td><td>${cg4x}/${cg4y} (${cg4z})</td><td>${cmx}/${cmy} (${cmz})</td><td>${allx}/${ally} (${allz})</td></tr>" >> $output
+	else
 		echo "<tr><td>$name</td><td>${cax}/${cay} (${caz}%)</td><td>${ca1x}/${ca1y} (${ca1z}%)</td><td>${ca2x}/${ca2y} (${ca2z}%)</td><td>${cgx}/${cgy} (${cgz}%)</td><td>${cg1x}/${cg1y} (${cg1z}%)</td><td>${cg2x}/${cg2y} (${cg2z}%)</td><td>${cg3x}/${cg3y} (${cg3z}%)</td><td>${cg4x}/${cg4y} (${cg4z}%)</td><td>${cmx}/${cmy} (${cmz}%)</td><td>${allx}/${ally} (${allz}%)</td></tr>" >> $output
+	fi
 done < $outdir/result.txt
 echo "</table>" >> $output
 echo "<a href='unmatched.txt'>unmatched</a><br /><a href='motif_per_seq.txt'>motif per sequence</a><br />" >> $output