Mercurial > repos > davidvanzessen > mutation_analysis
changeset 25:58a62d2c0377 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Tue, 07 Apr 2015 07:32:43 -0400 |
| parents | 31eee1b3d7df |
| children | 2433a1e110e1 |
| files | mutation_analysis.r wrapper.sh |
| diffstat | 2 files changed, 18 insertions(+), 14 deletions(-) [+] |
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--- 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)
--- 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