# HG changeset patch
# User davidvanzessen
# Date 1446466236 18000
# Node ID e022c21f8c479df0392d4b71097cdc52ad459946
# Parent  7377bf7e632d782b300b67f9a41bb2bb543226f5
Uploaded

diff -r 7377bf7e632d -r e022c21f8c47 mutation_analysis.r
--- a/mutation_analysis.r	Mon Nov 02 04:52:26 2015 -0500
+++ b/mutation_analysis.r	Mon Nov 02 07:10:36 2015 -0500
@@ -145,6 +145,9 @@
 CDR_nonSilentMutations_columns = paste(CDRRegions, ".IMGT.Nb.of.nonsilent.mutations", sep="")
 dat$nonSilentMutationsCDR = apply(dat, FUN=sum_by_row, 1, columns=CDR_nonSilentMutations_columns)
 
+mutation.sum.columns = c("Sequence.ID", "VRegionMutations", "VRegionNucleotides", "transitionMutations", "transversionMutations", "transitionMutationsAtGC", "silentMutationsFR", "nonSilentMutationsFR", "silentMutationsCDR", "nonSilentMutationsCDR")
+
+write.table(dat[,mutation.sum.columns], "mutation_by_id.txt", sep="\t",quote=F,row.names=F,col.names=T)
 
 setwd(outputdir)
 
diff -r 7377bf7e632d -r e022c21f8c47 wrapper.sh
--- a/wrapper.sh	Mon Nov 02 04:52:26 2015 -0500
+++ b/wrapper.sh	Mon Nov 02 07:10:36 2015 -0500
@@ -88,7 +88,7 @@
 	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 /><a href='merged.txt'>all data</a><br />" >> $output
+echo "<a href='unmatched.txt'>unmatched</a><br /><a href='motif_per_seq.txt'>motif per sequence</a><br /><a href='merged.txt'>all data</a><br /><a href='mutation_by_id.txt'>mutations by id</a><br />" >> $output
 
 
 echo "<img src='all.png'/><br />" >> $output