Mercurial > repos > davidvanzessen > mutation_analysis

changeset 40:e022c21f8c47 draft

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Uploaded
author davidvanzessen
date Mon, 02 Nov 2015 07:10:36 -0500
parents 7377bf7e632d
children 1b45c7d7d941
files mutation_analysis.r wrapper.sh
diffstat 2 files changed, 4 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- 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)
 
--- 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