Mercurial > repos > davidvanzessen > mutation_analysis

diff wrapper.sh @ 39:7377bf7e632d draft

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Uploaded
author davidvanzessen
date Mon, 02 Nov 2015 04:52:26 -0500
parents 8dba36531e6e
children e022c21f8c47
line wrap: on
line diff
--- a/wrapper.sh	Tue Aug 04 08:55:14 2015 -0400
+++ b/wrapper.sh	Mon Nov 02 04:52:26 2015 -0500
@@ -24,6 +24,7 @@
 fi
 
 cat $PWD/files/*/1_* > $PWD/summary.txt
+cat $PWD/files/*/6_* > $PWD/junction.txt
 cat $PWD/files/*/7_* > $PWD/mutationanalysis.txt
 cat $PWD/files/*/8_* > $PWD/mutationstats.txt
 cat $PWD/files/*/10_* > $PWD/hotspots.txt
@@ -53,7 +54,7 @@
 
 
 echo "merging"
-Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $outdir/identified_genes.txt $outdir/merged.txt $outdir/unmatched.txt $method $functionality $unique
+Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/junction.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $outdir/identified_genes.txt $outdir/merged.txt $outdir/unmatched.txt $method $functionality $unique
 
 genes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm"
 echo "R mutation analysis"