Mercurial > repos > davidvanzessen > shm_csr

diff wrapper.sh @ 40:ca2512e1e3ab draft

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Uploaded
author davidvanzessen
date Thu, 29 Dec 2016 07:05:45 -0500
parents a24f8c93583a
children b8ac74723ab0
line wrap: on
line diff
--- a/wrapper.sh	Thu Dec 22 09:39:27 2016 -0500
+++ b/wrapper.sh	Thu Dec 29 07:05:45 2016 -0500
@@ -43,6 +43,7 @@
 
 cat "`find $PWD/files/ -name "1_*"`" > $PWD/summary.txt
 cat "`find $PWD/files/ -name "3_*"`" > $PWD/sequences.txt
+cat "`find $PWD/files/ -name "4_*"`" > $PWD/gapped_aa.txt
 cat "`find $PWD/files/ -name "5_*"`" > $PWD/aa.txt
 cat "`find $PWD/files/ -name "6_*"`" > $PWD/junction.txt
 cat "`find $PWD/files/ -name "7_*"`" > $PWD/mutationanalysis.txt
@@ -64,7 +65,7 @@
 echo "---------------- merge_and_filter.r ----------------"
 echo "---------------- merge_and_filter.r ----------------<br />" >> $log
 
-Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $PWD/aa.txt $outdir/identified_genes.txt $outdir/merged.txt $outdir/before_unique_filter.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${class_filter} ${empty_region_filter} 2>&1
+Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt "$PWD/gapped_aa.txt" $outdir/identified_genes.txt $outdir/merged.txt $outdir/before_unique_filter.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${class_filter} ${empty_region_filter} 2>&1
 
 if [[ "$fast" == "no" ]] ; then