diff wrapper.sh @ 5:d8de51314d3f draft

Uploaded

--- a/wrapper.sh	Wed Aug 13 09:09:56 2014 -0400
+++ b/wrapper.sh	Thu Aug 14 07:17:26 2014 -0400
@@ -1,3 +1,4 @@
+
 #!/bin/bash
 dir="$(cd "$(dirname "$0")" && pwd)"
 
@@ -48,7 +49,7 @@
 		filtered="$PWD/filtered_${id}.txt"
 		cat $PWD/$id/*/1_* > $summaryfile
 		cat $PWD/$id/*/2_* > $gappedfile
-		Rscript $dir/filter.r $summaryfile $gappedfile "$selection" $filtered
+		Rscript $dir/filter.r $summaryfile $gappedfile "$selection" $filtered 2>&1
 		
 		final="$PWD/final_${id}.txt"
 		cat $filtered | cut -f2,4,7 > $final
@@ -64,9 +65,9 @@
 
 echo "$workdir/${outID}.txt"
 
-rows=`tail -n +2 $workdir/${outID}.txt | grep -n 'Group' | grep -Eoh '^[0-9]+' | tr '\n' ' '`
+rows=`tail -n +2 $workdir/${outID}.txt | grep -v "All sequences combined" | grep -n 'Group' | grep -Eoh '^[0-9]+' | tr '\n' ' '`
 rows=($rows)
-unset rows[${#rows[@]}-1]
+#unset rows[${#rows[@]}-1]
 
 cd $dir
 Rscript --verbose $dir/comparePDFs.r $workdir/${outID}.RData $output ${rows[@]} 2>&1