diff wrapper.sh @ 3:38c038c17d0c draft

Uploaded

--- a/wrapper.sh	Wed Aug 13 07:32:38 2014 -0400
+++ b/wrapper.sh	Wed Aug 13 09:07:54 2014 -0400
@@ -14,6 +14,7 @@
 IDs=($IDs)
 ref=${10}
 output=${11}
+selection=${12}
 outID="result"
 
 echo "testID = $testID"
@@ -42,9 +43,16 @@
 		id=${IDs[$count]}
 		echo "id=$id"
 		unzip $current -d $PWD/$id/ >> $PWD/unziplog.log
-		filename="$PWD/gappednt_${id}.txt"
-		cat $PWD/$id/*/2_* | cut -f2,4,7 > $filename
-		python $dir/script_imgt.py --input $filename --ref $ref --output $fasta --id $id
+		summaryfile="$PWD/summary_${id}.txt"
+		gappedfile="$PWD/gappednt_${id}.txt"
+		filtered="$PWD/filtered_${id}.txt"
+		cat $PWD/$id/*/1_* > $summaryfile
+		cat $PWD/$id/*/2_* > $gappedfile
+		Rscript $dir/filter.r $summaryfile $gappedfile "$selection" $filtered
+		
+		final="$PWD/final_${id}.txt"
+		cat $filtered | cut -f2,4,7 > $final
+		python $dir/script_imgt.py --input $final --ref $ref --output $fasta --id $id
 	else
 		python $dir/script_xlsx.py --input $current --ref $ref --output $fasta
 	fi