diff bin/apply_cutoff.sh @ 1:adc0f7765d85 draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bin/apply_cutoff.sh	Thu Sep 07 15:06:58 2017 -0400
@@ -0,0 +1,36 @@
+#SrcFolder="/data/zhang/wuj/scripts/SpliceTrap.0.8";
+
+outputname=$1;
+CutoffLevel=$2;
+Outputfolder=$3
+SrcFolder=$5
+JunctionCut=$4
+noIRM=$8
+
+echo "CUTOFF: Entering cutoff step...";
+echo "CUTOFF: Cache folder: $outputname.filter"
+mkdir $Outputfolder/$outputname.filter
+cd $Outputfolder/$outputname.filter
+ln -s ../$outputname.ratio
+ln -s ../$outputname.nums
+echo "CUTOFF: spliting file....and generating shell scripts..."
+split -11000 $outputname.ratio
+
+for ratiofiles in  x*
+do
+        echo "perl $SrcFolder/ApplyCutoff.jie.pl $ratiofiles $CutoffLevel $JunctionCut $noIRM > $ratiofiles.out" >>filter.sh
+done
+
+echo "CUTOFF: submit scripts..."
+perl $SrcFolder/batchqsub.pl filter.sh
+echo "CUTOFF: merging file...."
+cat *.out >../$outputname.raw
+cd ../
+#perl /data/zhang/wuj/tools/SpliceTrap.0.8/ApplyCutoff.jie.pl $outputname.ratio $outputname.nums 8 >$outputname.txt
+if [ "$noIRM" ];then
+	awk '{printf $22"\t"$2"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$12"\t"$13"\t"$14"\t"$15"\n"}' $outputname.raw >$outputname.txt
+else
+	awk '{printf $22"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$12"\t"$13"\t"$14"\t"$15"\n"}' $outputname.raw >$outputname.txt
+fi
+rm $outputname.filter -rf
+