Mercurial > repos > bioitcore > splicetrap
view bin/apply_cutoff.sh @ 4:cd336e593a92 draft
planemo upload
author | bioitcore |
---|---|
date | Thu, 07 Sep 2017 16:53:12 -0400 |
parents | adc0f7765d85 |
children |
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#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