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1 #SrcFolder="/data/zhang/wuj/scripts/SpliceTrap.0.8";
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2
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3 outputname=$1;
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4 CutoffLevel=$2;
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5 Outputfolder=$3
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6 SrcFolder=$5
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7 JunctionCut=$4
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8 noIRM=$8
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9
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10 echo "CUTOFF: Entering cutoff step...";
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11 echo "CUTOFF: Cache folder: $outputname.filter"
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12 mkdir $Outputfolder/$outputname.filter
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13 cd $Outputfolder/$outputname.filter
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14 ln -s ../$outputname.ratio
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15 ln -s ../$outputname.nums
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16 echo "CUTOFF: spliting file....and generating shell scripts..."
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17 split -11000 $outputname.ratio
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18
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19 for ratiofiles in x*
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20 do
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21 echo "perl $SrcFolder/ApplyCutoff.jie.pl $ratiofiles $CutoffLevel $JunctionCut $noIRM > $ratiofiles.out" >>filter.sh
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22 done
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23
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24 echo "CUTOFF: submit scripts..."
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25 perl $SrcFolder/batchqsub.pl filter.sh
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26 echo "CUTOFF: merging file...."
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27 cat *.out >../$outputname.raw
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28 cd ../
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29 #perl /data/zhang/wuj/tools/SpliceTrap.0.8/ApplyCutoff.jie.pl $outputname.ratio $outputname.nums 8 >$outputname.txt
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30 if [ "$noIRM" ];then
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31 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
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32 else
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33 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
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34 fi
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35 rm $outputname.filter -rf
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36
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