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1 #!/bin/bash
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2 dir="$(cd "$(dirname "$0")" && pwd)"
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3
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4 #define_clones.sh $input $noparse $scores $regions $out_file
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5
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6 type=$1
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7 input=$2
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8
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9 mkdir -p $PWD/outdir
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10
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11 cp $input $PWD/input.tab #file has to have a ".tab" extension
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12
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13 if [ "bygroup" == "$type" ] ; then
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14 mode=$3
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15 act=$4
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16 model=$5
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17 norm=$6
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18 sym=$7
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19 link=$8
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20 dist=$9
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21 output=${10}
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22 output2=${11}
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23
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72
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24 DefineClones.py -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --mode $mode --act $act --model $model --dist $dist --norm $norm --sym $sym --link $link
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25
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26 Rscript $dir/define_clones.r $PWD/outdir/output_clone-pass.tab $output2 2>&1
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27 else
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28 method=$3
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29 output=$4
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30 output2=$5
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31
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72
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32 DefineClones.py hclust -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --method $method
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33
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34 Rscript $dir/define_clones.r $PWD/outdir/output_clone-pass.tab $output2 2>&1
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35 fi
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36
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37 cp $PWD/outdir/output_clone-pass.tab $output
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38
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39 rm -rf $PWD/outdir/
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