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comparison change_o/define_clones.sh @ 81:b6f9a640e098 draft

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author davidvanzessen
date Fri, 19 Feb 2021 15:10:54 +0000
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children a103134ee6e0
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80:a4617f1d1d89 81:b6f9a640e098
1 #!/bin/bash
2 dir="$(cd "$(dirname "$0")" && pwd)"
3
4 #define_clones.sh $input $noparse $scores $regions $out_file
5
6 type=$1
7 input=$2
8
9 mkdir -p $PWD/outdir
10
11 cp $input $PWD/input.tab #file has to have a ".tab" extension
12
13 if [ "bygroup" == "$type" ] ; then
14 mode=$3
15 act=$4
16 model=$5
17 norm=$6
18 sym=$7
19 link=$8
20 dist=$9
21 output=${10}
22 output2=${11}
23
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
25
26 Rscript $dir/define_clones.r $PWD/outdir/output_clone-pass.tab $output2 2>&1
27 else
28 method=$3
29 output=$4
30 output2=$5
31
32 DefineClones.py hclust -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --method $method
33
34 Rscript $dir/define_clones.r $PWD/outdir/output_clone-pass.tab $output2 2>&1
35 fi
36
37 cp $PWD/outdir/output_clone-pass.tab $output
38
39 rm -rf $PWD/outdir/