|
82
|
1 #!/bin/bash
|
|
|
2 # something to make it commit, with unix line ends
|
|
|
3 dir="$(cd "$(dirname "$0")" && pwd)"
|
|
|
4
|
|
|
5 #define_clones.sh $input $noparse $scores $regions $out_file
|
|
|
6
|
|
|
7 type=$1
|
|
|
8 input=$2
|
|
|
9
|
|
|
10 mkdir -p $PWD/outdir
|
|
|
11
|
|
|
12 cp $input $PWD/input.tab #file has to have a ".tab" extension
|
|
|
13
|
|
|
14 if [ "bygroup" == "$type" ] ; then
|
|
|
15 mode=$3
|
|
|
16 act=$4
|
|
|
17 model=$5
|
|
|
18 norm=$6
|
|
|
19 sym=$7
|
|
|
20 link=$8
|
|
|
21 dist=$9
|
|
|
22 output=${10}
|
|
|
23 output2=${11}
|
|
|
24
|
|
|
25 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
|
|
|
26
|
|
|
27 Rscript $dir/define_clones.r $PWD/outdir/output_clone-pass.tab $output2 2>&1
|
|
|
28 else
|
|
|
29 method=$3
|
|
|
30 output=$4
|
|
|
31 output2=$5
|
|
|
32
|
|
|
33 DefineClones.py hclust -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --method $method
|
|
|
34
|
|
|
35 Rscript $dir/define_clones.r $PWD/outdir/output_clone-pass.tab $output2 2>&1
|
|
|
36 fi
|
|
|
37
|
|
|
38 cp $PWD/outdir/output_clone-pass.tab $output
|
|
|
39
|
|
|
40 rm -rf $PWD/outdir/
|
