Mercurial > repos > davidvanzessen > change_o

comparison define_clones.sh @ 0:183edf446dcf draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author davidvanzessen
date Mon, 17 Jul 2017 07:44:27 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:183edf446dcf
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 echo "defineclones: $PWD/outdir"
12
13 cp $input $PWD/input.tab #file has to have a ".tab" extension
14
15 if [ "bygroup" == "$type" ] ; then
16 mode=$3
17 act=$4
18 model=$5
19 norm=$6
20 sym=$7
21 link=$8
22 dist=$9
23 output=${10}
24 output2=${11}
25
26 python3 $dir/DefineClones.py bygroup -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
27 #/home/galaxy/anaconda3/bin/python $dir/DefineClones.py bygroup -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
28
29 Rscript $dir/define_clones.r $PWD/outdir/output_clone-pass.tab $output2 2>&1
30 else
31 method=$3
32 output=$4
33 output2=$5
34
35 python3 $dir/DefineClones.py hclust -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --method $method
36 #/home/galaxy/anaconda3/bin/python $dir/DefineClones.py hclust -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --method $method
37
38 Rscript $dir/define_clones.r $PWD/outdir/output_clone-pass.tab $output2 2>&1
39 fi
40
41 cp $PWD/outdir/output_clone-pass.tab $output