Mercurial > repos > davidvanzessen > mutation_analysis

comparison change_o/define_clones.sh @ 120:613278c1bde0 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author davidvanzessen
date Tue, 16 Aug 2016 09:10:50 -0400
parents
children e87dcca14bd6
comparison
equal deleted inserted replaced
119:626a956f3811 120:613278c1bde0
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 /data/users/david/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
25 #/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
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 /data/users/david/anaconda3/bin/python $dir/DefineClones.py hclust -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --method $method
34 #/home/galaxy/anaconda3/bin/python $dir/DefineClones.py hclust -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --method $method
35
36 Rscript $dir/define_clones.r $PWD/outdir/output_clone-pass.tab $output2 2>&1
37 fi
38
39 cp $PWD/outdir/output_clone-pass.tab $output