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comparison define_clones.sh @ 0:dda9b2e72e2b draft

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author davidvanzessen
date Tue, 03 May 2016 09:52:21 -0400
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children 326165da9ece
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-1:000000000000 0:dda9b2e72e2b
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 $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
23 /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
24 else
25 method=$3
26 output=$4
27
28 /data/users/david/anaconda3/bin/python $dir/DefineClones.py hclust -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --method $method
29 fi
30
31 cp $PWD/outdir/output_clone-pass.tab $output