Mercurial > repos > davidvanzessen > mutation_analysis

comparison wrapper.sh @ 3:a0b27058dcac draft

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Uploaded
author davidvanzessen
date Wed, 17 Sep 2014 07:25:17 -0400
parents 2f4298673519
children 069419cccba4
comparison
equal deleted inserted replaced
2:2f4298673519 3:a0b27058dcac
1 #!/bin/bash 1 #!/bin/bash
2 dir="$(cd "$(dirname "$0")" && pwd)" 2 dir="$(cd "$(dirname "$0")" && pwd)"
3
4 input=$1 3 input=$1
5 output=$2 4 output=$2
6 outdir=$3 5 outdir=$3
7 title=$4 6 title=$4
8 mkdir $outdir 7 mkdir $outdir
10 unzip $input -d $PWD/files/ > $PWD/unziplog.log 9 unzip $input -d $PWD/files/ > $PWD/unziplog.log
11 cat $PWD/files/*/1_* > $PWD/summary.txt 10 cat $PWD/files/*/1_* > $PWD/summary.txt
12 cat $PWD/files/*/7_* > $PWD/mutationanalysis.txt 11 cat $PWD/files/*/7_* > $PWD/mutationanalysis.txt
13 cat $PWD/files/*/8_* > $PWD/mutationstats.txt 12 cat $PWD/files/*/8_* > $PWD/mutationstats.txt
14 cat $PWD/files/*/10_* > $PWD/hotspots.txt 13 cat $PWD/files/*/10_* > $PWD/hotspots.txt
14
15 cp $dir/HS12RSS.txt $outdir/ 15 cp $dir/HS12RSS.txt $outdir/
16 cp $dir/HS23RSS.txt $outdir/ 16 cp $dir/HS23RSS.txt $outdir/
17 17
18 mkdir $outdir/identification/ 18 mkdir $outdir/identification/
19 python $dir/gene_identification.py --input $PWD/summary.txt --outdir $outdir/identification/ 19 python $dir/gene_identification.py --input $PWD/summary.txt --outdir $outdir/identification/