Mercurial > repos > davidvanzessen > mutation_analysis

comparison wrapper.sh @ 35:8dba36531e6e draft

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Uploaded
author davidvanzessen
date Tue, 23 Jun 2015 10:54:05 -0400
parents d436daae9d68
children 7377bf7e632d
comparison
equal deleted inserted replaced
34:d436daae9d68 35:8dba36531e6e
9 include_fr1=$6 9 include_fr1=$6
10 functionality=$7 10 functionality=$7
11 unique=$8 11 unique=$8
12 mkdir $outdir 12 mkdir $outdir
13 13
14 unzip $input -d $PWD/files/ > $PWD/unziplog.log 14 type="`file $input`"
15 if [[ "$type" == *"Zip archive"* ]] ; then
16 echo "Zip archive"
17 echo "unzip $input -d $PWD/files/"
18 unzip $input -d $PWD/files/
19 elif [[ "$type" == *"XZ compressed data"* ]] ; then
20 echo "ZX archive"
21 echo "tar -xJf $input -C $PWD/files/"
22 mkdir -p $PWD/files/$title
23 tar -xJf $input -C $PWD/files/$title
24 fi
25
15 cat $PWD/files/*/1_* > $PWD/summary.txt 26 cat $PWD/files/*/1_* > $PWD/summary.txt
16 cat $PWD/files/*/7_* > $PWD/mutationanalysis.txt 27 cat $PWD/files/*/7_* > $PWD/mutationanalysis.txt
17 cat $PWD/files/*/8_* > $PWD/mutationstats.txt 28 cat $PWD/files/*/8_* > $PWD/mutationstats.txt
18 cat $PWD/files/*/10_* > $PWD/hotspots.txt 29 cat $PWD/files/*/10_* > $PWD/hotspots.txt
19 30