Mercurial > repos > davidvanzessen > mutation_analysis

comparison wrapper.sh @ 15:8a40634fd4b3 draft

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Uploaded
author davidvanzessen
date Mon, 30 Mar 2015 05:11:25 -0400
parents 257e98fd3b54
children 2bb24ebbbc38
comparison
equal deleted inserted replaced
14:6f8392d090bd 15:8a40634fd4b3
10 unzip $input -d $PWD/files/ > $PWD/unziplog.log 10 unzip $input -d $PWD/files/ > $PWD/unziplog.log
11 cat $PWD/files/*/1_* > $PWD/summary.txt 11 cat $PWD/files/*/1_* > $PWD/summary.txt
12 cat $PWD/files/*/7_* > $PWD/mutationanalysis.txt 12 cat $PWD/files/*/7_* > $PWD/mutationanalysis.txt
13 cat $PWD/files/*/8_* > $PWD/mutationstats.txt 13 cat $PWD/files/*/8_* > $PWD/mutationstats.txt
14 cat $PWD/files/*/10_* > $PWD/hotspots.txt 14 cat $PWD/files/*/10_* > $PWD/hotspots.txt
15
16 echo "${BLASTN_DIR}"
15 17
16 18
17 echo "identification" 19 echo "identification"
18 python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/annotatedsummary.txt 20 python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/annotatedsummary.txt
19 echo "merging" 21 echo "merging"