Mercurial > repos > davidvanzessen > mutation_analysis

comparison wrapper.sh @ 39:7377bf7e632d draft

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Uploaded
author davidvanzessen
date Mon, 02 Nov 2015 04:52:26 -0500
parents 8dba36531e6e
children e022c21f8c47
comparison
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38:6b6dbbcc771d 39:7377bf7e632d
22 mkdir -p $PWD/files/$title 22 mkdir -p $PWD/files/$title
23 tar -xJf $input -C $PWD/files/$title 23 tar -xJf $input -C $PWD/files/$title
24 fi 24 fi
25 25
26 cat $PWD/files/*/1_* > $PWD/summary.txt 26 cat $PWD/files/*/1_* > $PWD/summary.txt
27 cat $PWD/files/*/6_* > $PWD/junction.txt
27 cat $PWD/files/*/7_* > $PWD/mutationanalysis.txt 28 cat $PWD/files/*/7_* > $PWD/mutationanalysis.txt
28 cat $PWD/files/*/8_* > $PWD/mutationstats.txt 29 cat $PWD/files/*/8_* > $PWD/mutationstats.txt
29 cat $PWD/files/*/10_* > $PWD/hotspots.txt 30 cat $PWD/files/*/10_* > $PWD/hotspots.txt
30 31
31 #BLASTN_DIR="/home/galaxy/tmp/blast/ncbi-blast-2.2.30+/bin" 32 #BLASTN_DIR="/home/galaxy/tmp/blast/ncbi-blast-2.2.30+/bin"
51 fi 52 fi
52 53
53 54
54 55
55 echo "merging" 56 echo "merging"
56 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $outdir/identified_genes.txt $outdir/merged.txt $outdir/unmatched.txt $method $functionality $unique 57 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/junction.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $outdir/identified_genes.txt $outdir/merged.txt $outdir/unmatched.txt $method $functionality $unique
57 58
58 genes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm" 59 genes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm"
59 echo "R mutation analysis" 60 echo "R mutation analysis"
60 Rscript $dir/mutation_analysis.r $outdir/merged.txt $genes $outdir ${include_fr1} 2>&1 61 Rscript $dir/mutation_analysis.r $outdir/merged.txt $genes $outdir ${include_fr1} 2>&1
61 echo "python mutation analysis" 62 echo "python mutation analysis"