Mercurial > repos > davidvanzessen > mutation_analysis

comparison wrapper.sh @ 12:257e98fd3b54 draft

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author davidvanzessen
date Mon, 30 Mar 2015 05:06:45 -0400
parents 069419cccba4
children 8a40634fd4b3
comparison
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11:b0242cd1da34 12:257e98fd3b54
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 15
16 16
17 echo "identification" 17 echo "identification"
18 python $dir/gene_identification.py --input $PWD/summary.txt --output $PWD/annotatedsummary.txt 18 python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/annotatedsummary.txt
19 echo "merging" 19 echo "merging"
20 Rscript $dir/merge_and_filter.r $PWD/annotatedsummary.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $outdir/merged.txt $outdir/unmatched.txt 20 Rscript $dir/merge_and_filter.r $outdir/annotatedsummary.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $outdir/merged.txt $outdir/unmatched.txt
21 21
22 genes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm" 22 genes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm"
23 echo "R mutation analysis" 23 echo "R mutation analysis"
24 Rscript $dir/mutation_analysis.r $outdir/merged.txt $genes $outdir 2>&1 24 Rscript $dir/mutation_analysis.r $outdir/merged.txt $genes $outdir 2>&1
25 echo "python mutation analysis" 25 echo "python mutation analysis"