Mercurial > repos > davidvanzessen > mutation_analysis

comparison wrapper.sh @ 31:c623690e3b81 draft

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author davidvanzessen
date Thu, 09 Apr 2015 08:52:18 -0400
parents 2433a1e110e1
children 2a7343e4be5a
comparison
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30:7e44617c9ca4 31:c623690e3b81
44 44
45 genes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm" 45 genes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm"
46 echo "R mutation analysis" 46 echo "R mutation analysis"
47 Rscript $dir/mutation_analysis.r $outdir/merged.txt $genes $outdir ${include_fr1} 2>&1 47 Rscript $dir/mutation_analysis.r $outdir/merged.txt $genes $outdir ${include_fr1} 2>&1
48 echo "python mutation analysis" 48 echo "python mutation analysis"
49 python $dir/mutation_analysis.py --input $outdir/merged.txt --genes $genes --output $outdir/hotspot_analysis.txt 49 python $dir/mutation_analysis.py --input $outdir/merged.txt --genes $genes --includefr1 "${inlcude_fr1}" --output $outdir/hotspot_analysis.txt
50 echo "R AA histogram" 50 echo "R AA histogram"
51 Rscript $dir/aa_histogram.r $outdir/aa_mutations.txt $outdir/aa_histogram.png 2>&1 51 Rscript $dir/aa_histogram.r $outdir/aa_mutations.txt $outdir/aa_histogram.png 2>&1
52 52
53 cat $outdir/mutations.txt $outdir/hotspot_analysis.txt > $outdir/result.txt 53 cat $outdir/mutations.txt $outdir/hotspot_analysis.txt > $outdir/result.txt
54 54