Mercurial > repos > davidvanzessen > mutation_analysis

comparison wrapper.sh @ 52:d3542f87a304 draft

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Uploaded
author davidvanzessen
date Fri, 29 Jan 2016 08:11:31 -0500
parents 8ba6afa1247a
children 7290a88ea202
comparison
equal deleted inserted replaced
51:d4e72eeea640 52:d3542f87a304
8 title=$5 8 title=$5
9 include_fr1=$6 9 include_fr1=$6
10 functionality=$7 10 functionality=$7
11 unique=$8 11 unique=$8
12 naive_output=$9 12 naive_output=$9
13 filter_unique=${10}
13 mkdir $outdir 14 mkdir $outdir
14 15
15 type="`file $input`" 16 type="`file $input`"
16 if [[ "$type" == *"Zip archive"* ]] ; then 17 if [[ "$type" == *"Zip archive"* ]] ; then
17 echo "Zip archive" 18 echo "Zip archive"
55 fi 56 fi
56 57
57 58
58 59
59 echo "merging" 60 echo "merging"
60 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $outdir/identified_genes.txt $outdir/merged.txt $outdir/unmatched.txt $method $functionality $unique 61 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $outdir/identified_genes.txt $outdir/merged.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique}
61 62
62 genes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm" 63 genes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm"
63 echo "R mutation analysis" 64 echo "R mutation analysis"
64 Rscript $dir/mutation_analysis.r $outdir/merged.txt $genes $outdir ${include_fr1} 2>&1 65 Rscript $dir/mutation_analysis.r $outdir/merged.txt $genes $outdir ${include_fr1} 2>&1
65 echo "python mutation analysis" 66 echo "python mutation analysis"