Mercurial > repos > davidvanzessen > mutation_analysis

comparison wrapper.sh @ 41:1b45c7d7d941 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author davidvanzessen
date Mon, 02 Nov 2015 09:20:13 -0500
parents e022c21f8c47
children 7304b91757a8
comparison
equal deleted inserted replaced
40:e022c21f8c47 41:1b45c7d7d941
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/*/3_* > $PWD/sequences.txt
27 cat $PWD/files/*/6_* > $PWD/junction.txt 28 cat $PWD/files/*/6_* > $PWD/junction.txt
28 cat $PWD/files/*/7_* > $PWD/mutationanalysis.txt 29 cat $PWD/files/*/7_* > $PWD/mutationanalysis.txt
29 cat $PWD/files/*/8_* > $PWD/mutationstats.txt 30 cat $PWD/files/*/8_* > $PWD/mutationstats.txt
30 cat $PWD/files/*/10_* > $PWD/hotspots.txt 31 cat $PWD/files/*/10_* > $PWD/hotspots.txt
31 32
52 fi 53 fi
53 54
54 55
55 56
56 echo "merging" 57 echo "merging"
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 58 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
58 59
59 genes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm" 60 genes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm"
60 echo "R mutation analysis" 61 echo "R mutation analysis"
61 Rscript $dir/mutation_analysis.r $outdir/merged.txt $genes $outdir ${include_fr1} 2>&1 62 Rscript $dir/mutation_analysis.r $outdir/merged.txt $genes $outdir ${include_fr1} 2>&1
62 echo "python mutation analysis" 63 echo "python mutation analysis"