Mercurial > repos > davidvanzessen > mutation_analysis

comparison wrapper.sh @ 66:88e0e7665086 draft

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author davidvanzessen
date Wed, 06 Apr 2016 05:54:13 -0400
parents 0fdd90f7c654
children 7acdcd5c52ef
comparison
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65:ae8b721a2964 66:88e0e7665086
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 filter_unique=${10}
14 class_filter=${11}
14 mkdir $outdir 15 mkdir $outdir
15 16
16 echo "---------------- read parameters ----------------" 17 echo "---------------- read parameters ----------------"
17 echo "---------------- read parameters ----------------<br />" > $output 18 echo "---------------- read parameters ----------------<br />" > $output
18 19
76 fi 77 fi
77 78
78 echo "---------------- merge_and_filter.r ----------------" 79 echo "---------------- merge_and_filter.r ----------------"
79 echo "---------------- merge_and_filter.r ----------------<br />" >> $output 80 echo "---------------- merge_and_filter.r ----------------<br />" >> $output
80 81
81 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} 82 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} ${class_filter}
82 83
83 echo "---------------- mutation_analysis.r ----------------" 84 echo "---------------- mutation_analysis.r ----------------"
84 echo "---------------- mutation_analysis.r ----------------<br />" >> $output 85 echo "---------------- mutation_analysis.r ----------------<br />" >> $output
85 86
86 genes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm" 87 genes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm"