Mercurial > repos > davidvanzessen > mutation_analysis

comparison wrapper.sh @ 90:f0e8dac22c6e draft

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Uploaded
author davidvanzessen
date Wed, 01 Jun 2016 05:03:24 -0400
parents 480fdd383fdb
children b869a126e2c4
comparison
equal deleted inserted replaced
89:480fdd383fdb 90:f0e8dac22c6e
74 fi 74 fi
75 75
76 echo "---------------- merge_and_filter.r ----------------" 76 echo "---------------- merge_and_filter.r ----------------"
77 echo "---------------- merge_and_filter.r ----------------<br />" >> $output 77 echo "---------------- merge_and_filter.r ----------------<br />" >> $output
78 78
79 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} 2>&1 79 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/before_unique_filter.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${class_filter} 2>&1
80 80
81 echo "---------------- mutation_analysis.r ----------------" 81 echo "---------------- mutation_analysis.r ----------------"
82 echo "---------------- mutation_analysis.r ----------------<br />" >> $output 82 echo "---------------- mutation_analysis.r ----------------<br />" >> $output
83 83
84 classes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm,unmatched" 84 classes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm,unmatched"
102 102
103 echo "---------------- sequence_overview.r ----------------" 103 echo "---------------- sequence_overview.r ----------------"
104 104
105 mkdir $outdir/sequence_overview 105 mkdir $outdir/sequence_overview
106 106
107 Rscript $dir/sequence_overview.r $outdir/identified_genes.txt $PWD/sequences.txt $outdir/merged.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt 2>&1 107 #Rscript $dir/sequence_overview.r $outdir/identified_genes.txt $PWD/sequences.txt $outdir/merged.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt 2>&1
108 #Rscript $dir/sequence_overview.r $outdir/before_unique_filter.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt 2>&1 108 Rscript $dir/sequence_overview.r $outdir/before_unique_filter.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt 2>&1
109 109
110 echo "<table border='1'>" > $outdir/base_overview.html 110 echo "<table border='1'>" > $outdir/base_overview.html
111 111
112 while read ID class seq A C G T 112 while read ID class seq A C G T
113 do 113 do