Mercurial > repos > davidvanzessen > mutation_analysis

comparison wrapper.sh @ 85:07f7da724a77 draft

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Uploaded
author davidvanzessen
date Thu, 26 May 2016 08:18:13 -0400
parents 041f94f50b34
children 480fdd383fdb
comparison
equal deleted inserted replaced
84:041f94f50b34 85:07f7da724a77
88 88
89 classes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm,unmatched" 89 classes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm,unmatched"
90 echo "R mutation analysis" 90 echo "R mutation analysis"
91 Rscript $dir/mutation_analysis.r $outdir/merged.txt $classes $outdir ${include_fr1} 2>&1 91 Rscript $dir/mutation_analysis.r $outdir/merged.txt $classes $outdir ${include_fr1} 2>&1
92 92
93 #echo "." > $output
94 #exit 0
95
96
97 93
98 echo "---------------- mutation_analysis.py ----------------" 94 echo "---------------- mutation_analysis.py ----------------"
99 echo "---------------- mutation_analysis.py ----------------<br />" >> $output 95 echo "---------------- mutation_analysis.py ----------------<br />" >> $output
100 96
101 python $dir/mutation_analysis.py --input $outdir/merged.txt --genes $classes --includefr1 "${include_fr1}" --output $outdir/hotspot_analysis.txt 97 python $dir/mutation_analysis.py --input $outdir/merged.txt --genes $classes --includefr1 "${include_fr1}" --output $outdir/hotspot_analysis.txt
117 113
118 echo "<table border='1'>" > $outdir/base_overview.html 114 echo "<table border='1'>" > $outdir/base_overview.html
119 115
120 while read ID class seq A C G T 116 while read ID class seq A C G T
121 do 117 do
122 echo "<tr><td>$ID</td><td>$class</td><td>$A</td><td>$C</td><td>$G</td><td>$T</td></tr>" >> $outdir/base_overview.html 118 echo "<tr><td>$ID</td><td>$seq</td><td>$class</td><td>$A</td><td>$C</td><td>$G</td><td>$T</td></tr>" >> $outdir/base_overview.html
123 done < $outdir/sequence_overview/ntoverview.txt 119 done < $outdir/sequence_overview/ntoverview.txt
124 120
125 121
126 echo "<html><center><h1>$title</h1></center>" > $output 122 echo "<html><center><h1>$title</h1></center>" > $output
127 123