Mercurial > repos > davidvanzessen > mutation_analysis
comparison wrapper.sh @ 104:603a10976e9c draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Wed, 22 Jun 2016 10:07:28 -0400 |
| parents | e6bc976760d4 |
| children | e4957ad476a2 |
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| 103:e21cbe15381f | 104:603a10976e9c |
|---|---|
| 146 python $dir/mutation_analysis.py --input $outdir/merged.txt --genes $classes --includefr1 "${include_fr1}" --output $outdir/hotspot_analysis.txt | 146 python $dir/mutation_analysis.py --input $outdir/merged.txt --genes $classes --includefr1 "${include_fr1}" --output $outdir/hotspot_analysis.txt |
| 147 | 147 |
| 148 echo "---------------- aa_histogram.r ----------------" | 148 echo "---------------- aa_histogram.r ----------------" |
| 149 echo "---------------- aa_histogram.r ----------------<br />" >> $output | 149 echo "---------------- aa_histogram.r ----------------<br />" >> $output |
| 150 | 150 |
| 151 Rscript $dir/aa_histogram.r $outdir/aa_mutations.txt $outdir/aa_histogram.png 2>&1 | 151 Rscript $dir/aa_histogram.r $outdir/aa_mutations.txt $outdir/aa_histogram.png "" 2>&1 |
| 152 Rscript $dir/aa_histogram.r $outdir/aa_mutations_ca.txt $outdir/aa_histogram_ca.png "ca" 2>&1 | |
| 153 Rscript $dir/aa_histogram.r $outdir/aa_mutations_cg.txt $outdir/aa_histogram_cg.png "cg" 2>&1 | |
| 154 Rscript $dir/aa_histogram.r $outdir/aa_mutations_cm.txt $outdir/aa_histogram_cm.png "cm" 2>&1 | |
| 152 | 155 |
| 153 genes=(ca ca1 ca2 cg cg1 cg2 cg3 cg4 cm) | 156 genes=(ca ca1 ca2 cg cg1 cg2 cg3 cg4 cm) |
| 154 | 157 |
| 155 funcs=(sum mean median) | 158 funcs=(sum mean median) |
| 156 | 159 |
| 277 fi | 280 fi |
| 278 if [ -a $outdir/aa_histogram.png ] | 281 if [ -a $outdir/aa_histogram.png ] |
| 279 then | 282 then |
| 280 echo "<img src='aa_histogram.png'/><br />" >> $output | 283 echo "<img src='aa_histogram.png'/><br />" >> $output |
| 281 echo "<a href='aa_histogram.txt'>download data</a><br />" >> $output | 284 echo "<a href='aa_histogram.txt'>download data</a><br />" >> $output |
| 285 echo "<img src='aa_histogram_ca.png'/><br />" >> $output | |
| 286 echo "<a href='aa_histogram_ca.txt'>download data</a><br />" >> $output | |
| 287 echo "<img src='aa_histogram_cg.png'/><br />" >> $output | |
| 288 echo "<a href='aa_histogram_cg.txt'>download data</a><br />" >> $output | |
| 289 echo "<img src='aa_histogram_cm.png'/><br />" >> $output | |
| 290 echo "<a href='aa_histogram_cm.txt'>download data</a><br />" >> $output | |
| 282 fi | 291 fi |
| 283 | 292 |
| 284 for gene in ${genes[@]} | 293 for gene in ${genes[@]} |
| 285 do | 294 do |
| 286 echo "<table border='1'><caption>$gene transition table</caption>" >> $output | 295 echo "<table border='1'><caption>$gene transition table</caption>" >> $output |