Mercurial > repos > davidvanzessen > mutation_analysis

comparison wrapper.sh @ 81:a778156dad3d draft

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Uploaded
author davidvanzessen
date Tue, 17 May 2016 04:17:38 -0400
parents a4c2ddeadec0
children 564c4f6da203
comparison
equal deleted inserted replaced
80:a4c2ddeadec0 81:a778156dad3d
165 echo "<a href='merged.txt'>all data</a><br />" >> $output 165 echo "<a href='merged.txt'>all data</a><br />" >> $output
166 echo "<a href='mutation_by_id.txt'>mutations by id</a><br />" >> $output 166 echo "<a href='mutation_by_id.txt'>mutations by id</a><br />" >> $output
167 echo "<a href='aa_id_mutations.txt'>AA mutations location by id</a><br />" >> $output 167 echo "<a href='aa_id_mutations.txt'>AA mutations location by id</a><br />" >> $output
168 echo "<a href='absent_aa_id.txt'>Absant AA locations by id</a><br />" >> $output 168 echo "<a href='absent_aa_id.txt'>Absant AA locations by id</a><br />" >> $output
169 echo "<a href='sequence_overview/index.html'>Sequence Overview</a><br />" >> $output 169 echo "<a href='sequence_overview/index.html'>Sequence Overview</a><br />" >> $output
170 echo "<a href='base_overview.html'>Base overview</a><br />" >> $output
170 171
171 echo "---------------- images ----------------" 172 echo "---------------- images ----------------"
172 173
173 echo "<img src='all.png'/><br />" >> $output 174 echo "<img src='all.png'/><br />" >> $output
174 echo "<a href='all.txt'>download data</a><br />" >> $output 175 echo "<a href='all.txt'>download data</a><br />" >> $output
227 then 228 then
228 echo "---------------- imgt_loader.r ----------------" 229 echo "---------------- imgt_loader.r ----------------"
229 #python $dir/imgt_loader.py --summ $PWD/summary.txt --aa $PWD/aa.txt --junction $PWD/junction.txt --output $naive_output 230 #python $dir/imgt_loader.py --summ $PWD/summary.txt --aa $PWD/aa.txt --junction $PWD/junction.txt --output $naive_output
230 Rscript --verbose $dir/imgt_loader.r $PWD/summary.txt $PWD/aa.txt $PWD/junction.txt $outdir/loader_output.txt 2>&1 231 Rscript --verbose $dir/imgt_loader.r $PWD/summary.txt $PWD/aa.txt $PWD/junction.txt $outdir/loader_output.txt 2>&1
231 echo "---------------- naive_output.r ----------------" 232 echo "---------------- naive_output.r ----------------"
232 Rscript $dir/naive_output.r $outdir/loader_output.txt $outdir/merged.txt ${naive_output_ca} ${naive_output_cg} ${naive_output_cm} 2>&1 233 Rscript $dir/naive_output.r $outdir/loader_output.txt $outdir/merged.txt ${naive_output_ca} ${naive_output_cg} ${naive_output_cm} $outdir/ntoverview.txt $outdir/ntsum.txt 2>&1
233 fi 234 fi
234 235
235 echo "---------------- sequence_overview.r ----------------" 236 echo "---------------- sequence_overview.r ----------------"
236 237
237 mkdir $outdir/sequence_overview 238 mkdir $outdir/sequence_overview
238 239
239 Rscript $dir/sequence_overview.r $outdir/identified_genes.txt $PWD/sequences.txt $outdir/sequence_overview 2>&1 240 Rscript $dir/sequence_overview.r $outdir/identified_genes.txt $PWD/sequences.txt $outdir/sequence_overview 2>&1
240 241
241 242 echo "<table border='1'>" > $outdir/base_overview.html
243
244 while read ID class seq A C G T
245 do
246 echo "<tr><td>$ID</td><td>$class</td><td>$A</td><td>$C</td><td>$G</td><td>$T</td></tr>" >> $outdir/base_overview.html
247 done < $outdir/sequence_overview/ntoverview.txt
248
249 echo "</table>" >> $outdir/base_overview.html
250
251 echo "---------------- Done! ----------------"
242 252
243 253
244 254
245 255
246 256