Mercurial > repos > davidvanzessen > mutation_analysis

comparison wrapper.sh @ 105:e4957ad476a2 draft

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author davidvanzessen
date Thu, 23 Jun 2016 03:58:03 -0400
parents 603a10976e9c
children 01c9993865af
comparison
equal deleted inserted replaced
104:603a10976e9c 105:e4957ad476a2
144 echo "---------------- mutation_analysis.py ----------------<br />" >> $log 144 echo "---------------- mutation_analysis.py ----------------<br />" >> $log
145 145
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 />" >> $log
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
153 echo "---------------- aa_histogram.r ca ----------------"
154 echo "---------------- aa_histogram.r ca ----------------<br />" >> $log
155
152 Rscript $dir/aa_histogram.r $outdir/aa_mutations_ca.txt $outdir/aa_histogram_ca.png "ca" 2>&1 156 Rscript $dir/aa_histogram.r $outdir/aa_mutations_ca.txt $outdir/aa_histogram_ca.png "ca" 2>&1
157
158 echo "---------------- aa_histogram.r cg ----------------"
159 echo "---------------- aa_histogram.r cg ----------------<br />" >> $log
160
153 Rscript $dir/aa_histogram.r $outdir/aa_mutations_cg.txt $outdir/aa_histogram_cg.png "cg" 2>&1 161 Rscript $dir/aa_histogram.r $outdir/aa_mutations_cg.txt $outdir/aa_histogram_cg.png "cg" 2>&1
162
163 echo "---------------- aa_histogram.r cm ----------------"
164 echo "---------------- aa_histogram.r cm ----------------<br />" >> $log
165
154 Rscript $dir/aa_histogram.r $outdir/aa_mutations_cm.txt $outdir/aa_histogram_cm.png "cm" 2>&1 166 Rscript $dir/aa_histogram.r $outdir/aa_mutations_cm.txt $outdir/aa_histogram_cm.png "cm" 2>&1
155 167
156 genes=(ca ca1 ca2 cg cg1 cg2 cg3 cg4 cm) 168 genes=(ca ca1 ca2 cg cg1 cg2 cg3 cg4 cm)
157 169
158 funcs=(sum mean median) 170 funcs=(sum mean median)
365 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>&1 377 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
366 fi 378 fi
367 379
368 echo "</table>" >> $outdir/base_overview.html 380 echo "</table>" >> $outdir/base_overview.html
369 381
382 mv $log $outdir/log.html
383
384 cp $outdir/index.html $log
385
370 echo "---------------- Done! ----------------" 386 echo "---------------- Done! ----------------"
371 echo "---------------- Done! ----------------<br />" >> $log 387 echo "---------------- Done! ----------------<br />" >> $log
372 388
373 mv $log $outdir/log.html
374
375 mv $outdir/index.html $log
376