Mercurial > repos > davidvanzessen > mutation_analysis

comparison wrapper.sh @ 107:01c9993865af draft

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author davidvanzessen
date Wed, 13 Jul 2016 08:04:13 -0400
parents e4957ad476a2
children 6add3e66f4fa
comparison
equal deleted inserted replaced
106:074ae1e30e8f 107:01c9993865af
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 />" >> $log 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 cp $outdir/aa_mutations.txt $outdir/aa_mutations_count.txt
152 152 Rscript $dir/aa_histogram.r $outdir/aa_id_mutations.txt $outdir/absent_aa_id.txt "ca,cg,cm" $outdir/ 2>&1
153 echo "---------------- aa_histogram.r ca ----------------" 153 mv $outdir/aa_histogram_.png $outdir/aa_histogram.png
154 echo "---------------- aa_histogram.r ca ----------------<br />" >> $log
155
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
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
166 Rscript $dir/aa_histogram.r $outdir/aa_mutations_cm.txt $outdir/aa_histogram_cm.png "cm" 2>&1
167 154
168 genes=(ca ca1 ca2 cg cg1 cg2 cg3 cg4 cm) 155 genes=(ca ca1 ca2 cg cg1 cg2 cg3 cg4 cm)
169 156
170 funcs=(sum mean median) 157 funcs=(sum mean median)
171 158
382 mv $log $outdir/log.html 369 mv $log $outdir/log.html
383 370
384 cp $outdir/index.html $log 371 cp $outdir/index.html $log
385 372
386 echo "---------------- Done! ----------------" 373 echo "---------------- Done! ----------------"
387 echo "---------------- Done! ----------------<br />" >> $log 374 echo "---------------- Done! ----------------<br />" >> $outdir/log.html
388 375