Mercurial > repos > davidvanzessen > mutation_analysis

comparison wrapper.sh @ 108:6add3e66f4fa draft

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author davidvanzessen
date Wed, 13 Jul 2016 09:04:15 -0400
parents 01c9993865af
children ade5cf6fd2dc
comparison
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107:01c9993865af 108:6add3e66f4fa
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 cp $outdir/aa_mutations.txt $outdir/aa_mutations_count.txt
152 Rscript $dir/aa_histogram.r $outdir/aa_id_mutations.txt $outdir/absent_aa_id.txt "ca,cg,cm" $outdir/ 2>&1 151 Rscript $dir/aa_histogram.r $outdir/aa_id_mutations.txt $outdir/absent_aa_id.txt "ca,cg,cm" $outdir/ 2>&1
153 mv $outdir/aa_histogram_.png $outdir/aa_histogram.png 152 mv $outdir/aa_histogram_.png $outdir/aa_histogram.png
153 mv $outdir/aa_histogram_.txt $outdir/aa_histogram.txt
154 154
155 genes=(ca ca1 ca2 cg cg1 cg2 cg3 cg4 cm) 155 genes=(ca ca1 ca2 cg cg1 cg2 cg3 cg4 cm)
156 156
157 funcs=(sum mean median) 157 funcs=(sum mean median)
158 158