Mercurial > repos > davidvanzessen > mutation_analysis

comparison wrapper.sh @ 80:a4c2ddeadec0 draft

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Uploaded
author davidvanzessen
date Thu, 12 May 2016 10:51:55 -0400
parents 0513b46178c4
children a778156dad3d
comparison
equal deleted inserted replaced
79:0513b46178c4 80:a4c2ddeadec0
225 225
226 if [[ "$naive_output" != "None" ]] 226 if [[ "$naive_output" != "None" ]]
227 then 227 then
228 echo "---------------- imgt_loader.r ----------------" 228 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 229 #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 ${naive_output_ca} 2>&1 230 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 ----------------" 231 echo "---------------- naive_output.r ----------------"
232 Rscript $dir/naive_output.r $naive_output_ca $outdir/merged.txt $naive_output_ca $naive_output_cg $naive_output_cm 2>&1 232 Rscript $dir/naive_output.r $outdir/loader_output.txt $outdir/merged.txt ${naive_output_ca} ${naive_output_cg} ${naive_output_cm} 2>&1
233 fi 233 fi
234 234
235 echo "---------------- sequence_overview.r ----------------" 235 echo "---------------- sequence_overview.r ----------------"
236 236
237 mkdir $outdir/sequence_overview 237 mkdir $outdir/sequence_overview