Mercurial > repos > davidvanzessen > shm_csr

comparison wrapper.sh @ 4:477e95b098fd draft

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Uploaded
author davidvanzessen
date Mon, 31 Oct 2016 05:05:26 -0400
parents 275ab5175fd6
children 012a738edf5a
comparison
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3:275ab5175fd6 4:477e95b098fd
157 echo "---------------- shm_csr.r ----------------<br />" >> $log 157 echo "---------------- shm_csr.r ----------------<br />" >> $log
158 158
159 classes="IGA,IGA1,IGA2,IGG,IGG1,IGG2,IGG3,IGG4,IGM,unmatched" 159 classes="IGA,IGA1,IGA2,IGG,IGG1,IGG2,IGG3,IGG4,IGM,unmatched"
160 echo "R mutation analysis" 160 echo "R mutation analysis"
161 Rscript $dir/shm_csr.r $outdir/merged.txt $classes $outdir ${empty_region_filter} 2>&1 161 Rscript $dir/shm_csr.r $outdir/merged.txt $classes $outdir ${empty_region_filter} 2>&1
162
163 162
164 echo "---------------- shm_csr.py ----------------" 163 echo "---------------- shm_csr.py ----------------"
165 echo "---------------- shm_csr.py ----------------<br />" >> $log 164 echo "---------------- shm_csr.py ----------------<br />" >> $log
166 165
167 python $dir/shm_csr.py --input $outdir/merged.txt --genes $classes --empty_region_filter "${empty_region_filter}" --output $outdir/hotspot_analysis.txt 166 python $dir/shm_csr.py --input $outdir/merged.txt --genes $classes --empty_region_filter "${empty_region_filter}" --output $outdir/hotspot_analysis.txt