Mercurial > repos > davidvanzessen > mutation_analysis

comparison wrapper.sh @ 69:7acdcd5c52ef draft

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Uploaded
author davidvanzessen
date Fri, 22 Apr 2016 05:07:10 -0400
parents 88e0e7665086
children becea91089ed
comparison
equal deleted inserted replaced
68:3636d5aaa127 69:7acdcd5c52ef
7 outdir=$4 7 outdir=$4
8 title=$5 8 title=$5
9 include_fr1=$6 9 include_fr1=$6
10 functionality=$7 10 functionality=$7
11 unique=$8 11 unique=$8
12 naive_output=$9 12 naive_output_ca=$9
13 filter_unique=${10} 13 naive_output_cg=${10}
14 class_filter=${11} 14 naive_output_cm=${11}
15 filter_unique=${12}
16 class_filter=${13}
15 mkdir $outdir 17 mkdir $outdir
16 18
17 echo "---------------- read parameters ----------------" 19 echo "---------------- read parameters ----------------"
18 echo "---------------- read parameters ----------------<br />" > $output 20 echo "---------------- read parameters ----------------<br />" > $output
19 21
220 222
221 if [[ "$naive_output" != "None" ]] 223 if [[ "$naive_output" != "None" ]]
222 then 224 then
223 echo "---------------- imgt_loader.r ----------------" 225 echo "---------------- imgt_loader.r ----------------"
224 #python $dir/imgt_loader.py --summ $PWD/summary.txt --aa $PWD/aa.txt --junction $PWD/junction.txt --output $naive_output 226 #python $dir/imgt_loader.py --summ $PWD/summary.txt --aa $PWD/aa.txt --junction $PWD/junction.txt --output $naive_output
225 Rscript --verbose $dir/imgt_loader.r $PWD/summary.txt $PWD/aa.txt $PWD/junction.txt ${naive_output} 2>&1 227 Rscript --verbose $dir/imgt_loader.r $PWD/summary.txt $PWD/aa.txt $PWD/junction.txt ${naive_output_ca} 2>&1
226 echo "---------------- naive_output.r ----------------" 228 echo "---------------- naive_output.r ----------------"
227 Rscript $dir/naive_output.r $naive_output $outdir/merged.txt $naive_output 2>&1 229 Rscript $dir/naive_output.r $naive_output_ca $outdir/merged.txt $naive_output_ca $naive_output_cg $naive_output_cm 2>&1
228 fi 230 fi
229 231
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232 234