Mercurial > repos > davidvanzessen > argalaxy_tools

comparison imgt_loader/imgt_loader.sh @ 40:106275b54470 draft

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Uploaded
author davidvanzessen
date Tue, 30 May 2017 07:26:33 -0400
parents 798b62942b4b
children 124b7fd92a3e
comparison
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39:bad6a9a53ae7 40:106275b54470
64 find $PWD/$name/files -iname "3_*" -exec cat {} + > $PWD/$name/sequences.txt 64 find $PWD/$name/files -iname "3_*" -exec cat {} + > $PWD/$name/sequences.txt
65 find $PWD/$name/files -iname "4_*" -exec cat {} + > $PWD/$name/gapped_aa.txt 65 find $PWD/$name/files -iname "4_*" -exec cat {} + > $PWD/$name/gapped_aa.txt
66 find $PWD/$name/files -iname "5_*" -exec cat {} + > $PWD/$name/aa.txt 66 find $PWD/$name/files -iname "5_*" -exec cat {} + > $PWD/$name/aa.txt
67 find $PWD/$name/files -iname "6_*" -exec cat {} + > $PWD/$name/junction.txt 67 find $PWD/$name/files -iname "6_*" -exec cat {} + > $PWD/$name/junction.txt
68 68
69 echo "summ.txt `cat $PWD/$name/summ.txt | wc -l`"
70 echo "aa.txt `cat $PWD/$name/aa.txt | wc -l`"
71
69 #python $dir/imgt_loader.py --summ $PWD/$name/summ.txt --aa $PWD/$name/aa.txt --junction $PWD/$name/junction.txt --output $output 72 #python $dir/imgt_loader.py --summ $PWD/$name/summ.txt --aa $PWD/$name/aa.txt --junction $PWD/$name/junction.txt --output $output
70 73
71 Rscript --verbose $dir/imgt_loader.r $PWD/$name/summ.txt $PWD/$name/sequences.txt $PWD/$name/aa.txt $PWD/$name/junction.txt $PWD/$name/gapped_aa.txt $output 2>&1 74 Rscript --verbose $dir/imgt_loader.r $PWD/$name/summ.txt $PWD/$name/sequences.txt $PWD/$name/aa.txt $PWD/$name/junction.txt $PWD/$name/gapped_aa.txt $output 2>&1