Mercurial > repos > davidvanzessen > argalaxy_tools
diff imgt_loader/imgt_loader.sh @ 20:9185c3dfc679 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Fri, 27 Jan 2017 03:44:18 -0500 |
| parents | afe85eb6572e |
| children | 798b62942b4b |
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--- a/imgt_loader/imgt_loader.sh Thu Dec 22 03:43:02 2016 -0500 +++ b/imgt_loader/imgt_loader.sh Fri Jan 27 03:44:18 2017 -0500 @@ -61,9 +61,10 @@ tar xJf $input -C $PWD/$name/files fi find $PWD/$name/files -iname "1_*" -exec cat {} + > $PWD/$name/summ.txt +find $PWD/$name/files -iname "3_*" -exec cat {} + > $PWD/$name/sequences.txt find $PWD/$name/files -iname "5_*" -exec cat {} + > $PWD/$name/aa.txt find $PWD/$name/files -iname "6_*" -exec cat {} + > $PWD/$name/junction.txt #python $dir/imgt_loader.py --summ $PWD/$name/summ.txt --aa $PWD/$name/aa.txt --junction $PWD/$name/junction.txt --output $output -Rscript --verbose $dir/imgt_loader.r $PWD/$name/summ.txt $PWD/$name/aa.txt $PWD/$name/junction.txt $output 2>&1 +Rscript --verbose $dir/imgt_loader.r $PWD/$name/summ.txt $PWD/$name/sequences.txt $PWD/$name/aa.txt $PWD/$name/junction.txt $output 2>&1