Mercurial > repos > davidvanzessen > argalaxy_tools

diff imgt_loader/imgt_loader.sh @ 35:d7580295e13b draft

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author davidvanzessen
date Fri, 22 Jan 2016 08:45:29 -0500
parents 010402c959aa
children
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--- a/imgt_loader/imgt_loader.sh	Mon Jan 18 07:55:31 2016 -0500
+++ b/imgt_loader/imgt_loader.sh	Fri Jan 22 08:45:29 2016 -0500
@@ -64,4 +64,6 @@
 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
+#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