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