diff imgt_loader/imgt_loader.sh @ 28:798b62942b4b draft

Uploaded
author davidvanzessen
date Wed, 01 Mar 2017 10:41:30 -0500
parents 9185c3dfc679
children 106275b54470
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--- a/imgt_loader/imgt_loader.sh	Tue Feb 28 08:10:34 2017 -0500
+++ b/imgt_loader/imgt_loader.sh	Wed Mar 01 10:41:30 2017 -0500
@@ -62,9 +62,10 @@
 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 "4_*" -exec cat {} + > $PWD/$name/gapped_aa.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/sequences.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 $PWD/$name/gapped_aa.txt $output 2>&1