Mercurial > repos > davidvanzessen > argalaxy_tools

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

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Uploaded
author davidvanzessen
date Wed, 01 Mar 2017 10:41:30 -0500
parents 9185c3dfc679
children 106275b54470
comparison
equal deleted inserted replaced
27:b539aeb75980 28:798b62942b4b
60 echo "Trying: tar -xJf $input -C $PWD/files/" 60 echo "Trying: tar -xJf $input -C $PWD/files/"
61 tar xJf $input -C $PWD/$name/files 61 tar xJf $input -C $PWD/$name/files
62 fi 62 fi
63 find $PWD/$name/files -iname "1_*" -exec cat {} + > $PWD/$name/summ.txt 63 find $PWD/$name/files -iname "1_*" -exec cat {} + > $PWD/$name/summ.txt
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 "5_*" -exec cat {} + > $PWD/$name/aa.txt 66 find $PWD/$name/files -iname "5_*" -exec cat {} + > $PWD/$name/aa.txt
66 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
67 68
68 #python $dir/imgt_loader.py --summ $PWD/$name/summ.txt --aa $PWD/$name/aa.txt --junction $PWD/$name/junction.txt --output $output 69 #python $dir/imgt_loader.py --summ $PWD/$name/summ.txt --aa $PWD/$name/aa.txt --junction $PWD/$name/junction.txt --output $output
69 70
70 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 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