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comparison wrapper.sh @ 14:59765d2c8890 draft

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Uploaded
author davidvanzessen
date Fri, 11 Nov 2016 07:31:48 -0500
parents ad9be244b104
children 4e596473c25c
comparison
equal deleted inserted replaced
13:933fb21568ce 14:59765d2c8890
60 python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt 60 python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt
61 61
62 echo "---------------- merge_and_filter.r ----------------" 62 echo "---------------- merge_and_filter.r ----------------"
63 echo "---------------- merge_and_filter.r ----------------<br />" >> $log 63 echo "---------------- merge_and_filter.r ----------------<br />" >> $log
64 64
65 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $outdir/identified_genes.txt $outdir/merged.txt $outdir/before_unique_filter.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${class_filter} ${empty_region_filter} 2>&1 65 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $PWD/aa.txt $outdir/identified_genes.txt $outdir/merged.txt $outdir/before_unique_filter.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${class_filter} ${empty_region_filter} 2>&1
66 66
67 if [[ "$fast" == "no" ]] ; then 67 if [[ "$fast" == "no" ]] ; then
68 68
69 echo "---------------- creating new IMGT zips ----------------" 69 echo "---------------- creating new IMGT zips ----------------"
70 echo "---------------- creating new IMGT zips ----------------<br />" >> $log 70 echo "---------------- creating new IMGT zips ----------------<br />" >> $log