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comparison wrapper.sh @ 49:f5fe63533c58 draft

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Uploaded
author davidvanzessen
date Thu, 11 May 2017 10:21:39 -0400
parents 64711f461c8e
children 6cd12c71c3d3
comparison
equal deleted inserted replaced
48:c5295dd10dfc 49:f5fe63533c58
15 naive_output_cg=${11} 15 naive_output_cg=${11}
16 naive_output_cm=${12} 16 naive_output_cm=${12}
17 naive_output_ce=${13} 17 naive_output_ce=${13}
18 naive_output_all=${14} 18 naive_output_all=${14}
19 filter_unique=${15} 19 filter_unique=${15}
20 class_filter=${16} 20 filter_unique_count=${16}
21 empty_region_filter=${17} 21 class_filter=${17}
22 fast=${18} 22 empty_region_filter=${18}
23 fast=${19}
24
23 mkdir $outdir 25 mkdir $outdir
24 26
25 tar -xzf $dir/style.tar.gz -C $outdir 27 tar -xzf $dir/style.tar.gz -C $outdir
26 28
27 echo "---------------- read parameters ----------------" 29 echo "---------------- read parameters ----------------"
63 python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt 65 python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt
64 66
65 echo "---------------- merge_and_filter.r ----------------" 67 echo "---------------- merge_and_filter.r ----------------"
66 echo "---------------- merge_and_filter.r ----------------<br />" >> $log 68 echo "---------------- merge_and_filter.r ----------------<br />" >> $log
67 69
68 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt "$PWD/gapped_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 70 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt "$PWD/gapped_aa.txt" $outdir/identified_genes.txt $outdir/merged.txt $outdir/before_unique_filter.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${filter_unique_count} ${class_filter} ${empty_region_filter} 2>&1
69 71
70 if [[ "$fast" == "no" ]] ; then 72 if [[ "$fast" == "no" ]] ; then
71 73
72 echo "---------------- creating new IMGT zips ----------------" 74 echo "---------------- creating new IMGT zips ----------------"
73 echo "---------------- creating new IMGT zips ----------------<br />" >> $log 75 echo "---------------- creating new IMGT zips ----------------<br />" >> $log