Mercurial > repos > davidvanzessen > shm_csr

comparison wrapper.sh @ 40:ca2512e1e3ab draft

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Uploaded
author davidvanzessen
date Thu, 29 Dec 2016 07:05:45 -0500
parents a24f8c93583a
children b8ac74723ab0
comparison
equal deleted inserted replaced
39:a24f8c93583a 40:ca2512e1e3ab
41 tar -xJf $input -C "$PWD/files/$title" 41 tar -xJf $input -C "$PWD/files/$title"
42 fi 42 fi
43 43
44 cat "`find $PWD/files/ -name "1_*"`" > $PWD/summary.txt 44 cat "`find $PWD/files/ -name "1_*"`" > $PWD/summary.txt
45 cat "`find $PWD/files/ -name "3_*"`" > $PWD/sequences.txt 45 cat "`find $PWD/files/ -name "3_*"`" > $PWD/sequences.txt
46 cat "`find $PWD/files/ -name "4_*"`" > $PWD/gapped_aa.txt
46 cat "`find $PWD/files/ -name "5_*"`" > $PWD/aa.txt 47 cat "`find $PWD/files/ -name "5_*"`" > $PWD/aa.txt
47 cat "`find $PWD/files/ -name "6_*"`" > $PWD/junction.txt 48 cat "`find $PWD/files/ -name "6_*"`" > $PWD/junction.txt
48 cat "`find $PWD/files/ -name "7_*"`" > $PWD/mutationanalysis.txt 49 cat "`find $PWD/files/ -name "7_*"`" > $PWD/mutationanalysis.txt
49 cat "`find $PWD/files/ -name "8_*"`" > $PWD/mutationstats.txt 50 cat "`find $PWD/files/ -name "8_*"`" > $PWD/mutationstats.txt
50 cat "`find $PWD/files/ -name "10_*"`" > $PWD/hotspots.txt 51 cat "`find $PWD/files/ -name "10_*"`" > $PWD/hotspots.txt
62 python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt 63 python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt
63 64
64 echo "---------------- merge_and_filter.r ----------------" 65 echo "---------------- merge_and_filter.r ----------------"
65 echo "---------------- merge_and_filter.r ----------------<br />" >> $log 66 echo "---------------- merge_and_filter.r ----------------<br />" >> $log
66 67
67 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 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} ${empty_region_filter} 2>&1
68 69
69 if [[ "$fast" == "no" ]] ; then 70 if [[ "$fast" == "no" ]] ; then
70 71
71 echo "---------------- creating new IMGT zips ----------------" 72 echo "---------------- creating new IMGT zips ----------------"
72 echo "---------------- creating new IMGT zips ----------------<br />" >> $log 73 echo "---------------- creating new IMGT zips ----------------<br />" >> $log