Mercurial > repos > davidvanzessen > shm_csr

comparison wrapper.sh @ 34:96c1276ceefe draft

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Uploaded
author davidvanzessen
date Fri, 16 Dec 2016 09:53:09 -0500
parents 22fabe161cf3
children 744e5e2e3556
comparison
equal deleted inserted replaced
33:22fabe161cf3 34:96c1276ceefe
4 input=$1 4 input=$1
5 method=$2 5 method=$2
6 log=$3 #becomes the main html page at the end 6 log=$3 #becomes the main html page at the end
7 outdir=$4 7 outdir=$4
8 output="$outdir/index.html" #copied to $log location at the end 8 output="$outdir/index.html" #copied to $log location at the end
9 title=$5 9 title="$5"
10 include_fr1=$6 10 include_fr1=$6
11 functionality=$7 11 functionality=$7
12 unique=$8 12 unique=$8
13 naive_output=$9 13 naive_output=$9
14 naive_output_ca=${10} 14 naive_output_ca=${10}
35 echo "unzip $input -d $PWD/files/" 35 echo "unzip $input -d $PWD/files/"
36 unzip $input -d $PWD/files/ 36 unzip $input -d $PWD/files/
37 elif [[ "$type" == *"XZ compressed data"* ]] ; then 37 elif [[ "$type" == *"XZ compressed data"* ]] ; then
38 echo "ZX archive" 38 echo "ZX archive"
39 echo "tar -xJf $input -C $PWD/files/" 39 echo "tar -xJf $input -C $PWD/files/"
40 mkdir -p $PWD/files/$title 40 mkdir -p "$PWD/files/$title"
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 "5_*"` > $PWD/aa.txt 46 cat `find $PWD/files/ -name "5_*"` > $PWD/aa.txt
437 fi 437 fi
438 438
439 mkdir $outdir/baseline/IGG 439 mkdir $outdir/baseline/IGG
440 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then 440 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
441 cd $outdir/baseline/IGG 441 cd $outdir/baseline/IGG
442 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGG.txz "cg" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGG.pdf" "Sequence.ID" "$outdir/baseline_IGG.txt" 442 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGG.txz "IGG" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGG.pdf" "Sequence.ID" "$outdir/baseline_IGG.txt"
443 else 443 else
444 echo "No IGG sequences" > "$outdir/baseline_IGG.txt" 444 echo "No IGG sequences" > "$outdir/baseline_IGG.txt"
445 fi 445 fi
446 446
447 mkdir $outdir/baseline/IGM 447 mkdir $outdir/baseline/IGM