Mercurial > repos > davidvanzessen > complete_immunerepertoire_igg
comparison imgt_loader.sh @ 5:3287f7b9c47d draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Fri, 05 Sep 2014 04:19:58 -0400 |
| parents | |
| children | 70c8234acaf3 |
comparison
equal
deleted
inserted
replaced
| 4:24d5d9120d93 | 5:3287f7b9c47d |
|---|---|
| 1 #!/bin/bash | |
| 2 input=$1 | |
| 3 output=$2 | |
| 4 name=$3 | |
| 5 dir="$(cd "$(dirname "$0")" && pwd)" | |
| 6 mkdir -p $PWD/$name/files | |
| 7 f=$(file $input) | |
| 8 zip7Type="7-zip archive" | |
| 9 tarType="tar archive" | |
| 10 bzip2Type="bzip2 compressed" | |
| 11 gzipType="gzip compressed" | |
| 12 zipType="Zip archive" | |
| 13 rarType="RAR archive" | |
| 14 | |
| 15 if [[ "$f" == *"$zip7Type"* ]]; then | |
| 16 echo "7-zip" | |
| 17 echo "Trying: 7za e $input -o$PWD/files/" | |
| 18 7za e $input -o$PWD/$name/files | |
| 19 fi | |
| 20 | |
| 21 if [[ "$f" == *"$tarType"* ]] | |
| 22 then | |
| 23 echo "tar archive" | |
| 24 echo "Trying: tar xvf $input -C $PWD/files/" | |
| 25 tar xvf $input -C $PWD/$name/files | |
| 26 fi | |
| 27 | |
| 28 if [[ "$f" == *"$bzip2Type"* ]] | |
| 29 then | |
| 30 echo "bzip2 compressed data" | |
| 31 echo "Trying: tar jxf $input -C $PWD/files/" | |
| 32 tar jxf $input -C $PWD/$name/files | |
| 33 fi | |
| 34 | |
| 35 if [[ "$f" == *"$gzipType"* ]] | |
| 36 then | |
| 37 echo "gzip compressed data" | |
| 38 echo "Trying: tar xvzf $input -C $PWD/files/" | |
| 39 tar xvzf $input -C $PWD/$name/files | |
| 40 fi | |
| 41 | |
| 42 if [[ "$f" == *"$zipType"* ]] | |
| 43 then | |
| 44 echo "Zip archive" | |
| 45 echo "Trying: unzip $input -d $PWD/files/" | |
| 46 unzip $input -d $PWD/$name/files > $PWD/unziplog.log | |
| 47 fi | |
| 48 | |
| 49 if [[ "$f" == *"$rarType"* ]] | |
| 50 then | |
| 51 echo "RAR archive" | |
| 52 echo "Trying: unrar e $input $PWD/files/" | |
| 53 unrar e $input $PWD/$name/files | |
| 54 fi | |
| 55 find $PWD/$name/files -iname "1_*" -exec cat {} + > $PWD/$name/summ.txt | |
| 56 find $PWD/$name/files -iname "5_*" -exec cat {} + > $PWD/$name/aa.txt | |
| 57 find $PWD/$name/files -iname "6_*" -exec cat {} + > $PWD/$name/junction.txt | |
| 58 | |
| 59 python $dir/imgt_loader.py --summ $PWD/$name/summ.txt --aa $PWD/$name/aa.txt --junction $PWD/$name/junction.txt --output $output |