|
12
|
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 $input)
|
|
|
8 zip7Type="7-zip archive"
|
|
|
9 tarType="tar archive"
|
|
|
10 bzip2Type="bzip2 compressed"
|
|
|
11 gzipType="gzip compressed"
|
|
|
12 zipType="Zip archive"
|
|
|
13 rarType="RAR archive"
|
|
|
14 zxType="XZ compressed data"
|
|
|
15
|
|
|
16 if [[ "$f" == *"$zip7Type"* ]]; then
|
|
|
17 echo "7-zip"
|
|
|
18 echo "Trying: 7za e $input -o$PWD/files/"
|
|
|
19 7za e $input -o$PWD/$name/files
|
|
|
20 fi
|
|
|
21
|
|
|
22 if [[ "$f" == *"$tarType"* ]]
|
|
|
23 then
|
|
|
24 echo "tar archive"
|
|
|
25 echo "Trying: tar xvf $input -C $PWD/files/"
|
|
|
26 tar -xvf $input -C $PWD/$name/files
|
|
|
27 fi
|
|
|
28
|
|
|
29 if [[ "$f" == *"$bzip2Type"* ]]
|
|
|
30 then
|
|
|
31 echo "bzip2 compressed data"
|
|
|
32 echo "Trying: tar jxf $input -C $PWD/files/"
|
|
|
33 tar -jxf $input -C $PWD/$name/files
|
|
|
34 fi
|
|
|
35
|
|
|
36 if [[ "$f" == *"$gzipType"* ]]
|
|
|
37 then
|
|
|
38 echo "gzip compressed data"
|
|
|
39 echo "Trying: tar xvzf $input -C $PWD/files/"
|
|
|
40 tar -xvzf $input -C $PWD/$name/files
|
|
|
41 fi
|
|
|
42
|
|
|
43 if [[ "$f" == *"$zipType"* ]]
|
|
|
44 then
|
|
|
45 echo "Zip archive"
|
|
|
46 echo "Trying: unzip $input -d $PWD/files/"
|
|
|
47 unzip $input -d $PWD/$name/files > $PWD/unziplog.log
|
|
|
48 fi
|
|
|
49
|
|
|
50 if [[ "$f" == *"$rarType"* ]]
|
|
|
51 then
|
|
|
52 echo "RAR archive"
|
|
|
53 echo "Trying: unrar e $input $PWD/files/"
|
|
|
54 unrar e $input $PWD/$name/files
|
|
|
55 fi
|
|
|
56
|
|
|
57 if [[ "$f" == *"$zxType"* ]]
|
|
|
58 then
|
|
|
59 echo "xz compressed data"
|
|
|
60 echo "Trying: tar -xJf $input -C $PWD/files/"
|
|
|
61 tar xJf $input -C $PWD/$name/files
|
|
|
62 fi
|
|
|
63 find $PWD/$name/files -iname "1_*" -exec cat {} + > $PWD/$name/summ.txt
|
|
|
64 find $PWD/$name/files -iname "5_*" -exec cat {} + > $PWD/$name/aa.txt
|
|
|
65 find $PWD/$name/files -iname "6_*" -exec cat {} + > $PWD/$name/junction.txt
|
|
|
66
|
|
|
67 python $dir/imgt_loader.py --summ $PWD/$name/summ.txt --aa $PWD/$name/aa.txt --junction $PWD/$name/junction.txt --output $output
|
