Mercurial > repos > davidvanzessen > argalaxy_tools

comparison imgt_loader/imgt_loader.sh @ 58:a073fa12ef98 draft

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author davidvanzessen
date Fri, 18 Mar 2016 08:02:22 -0400
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57:16c7fc1c4bf8 58:a073fa12ef98
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
68
69 Rscript --verbose $dir/imgt_loader.r $PWD/$name/summ.txt $PWD/$name/aa.txt $PWD/$name/junction.txt $output 2>&1