Mercurial > repos > davidvanzessen > combined_immune_repertoire_imgt
comparison immunerepertoirecombined_imgt/imgtconvert.sh @ 0:e71c59b72669 draft
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| author | davidvanzessen |
|---|---|
| date | Mon, 09 Dec 2013 03:45:21 -0500 |
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| children |
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| -1:000000000000 | 0:e71c59b72669 |
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| 1 #!/bin/bash | |
| 2 dir="$(cd "$(dirname "$0")" && pwd)" | |
| 3 mkdir $PWD/$2_$3 | |
| 4 | |
| 5 | |
| 6 #!/bin/bash | |
| 7 f=$(file $1) | |
| 8 zip7Type="7-zip archive" | |
| 9 tarType="tar archive" | |
| 10 bzip2Type="bzip2 compressed" | |
| 11 gzipType="gzip compressed" | |
| 12 zipType="Zip archive" | |
| 13 rarType="RAR archive" | |
| 14 | |
| 15 if [[ "$f" == *"$zip7Type"* ]]; then | |
| 16 echo "7-zip" | |
| 17 echo "Trying: 7za e $1 -o$PWD/$2_$3/" | |
| 18 7za e $1 -o$PWD/$2_$3/ | |
| 19 fi | |
| 20 | |
| 21 if [[ "$f" == *"$tarType"* ]] | |
| 22 then | |
| 23 echo "tar archive" | |
| 24 echo "Trying: tar xvf $1 -C $PWD/$2_$3/" | |
| 25 tar xvf $1 -C $PWD/$2_$3/ | |
| 26 fi | |
| 27 | |
| 28 if [[ "$f" == *"$bzip2Type"* ]] | |
| 29 then | |
| 30 echo "bzip2 compressed data" | |
| 31 echo "Trying: tar jxf $1 -C $PWD/$2_$3/" | |
| 32 tar jxf $1 -C $PWD/$2_$3/ | |
| 33 fi | |
| 34 | |
| 35 if [[ "$f" == *"$gzipType"* ]] | |
| 36 then | |
| 37 echo "gzip compressed data" | |
| 38 echo "Trying: tar xvzf $1 -C $PWD/$2_$3/" | |
| 39 tar xvzf $1 -C $PWD/$2_$3/ | |
| 40 fi | |
| 41 | |
| 42 if [[ "$f" == *"$zipType"* ]] | |
| 43 then | |
| 44 echo "Zip archive" | |
| 45 echo "Trying: unzip $1 -d $PWD/$2_$3/" | |
| 46 unzip $1 -d $PWD/$2_$3/ | |
| 47 fi | |
| 48 | |
| 49 if [[ "$f" == *"$rarType"* ]] | |
| 50 then | |
| 51 echo "RAR archive" | |
| 52 echo "Trying: unrar e $1 $PWD/$2_$3/" | |
| 53 unrar e $1 $PWD/$2_$3/ | |
| 54 fi | |
| 55 find $PWD/$2_$3/ -type f | grep -v "1_Summary_\|5_AA-sequences_\|6_Junction_" | xargs rm -f | |
| 56 python $dir/imgtconvert.py --input $PWD/$2_$3 --output $4 | |
| 57 |