Mercurial > repos > davidvanzessen > complete_immunerepertoire_igg
diff imgtconvert.sh @ 4:24d5d9120d93 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Thu, 04 Sep 2014 07:59:02 -0400 |
| parents | 7d97fa9a0423 |
| children |
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--- a/imgtconvert.sh Thu Sep 04 07:51:11 2014 -0400 +++ b/imgtconvert.sh Thu Sep 04 07:59:02 2014 -0400 @@ -1,6 +1,6 @@ #!/bin/bash dir="$(cd "$(dirname "$0")" && pwd)" -mkdir $PWD/$2_$3 +mkdir $PWD/files #!/bin/bash @@ -14,44 +14,44 @@ if [[ "$f" == *"$zip7Type"* ]]; then echo "7-zip" - echo "Trying: 7za e $1 -o$PWD/$2_$3/" - 7za e $1 -o$PWD/$2_$3/ + echo "Trying: 7za e $1 -o$PWD/files/" + 7za e $1 -o$PWD/files/ fi if [[ "$f" == *"$tarType"* ]] then echo "tar archive" - echo "Trying: tar xvf $1 -C $PWD/$2_$3/" - tar xvf $1 -C $PWD/$2_$3/ + echo "Trying: tar xvf $1 -C $PWD/files/" + tar xvf $1 -C $PWD/files/ fi if [[ "$f" == *"$bzip2Type"* ]] then echo "bzip2 compressed data" - echo "Trying: tar jxf $1 -C $PWD/$2_$3/" - tar jxf $1 -C $PWD/$2_$3/ + echo "Trying: tar jxf $1 -C $PWD/files/" + tar jxf $1 -C $PWD/files/ fi if [[ "$f" == *"$gzipType"* ]] then echo "gzip compressed data" - echo "Trying: tar xvzf $1 -C $PWD/$2_$3/" - tar xvzf $1 -C $PWD/$2_$3/ + echo "Trying: tar xvzf $1 -C $PWD/files/" + tar xvzf $1 -C $PWD/files/ fi if [[ "$f" == *"$zipType"* ]] then echo "Zip archive" - echo "Trying: unzip $1 -d $PWD/$2_$3/" - unzip $1 -d $PWD/$2_$3/ + echo "Trying: unzip $1 -d $PWD/files/" + unzip $1 -d $PWD/files/ > $PWD/unziplog.log fi if [[ "$f" == *"$rarType"* ]] then echo "RAR archive" - echo "Trying: unrar e $1 $PWD/$2_$3/" - unrar e $1 $PWD/$2_$3/ + echo "Trying: unrar e $1 $PWD/files/" + unrar e $1 $PWD/files/ fi -find $PWD/$2_$3/ -type f | grep -v "1_Summary_\|5_AA-sequences_\|6_Junction_" | xargs rm -f -python $dir/imgtconvert.py --input $PWD/$2_$3 --output $4 +find $PWD/files/ -type f | grep -v "1_Summary_\|5_AA-sequences_\|6_Junction_" | xargs rm -f +python $dir/imgtconvert.py --input $PWD/files --output $2