Mercurial > repos > davidvanzessen > argalaxy_tools
diff imgt_loader/imgt_loader.sh @ 53:0ef7f80ea061 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Thu, 25 Feb 2021 13:39:50 +0000 |
| parents | 124b7fd92a3e |
| children |
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--- a/imgt_loader/imgt_loader.sh Thu Feb 25 13:36:15 2021 +0000 +++ b/imgt_loader/imgt_loader.sh Thu Feb 25 13:39:50 2021 +0000 @@ -1,74 +1,74 @@ -#!/bin/bash -input=$1 -output=$2 -name=$3 -dir="$(cd "$(dirname "$0")" && pwd)" -mkdir -p $PWD/$name/files -f=$(file $input) -zip7Type="7-zip archive" -tarType="tar archive" -bzip2Type="bzip2 compressed" -gzipType="gzip compressed" -zipType="Zip archive" -rarType="RAR archive" -zxType="XZ compressed data" - -if [[ "$f" == *"$zip7Type"* ]]; then - echo "7-zip" - echo "Trying: 7za e $input -o$PWD/files/" - 7za e $input -o$PWD/$name/files -fi - -if [[ "$f" == *"$tarType"* ]] -then - echo "tar archive" - echo "Trying: tar xvf $input -C $PWD/files/" - tar -xvf $input -C $PWD/$name/files -fi - -if [[ "$f" == *"$bzip2Type"* ]] -then - echo "bzip2 compressed data" - echo "Trying: tar jxf $input -C $PWD/files/" - tar -jxf $input -C $PWD/$name/files -fi - -if [[ "$f" == *"$gzipType"* ]] -then - echo "gzip compressed data" - echo "Trying: tar xvzf $input -C $PWD/files/" - tar -xvzf $input -C $PWD/$name/files -fi - -if [[ "$f" == *"$zipType"* ]] -then - echo "Zip archive" - echo "Trying: unzip $input -d $PWD/files/" - unzip $input -d $PWD/$name/files > $PWD/unziplog.log -fi - -if [[ "$f" == *"$rarType"* ]] -then - echo "RAR archive" - echo "Trying: unrar e $input $PWD/files/" - unrar e $input $PWD/$name/files -fi - -if [[ "$f" == *"$zxType"* ]] -then - echo "xz compressed data" - echo "Trying: tar -xJf $input -C $PWD/files/" - tar xJf $input -C $PWD/$name/files -fi -find $PWD/$name/files -iname "1_*" -exec cat {} + > $PWD/$name/summ.txt -find $PWD/$name/files -iname "3_*" -exec cat {} + > $PWD/$name/sequences.txt -find $PWD/$name/files -iname "4_*" -exec cat {} + > $PWD/$name/gapped_aa.txt -find $PWD/$name/files -iname "5_*" -exec cat {} + > $PWD/$name/aa.txt -find $PWD/$name/files -iname "6_*" -exec cat {} + > $PWD/$name/junction.txt - -echo "summ.txt `cat $PWD/$name/summ.txt | wc -l`" -echo "aa.txt `cat $PWD/$name/aa.txt | wc -l`" - -#python $dir/imgt_loader.py --summ $PWD/$name/summ.txt --aa $PWD/$name/aa.txt --junction $PWD/$name/junction.txt --output $output - -Rscript --verbose $dir/imgt_loader.r $PWD/$name/summ.txt $PWD/$name/sequences.txt $PWD/$name/aa.txt $PWD/$name/junction.txt $PWD/$name/gapped_aa.txt $output 2>&1 +#!/bin/bash +input=$1 +output=$2 +name=$3 +dir="$(cd "$(dirname "$0")" && pwd)" +mkdir -p $PWD/$name/files +f=$(file $input) +zip7Type="7-zip archive" +tarType="tar archive" +bzip2Type="bzip2 compressed" +gzipType="gzip compressed" +zipType="Zip archive" +rarType="RAR archive" +zxType="XZ compressed data" + +if [[ "$f" == *"$zip7Type"* ]]; then + echo "7-zip" + echo "Trying: 7za e $input -o$PWD/files/" + 7za e $input -o$PWD/$name/files +fi + +if [[ "$f" == *"$tarType"* ]] +then + echo "tar archive" + echo "Trying: tar xvf $input -C $PWD/files/" + tar -xvf $input -C $PWD/$name/files +fi + +if [[ "$f" == *"$bzip2Type"* ]] +then + echo "bzip2 compressed data" + echo "Trying: tar jxf $input -C $PWD/files/" + tar -jxf $input -C $PWD/$name/files +fi + +if [[ "$f" == *"$gzipType"* ]] +then + echo "gzip compressed data" + echo "Trying: tar xvzf $input -C $PWD/files/" + tar -xvzf $input -C $PWD/$name/files +fi + +if [[ "$f" == *"$zipType"* ]] +then + echo "Zip archive" + echo "Trying: unzip $input -d $PWD/files/" + unzip $input -d $PWD/$name/files > $PWD/unziplog.log +fi + +if [[ "$f" == *"$rarType"* ]] +then + echo "RAR archive" + echo "Trying: unrar e $input $PWD/files/" + unrar e $input $PWD/$name/files +fi + +if [[ "$f" == *"$zxType"* ]] +then + echo "xz compressed data" + echo "Trying: tar -xJf $input -C $PWD/files/" + tar xJf $input -C $PWD/$name/files +fi +find $PWD/$name/files -iname "1_*" -exec cat {} + > $PWD/$name/summ.txt +find $PWD/$name/files -iname "3_*" -exec cat {} + > $PWD/$name/sequences.txt +find $PWD/$name/files -iname "4_*" -exec cat {} + > $PWD/$name/gapped_aa.txt +find $PWD/$name/files -iname "5_*" -exec cat {} + > $PWD/$name/aa.txt +find $PWD/$name/files -iname "6_*" -exec cat {} + > $PWD/$name/junction.txt + +echo "summ.txt `cat $PWD/$name/summ.txt | wc -l`" +echo "aa.txt `cat $PWD/$name/aa.txt | wc -l`" + +#python $dir/imgt_loader.py --summ $PWD/$name/summ.txt --aa $PWD/$name/aa.txt --junction $PWD/$name/junction.txt --output $output + +Rscript --verbose $dir/imgt_loader.r $PWD/$name/summ.txt $PWD/$name/sequences.txt $PWD/$name/aa.txt $PWD/$name/junction.txt $PWD/$name/gapped_aa.txt $output 2>&1