diff imgt_loader/imgt_loader.sh @ 0:afe85eb6572e draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/imgt_loader/imgt_loader.sh	Mon Aug 29 05:41:20 2016 -0400
@@ -0,0 +1,69 @@
+#!/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 "5_*" -exec cat {} + > $PWD/$name/aa.txt
+find $PWD/$name/files -iname "6_*" -exec cat {} + > $PWD/$name/junction.txt
+
+#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/aa.txt $PWD/$name/junction.txt $output 2>&1