--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/immunerepertoirecombined_imgt/imgtconvert.sh	Mon Dec 09 03:45:21 2013 -0500
@@ -0,0 +1,57 @@
+#!/bin/bash
+dir="$(cd "$(dirname "$0")" && pwd)"
+mkdir $PWD/$2_$3
+
+
+#!/bin/bash
+f=$(file $1)
+zip7Type="7-zip archive"
+tarType="tar archive"
+bzip2Type="bzip2 compressed"
+gzipType="gzip compressed"
+zipType="Zip archive"
+rarType="RAR archive"
+
+if [[ "$f" == *"$zip7Type"* ]]; then
+	echo "7-zip"
+	echo "Trying: 7za e $1 -o$PWD/$2_$3/"
+	7za e $1 -o$PWD/$2_$3/
+fi
+
+if [[ "$f" == *"$tarType"* ]]
+then
+	echo "tar archive"
+	echo "Trying: tar xvf $1 -C $PWD/$2_$3/"
+	tar xvf $1 -C $PWD/$2_$3/
+fi
+
+if [[ "$f" == *"$bzip2Type"* ]]
+then
+	echo "bzip2 compressed data"
+	echo "Trying: tar jxf $1 -C $PWD/$2_$3/"
+	tar jxf $1 -C $PWD/$2_$3/
+fi
+
+if [[ "$f" == *"$gzipType"* ]]
+then
+	echo "gzip compressed data"
+	echo "Trying: tar xvzf $1 -C $PWD/$2_$3/"
+	tar xvzf $1 -C $PWD/$2_$3/
+fi
+
+if [[ "$f" == *"$zipType"* ]]
+then
+	echo "Zip archive"
+	echo "Trying: unzip $1 -d $PWD/$2_$3/"
+	unzip $1 -d $PWD/$2_$3/
+fi
+
+if [[ "$f" == *"$rarType"* ]]
+then
+	echo "RAR archive"
+	echo "Trying: unrar e $1 $PWD/$2_$3/"
+	unrar e $1 $PWD/$2_$3/
+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
+