--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/from_imgt.sh	Fri Jul 24 04:44:39 2015 -0400
@@ -0,0 +1,104 @@
+set -e
+
+dir="$(cd "$(dirname "$0")" && pwd)"
+
+args=($@)
+inputs=(${args[@]:1})
+output="${args[0]}"
+echo "$PWD"
+
+function get_summary_file
+{
+	imgt_zip=$1
+	summary_file=$2
+	
+	mkdir ${PWD}/tmp/
+	type="`file ${imgt_zip}`"
+	if [[ "$type" == *"Zip archive"* ]] ; then
+		unzip ${imgt_zip} -d $PWD/tmp/
+	elif [[ "$type" == *"XZ compressed data"* ]] ; then
+		mkdir "$PWD/tmp/files"
+		tar -xJf ${imgt_zip} -C $PWD/tmp/files
+	fi
+	
+	cat $PWD/tmp/*/1_* > ${summary_file}
+	rm -rf $PWD/tmp
+}
+
+index=0
+
+echo -e "Patient\tReceptor\tSample\tCell_Count\tClone_Molecule_Count_From_Spikes\tLog10_Frequency\tTotal_Read_Count\tV_Segment_Major_Gene\tJ_Segment_Major_Gene\tClone_Sequence\tCDR3_Sense_Sequence\tRelated_to_leukemia_clone" > "$output"
+
+while true
+do
+	patient="${inputs[$index]}"
+	index=$((index + 1))
+	cell_count="${inputs[$index]}"
+	index=$((index + 1))
+	receptor="${inputs[$index]}"
+	index=$((index + 1))
+	sample_count="${inputs[$index]}"
+	index=$((index + 1))
+	
+	sample_name="${inputs[$index]}"
+	index=$((index + 1))
+	
+	sample_file="${inputs[$index]}"
+	index=$((index + 1))
+	
+	echo "patient: $patient"
+	echo "cell_count: ${cell_count}"
+	echo "receptor: $receptor"
+	echo "sample_count: ${sample_count}"
+	echo "sample_name: ${sample_name}"
+	echo "sample_file: ${sample_file}"
+	
+	get_summary_file ${sample_file} ${PWD}/summ.txt
+	
+	Rscript --verbose $dir/from_imgt.r ${PWD}/summ.txt ${patient} ${sample_name} ${cell_count} ${receptor} ${PWD}/tmp.txt 2>&1
+	cat "${PWD}/tmp.txt" >> "$output"
+	
+	if [[ "${sample_count}" -gt "1" ]]; then
+		sample_name="${inputs[$index]}"
+		index=$((index + 1))
+		
+		sample_file="${inputs[$index]}"
+		index=$((index + 1))
+		
+		echo "sample_name: ${sample_name}"
+		echo "sample_file: ${sample_file}"
+		
+		get_summary_file ${sample_file} ${PWD}/summ.txt
+		
+		Rscript --verbose $dir/from_imgt.r ${PWD}/summ.txt ${patient} ${sample_name} ${cell_count} ${receptor} ${PWD}/tmp.txt 2>&1
+		cat "${PWD}/tmp.txt" >> "$output"
+	fi
+	
+	if [[ "${sample_count}" -eq "3" ]]; then		
+		sample_name="${inputs[$index]}"
+		index=$((index + 1))
+		
+		sample_file="${inputs[$index]}"
+		index=$((index + 1))
+		
+		echo "sample_name: ${sample_name}"
+		echo "sample_file: ${sample_file}"
+				
+		get_summary_file ${sample_file} ${PWD}/summ.txt
+		
+		Rscript --verbose $dir/from_imgt.r ${PWD}/summ.txt ${patient} ${sample_name} ${cell_count} ${receptor} ${PWD}/tmp.txt 2>&1
+		cat "${PWD}/tmp.txt" >> "$output"
+	fi
+	if [[ "${index}" -eq "${#inputs[@]}" ]]; then
+		exit 0
+	fi
+done
+
+
+
+
+
+
+
+
+