--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dexseq-hts_1.0/src/DEXseq-hts.sh	Tue Oct 08 08:22:45 2013 -0400
@@ -0,0 +1,98 @@
+#/bin/bash
+##
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 3 of the License, or
+# (at your option) any later version.
+#
+# Copyright (C) 2013 Memorial Sloan-Kettering Cancer Center 
+##
+
+set -e 
+
+PROG=`basename $0`
+DIR=`dirname $0`
+
+. ${DIR}/../bin/dexseq_config.sh
+
+echo
+echo ${PROG}: Oqtans http://galaxy.cbio.mskcc.org Galaxy wrapper for the DEXSeq version ${DEXSEQ_VERSION}.
+echo
+echo DEXSeq: Detecting differential usage of exons from RNA-seq data.
+echo 
+
+## input arguments from the interface 
+GFF_IN=${1}
+shift
+MATE_PAIR=${1}
+shift
+LIBTP=${1}
+shift
+minQL=${1}
+shift
+RES_FILE=${1}
+shift
+RES_WD=${1}
+shift
+
+## associated array with sequencing type.
+declare -A SEQ_TYPE=( [no]=SE [yes]=PE )
+
+echo %%%%%%%%%%%%%%%%%%%%%%%
+echo % 1. Data preparation %
+echo %%%%%%%%%%%%%%%%%%%%%%%
+echo
+
+mkdir -p ${RES_WD}
+echo extra file path $RES_WD
+tmpGTF=`mktemp --tmpdir=/tmp`
+
+echo load the genome annotation in GFF file 
+
+${PYTHON_PATH} ${DIR}/dexseq_prepare_annotation.py ${GFF_IN} ${tmpGTF}
+echo genome annotation stored in ${tmpGTF} 
+echo
+
+echo %%%%%%%%%%%%%%%%%%%%
+echo % 2. Read counting %
+echo %%%%%%%%%%%%%%%%%%%%
+echo
+
+tmpFILE=`mktemp --tmpdir=/tmp`
+echo $tmpFILE
+echo -e '\t'condition'\t'libType > ${tmpFILE}_CONDITIONS.tab
+
+COND=0
+for REPLICATE_GROUP in $@
+do
+    IFS=':'
+    COND=$((COND+1))
+    for BAM_FILE in ${REPLICATE_GROUP}
+    do
+        ## different group information 
+        REPNAME=$(basename ${BAM_FILE%.dat})
+        echo -e ${REPNAME}"\t"$COND"\t"${SEQ_TYPE[$MATE_PAIR]} >> ${tmpFILE}_CONDITIONS.tab
+        
+        ## counting the reads 
+        ${SAMTOOLS_DIR}/samtools view -h $BAM_FILE | ${PYTHON_PATH} ${DIR}/dexseq_count.py -p ${MATE_PAIR} -s ${LIBTP} -a ${minQL} ${tmpGTF} - ${RES_WD}/${REPNAME}
+
+        echo 
+    done
+    echo conuted condition ${COND} 
+done
+echo counted reads map to each exon.
+echo 
+
+echo %%%%%%%%%%%%%%%%%%%%%%%%%%%
+echo % 3. Differential testing %
+echo %%%%%%%%%%%%%%%%%%%%%%%%%%%
+echo
+
+echo "cat ${DIR}/run_DEXseq.R | $R_PATH --slave --args $tmpFILE $RES_WD $tmpGTF ${RES_FILE} $#" 
+cat ${DIR}/run_DEXseq.R | $R_PATH --slave --args $tmpFILE $RES_WD $tmpGTF ${RES_FILE} 
+
+## clean up
+rm -fr ${RES_WD} ${tmpGTF} ${tmpFILE} 
+echo %%%%%%%%
+echo % Done %
+echo %%%%%%%%