diff rDiff/bin/rdiff @ 2:233c30f91d66

updated python based GFF parsing module which will handle GTF/GFF/GFF3 file types

--- a/rDiff/bin/rdiff	Thu Feb 14 23:38:36 2013 -0500
+++ b/rDiff/bin/rdiff	Tue Oct 08 07:15:44 2013 -0400
@@ -161,19 +161,19 @@
 echo
 
 #Check wether results directory exists
-#if [ -d $RDIFF_RES_DIR ]
-#then       
-#	echo "Writting results to: $RDIFF_RES_DIR"
-#else
-#	mkdir $RDIFF_RES_DIR
-#fi 
+if [ -d $RDIFF_RES_DIR ]
+then       
+	echo "Writting results to: $RDIFF_RES_DIR"
+else
+	mkdir $RDIFF_RES_DIR
+fi 
 
 
 echo 1a. load the genome annotation in GFF3 format, create an annotation object #\[Log file in ${RDIFF_RES_DIR}}/elegans-gff2anno.log\]
-export PYTHONPATH=$PYTHONPATH:$RDIFF_PYTHON_PATH:${SCIPY_PATH}
-${RDIFF_PYTHON_PATH} -W ignore::RuntimeWarning ${DIR}/../tools/ParseGFF.py ${GFF_INPUT} ${RDIFF_RES_DIR}/genes.mat #> ${RDIFF_RES_DIR}}/elegans-gff2anno.log
-${DIR}/../bin/genes_cell2struct ${RDIFF_RES_DIR}/genes.mat 
+export PYTHONPATH=$PYTHONPATH:$RDIFF_PYTHON_PATH
+touch ${RDIFF_RES_DIR}/genes.mat
 
+${RDIFF_PYTHON_PATH} ${DIR}/../tools/GFFParser.py ${GFF_INPUT} ${RDIFF_RES_DIR}/genes.mat #> ${RDIFF_RES_DIR}}/elegans-gff2anno.log
 
 PARAM_VECT="$PARAM_VECT""GFF_INPUT:${RDIFF_RES_DIR}/genes.mat;"
 
@@ -183,4 +183,3 @@
 echo
 
 exec ${DIR}/start_interpreter.sh ${PROG} "$PARAM_VECT"
-