Mercurial > repos > vipints > rdiff
diff rDiff/bin/rdiff @ 2:233c30f91d66
updated python based GFF parsing module which will handle GTF/GFF/GFF3 file types
author | vipints <vipin@cbio.mskcc.org> |
---|---|
date | Tue, 08 Oct 2013 07:15:44 -0400 |
parents | 0f80a5141704 |
children |
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--- 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" -