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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
comparison
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0:0f80a5141704 2:233c30f91d66
159 echo % 1. Data preparation % 159 echo % 1. Data preparation %
160 echo %%%%%%%%%%%%%%%%%%%%%%% 160 echo %%%%%%%%%%%%%%%%%%%%%%%
161 echo 161 echo
162 162
163 #Check wether results directory exists 163 #Check wether results directory exists
164 #if [ -d $RDIFF_RES_DIR ] 164 if [ -d $RDIFF_RES_DIR ]
165 #then 165 then
166 # echo "Writting results to: $RDIFF_RES_DIR" 166 echo "Writting results to: $RDIFF_RES_DIR"
167 #else 167 else
168 # mkdir $RDIFF_RES_DIR 168 mkdir $RDIFF_RES_DIR
169 #fi 169 fi
170 170
171 171
172 echo 1a. load the genome annotation in GFF3 format, create an annotation object #\[Log file in ${RDIFF_RES_DIR}}/elegans-gff2anno.log\] 172 echo 1a. load the genome annotation in GFF3 format, create an annotation object #\[Log file in ${RDIFF_RES_DIR}}/elegans-gff2anno.log\]
173 export PYTHONPATH=$PYTHONPATH:$RDIFF_PYTHON_PATH:${SCIPY_PATH} 173 export PYTHONPATH=$PYTHONPATH:$RDIFF_PYTHON_PATH
174 ${RDIFF_PYTHON_PATH} -W ignore::RuntimeWarning ${DIR}/../tools/ParseGFF.py ${GFF_INPUT} ${RDIFF_RES_DIR}/genes.mat #> ${RDIFF_RES_DIR}}/elegans-gff2anno.log 174 touch ${RDIFF_RES_DIR}/genes.mat
175 ${DIR}/../bin/genes_cell2struct ${RDIFF_RES_DIR}/genes.mat
176 175
176 ${RDIFF_PYTHON_PATH} ${DIR}/../tools/GFFParser.py ${GFF_INPUT} ${RDIFF_RES_DIR}/genes.mat #> ${RDIFF_RES_DIR}}/elegans-gff2anno.log
177 177
178 PARAM_VECT="$PARAM_VECT""GFF_INPUT:${RDIFF_RES_DIR}/genes.mat;" 178 PARAM_VECT="$PARAM_VECT""GFF_INPUT:${RDIFF_RES_DIR}/genes.mat;"
179 179
180 echo %%%%%%%%%%%%%%%%%%%%%%%%%%% 180 echo %%%%%%%%%%%%%%%%%%%%%%%%%%%
181 echo % 2. Differential testing % 181 echo % 2. Differential testing %
182 echo %%%%%%%%%%%%%%%%%%%%%%%%%%% 182 echo %%%%%%%%%%%%%%%%%%%%%%%%%%%
183 echo 183 echo
184 184
185 exec ${DIR}/start_interpreter.sh ${PROG} "$PARAM_VECT" 185 exec ${DIR}/start_interpreter.sh ${PROG} "$PARAM_VECT"
186