Setting up project

@@ -3,6 +3,8 @@ echo 'Preprocessing files...'
 ORIGINAL_CORPUS_PATH=/export/space1/users/compu2/bionlp/conditional-random-fields/data-sets/original
 CORPUS_PATH=/export/space1/users/compu2/bionlp/conditional-random-fields/data-sets
 TERM_PATH=/export/space1/users/compu2/bionlp/conditional-random-fields/dictionaries
+POST_PATH=/home/cmendezc/STANFORD_POSTAGGER/stanford-postagger-2015-12-09
+LEMMA_PATH/home/cmendezc/BIO_LEMMATIZER
 
 PRE=TRUE
 echo "   Preprocessing: $PRE"
@@ -19,34 +21,33 @@ if [ "$PRE" = "TRUE" ]; then
 echo "Preprocessing..."
 INPUT_PATH=$ORIGINAL_CORPUS_PATH
 OUTPUT_PATH=$CORPUS_PATH/preprocessed
-python3.4 preprocessingTermDetection.py --inputPath $INPUT_PATH --outputPath $OUTPUT_PATH --termDetection --termPath $TERM_PATH --termFiles termFilesLength_LREGULONDB.json > outputPreprocessing_lregulondb.txt
-# python3.4 preprocessingTermDetection.py --inputPath $INPUT_PATH --outputPath $OUTPUT_PATH > outputPreprocessing_lregulondb.txt
+python3.4 preprocessingTermDetection.py --inputPath $INPUT_PATH --outputPath $OUTPUT_PATH --termDetection --termPath $TERM_PATH --termFiles termFilesLength.json > outputPreprocessing.txt
 fi
 
 if [ "$POS" = "TRUE" ]; then
 echo "POS Tagging..."
 INPUT_PATH=$CORPUS_PATH/preprocessed
 OUTPUT_PATH=$CORPUS_PATH/pos
-python3.4 posTaggingStanford.py --inputPath $INPUT_PATH --outputPath $OUTPUT_PATH --taggerPath /home/cmendezc/STANFORD_POSTAGGER/stanford-postagger-2015-12-09 --biolemmatizer > outputPOST_lregulondb.txt
+python3.4 posTaggingStanford.py --inputPath $INPUT_PATH --outputPath $OUTPUT_PATH --taggerPath $POST_PATH --biolemmatizer > outputPOST.txt
 fi
 
 if [ "$LEMMA" = "TRUE" ]; then
 echo "Lemmatization..."
 INPUT_PATH=$CORPUS_PATH/pos
 OUTPUT_PATH=$CORPUS_PATH/lemma
-python3.4 biolemmatizing.py --inputPath $INPUT_PATH --outputPath $OUTPUT_PATH --biolemmatizerPath /home/cmendezc/BIO_LEMMATIZER  > outputLemma_lregulondb.txt
+python3.4 biolemmatizing.py --inputPath $INPUT_PATH --outputPath $OUTPUT_PATH --biolemmatizerPath $LEMMA_PATH  > outputLemma.txt
 fi
 
 if [ "$TERM" = "TRUE" ]; then
 echo "Terminological tagging..."
 INPUT_PATH=$CORPUS_PATH/lemma
 OUTPUT_PATH=$CORPUS_PATH/term
-python3.4 biologicalTermTagging.py --inputPath $INPUT_PATH --outputPath $OUTPUT_PATH --termPath $TERM_PATH --termFiles termFilesTag_LREGULONDB.json > outputTerm_lregulondb.txt
+python3.4 biologicalTermTagging.py --inputPath $INPUT_PATH --outputPath $OUTPUT_PATH --termPath $TERM_PATH --termFiles termFilesTag.json > outputTerm.txt
 fi
 
 if [ "$TRANS" = "TRUE" ]; then
 echo "Transformation..."
 INPUT_PATH=$CORPUS_PATH/term
 OUTPUT_PATH=$CORPUS_PATH/transformed
-python3.4 transforming.py --inputPath $INPUT_PATH --outputPath $OUTPUT_PATH --minWordsInLine 5 > outputTransformation_lregulondb.txt
+python3.4 transforming.py --inputPath $INPUT_PATH --outputPath $OUTPUT_PATH --minWordsInLine 5 > outputTransformation.txt
 fi