Setting up project

+# -*- coding: UTF-8 -*-
+
+from optparse import OptionParser
+import os
+import sys
+from time import time
+from subprocess import call
+
+__author__ = 'CMendezC'
+
+# Objective: Lemmatizing several files with BIOLemmatizer.
+
+# Parameters:
+#   1) --inputPath Path to read TXT files.
+#   2) --outputPath Path to place POST files.
+#   3) --biolemmatizerPath Path BIOLemmatizer command.
+
+# Input:
+#   1) POS Tagged files in format:
+#   Rob	NNP
+#   is	VBZ
+#   a	DT
+#   transcriptional	JJ
+#   dual	JJ
+#   regulator	NN
+#   .	.
+#
+#   Its	PRP$
+#   N-terminal	JJ ...
+
+# Output:
+#   1) BIOLemmatized files.
+
+# Execution:
+# python biolemmatizing.py --inputPath C:\Users\cmendezc\Documents\GENOMICAS\AUTOMATIC_SUMMARIZATION_TFS\corpus\TF_PMIDs_TXT\ECK120012096_GntR\post --outputPath C:\Users\cmendezc\Documents\GENOMICAS\AUTOMATIC_SUMMARIZATION_TFS\corpus\TF_PMIDs_TXT\ECK120012096_GntR\lemma --biolemmatizerPath C:\Users\cmendezc\Documents\GENOMICAS\BIO_LEMMATIZER
+
+# FhlA
+# python biolemmatizing.py --inputPath C:\Users\cmendezc\Documents\GENOMICAS\AUTOMATIC_SUMMARIZATION_TFS\corpus\TF_PMIDs_TXT_ECK120011394_FhlA\post --outputPath C:\Users\cmendezc\Documents\GENOMICAS\AUTOMATIC_SUMMARIZATION_TFS\corpus\TF_PMIDs_TXT_ECK120011394_FhlA\lemma --biolemmatizerPath C:\Users\cmendezc\Documents\GENOMICAS\BIO_LEMMATIZER
+
+# MarA
+# python biolemmatizing.py --inputPath C:\Users\cmendezc\Documents\GENOMICAS\AUTOMATIC_SUMMARIZATION_TFS\corpus\TF_PMIDs_TXT_ECK120011412_MarA\post --outputPath C:\Users\cmendezc\Documents\GENOMICAS\AUTOMATIC_SUMMARIZATION_TFS\corpus\TF_PMIDs_TXT_ECK120011412_MarA\lemma --biolemmatizerPath C:\Users\cmendezc\Documents\GENOMICAS\BIO_LEMMATIZER
+
+# ArgR
+# python biolemmatizing.py --inputPath C:\Users\cmendezc\Documents\GENOMICAS\AUTOMATIC_SUMMARIZATION_TFS\corpus\TF_PMIDs_TXT_ECK120011670_ArgR\post --outputPath C:\Users\cmendezc\Documents\GENOMICAS\AUTOMATIC_SUMMARIZATION_TFS\corpus\TF_PMIDs_TXT_ECK120011670_ArgR\lemma --biolemmatizerPath C:\Users\cmendezc\Documents\GENOMICAS\BIO_LEMMATIZER
+
+# CytR
+# python biolemmatizing.py --inputPath C:\Users\cmendezc\Documents\GENOMICAS\AUTOMATIC_SUMMARIZATION_TFS\corpus\TF_PMIDs_TXT_ECK120012407_CytR\post --outputPath C:\Users\cmendezc\Documents\GENOMICAS\AUTOMATIC_SUMMARIZATION_TFS\corpus\TF_PMIDs_TXT_ECK120012407_CytR\lemma --biolemmatizerPath C:\Users\cmendezc\Documents\GENOMICAS\BIO_LEMMATIZER
+
+# Rob
+# python biolemmatizing.py --inputPath C:\Users\cmendezc\Documents\GENOMICAS\AUTOMATIC_SUMMARIZATION_TFS\corpus\TF_PMIDs_TXT_ECK120011190_Rob\post --outputPath C:\Users\cmendezc\Documents\GENOMICAS\AUTOMATIC_SUMMARIZATION_TFS\corpus\TF_PMIDs_TXT_ECK120011190_Rob\lemma --biolemmatizerPath C:\Users\cmendezc\Documents\GENOMICAS\BIO_LEMMATIZER
+
+# EXTRACTING REGULATORY INTERACTIONS
+# python biolemmatizing.py --inputPath C:\Users\cmendezc\Documents\GENOMICAS\EXTRACTING_REGULATORY_INTERACTIONS\corpus_ecoli\post --outputPath C:\Users\cmendezc\Documents\GENOMICAS\EXTRACTING_REGULATORY_INTERACTIONS\corpus_ecoli\lemma  --biolemmatizerPath C:\Users\cmendezc\Documents\GENOMICAS\BIO_LEMMATIZER
+
+###########################################################
+#                       MAIN PROGRAM                      #
+###########################################################
+
+if __name__ == "__main__":
+    # Parameter definition
+    parser = OptionParser()
+    parser.add_option("-i", "--inputPath", dest="inputPath",
+                      help="Path to read TXT files", metavar="PATH")
+    parser.add_option("-o", "--outputPath", dest="outputPath",
+                      help="Path to place POST files", metavar="PATH")
+    parser.add_option("-a", "--biolemmatizerPath", dest="biolemmatizerPath", default="",
+                      help="Path BIOLemmatizer", metavar="PATH")
+
+    (options, args) = parser.parse_args()
+    if len(args) > 0:
+        parser.error("None parameters indicated.")
+        sys.exit(1)
+
+    # Printing parameter values
+    print('-------------------------------- PARAMETERS --------------------------------')
+    print("Path to read input files: " + str(options.inputPath))
+    print("Path to place output files: " + str(options.outputPath))
+    print("Path BIOLemmatizer command: " + str(options.biolemmatizerPath))
+
+    filesTagged = 0
+    t0 = time()
+    print("Lemmatizing corpus...")
+    # Walk directory to read files
+    for path, dirs, files in os.walk(options.inputPath):
+        # For each file in dir
+        for file in files:
+            print("   Lemmatizing file..." + str(file))
+            try:
+
+                #java -Xmx1G -jar biolemmatizer-core-1.2-jar-with-dependencies.jar
+                # -i C:\Users\cmendezc\Documents\GENOMICAS\AUTOMATIC_SUMMARIZATION_TFS\corpus\aspectsOfInterest_TrainingSet\sentences_POST_Test.Stanford.post.biolemm.txt
+                # -o C:\Users\cmendezc\Documents\GENOMICAS\AUTOMATIC_SUMMARIZATION_TFS\corpus\aspectsOfInterest_TrainingSet\sentences_POST_Test.Stanford.post.biolemm.lemm.txt
+
+                taggerPath = os.path.join('java')
+                command = taggerPath + " -Xmx1G -jar " + os.path.join(options.biolemmatizerPath, 'biolemmatizer-core-1.2-jar-with-dependencies.jar') + \
+                                    ' -i ' + os.path.join(options.inputPath, file) + \
+                                    ' -o ' + os.path.join(options.outputPath, file.replace('pos.txt', 'lem.txt'))
+                #print(command)
+                retcode = call(command, shell=True)
+                if retcode < 0:
+                    print("   Child was terminated by signal", -retcode, file=sys.stderr)
+                else:
+                    print("   Child returned", retcode, file=sys.stderr)
+                    filesTagged += 1
+            except OSError as e:
+                print("   Execution failed:", e, file=sys.stderr)
+
+    # Imprime archivos procesados
+    print()
+    print("Files BIOLemmatized: " + str(filesTagged))
+    print("Files BIOLemmatized in: %fs" % (time() - t0))