biologicalTermTagging.py
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# -*- coding: UTF-8 -*-
import json
from optparse import OptionParser
import os
import sys
from time import time
from nltk.corpus import words
__author__ = 'CMendezC'
# Objective: Tagging biological terms from lists of terms related to aspects of interest:
# 1) Changing POS tag by term tag
# Parameters:
# 1) --inputPath Path to read input files.
# 2) --outputPath Path to place output files.
# 3) --termPath Path to read term lists
# 4) --termFiles JSON file with terms files and tags
# 5) --crf Let POS tag instead of substituting it by term or freq tag
# Output:
# 1) Files with biological terms tagged
# Execution:
# python biologicalTermTagging.py --inputPath C:\Users\cmendezc\Documents\GENOMICAS\AUTOMATIC_SUMMARIZATION_TFS\corpus\TF_PMIDs_TXT\ECK120012096_GntR\lemma --outputPath C:\Users\cmendezc\Documents\GENOMICAS\AUTOMATIC_SUMMARIZATION_TFS\corpus\TF_PMIDs_TXT\ECK120012096_GntR\term --termPath C:\Users\cmendezc\Documents\GENOMICAS\AUTOMATIC_SUMMARIZATION_TFS\resources\termLists --termFiles termFilesTag.json
# FhlA
# python biologicalTermTagging.py --inputPath C:\Users\cmendezc\Documents\GENOMICAS\AUTOMATIC_SUMMARIZATION_TFS\corpus\TF_PMIDs_TXT_ECK120011394_FhlA\lemma --outputPath C:\Users\cmendezc\Documents\GENOMICAS\AUTOMATIC_SUMMARIZATION_TFS\corpus\TF_PMIDs_TXT_ECK120011394_FhlA\term --termPath C:\Users\cmendezc\Documents\GENOMICAS\AUTOMATIC_SUMMARIZATION_TFS\resources\termLists --termFiles termFilesTag.json
# MarA
# python biologicalTermTagging.py --inputPath C:\Users\cmendezc\Documents\GENOMICAS\AUTOMATIC_SUMMARIZATION_TFS\corpus\TF_PMIDs_TXT_ECK120011412_MarA\lemma --outputPath C:\Users\cmendezc\Documents\GENOMICAS\AUTOMATIC_SUMMARIZATION_TFS\corpus\TF_PMIDs_TXT_ECK120011412_MarA\term --termPath C:\Users\cmendezc\Documents\GENOMICAS\AUTOMATIC_SUMMARIZATION_TFS\resources\termLists --termFiles termFilesTag.json
# ArgR
# python biologicalTermTagging.py --inputPath C:\Users\cmendezc\Documents\GENOMICAS\AUTOMATIC_SUMMARIZATION_TFS\corpus\TF_PMIDs_TXT_ECK120011670_ArgR\lemma --outputPath C:\Users\cmendezc\Documents\GENOMICAS\AUTOMATIC_SUMMARIZATION_TFS\corpus\TF_PMIDs_TXT_ECK120011670_ArgR\term --termPath C:\Users\cmendezc\Documents\GENOMICAS\AUTOMATIC_SUMMARIZATION_TFS\resources\termLists --termFiles termFilesTag.json
# CytR
# python biologicalTermTagging.py --inputPath C:\Users\cmendezc\Documents\GENOMICAS\AUTOMATIC_SUMMARIZATION_TFS\corpus\TF_PMIDs_TXT_ECK120012407_CytR\lemma --outputPath C:\Users\cmendezc\Documents\GENOMICAS\AUTOMATIC_SUMMARIZATION_TFS\corpus\TF_PMIDs_TXT_ECK120012407_CytR\term --termPath C:\Users\cmendezc\Documents\GENOMICAS\AUTOMATIC_SUMMARIZATION_TFS\resources\termLists --termFiles termFilesTag.json
# Rob
# python biologicalTermTagging.py --inputPath C:\Users\cmendezc\Documents\GENOMICAS\AUTOMATIC_SUMMARIZATION_TFS\corpus\TF_PMIDs_TXT_ECK120011190_Rob\lemma --outputPath C:\Users\cmendezc\Documents\GENOMICAS\AUTOMATIC_SUMMARIZATION_TFS\corpus\TF_PMIDs_TXT_ECK120011190_Rob\term --termPath C:\Users\cmendezc\Documents\GENOMICAS\AUTOMATIC_SUMMARIZATION_TFS\resources\termLists --termFiles termFilesTag.json
###########################################################
# MAIN PROGRAM #
###########################################################
if __name__ == "__main__":
# Parameter definition
parser = OptionParser()
parser.add_option("--inputPath", dest="inputPath",
help="Path to read input files", metavar="PATH")
parser.add_option("--outputPath", dest="outputPath",
help="Path to place transformed files", metavar="PATH")
parser.add_option("--termPath", dest="termPath",
help="Path to read term files", metavar="PATH")
parser.add_option("--termFiles", dest="termFiles",
help="JSON file with terms files and tags", metavar="FILE")
parser.add_option("--crf", default=False,
action="store_true", dest="crf",
help="Let POS tag instead of substituting it by term or freq tag?")
parser.add_option("--termLower", default=False,
action="store_true", dest="termLower",
help="Compare with terms in lower case?")
parser.add_option("--termCapitalize", default=False,
action="store_true", dest="termCapitalize",
help="Compare with capitalize terms?")
(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 transformed files: " + str(options.outputPath))
print("Path to read term files: " + str(options.termPath))
print("Let POS tag instead of substituting it by term or freq tag? " + str(options.crf))
print("Compare with terms in lower case? " + str(options.termLower))
print("Compare with capitalize terms? " + str(options.termCapitalize))
##### LOADING BIOLOGICAL TERM FILES #####
# hashTermFiles = {
# 'DFAM': ['domain_families_1grams.txt', 'domain_families_2grams.txt', 'domain_families_3grams.txt', 'domain_families_4grams.txt', 'domain_families_5Moregrams.txt'],
# 'MF': ['domain_function_1grams.txt', 'domain_function_2grams.txt', 'domain_function_3grams.txt', 'domain_function_4grams.txt' , 'domain_function_5Moregrams.txt'],
# 'RP': ['regulatory_Processes_GO_1grams.txt', 'regulatory_Processes_GO_2grams.txt', 'regulatory_Processes_GO_3grams.txt', 'regulatory_Processes_GO_4grams.txt', 'regulatory_Processes_GO_5Moregrams.txt'],
# 'DPOS': ['domain_position_1grams.txt', 'domain_position_2grams.txt', 'domain_position_5Moregrams.txt'],
# 'DMOT': ['domain_structural_motif_1grams.txt', 'domain_structural_motif_2grams.txt'],
# 'TF': ['tfs.txt']
# }
# hashTerms = {
# 'DFAM': [],
# 'MF': [],
# 'RP': [],
# 'DPOS': [],
# 'DMOT': [],
# 'TF': []
# }
print('Loading biological term files...')
with open(os.path.join(options.termPath, options.termFiles)) as data_file:
lists = json.load(data_file)
hashTermFiles = lists["hashTermFiles"]
hashTerms = lists["hashTerms"]
for key in hashTermFiles.keys():
for f in hashTermFiles[key]:
# print('File: ' + f)
with open(os.path.join(options.termPath, f), "r", encoding="utf-8", errors="replace") as iFile:
for line in iFile:
line = line.strip('\n')
line = line.replace(' ', '-')
if line not in hashTerms[key]:
hashTerms[key].append(line)
if options.termLower:
hashTerms[key].append(line.lower())
if options.termCapitalize:
hashTerms[key].append(line.capitalize())
print(' Terms read {} size: {}'.format(key, len(hashTerms[key])))
regularWords = words.words('en')
print()
filesPreprocessed = 0
t0 = time()
print("Biological term tagging files...")
# Walk directory to read files
for path, dirs, files in os.walk(options.inputPath):
# For each file in dir
for file in files:
print(" Biological term tagging file..." + str(file))
with open(os.path.join(path, file), "r", encoding="utf-8", errors="replace") as iFile:
# Create output file to write
with open(os.path.join(options.outputPath, file.replace('lem.txt', 'term.txt')), "w", encoding="utf-8") as oFile:
for line in iFile:
if line == '\n':
oFile.write(line)
else:
line = line.strip('\n')
listLine1 = line.split('\t')
if len(listLine1) < 3:
continue
word = listLine1[0]
pos = listLine1[1]
listLine2 = listLine1[2].split(' ')
lemma = listLine2[0]
if len(word) > 1:
for termTag in hashTerms:
if termTag == "TF":
for term in hashTerms[termTag]:
if (word == term) or (word.startswith(term) and lemma not in regularWords):
print(" TAG WORD {} AS TF CAUSE START WITH TF {} OR IT IS EQUAL".format(word, term))
if listLine1[1].startswith("NN"):
# line = listLine1[0] + '\t' + listLine1[1] + '\t' + listLine2[0] + ' ' + termTag + ' TermTag'
line = listLine1[0] + '\t' + termTag + '\t' + listLine2[0] + ' ' + termTag + ' TermTag'
elif termTag == "EFFECT":
if word.lower() in hashTerms[termTag]:
line = word + '\t' + termTag + '\t' + lemma + ' ' + termTag + ' TermTag'
elif termTag == "DIS":
for term in hashTerms[termTag]:
if lemma.startswith(term) and (pos not in ["CC", "DT", "FW", "CD", "IN", "PRP$", "JJ", "JJR", "JJS", "VBN", "RB"]):
line = word + '\t' + termTag + '\t' + lemma + ' ' + termTag + ' TermTag'
else:
if word in hashTerms[termTag]:
# listLine2 = listLine1[2].split(' ')
if termTag in ["GENE", "TU"]:
if listLine1[1].startswith("NN"):
# line = listLine1[0] + '\t' + listLine1[1] + '\t' + listLine2[0] + ' ' + termTag + ' TermTag'
line = listLine1[0] + '\t' + termTag + '\t' + listLine2[0] + ' ' + termTag + ' TermTag'
elif termTag in ["GC"]:
if pos not in ["CC", "DT", "FW", "CD", "IN", "PRP$", "NNP"]:
# line = listLine1[0] + '\t' + listLine1[1] + '\t' + listLine2[0] + ' ' + termTag + ' TermTag'
line = word + '\t' + termTag + '\t' + lemma + ' ' + termTag + ' TermTag'
else:
if termTag in ['FWDOM', 'FWRP']:
# line = listLine1[0] + '\t' + listLine1[1] + '\t' + listLine2[0] + ' ' + termTag + ' FreqTag'
line = listLine1[0] + '\t' + termTag + '\t' + listLine2[0] + ' ' + termTag + ' FreqTag'
else:
# line = listLine1[0] + '\t' + listLine1[1] + '\t' + listLine2[0] + ' ' + termTag + ' TermTag'
# line = listLine1[0] + '\t' + termTag + '\t' + listLine2[0] + ' ' + termTag + ' TermTag'
line = word + '\t' + termTag + '\t' + lemma + ' ' + termTag + ' TermTag'
oFile.write(line + '\n')
filesPreprocessed += 1
# Imprime archivos procesados
print()
print("Files preprocessed: " + str(filesPreprocessed))
print("In: %fs" % (time() - t0))