ri-openie-extraction-v02.py
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# -*- coding: UTF-8 -*-
from optparse import OptionParser
import sys
import os
import json
import operator
from general_functions import getTypeRegulation
import re
from nltk.corpus import words
__author__ = 'CMendezC'
# Objective: obtain predicted ris from triplets extracted by OpenIE Stanford CoreNLP
# Input format:
# WARNING: Only one sentence per line
# Parameters:
# 1) --inputPath Input path
# 2) --inputFile Inpupt file
# 3) --outputPath Output path
# 5) --diccPath Dictionary path
# 6) --diccFile JSON file with entity dictionaries
# 7) --diccEffect File with normalized effects
# 8) --format Output format: standoff, tabs
# 9) --diccEPAth Dictionary path diccEffect
# Ouput:
# 1) File with predicted ris.
# Format standoff:
# T1 TF 0 0 MetR
# T2 TU 0 0 metH
# T3 GENE 0 0 metH
# T1 Growth_condition 88 137 mitochondrial electron transport chain inhibitors
# T2 Growth_condition 150 179 switch rich to minimal medium
# R1 Interaction.activator Target:T3 Agent:T1
# R2 Interaction.activator Target:T2 Agent:T1
# Execution
# python3.4 ri-openie-extraction.py
# --inputFile /home/cmendezc/bitbucket_repositories/automatic-extraction-ris-gcs/rie-gce-system/predicted-ris/predicted-ris.reverb
# --outputPath /home/cmendezc/bitbucket_repositories/automatic-extraction-ris-gcs/rie-gce-system/processing-ris
# --diccPath /home/cmendezc/terminologicalResources
# --diccFile normalized_Effects_Type.json
# --diccEffect termFilesTag_RIE_GCE_SYSTEM_ECCO.jsong
# --format standoff
###########################################################
# MAIN PROGRAM #
###########################################################
def getPosWord(wordPos, endPos, text, termList, type_entity=""):
#print("GETPOSWORD wordPOs {}".format(wordPos))
offsetStart = 0
wordNum = 0
listText = text.split()
for w in listText:
# if filenameBefore.find('000-2') > -1:
# print("Word {} in wordNum {} with wordPos {}".format(w, wordNum, wordPos))
if wordNum >= int(wordPos):
# for tok in word.split():
for t in termList:
# For entities starting word: if w == t or (w.startswith(t) and w not in regularWords):
if w == t:
if type_entity == "EFFECT":
# To change regulation effect in:
# negative regulator --> repressor
# positively regulates --> activator
print("text: {}".format(text))
new_w = getTypeRegulation(w, int(wordPos), text, "word")
return [new_w, offsetStart, offsetStart + len(w) - 1]
else:
return [w, offsetStart, offsetStart + len(w) - 1]
#else:
wordNum += 1
offsetStart += len(w) + 1
if wordNum > int(endPos):
return None
return None
def getIdEntity(aList, etype, idE):
entity = aList[0]
if etype == "EFFECT":
normalizedEffect = entity
# print("EFFECT: {}".format(entity))
if entity in hashEffects:
normalizedEffect = hashEffects[entity]
etype += "." + normalizedEffect
# print("EFFECT: {}".format(entity))
entityPosStart = aList[1]
entityPosEnd = aList[2]
keyEntity = "{} {} {} {}".format(etype, entityPosStart, entityPosEnd, entity)
#if filenameBefore.find('061-02') > -1:
# print("keyEntity: {}".format(keyEntity))
# print("idE: {}".format(idE))
# print("hashEntities: {}".format(hashEntities))
if keyEntity not in hashEntities:
idE += 1
idEntity = "T{}".format(idE)
#if filenameBefore.find('061-02') > -1:
# print("idEntity not in hashEntities: {}".format(keyEntity))
# print("idE not in hashEntities: {}".format(idE))
hashEntities[keyEntity] = idEntity
#print("New entity {}: {}".format(idEntity, keyEntity))
return idEntity, idE
else:
idEntity = hashEntities[keyEntity]
return idEntity, idE
def getIdInteraction(regulator, regulated, effect, idI, hashInt):
#print("hashInt: {}".format(hashInt))
keyInteraction = "{} {} {}".format(regulator, regulated, effect)
if keyInteraction not in hashInt:
idI += 1
idInteraction = "R{}".format(idI)
hashInt[keyInteraction] = idInteraction
#print("New interaction {}: {}".format(idInteraction, keyInteraction))
#return idInteraction, idI
else:
idInteraction = hashInt[keyInteraction]
return idInteraction, idI
def saveFiles(filename, hashE, hashI, s, effect):
if effect:
outputPath = os.path.join(options.outputPath, "complete-ris")
else:
outputPath = os.path.join(options.outputPath, "incomplete-ris")
with open(os.path.join(outputPath, filename[:file.find(".")] + ".a1"), mode="w") as a1File:
#with open(os.path.join(outputPath, filename[:file.find(".")] + ".a1"), mode="a+") as a1File:
for k, v in sorted(hashE.items(), key=operator.itemgetter(1)):
aList = k.split()
a1File.write("{}\t{} {} {}\t{}\n".format(v, aList[0], aList[1], aList[2], aList[3]))
with open(os.path.join(outputPath, filename[:file.find(".")] + ".a2"), mode="w") as a2File:
#with open(os.path.join(outputPath, filename[:file.find(".")] + ".a2"), mode="a+") as a2File:
for k, v in sorted(hashI.items(), key=operator.itemgetter(1)):
aList = k.split()
a2File.write("{}\tInteraction.{} Target:{} Agent:{}\n".format(v, aList[2], aList[1], aList[0]))
with open(os.path.join(outputPath, filename[:file.find(".")] + ".txt"), mode="w") as txtFile:
txtFile.write(s)
def loadFileEntities(filename, outputPath, hashTemp):
idE = 1
try:
with open(os.path.join(outputPath, filename[:file.find(".")] + ".a1"), mode="r") as a1File:
for line in a1File:
line = line.strip('\n')
listLine1 = line.split('\t')
listLine2 = listLine1[1].split(' ')
etype = listLine2[0]
entityPosStart = listLine2[1]
entityPosEnd = listLine2[2]
entity = listLine1[2]
keyEntity = "{} {} {} {}".format(etype, entityPosStart, entityPosEnd, entity)
idEntity = listLine1[0]
if keyEntity not in hashTemp:
hashTemp[keyEntity] = idEntity
if int(idEntity[1:]) > idE:
idE = int(idEntity[1:])
except IOError:
print("IOError file, idEntity starts in 1: {}".format(os.path.join(outputPath, filename[:file.find(".")] + ".a1")))
# idE = 1
return idE
def loadFileInteractions(filename, outputPath, hashTemp):
idI = 1
try:
with open(os.path.join(outputPath, filename[:file.find(".")] + ".a2"), mode="r") as a2File:
for line in a2File:
#print("Line a2: {}".format(line))
line = line.strip('\n')
listLine1 = line.split('\t')
listLine2 = listLine1[1].split(' ')
regulator = listLine2[2]
regulator = regulator[regulator.find(":") + 1:]
regulated = listLine2[1]
regulated = regulated[regulated.find(":") + 1:]
effect = listLine2[0]
effect = effect[effect.find(".") + 1:]
idInteraction = listLine1[0]
keyInteraction = "{} {} {}".format(regulator, regulated, effect)
if keyInteraction not in hashTemp:
hashTemp[keyInteraction] = idInteraction
if int(idInteraction[1:]) > idI:
idI = int(idInteraction[1:])
except IOError:
print("IOError file, idInteraction starts in 1: {}".format(os.path.join(outputPath, filename[:file.find(".")] + ".a2")))
# idI = 1
return idI
if __name__ == "__main__":
# Parameter definition
parser = OptionParser()
parser.add_option("--inputPath", dest="inputPath",
help="Input path", metavar="PATH")
parser.add_option("--inputFile", dest="inputFile",
help="Input file", metavar="FILE")
parser.add_option("--outputPath", dest="outputPath",
help="Output path", metavar="PATH")
#parser.add_option("--outputFile", dest="outputFile",
#help="Output file", metavar="FILE")
parser.add_option("--diccPath", dest="diccPath",
help="Path to read dictionaries", metavar="PATH")
parser.add_option("--diccFile", dest="diccFile",
help="JSON file with entity dictionaries", metavar="FILE")
parser.add_option("--diccEffect", dest="diccEffect",
help="File with normalized effects", metavar="FILE")
parser.add_option("--format", dest="format",
help="Output format: standoff", metavar="TEXT")
parser.add_option("--diccEPAth", dest="diccEPAth",
help="File with normalized effects", metavar="FILE")
(options, args) = parser.parse_args()
if len(args) > 0:
parser.error("None parameter entered.")
sys.exit(1)
# Printing parameter values
print('-------------------------------- PARAMETERS --------------------------------')
print("Input path: " + str(options.inputPath))
print("Input file: " + str(options.inputFile))
print("Output path: " + str(options.outputPath))
#print("Output file: " + str(options.outputFile))
print("Path to read dictionaries: " + str(options.diccPath))
print("JSON file with entity dictionaries: " + str(options.diccFile))
print("Path to read normalized effects: " + str(options.diccEPAth))
print("File with normalized effects: " + str(options.diccEffect))
print("Output format: " + str(options.format))
regularWords = words.words('en')
print('Loading dictionaries...')
with open(os.path.join(options.diccPath, options.diccFile)) as diccFile:
hashDicc = json.load(diccFile)
# hashTermFiles = hashDicc["hashTermFiles"]
# hashTerms = hashDicc["hashTerms"]
# for key in hashTermFiles.keys():
# for f in hashTermFiles[key]:
# # print('File: ' + f)
# with open(os.path.join(options.diccPath, 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])))
# Loading normalized effects
print('Loading normalized effects...')
with open(os.path.join(options.diccEPAth, options.diccEffect)) as diccFile:
hashEffects = json.load(diccFile)
files = {}
hashEntities = {}
hashInteractions = {}
hashInteractionsEffect = {}
idEntities = 1
idInteractions = 1
idInteractionsEffect = 1
filenameBefore = ''
regexNumFile = re.compile(r'_([0-9]+)[.-]')
numFile = ""
inumFile = 0
hashTerms = {"TF": [], "TU": [], "EFFECT": [], "GENE": []}
with open(os.path.join(options.inputPath, options.inputFile)) as iFile:
for line in iFile:
line = line.rstrip('\n')
listLine = line.split('\t')
file = listLine[0]
filename = file.split("/")[-1]
filename = filename[:-4]
if filename not in files:
# New file, that is, new sentence
files[filename] = 1
if len(files) > 1:
if len(hashEntities) > 0:
#if filenameBefore.find('061-02') > -1:
# print("filenameBefore: {}".format(filenameBefore))
# print("Save hashEntities: {}".format(hashEntities))
# print("Save hashInteractions: {}".format(hashInteractions))
# print("Save hashInteractionsEffect: {}".format(hashInteractionsEffect))
saveFiles(filenameBefore, hashEntities, hashInteractions, sent, effect=False)
saveFiles(filenameBefore, hashEntities, hashInteractionsEffect, sent, effect=True)
filenameBefore = filename
hashEntities = {}
hashInteractions = {}
hashInteractionsEffect = {}
idEntities = 1
idInteractions = 1
idInteractionsEffect = 1
outputPath = os.path.join(options.outputPath, "complete-ris")
idEntities = loadFileEntities(filename, outputPath, hashEntities)
idInteractionsEffect = loadFileInteractions(filename, outputPath, hashInteractionsEffect)
outputPath = os.path.join(options.outputPath, "incomplete-ris")
idInteractions = loadFileInteractions(filename, outputPath, hashInteractions)
result = regexNumFile.search(filenameBefore)
if result:
inumFile = int(result.group(1))
numFile = str(inumFile)
print("Numfile: {}".format(numFile))
else:
print("WARNING: numfile not found in filename")
hashTerms = {"TF": [], "TU": [], "EFFECT": [], "GENE": []}
if numFile in hashDicc:
hashTemp = hashDicc[numFile]
#print("hashDicc[numFile]: {}".format(hashTemp))
for k, v in hashTemp.items():
if v == "TF":
# print("Verifiying TF")
if "TF" in hashTerms:
# print(" TF {}".format(k))
hashTerms["TF"].append(k)
else:
hashTerms["TF"] = [k]
elif v == "GENE":
if "GENE" in hashTerms:
hashTerms["GENE"].append(k)
else:
hashTerms["GENE"] = [k]
elif v == "TU":
if "TU" in hashTerms:
hashTerms["TU"].append(k)
else:
hashTerms["TU"] = [k]
elif v == "EFFECT":
if "EFFECT" in hashTerms:
hashTerms["EFFECT"].append(k)
else:
hashTerms["EFFECT"] = [k]
else:
print("WARNING: entity not found in dictionaries")
else:
print("WARNING: numfile not found in dictionaries")
#if filename.find('061-02') > -1:
# print("filename: {}".format(filename))
# print("Load hashEntities: {}".format(hashEntities))
# print("Load hashInteractions: {}".format(hashInteractions))
# print("Load hashInteractionsEffect: {}".format(hashInteractionsEffect))
wordA = listLine[2]
wordB = listLine[3]
wordC = listLine[4]
startA = listLine[5]
endA = listLine[6]
startB = listLine[7]
endB = listLine[8]
startC = listLine[9]
endC = listLine[10]
sent = listLine[12]
lemmaA = listLine[2]
lemmaB = listLine[3]
lemmaC = listLine[4]
# Return [tok, offsetStart, offsetEnd ]
# print("hashTerms[TF]: {}".format(hashTerms["TF"]))
listRegulator = getPosWord(startA, endA, sent, hashTerms["TF"])
if listRegulator is not None:
#if filenameBefore.find('061-02') > -1:
# print(">> Regulator found: {}".format(listRegulator[0]))
listRegulated = getPosWord(startC, endC, sent, hashTerms["GENE"])
if listRegulated is not None:
#if filenameBefore.find('061-02') > -1:
# print(">> Regulated GENE found: {}".format(listRegulated[0]))
idRegulator, idEntities = getIdEntity(listRegulator, "TF", idEntities)
idRegulated, idEntities = getIdEntity(listRegulated, "GENE", idEntities)
idInteraction, idInteractions = getIdInteraction(idRegulator, idRegulated, "regulator", idInteractions, hashInteractions)
#print("Review EFFECT")
listEffect = getPosWord(startB, endB, sent, hashTerms["EFFECT"], "EFFECT")
if listEffect is not None:
idEffect, idEntities = getIdEntity(listEffect, "EFFECT", idEntities)
idInteraction, idInteractionsEffect = getIdInteraction(idRegulator, idRegulated, idEffect, idInteractionsEffect, hashInteractionsEffect)
else:
listRegulated = getPosWord(startC, endC, sent, hashTerms["TU"])
if listRegulated is not None:
#if filenameBefore.find('061-02') > -1:
# print(">> Regulated TU found: {}".format(listRegulated[0]))
idRegulator, idEntities = getIdEntity(listRegulator, "TF", idEntities)
idRegulated, idEntities = getIdEntity(listRegulated, "TU", idEntities)
idInteraction, idInteractions = getIdInteraction(idRegulator, idRegulated, "regulator", idInteractions, hashInteractions)
#print("Review EFFECT")
listEffect = getPosWord(startB, endB, sent, hashTerms["EFFECT"], "EFFECT")
if listEffect is not None:
idEffect, idEntities = getIdEntity(listEffect, "EFFECT", idEntities)
idInteraction, idInteractionsEffect = getIdInteraction(idRegulator, idRegulated, idEffect, idInteractionsEffect, hashInteractionsEffect)
else:
listRegulator = getPosWord(startC, endC, sent, hashTerms["TF"])
if listRegulator is not None:
#if filenameBefore.find('061-02') > -1:
# print(">> Regulator found: {}".format(listRegulator[0]))
listRegulated = getPosWord(startA, endA, sent, hashTerms["GENE"])
if listRegulated is not None:
#if filenameBefore.find('061-02') > -1:
# print(">> Regulated GENE found: {}".format(listRegulated[0]))
idRegulator, idEntities = getIdEntity(listRegulator, "TF", idEntities)
idRegulated, idEntities = getIdEntity(listRegulated, "GENE", idEntities)
idInteraction, idInteractions = getIdInteraction(idRegulator, idRegulated, "regulator", idInteractions, hashInteractions)
#print("Review EFFECT")
listEffect = getPosWord(startB, endB, sent, hashTerms["EFFECT"], "EFFECT")
if listEffect is not None:
idEffect, idEntities = getIdEntity(listEffect, "EFFECT", idEntities)
idInteraction, idInteractionsEffect = getIdInteraction(idRegulator, idRegulated, idEffect, idInteractionsEffect, hashInteractionsEffect)
else:
listRegulated = getPosWord(startA, endA, sent, hashTerms["TU"])
if listRegulated is not None:
#if filenameBefore.find('061-02') > -1:
# print(">> Regulated TU found: {}".format(listRegulated[0]))
idRegulator, idEntities = getIdEntity(listRegulator, "TF", idEntities)
idRegulated, idEntities = getIdEntity(listRegulated, "TU", idEntities)
idInteraction, idInteractions = getIdInteraction(idRegulator, idRegulated, "regulator", idInteractions, hashInteractions)
#print("Review EFFECT")
listEffect = getPosWord(startB, endB, sent, hashTerms["EFFECT"], "EFFECT")
if listEffect is not None:
idEffect, idEntities = getIdEntity(listEffect, "EFFECT", idEntities)
idInteraction, idInteractionsEffect = getIdInteraction(idRegulator, idRegulated, idEffect, idInteractionsEffect, hashInteractionsEffect)
if len(files) > 1:
if len(hashEntities) > 0:
#print("filenameBefore: {}".format(filenameBefore))
#print("Save hashEntities: {}".format(hashEntities))
#print("Save hashInteractions: {}".format(hashInteractions))
#print("Save hashInteractionsEffect: {}".format(hashInteractionsEffect))
saveFiles(filenameBefore, hashEntities, hashInteractions, sent, effect=False)
saveFiles(filenameBefore, hashEntities, hashInteractionsEffect, sent, effect=True)