Carlos-Francisco Méndez-Cruz / automatic-extraction-growth-conditions

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Estefani Gaytan Nunez
e9ea7a32 1 parent 67d2b78c

upload

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Showing 9 changed files with 8 additions and 34 deletions
......@@ -34,7 +34,7 @@ echo
echo
echo "Add sentence-end-tag PGCGROWTHCONDITIONS"
#cext=$(grep -E ".*" $(cat $index | tr '\n' ' ')| sed 's/"//g'| sed 's/.tsv:/.tsv\t/' | tr '/' '\t'| cut -f8,9 | sort | uniq | awk 'BEGIN {FS="\t"} length($2) > 3 { print $_}' | sed 's/\\null\\/null/g'| sed 's/.tsv//g' | sed 's/-/\t/' | sed 's/-/\t/' )
cext=$(grep -E ".*" $(cat $index | tr '\n' ' ') | sed 's/\//\t/7'| cut -f2-3 | sed 's/-/\t/' | sed 's/-/\t/' | sed 's/.tsv:/\t/' | sed 's/\"//g' | sed 's/1.\tNeubauer//'| sort | uniq)
cext=$(grep -E ".*" $(cat $index | tr '\n' ' ') | sed 's/\//\t/7'| cut -f2-3 | sed 's/-/\t/' | sed 's/-/\t/' | sed 's/.tsv:/\t/' | sed 's/\"//g' | sed 's/1.\tNeubauer//'| sed 's/\\null\\/null/g' | sort | uniq)
echo "$cext" | cut -f4 | awk '{ print $_ " PGCGROWTHCONDITIONS" }' > $output
wc $output
echo "$cext" | cut -f1-3,5 > $mapping
......
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......@@ -61,6 +61,7 @@ import training_validation_v14 as training
# --variant 13
#python3 tagging.py --inputPath /home/egaytan/automatic-extraction-growth-conditions/predict-annot/input/ --outputPath /home/egaytan/automatic-extraction-growth-conditions/predict-annot/output/ --outputFileI annot-input_bg_outputI.txt --outputFileII annot-input_bg_outputII.txt --modelPath /home/egaytan/automatic-extraction-growth-conditions/CRF/models --modelName model_Run3_v10_S1_False_S2_True_S3_False_S4_False_Run3_v10 --infoPath /home/egaytan/automatic-extraction-growth-conditions/predict-annot/mapping --infoFile bg_sentences_midx.txt --variant 13 --S4 --S1 > ../../reports/output_tagging_report.txt
#python3 predict-annot/bin/tagging/tagging.py --inputPath /home/egaytan/automatic-extraction-growth-conditions/predict-annot/input/ --outputPath /home/egaytan/automatic-extraction-growth-conditions/predict-annot/output/ --outputFileI annot-input_bg_outputI_v4.txt --outputFileII annot-input_bg_outputII_v4 --modelPath /home/egaytan/automatic-extraction-growth-conditions/CRF/models --modelName model_Run3_v10_S1_False_S2_True_S3_False_S4_False_Run3_v10 --infoPath /home/egaytan/automatic-extraction-growth-conditions/predict-annot/mapping --infoFile bg_sentences_midx_v4.txt --variant 13 --S4 --S1 > predict-annot/reports/output_tagging_report_v4.txt
__author__ = 'egaytan'
......@@ -241,7 +242,7 @@ if __name__ == "__main__":
#print( DF(sentencesOutputDataI) )
#print( '\n'.join(sentencesOutputDataII) )
# Save tags
with open(os.path.join(options.outputPath, options.outFileII), "w") as oFile:
with open(os.path.join(options.outputPath, options.outFileII + '_' + options.modelName + '.txt'), "w") as oFile:
for line in sentencesOutputDataII:
#print(line)
oFile.write(line + '\n')
......
# -*- coding: UTF-8 -*-
import os
from optparse import OptionParser
from time import time
from collections import Counter
import nltk
import sklearn
import scipy.stats
import sys
#from sklearn.externals import joblib
import joblib
from sklearn.metrics import make_scorer
#from sklearn.cross_validation import cross_val_score
from sklearn.model_selection import cross_val_score
#from sklearn.grid_search import RandomizedSearchCV
from sklearn.model_selection import RandomizedSearchCV
import sklearn_crfsuite
from sklearn_crfsuite import scorers
from sklearn_crfsuite import metrics
from nltk.corpus import stopwords
#################################
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......@@ -2,7 +2,7 @@
--inputPath Path of training data set : /home/egaytan/automatic-extraction-growth-conditions/predict-annot/input/
--outputPath Output path to place output files: /home/egaytan/automatic-extraction-growth-conditions/predict-annot/output/
--outputFileI Output tagged file I : annot-input_bg_outputI_v4.txt
--outputFileII Output tagged file II : annot-input_bg_outputII_v4.txt
--outputFileII Output tagged file II : annot-input_bg_outputII_v4
--modelPath Path to read CRF model : /home/egaytan/automatic-extraction-growth-conditions/CRF/models
--modelName Model name : model_Run3_v10_S1_False_S2_True_S3_False_S4_False_Run3_v10
--infoPath Path of GSE-GSM index file : /home/egaytan/automatic-extraction-growth-conditions/predict-annot/mapping
......@@ -17,16 +17,16 @@
Filtering symbols ['.', ',', ':', ';', '?', '!', "'", '"', '<', '>', '(', ')', '-', '_', '/', '\\', '¿', '¡', '+', '{', '}', '[', ']', '*', '%', '$', '#', '&', '°', '`', '...']: False
-------------------------------- PROCESSING --------------------------------
Reading CRF model...
Reading CRF model done in: 0.009697s
Reading CRF model done in: 0.009390s
Processing corpus...
Preprocessing file...annot-input_bg_v3.txt
Sentences input data: 14716
Predicting tags with model
Prediction done in: 1.732606s
Prediction done in: 1.692121s
Tagging file
Preprocessing file...annot-input_bg_v4.txt
Sentences input data: 90904
Predicting tags with model
Prediction done in: 26.221746s
Prediction done in: 25.701133s
Tagging file
Processing corpus done in: 58.477312s
Processing corpus done in: 57.242562s
......