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data_refining.py
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import sys
import os
import shutil
import random
import glob, os
from shutil import copyfile
import re
import random
corpus_dir = "/Users/bingyushen/Documents/phylonegy/text-phylogeny-all-datasets/Reuters_Dataset/C50test"
tree_base_dir = "/Users/bingyushen/Documents/phylonegy/text-phylogeny-all-datasets/Reuters_Dataset/test_tree_base"
def prepare_doc():
for folder in os.listdir(corpus_dir):
if not folder.startswith('.') and os.path.isdir(os.path.join(corpus_dir, folder)):
folder_dir = corpus_dir+"/"+folder
outputfilename = folder_dir+"/"+folder+".txt"
newoutputfilename = folder_dir+".txt"
if os.path.exists(outputfilename):
open(outputfilename, 'w').close()
with open(newoutputfilename, 'w') as outputfile:
for files in os.listdir(folder_dir):
files_dir = folder_dir+"/"+files
with open(files_dir, 'rb') as readfile:
infile = readfile.read()
for line in infile:
outputfile.write(line)
outputfile.write("\n\n")
readfile.close()
print "files done ", files
outputfile.close()
print "done writing file ", newoutputfilename
def prepare_treebasefile():
for folder in os.listdir(corpus_dir):
if not folder.startswith('.') and os.path.isdir(os.path.join(corpus_dir, folder)):
folder_dir = corpus_dir + "/" + folder
file_a = random.choice(os.listdir(folder_dir))
old_path = os.path.join(folder_dir, file_a)
file_a_name = folder+"_"+file_a
new_path = os.path.join(tree_base_dir, file_a_name)
copyfile(old_path, new_path)
def prepare_corpus():
os.chdir("/Users/bingyushen/Documents/phylonegy/text-phylogeny-all-datasets/Reuters_Dataset/C50test/")
old_dir = "/Users/bingyushen/Documents/phylonegy/text-phylogeny-all-datasets/Reuters_Dataset/C50test"
corpus_dir = "/Users/bingyushen/Documents/phylonegy/text-phylogeny-all-datasets/Reuters_Dataset/test_corpus"
for file in glob.glob("*.txt"):
file_dir = old_dir + "/" + file
new_dir = corpus_dir + "/" + file
copyfile(file_dir, new_dir)
def generatetrainingdata():
trees_dir = "/Users/bingyushen/Downloads/drive-download-20161026T043937Z/1026_test_tree_10/Trees"
phyl_dir = "/Users/bingyushen/Downloads/drive-download-20161026T043937Z/1026_test_tree_10/Phylogenies"
for tree in os.listdir(trees_dir):
print "entering new tree", tree
doc = tree.split('_')[0]
print "doc: ", doc
tree_dir = os.path.join(trees_dir, tree)
treefiles = open(tree_dir,'r').read().split("<\\tphyldoc>")
edgefile_dir = os.path.join(phyl_dir, tree)
edgefile_dir = edgefile_dir.replace(".txt", ".phyl")
with open(edgefile_dir, 'r') as edgefile:
edges = edgefile.readlines()
# prepare edge table
tree_edge = [[0 for i in range(2)] for j in range(len(edges))]
# print tree_edge
for edge in edges:
# print edge
nodes = edge.split()
first_node = nodes[0]
second_node = nodes[2]
# print edges.index(edge)
tree_edge[edges.index(edge)][0] = int(first_node)
tree_edge[edges.index(edge)][1] = int(second_node)
labels = []
for i in range(len(treefiles)):
for j in range(len(treefiles)):
if i != j:
label = 0
sample1 = treefiles[i]
sample2 = treefiles[j]
for x in range(len(edges)):
if i==tree_edge[x][0] and j==tree_edge[x][1]:
# print "i: ", i, "j: ", j, "edgetable: " , tree_edge[x][0], tree_edge[x][1]
label = 1
writepostrainingsamples(sample1, sample2, doc, 1)
# print label
else:
# print "i: ", i, "j: ", j, "edgetable: ", tree_edge[x][0], tree_edge[x][1]
label = 0
writenegtrainingsamples(sample1, sample2, doc, 0)
# print label
# labels.append(label)
# print label
# print len(labels)
def writepostrainingsamples(sample1, sample2, doc, label):
rdscorpus = "/Users/bingyushen/Downloads/drive-download-20161026T043937Z/test_rdscorpus"
doc += '.rds'
docpath = os.path.join(rdscorpus, doc)
# print docpath
sample1 = sample1.replace('\n', '')
sample2 = sample2.replace('\n', '')
posfilepath = "/Users/bingyushen/Downloads/drive-download-20161026T043937Z/test_positive.txt"
with open(posfilepath, 'a') as postraining:
postraining.write("\"")
postraining.write(sample1)
postraining.write("\"")
postraining.write(",")
postraining.write('\"')
postraining.write(sample2)
postraining.write("\"")
postraining.write(",")
postraining.write(docpath)
postraining.write(",")
postraining.write(docpath)
postraining.write("\n")
postraining.close()
def writenegtrainingsamples(sample1, sample2, doc, label):
# a=0
rdscorpus = "/Users/bingyushen/Downloads/drive-download-20161026T043937Z/test_rdscorpus"
doc += '.rds'
docpath = os.path.join(rdscorpus, doc)
# print docpath
sample1 = sample1.replace('\n', '')
sample2 = sample2.replace('\n', '')
negfilepath = "/Users/bingyushen/Downloads/drive-download-20161026T043937Z/test_negative.txt"
with open(negfilepath, 'a') as negtraining:
negtraining.write("\"")
negtraining.write(sample1)
negtraining.write("\"")
negtraining.write(",")
negtraining.write('\"')
negtraining.write(sample2)
negtraining.write("\"")
negtraining.write(",")
negtraining.write(docpath)
negtraining.write(",")
negtraining.write(docpath)
negtraining.write("\n")
negtraining.close()
def cutnegtrainingfile():
negtrainingfile = "/Users/bingyushen/Documents/phylonegy/text-phylogeny-all-datasets/Reuters_Dataset/" \
"myresults/170219_tree_0.1/SVM_training_samples/negative1.txt"
newnegtrainingfile = "/Users/bingyushen/Documents/phylonegy/text-phylogeny-all-datasets/Reuters_Dataset" \
"/myresults/170219_tree_0.1/SVM_training_samples/new_negative1.txt"
with open(negtrainingfile, 'r') as negtraining:
negs = negtraining.readlines()
for x in range(230):
neg = random.choice(negs)
with open(newnegtrainingfile, 'a') as newnegtraining:
newnegtraining.write(neg)
if __name__ == "__main__":
cutnegtrainingfile()