To understand the values of each variable, I improved a script for replacement from Udacity class. I convert the codes in a function into regular codes. However, my codes do not work while the codes in the function do. I appreciate it if anyone can explain it. Please pay more attention to function "tokenize".
Below codes are from Udacity class (CopyRight belongs to Udacity).
# download necessary NLTK data
import nltk
nltk.download(['punkt', 'wordnet'])
# import statements
import re
import pandas as pd
from nltk.tokenize import word_tokenize
from nltk.stem import WordNetLemmatizer
url_regex = 'http[s]?://(?:[a-zA-Z]|[0-9]|[$-_#.&+]|[!*\(\),]|(?:%[0-9a-fA-F][0-9a-fA-F]))+'
def load_data():
df = pd.read_csv('corporate_messaging.csv', encoding='latin-1')
df = df[(df["category:confidence"] == 1) & (df['category'] != 'Exclude')]
X = df.text.values
y = df.category.values
return X, y
def tokenize(text):
detected_urls = re.findall(url_regex, text) # here, "detected_urls" is a list for sure
for url in detected_urls:
text = text.replace(url, "urlplaceholder") # I do not understand why it can work while does not work in my code if I do not convert it to string
tokens = word_tokenize(text)
lemmatizer = WordNetLemmatizer()
clean_tokens = []
for tok in tokens:
clean_tok = lemmatizer.lemmatize(tok).lower().strip()
clean_tokens.append(clean_tok)
return clean_tokens
X, y = load_data()
for message in X[:5]:
tokens = tokenize(message)
print(message)
print(tokens, '\n')
Below is its output:
I want to understand the variables' values in function "tokenize()". Following are my codes.
X, y = load_data()
detected_urls = []
for message in X[:5]:
detected_url = re.findall(url_regex, message)
detected_urls.append(detected_url)
print("detected_urs: ",detected_urls) #output a list without problems
# replace each url in text string with placeholder
i = 0
for url in detected_urls:
text = X[i].strip()
i += 1
print("LN1.url= ",url,"\ttext= ",text,"\n type(text)=",type(text))
url = str(url).strip() #if I do not convert it to string, it is a list. It does not work in text.replace() below, but works in above function.
if url in text:
print("yes")
else:
print("no") #always show no
text = text.replace(url, "urlplaceholder")
print("\nLN2.url=",url,"\ttext= ",text,"\n type(text)=",type(text),"\n===============\n\n")
The output is shown below.
The outputs for "LN1" and "LN2" are same. The "if" condition always output "no". I do not understand why it happens.
Any further help and advice would be highly appreciated.
Related
I have converted a .txt file to tfrecords with some changes to it. But now I want to convert or read same file so I could understand my data which is now changed. I am doing this for my knowledge graph project.
import numpy as np
import os
import tensorflow as tf
import tqdm
import pdb
import glob
import time
import sys
import re
import argparse
import fastBPE
import platform
use_py3 = platform.python_version()[0] == '3'
parser = argparse.ArgumentParser(description='TensorFlow code for creating TFRecords data')
parser.add_argument('--text_file', type=str, required=True,
help='location of text file to convert to TFRecords')
parser.add_argument('--control_code', type=str, required=True,
help='control code to use for this file. must be in the vocabulary, else it will error out.')
parser.add_argument('--sequence_len', type=int, required=True,
help='sequence length of model being fine-tuned (256 or 512)')
args = parser.parse_args()
path_to_train_file = fname = args.text_file
domain = [args.control_code]
train_text = open(path_to_train_file, 'rb').read().decode(encoding='utf-8')
bpe = fastBPE.fastBPE('../codes', '../vocab')
tokenized_train_text = bpe.apply([train_text.encode('ascii', errors='ignore') if not use_py3 else train_text])[0] # will NOT work for non-English texts
# if you want to run non-english text, please tokenize separately using ./fast applybpe and then run this script on the .bpe file with utf8 encoding
tokenized_train_text = re.findall(r'\S+|\n', tokenized_train_text)
tokenized_train_text = list(filter(lambda x: x != u'##', tokenized_train_text))
# load the vocabulary from file
vocab = open('../vocab').read().decode(encoding='utf-8').split('\n') if not use_py3 else open('../vocab', encoding='utf-8').read().split('\n')
vocab = list(map(lambda x: x.split(' ')[0], vocab)) + ['<unk>'] + ['\n']
print ('{} unique words'.format(len(vocab)))
if args.control_code not in vocab:
print('Provided control code is not in the vocabulary')
print('Please provide a different one; refer to the vocab file for allowable tokens')
sys.exit(1)
# Creating a mapping from unique characters to indices
word2idx = {u:i for i, u in enumerate(vocab)}
idx2word = np.array(vocab)
seq_length = args.sequence_len-1
def numericalize(x):
count = 0
for i in x:
if i not in word2idx:
print(i)
count += 1
return count>1, [word2idx.get(i, word2idx['<unk>']) for i in x]
tfrecords_fname = fname.lower()+'.tfrecords'
total = 0
skipped = 0
with tf.io.TFRecordWriter(tfrecords_fname) as writer:
for i in tqdm.tqdm(range(0, len(tokenized_train_text), seq_length)):
flag_input, inputs = numericalize(domain+tokenized_train_text[i:i+seq_length])
flag_output, outputs = numericalize(tokenized_train_text[i:i+seq_length+1])
total += 1
if flag_input or flag_output:
skipped += 1
continue
if len(inputs)!=seq_length+1 or len(outputs)!=seq_length+1:
break
example_proto = tf.train.Example(features=tf.train.Features(feature={'input': tf.train.Feature(int64_list=tf.train.Int64List(value=inputs)),
'output': tf.train.Feature(int64_list=tf.train.Int64List(value=outputs))}))
writer.write(example_proto.SerializeToString())
print('Done')
print('Skipped', skipped, 'of', total)
This is my code I want every changes in it except that to convert in tfrecords.
Read the TFRecord with a TFRecordDataset.
Then iterate through the TFRecordDataset and for each element, write to a new text file or print out the results.
https://www.tensorflow.org/api_docs/python/tf/data/TFRecordDataset
Being rather new to programming with python I tried to language detect segments of text in pandas data frame.
So first I made a function for the 'langdetect' package
import pandas as pd
from langdetect import detect
def language_detect(x):
lang = detect(x)
print(lang)
My second step would be to feed in the data frame for processing. All the segments that need detecting are in separate rows in the dataframe under the same column header.
result = [language_detect(x) for x in df['column_name']]
df['l_detect'] = pd.append(result)
In the output I see the texts being recognized properly.
But when I try to print result.
it returns me with only the value for every entry 'none'
So my questions are:
why do I get 'none' when the the print output from the function has the right values
How can I attach this to my current data frame, since when I try to append it I get 'none' on
every field as well.
Thanks in advance.
The problem is that result is empty because your function language_detect() doesn't return anything (it is only printing the results).
import pandas as pd
from langdetect import detect
lst = [('this is a test', 1), ('what language is this?', 4), ('stackoverflow is a website', 23)]
df = pd.DataFrame(lst, columns = ['text', 'something'])
def language_detect(x):
lang = detect(x)
print(lang)
result = [language_detect(x) for x in df['text']]
result
#Output:[None, None, None]
Just give it a return value:
def language_detect(x):
lang = detect(x)
return lang
df['l_detect'] = df['text'].apply(language_detect)
df.head()
#Output:
# text something l_detect
#0 this is a test 1 en
#1 what language is this? 4 en
#2 stackoverflow is a website 23 en
and it will work as expected.
at the moment I am able to create one CSV file with all the content I get at once.
Now I would like to create a list where I have different names in it.
How can I produce for every functioncall a different CSV file name? I thought about looping a list but I just want a +1 iteration at each call. I thought about saving my state somehow and use it in next functioncall. Everytime I initialize my variable with 0 and so I don't get 1. I think I could do it with Python Function Parameter calls but I have no idea how to use it. Can someone give me a little tip or example? If there are better ideas (maybe my idea is totally bullshit), how to solve this, just help please.
The comments in the code shall represent my imagination.
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from tenable.sc import SecurityCenter as SC
import os.path
import sys
import getpass
import csv
SC_HOST = '...'
def parse_entry(entry):
split_after_path = ''
ip = entry.get('ip', None)
pluginText = entry.get('pluginText', None)
if 'Path : ' in pluginText:
for line in pluginText.splitlines(0):
if 'Path : ' in line:
split_after_path_in_plugintext = line.split("Path : ",1)[1]
# place = ['place1', 'place2', 'place3', 'place4', 'place5']
# i = 0
# i = i+1
file_exists = os.path.isfile('testfile_path.csv')
# file_exists = os.path.isfile('testfile_path_'+place[i]+'.csv')
data = open('testfile_path.csv', 'a')
# data = open('testfile_path_'+place[i]+'.csv', 'a')
with data as csvfile:
header = ['IP Address', 'Path']
writer = csv.DictWriter(csvfile, lineterminator='\n', quoting=csv.QUOTE_NONNUMERIC, fieldnames=header)
if not file_exists:
writer.writeheader()
writer.writerow({'IP Address': ip, 'Path': split_after_path})
data.close()
def main():
sc_user = input('[<<] username: ')
sc_pass = getpass.getpass('[<<] password: ')
sc = SC(SC_HOST)
sc.login(sc_user, sc_pass)
# Query API for data
# asset = [12,13,14,25,29]
# i = 0
# assetid = asset[i]
# vuln = sc.analysis.vulns(('pluginID', '=', '25072')('asset','=','assetid'))
# i = i+1
vuln = sc.analysis.vulns(('pluginID', '=', '25072'),('asset','=','11'))
for entry in vuln:
parse_entry(entry)
sc.logout()
return 0
if __name__ == '__main__':
sys.exit(main())
The simplest and most obvious solution is to pass the full file path to your parse_entry function, ie:
def parse_entry(entry, filepath):
# ...
if 'Path : ' in pluginText:
for line in pluginText.splitlines(0):
if 'Path : ' in line:
# ...
file_exists = os.path.isfile(filepath)
with open(filepath, 'a') as csvfile:
# ...
Then in main() use enumerate() to build sequential filenames:
def main():
# ...
for i, entry in enumerate(vuln):
path = "'testfile_path{}.csv".format(i)
parse_entry(entry, path)
You can use a function attribute to keep track of the number of times the function has been called.
def parse_entry(entry):
parse_entry.i += 1
# outside the function you have to initialize the attribute
parse_entry.i = 0
Or you can look at other ways to initialize the function attribute in this post.
Alternatively, you can use glob to get the current number of files.
from glob import glob
i = len(glob('testfile_path_*.csv'))
# below is the sentiment analysis code written for sentence-level analysis
import glob
import os
import nltk.data
from nltk.sentiment.vader import SentimentIntensityAnalyzer
from nltk import sentiment
from nltk import word_tokenize
# Next, VADER is initialized so I can use it within the Python script
sid = SentimentIntensityAnalyzer()
# I will also initialize the 'english.pickle' function and give it a short
name
tokenizer = nltk.data.load('tokenizers/punkt/english.pickle')
#Each of the text file is listed from the folder speeches
files = glob.glob(os.path.join(os.getcwd(), 'cnn_articles', '*.txt'))
text = []
#iterate over the list getting each file
for file in files:
#open the file and then call .read() to get the text
with open(file) as f:
text.append(f.read())
text_str = "\n".join(text)
# This breaks up the paragraph into a list of strings.
sentences = tokenizer.tokenize(text_str )
sent = 0.0
count = 0
# Iterating through the list of sentences and extracting the compound scores
for sentence in sentences:
count +=1
scores = sid.polarity_scores(sentence)
sent += scores['compound'] #Adding up the overall compound sentiment
# print(sent, file=open('cnn_compound.txt', 'a'))
if count != 0:
sent = float(sent / count)
print(sent, file=open('cnn_compound.txt', 'a'))
With these lines of code, I have been able to get the average of all the compound sentiment values for all the text files. What I really want is the
average compound sentiment value for each text file, such that if I have 10
text files in the folder, I will have 10 floating point values representing
each of the text file. So that I can plot these values against each other.
Kindly assist me as I am very new to Python.
# below is the sentiment analysis code written for sentence-level analysis
import os, string, glob, pandas as pd, numpy as np
import nltk.data
from nltk.sentiment.vader import SentimentIntensityAnalyzer
from nltk import sentiment
from nltk import word_tokenize
# Next, VADER is initialized so I can use it within the Python
script
sid = SentimentIntensityAnalyzer()
exclude = set(string.punctuation)
# I will also initialize the 'english.pickle' function and give
it a short
name
tokenizer = nltk.data.load('tokenizers/punkt/english.pickle')
#Each of the text file is listed from the folder speeches
files = glob.glob(os.path.join(os.getcwd(), 'cnn_articles',
'*.txt'))
text = []
sent = 0.0
count = 0
cnt = 0
#iterate over the list getting each file
for file in files:
f = open(file).read().split('.')
cnt +=1
count = (len(f))
for sentence in f:
if sentence not in exclude:
scores = sid.polarity_scores(sentence)
print(scores)
break
sent += scores['compound']
average = round((sent/count), 4)
t = [cnt, average]
text.append(t)
break
df = pd.DataFrame(text, columns=['Article Number', 'Average
Value'])
#
#df.to_csv(r'Result.txt', header=True, index=None, sep='"\t\"
+"\t\"', mode='w')
df.to_csv('cnn_result.csv', index=None)
I have been using beautiful soup to extract info from the website http://slc.bioparadigms.org
But I am only interested in the diseases and OMIM number, so for each SLC transporter which i already have in a list i want to extract these 2 characteristics. The thing is that both are related to class prt_col2. So if i search for this class i get a lot of hits. How can I only get the diseases? Also sometimes there are no diseases related to the SLC transporter or sometimes there is no OMIM number. How can i extract the information? I put some screenshots below to show you how it looks like. Any help will be highly appreciated! This is my first post here so forgive me for any mistakes or missing information. Thank you!
http://imgur.com/aTiGi84 other one is /L65HSym
So ideally the output will be for example:
transporter: SLC1A1
Disease: Epilepsy
OMIM: 12345
Edit: the code i have so far:
import os
import re
from bs4 import BeautifulSoup as BS
import requests
import sys
import time
def hasNumbers(inputString): #get transporter names which contain numbers
return any(char.isdigit() for char in inputString)
def get_list(file): #get a list of transporters
transporter_list=[]
lines = [line.rstrip('\n') for line in open(file)]
for line in lines:
if 'SLC' in line and hasNumbers(line) == True:
get_SLC=line.split()
if 'SLC' in get_SLC[0]:
transporter_list.append(get_SLC[0])
return transporter_list
def get_transporter_webinfo(transporter_list):
output_Website=open("output_website.txt", "w") # get the website content of all transporters
for transporter in transporter_list:
text = requests.get('http://slc.bioparadigms.org/protein?GeneName=' + transporter).text
output_Website.write(text) #ouput from the SLC tables website
soup=BS(text, "lxml")
disease = soup(text=re.compile('Disease'))
characteristics=soup.find_all("span", class_="prt_col2")
memo=soup.find_all("span", class_='expandable prt_col2')
print(transporter,disease,characteristics[6],memo)
def convert(html_file):
file2= open(html_file, 'r')
clean_file= open('text_format_SLC','w')
soup=BS(file2,'lxml')
clean_file.write(soup.get_text())
clean_file.close()
def main():
start_time=time.time()
os.chdir('/home/Programming/Fun stuff')
sys.stdout= open("output_SLC.txt","w")
SLC_list=get_list("SLC.txt")
get_transporter_webinfo(SLC_list) #already have the website content so little redundant
print("this took",time.time() - start_time, "seconds to run")
convert("output_SLC.txt")
sys.stdout.close()
if __name__ == "__main__":
main()
No offence intended, I didn't feel like reading such a large piece of code as what you put in your question.
I would say it can be simplified.
You can get the complete list of links to the SLCs in the line at SLCs =. The next line shows how many there are, and the line beyond that exhibits the href attribute that the last link contains, as an example.
In each SLC's page I look for the string 'Disease' and then, if it's there, I navigate to the link nearby. I find the OMIM in a similar way.
Notice that I process only the first SLC.
>>> import requests
>>> import bs4
>>> main_url = 'http://slc.bioparadigms.org/'
>>> main_page = requests.get(main_url).content
>>> main_soup = bs4.BeautifulSoup(main_page, 'lxml')
>>> stem_url = 'http://slc.bioparadigms.org/protein?GeneName=SLC1A1'
>>> SLCs = main_soup.select('td.slct.tbl_cell.tbl_col1 a')
>>> len(SLCs)
418
>>> SLCs[-1].attrs['href']
'protein?GeneName=SLC52A3'
>>> stem_url = 'http://slc.bioparadigms.org/'
>>> for SLC in SLCs:
... SLC_page = requests.get(stem_url+SLC.attrs['href'], 'lxml').content
... SLC_soup = bs4.BeautifulSoup(SLC_page, 'lxml')
... disease = SLC_soup.find_all(string='Disease: ')
... if disease:
... disease = disease[0]
... diseases = disease.findParent().findNextSibling().text.strip()
... else:
... diseases = 'No diseases'
... OMIM = SLC_soup.find_all(string='OMIM:')
... if OMIM:
... OMIM = OMIM[0]
... number = OMIM.findParent().findNextSibling().text.strip()
... else:
... OMIM = 'No OMIM'
... number = -1
... SLC.text, number, diseases
... break
...
('SLC1A1', '133550', "Huntington's disease, epilepsy, ischemia, Alzheimer's disease, Niemann-Pick disease, obsessive-compulsive disorder")