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python3: Read huge file (~ 800 Gb), split the lines by condition, and append them to the end of new files in a memory-efficient way

I’m learning python 3, and I’m dealing with a huge txt file (~800Gb).
The enclosed function 'kmers_dic' while it read the main file, if the condition in if statement is satisfied, it should append the line in the previously created files (these files are 1024 and they are named with content of the kmers variable). The function work fine with a subset of the principal file, but when I run the code using the main file, my job is killed because I reached a memory usage limit.
def OpenFiles(i):
'''
A switch to handle file opening and reduce duplicated code
'''
open_method = {
"gz": gzip.open,
"norm": open
}
return open_method[i]
def rows(f, chunksize=102400, sep='\n'):
"""
Read a file where the row separator is '\n' lazily.
Default chunk size: 102400kB 100Mb.
Usage:
>>> with open('big.csv') as f:
>>> for r in rows(f):
>>> process(r)
"""
curr_row = ''
while True:
chunk = f.read(chunksize)
if chunk == '': # End of file
break
while True:
i = chunk.find(sep)
if i == -1:
break
yield curr_row + chunk[:i]
curr_row = ''
chunk = chunk[i+1:]
curr_row += chunk
def kmers_dic(input_file,kmers,out_dir):
'''
file writing by kmers
'''
#kmers_dic = set()
count_line=0
count_line_1=0
if input_file.endswith('.gz'):
nano_read = OpenFiles('gz')
else:
nano_read = OpenFiles('norm')
with nano_read(input_file, 'rt') as nano_f:
chunk = rows(nano_f,chunksize=2024,sep='\n')
for line in chunk:
count_line+=1
count_line_1+=1
sys.stdout.write('%s\r' % count_line)
sys.stdout.flush()
line = line.strip('\n')
line = line.split()
if line[2] in kmers:
kmer = line[2]
Out_f_name = out_dir+line[2]+'.lib'
file1 = open(Out_f_name, 'a')
##file1.write('\t'.join(line) + '\n') # print entire line
file1.write('\t'.join(line[1:4:]+line[6:9:]+line[9:13:]+line[15:]) + '\n')
file1.close()
print("lines: ",count_line_1)
I'm not understanding where is the issue.
Can you help me ?
Thanks in advance!
Best.

curr_row += chunk causes you keep all chunks in memory until you run out of free memory.

Python: Separating txt file to multiple files using a reoccuring symbol

I have a .txt file of amino acids separated by ">node" like this:
Filename.txt :
>NODE_1
MSETLVLTRPDDWHVHLRDGAALQSVVPYTARQFARAIAMPNLKPPITTAEQAQAYRERI
KFFLGTDSAPHASVMKENSVCGAGCFTALSALELYAEAFEAAGALDKLEAFASFHGADFY
GLPRNTTQVTLRKTEWTLPESVPFGEAAQLKPLRGGEALRWKLD*
>NODE_2
MSTWHKVQGRPKAQARRPGRKSKDDFVTRVEHDAKNDALLQLVRAEWAMLRSDIATFRGD
MVERFGKVEGEITGIKGQIDGLKGEMQGVKGEVEGLRGSLTTTQWVVGTAMALLAVVTQV
PSIISAYRFPPAGSSAFPAPGSLPTVPGSPASAASAP*
I want to separate this file into two (or as many as there are nodes) files;
Filename1.txt :
>NODE
MSETLVLTRPDDWHVHLRDGAALQSVVPYTARQFARAIAMPNLKPPITTAEQAQAYRERI
KFFLGTDSAPHASVMKENSVCGAGCFTALSALELYAEAFEAAGALDKLEAFASFHGADFY
GLPRNTTQVTLRKTEWTLPESVPFGEAAQLKPLRGGEALRWKLD*
Filename2.txt :
>NODE
MSTWHKVQGRPKAQARRPGRKSKDDFVTRVEHDAKNDALLQLVRAEWAMLRSDIATFRGD
MVERFGKVEGEITGIKGQIDGLKGEMQGVKGEVEGLRGSLTTTQWVVGTAMALLAVVTQV
PSIISAYRFPPAGSSAFPAPGSLPTVPGSPASAASAP*
With a number after the filename
This code works, however it deletes the ">NODE" line and does not create a file for the last node (the one without a '>' afterwards).
with open('FilePathway') as fo:
op = ''
start = 0
cntr = 1
for x in fo.read().split("\n"):
if x.startswith('>'):
if start == 1:
with open (str(cntr) + '.fasta','w') as opf:
opf.write(op)
opf.close()
op = ''
cntr += 1
else:
start = 1
else:
if op == '':
op = x
else:
op = op + '\n' + x
fo.close()
I can´t seem to find the mistake. Would be thankful if you could point it out to me.
Thank you for your help!
Hi again! Thank you for all the comments. With your help, I managed to get it to work perfectly. For anyone with similar problems, this is my final code:
import os
import glob
folder_path = 'FilePathway'
for filename in glob.glob(os.path.join(folder_path, '*.fasta')):
with open(filename) as fo:
for line in fo.readlines():
if line.startswith('>'):
original = line
content = [original]
fileno = 1
filename = filename
y = filename.replace(".fasta","_")
def writefasta():
global content, fileno
if len(content) > 1:
with open(f'{y}{fileno}.fasta', 'w') as fout:
fout.write(''.join(content))
content = [line]
fileno += 1
with open('FilePathway') as fin:
for line in fin:
if line.startswith('>NODE'):
writefasta()
else:
content.append(line)
writefasta()

You could do it like this:
def writefasta(d):
if len(d['content']) > 1:
with open(f'Filename{d["fileno"]}.fasta', 'w') as fout:
fout.write(''.join(d['content']))
d['content'] = ['>NODE\n']
d['fileno'] += 1
with open('test.fasta') as fin:
D = {'content': ['>NODE\n'], 'fileno': 1}
for line in fin:
if line.startswith('>NODE'):
writefasta(D)
else:
D['content'].append(line)
writefasta(D)

This would be better way. It is going to write only on odd iterations. So that, ">NODE" will be skipped and files will be created only for the real content.
with open('filename.txt') as fo:
cntr=1
for i,content in enumerate(fo.read().split("\n")):
if i%2 == 1:
with open (str(cntr) + '.txt','w') as opf:
opf.write(content)
cntr += 1
By the way, since you are using context manager, you dont need to close the file.
Context managers allow you to allocate and release resources precisely
when you want to. It opens the file, writes some data to it and then
closes it.
Please check: https://book.pythontips.com/en/latest/context_managers.html

with open('FileName') as fo:
cntr = 1
for line in fo.readlines():
with open (f'{str(cntr)}.fasta','w') as opf:
opf.write(line)
opf.close()
op = ''
cntr += 1
fo.close()

Extract IP addresses from text file without using REGEX

I am trying to extract IPv4 addresses from a text file and save them as a list to a new file, however, I can not use regex to parse the file, Instead, I have check the characters individually. Not really sure where to start with that, everything I find seems to have import re as the first line.
So far this is what I have,
#Opens and prints wireShark txt file
fileObject = open("wireShark.txt", "r")
data = fileObject.read()
print(data)
#Save IP adresses to new file
with open('wireShark.txt') as fin, open('IPAdressess.txt', 'wt') as fout:
list(fout.write(line) for line in fin if line.rstrip())
#Opens and prints IPAdressess txt file
fileObject = open("IPAdressess.txt", "r")
data = fileObject.read()
print(data)
#Close Files
fin.close()
fout.close()
So I open the file, and I have created the file that I will put the extracted IP's in, I just don't know ow to pull them without using REGEX.
Thanks for the help.

Here is a possible solution.
The function find_first_digit, position the index at the next digit in the text if any and return True. Else return False
The functions get_dot and get_num read a number/dot and, lets the index at the position just after the number/dot and return the number/dot as str. If one of those functions fails to get the number/dot raise an MissMatch exception.
In the main loop, find a digit, save the index and then try to get an ip.
If sucess, write it to output file.
If any of the called functions raises a MissMatch exception, set the current index to the saved index plus one and start over.
class MissMatch(Exception):pass
INPUT_FILE_NAME = 'text'
OUTPUT_FILE_NAME = 'ip_list'
def find_first_digit():
while True:
c = input_file.read(1)
if not c: # EOF found!
return False
elif c.isdigit():
input_file.seek(input_file.tell() - 1)
return True
def get_num():
num = input_file.read(1) # 1st digit
if not num.isdigit():
raise MissMatch
if num != '0':
for i in range(2): # 2nd 3th digits
c = input_file.read(1)
if c.isdigit():
num += c
else:
input_file.seek(input_file.tell() - 1)
break
return num
def get_dot():
if input_file.read(1) == '.':
return '.'
else:
raise MissMatch
with open(INPUT_FILE_NAME) as input_file, open(OUTPUT_FILE_NAME, 'w') as output_file:
while True:
ip = ''
if not find_first_digit():
break
saved_position = input_file.tell()
try:
ip = get_num() + get_dot() \
+ get_num() + get_dot() \
+ get_num() + get_dot() \
+ get_num()
except MissMatch:
input_file.seek(saved_position + 1)
else:
output_file.write(ip + '\n')

Hashing wordlist with big input output files in Python 3.8

I'm a beginner in coding and am trying to build a script that takes a txt file as an input, hash it and output to another txt file containing "string:hashedstring" in each line of it. The code is working properly. The problem I am facing now is that if the input file is big, it will consume all RAM and kill it. I tried to use chunks, but couldn't figure out how to use it with multiline input and output.
Any suggestions regarding other parts of the code other than the main subject here is very welcome, since I am just starting on this. Thanks.
import argparse
import hashlib
import os
import sys
def sofia_hash(msg):
h = ""
m = hashlib.md5()
m.update(msg.encode('utf-8'))
msg_md5 = m.digest()
for i in range(8):
n = (msg_md5[2*i] + msg_md5[2*i+1]) % 0x3e
if n > 9:
if n > 35:
n += 61
else:
n += 55
else:
n += 0x30
h += chr(n)
return h
top_parser = argparse.ArgumentParser(description='Sofiamass')
top_parser.add_argument('input', action="store", type=argparse.FileType('r', encoding='utf8'), help="Set input file")
top_parser.add_argument('output', action="store", help="Set output file")
args = top_parser.parse_args()
sofiainput = args.input.read().splitlines()
a = 0
try:
while a < len(sofiainput):
target_sofiainput = sofiainput[a]
etarget_sofiainput = (target_sofiainput).encode('utf-8')
try:
sofia_pass = sofia_hash(target_sofiainput)
x = True
except KeyboardInterrupt:
print ("\n[---]exiting now[---]")
if x == True:
with open(args.output, 'a') as sofiaoutput:
sofiaoutput.write(str(target_sofiainput) + ":" + str(sofia_pass) + "\n")
elif x == False:
print('error')
a += 1
except KeyboardInterrupt:
print ("\n[---]exiting now[---]")
except AttributeError:
pass

When you open the file with the open command, it creates a object called file handler. So, when you do:
with open('filepath.txt', 'r') as f:
for line in f:
print(line)
it only keeps the current line you are using in the RAM, thus achieving your objective to use as little as RAM as possible.

Splitting a text file

I have a folder with a set of text documents. I want to split each document to two or three documents, each one should be 45-70kb.
How сan I do it? I tried:
def split_file(filename, pattern, size):
with open(filename, 'rb') as f:
for index, line in enumerate(f, start=1):
with open(pattern.format(index), 'wb') as out:
n=0
for line in chain([line], f):
out.write(line)
n += len(line)
if n >= 450000 and n <=700000:
break
if __name__ == '__main__':
split_file('folderadress', 'part_{0:03d}.txt', 20000)
but it seems to me it's completely wrong.

This uses a different approach to yours. I have set the maximum size for each file to be 1000 bytes for testing purposes:
import glob
import os
dname = './gash' # directory name
unit_size = 1000 # maximum file size
for fname in glob.iglob("%s/*" % dname):
with open(fname, 'rb') as fo:
data = True
n = 1
while data:
# read returns "" (False) on EOF
data = fo.read(unit_size)
if data:
sub_fname = fname + str(n)
with open(sub_fname, 'wb') as out:
out.write(data)
n += 1
What this might do is to split a line between files, however you do not state if this could be an issue or not.