Efficiently remove the last two lines of an extremely large text file

Question

I have a very large file (~400 GB), and I need to remove the last 2 lines from it. I tried to use sed, but it ran for hours before I gave up. Is there a quick way of doing this, or am I stuck with sed?

Dennis Williamson · Accepted Answer · 2010-04-06T14:37:45.940

I haven't tried this on a large file to see how fast it is, but it should be fairly quick.

To use the script to remove lines from the end of a file:

./shorten.py 2 large_file.txt

It seeks to the end of the file, checks to make sure the last character is a newline, then reads each character one at a time going backwards until it's found three newlines and truncates the file just after that point. The change is made in place.

Edit: I've added a Python 2.4 version at the bottom.

Here is a version for Python 2.5/2.6:

#!/usr/bin/env python2.5
from __future__ import with_statement
# also tested with Python 2.6

import os, sys

if len(sys.argv) != 3:
    print sys.argv[0] + ": Invalid number of arguments."
    print "Usage: " + sys.argv[0] + " linecount filename"
    print "to remove linecount lines from the end of the file"
    exit(2)

number = int(sys.argv[1])
file = sys.argv[2]
count = 0

with open(file,'r+b') as f:
    f.seek(0, os.SEEK_END)
    end = f.tell()
    while f.tell() > 0:
        f.seek(-1, os.SEEK_CUR)
        char = f.read(1)
        if char != '\n' and f.tell() == end:
            print "No change: file does not end with a newline"
            exit(1)
        if char == '\n':
            count += 1
        if count == number + 1:
            f.truncate()
            print "Removed " + str(number) + " lines from end of file"
            exit(0)
        f.seek(-1, os.SEEK_CUR)

if count < number + 1:
    print "No change: requested removal would leave empty file"
    exit(3)

Here's a Python 3 version:

#!/usr/bin/env python3.0

import os, sys

if len(sys.argv) != 3:
    print(sys.argv[0] + ": Invalid number of arguments.")
    print ("Usage: " + sys.argv[0] + " linecount filename")
    print ("to remove linecount lines from the end of the file")
    exit(2)

number = int(sys.argv[1])
file = sys.argv[2]
count = 0

with open(file,'r+b', buffering=0) as f:
    f.seek(0, os.SEEK_END)
    end = f.tell()
    while f.tell() > 0:
        f.seek(-1, os.SEEK_CUR)
        print(f.tell())
        char = f.read(1)
        if char != b'\n' and f.tell() == end:
            print ("No change: file does not end with a newline")
            exit(1)
        if char == b'\n':
            count += 1
        if count == number + 1:
            f.truncate()
            print ("Removed " + str(number) + " lines from end of file")
            exit(0)
        f.seek(-1, os.SEEK_CUR)

if count < number + 1:
    print("No change: requested removal would leave empty file")
    exit(3)

Here is a Python 2.4 version:

#!/usr/bin/env python2.4

import sys

if len(sys.argv) != 3:
    print sys.argv[0] + ": Invalid number of arguments."
    print "Usage: " + sys.argv[0] + " linecount filename"
    print "to remove linecount lines from the end of the file"
    sys.exit(2)

number = int(sys.argv[1])
file = sys.argv[2]
count = 0
SEEK_CUR = 1
SEEK_END = 2

f = open(file,'r+b')
f.seek(0, SEEK_END)
end = f.tell()

while f.tell() > 0:
    f.seek(-1, SEEK_CUR)
    char = f.read(1)
    if char != '\n' and f.tell() == end:
        print "No change: file does not end with a newline"
        f.close()
        sys.exit(1)
    if char == '\n':
        count += 1
    if count == number + 1:
        f.truncate()
        print "Removed " + str(number) + " lines from end of file"
        f.close()
        sys.exit(0)
    f.seek(-1, SEEK_CUR)

if count < number + 1:
    print "No change: requested removal would leave empty file"
    f.close()
    sys.exit(3)

score 13 · Answer 2 · answered Apr 06 '10 at 05:54

13

you can try GNU head

head -n -2 file

answered Apr 06 '10 at 05:54

user31894

2,937

score 9 · Answer 3 · answered Apr 06 '10 at 12:53

I see my Debian Squeeze/testing systems (but not Lenny/stable) include a "truncate" command as part of the "coreutils" package.

With it you could simply do something like

truncate --size=-160 myfile

to remove 160 bytes from the end of the file (obviously you need to figure out exactly how many characters you need to remove).

Zac Thompson · Answer 4 · 2012-05-01T22:12:56.010

The problem with sed is that it is a stream editor -- it will process the entire file even if you only want to make modifications near the end. So no matter what, you are creating a new 400GB file, line by line. Any editor that operates on the whole file will probably have this problem.

If you know the number of lines, you could use head, but again this creates a new file instead of altering the existing one in place. You might get speed gains from the simplicity of the action, I guess.

You might have better luck using split to break the file into smaller pieces, editing the last one, and then using cat to combine them again, but I'm not sure if it will be any better. I would use byte counts rather than lines, otherwise it will probably be no faster at all -- you're still going to be creating a new 400GB file.

score 2 · Answer 5 · answered Apr 05 '10 at 23:27

2

Try VIM...I'm not sure if it will do the trick or not, as I've never used it on such a big file, but I've used it on smaller larger files in the past give it try.

answered Apr 05 '10 at 23:27

leeand00

23,552

score 1 · Answer 6 · answered Apr 05 '10 at 23:36

1

What kind of file and in what format? May be easier to use something like Perl dependent on what kind of file it is - text, graphics, binary? How is it formatted - CSV, TSV...

answered Apr 05 '10 at 23:36

Blackbeagle

6,702

score 1 · Answer 7 · answered Apr 06 '10 at 12:36

If you know the size of the file to the byte (400000000160 say) and you know that you need to remove exactly 160 characters to strip the last two lines, then something like

dd if=originalfile of=truncatedfile ibs=1 count=400000000000

should do the trick. It's been ages since I used dd in anger though; I seem to remember things go faster if you use a bigger block size, but whether you can do that depends on whether the lines you want to drop are at a nice multiple.

dd has some other options to pad text records out to a fixed size which might be useful as a preliminary pass.

timday · Answer 8 · 2010-04-06T12:54:27.437

1

If "truncate" command isn't available on your system (see my other answer), look at the "man 2 truncate" for the system call to truncate a file to a specified length.

Obviously you need to know how many characters you need to truncate the file to (size minus the length of the problem two lines; don't forget to count any cr/lf characters).

And make a backup of the file before you try this!

edited Apr 06 '10 at 12:54

answered Apr 06 '10 at 12:44

timday

812

Juve · Answer 9 · 2015-06-05T11:05:23.020

If you prefer unix-style solutions, you can have save and interactive line truncation using three lines of code (Tested on Mac and Linux).

small + safe unix-style line truncation (asks for confirmation):

n=2; file=test.csv; tail -n $n $file &&
read -p "truncate? (y/N)" -n1 key && [ "$key" == "y" ] &&
perl -e "truncate('$file', `wc -c <$file` - `tail -n $n $file | wc -c` )"

This solution relies on a few common unix-tools, but still uses perl -e "truncate(file,length)" as closest replacement for truncate(1), which is not available on all systems.

You may also use the following comprehensive reusable shell program, which provides a usage info and features truncation confirmation, option parsing, and error handling.

comprehensive line truncation script:

#!/usr/bin/env bash

usage(){
cat <<-EOF
  Usage:   $0 [-n NUM] [-h] FILE
  Options:
  -n NUM      number of lines to remove (default:1) from end of FILE
  -h          show this help
EOF
exit 1
}

num=1

for opt in $*; do case $opt in
  -n) num=$2;                 shift;;
  -h) usage;                  break;;
  *)  [ -f "$1" ] && file=$1; shift;;
esac done

[ -f "$file" ] || usage

bytes=`wc -c <$file`
size=`tail -n $num $file | wc -c`

echo "using perl 'truncate' to remove last $size of $bytes bytes:"
tail -n $num $file
read -p "truncate these lines? (y/N)" -n1 key && [ "$key" == "y" ] &&
perl -e "truncate('$file', $bytes - $size )"; echo ""
echo "new tail is:"; tail $file

Here is a usage example:

$ cat data/test.csv
1 nice data
2 cool data
3 just data

GARBAGE to be removed (incl. empty lines above and below)

$ ./rmtail.sh -n 3 data/test.csv
using perl 'truncate' to remove last 60 of 96 bytes:

GARBAGE to be removed (incl. empty lines above and below)

truncate these lines? (y/N)y
new tail is:
1 nice data
2 cool data
3 just data
$ cat data/test.csv
1 nice data
2 cool data
3 just data

score 0 · Answer 10 · answered Apr 16 '16 at 22:02

0

You can use Vim in Ex mode:

ex -sc '-,d|x' file

-, select last 2 lines
d delete
x save and close

answered Apr 16 '16 at 22:02

Zombo

1

Justin Smith · Answer 11 · 2010-04-07T00:27:01.250

0

#!/bin/sh

ed "$1" << HERE
$
d
d
w
HERE

changes are made in place. This is simpler and more efficient than the python script.

edited Apr 07 '10 at 00:27

answered Apr 07 '10 at 00:02

Justin Smith

4,166

score 0 · Answer 12 · answered Mar 05 '13 at 06:19

Modified the accepted answer to solve a similar problem. Could be tweaked a little bit to remove n lines.

import os

def clean_up_last_line(file_path):
    """
    cleanup last incomplete line from a file
    helps with an unclean shutdown of a program that appends to a file
    if \n is not the last character, remove the line
    """
    with open(file_path, 'r+b') as f:
        f.seek(0, os.SEEK_END)

        while f.tell() > 0: ## current position is greater than zero
            f.seek(-1, os.SEEK_CUR)

            if f.read(1) == '\n':
                f.truncate()
                break

            f.seek(-1, os.SEEK_CUR) ## don't quite understand why this has to be called again, but it doesn't work without it

And the corresponding test:

import unittest

class CommonUtilsTest(unittest.TestCase):

    def test_clean_up_last_line(self):
        """
        remove the last incomplete line from a huge file
        a line is incomplete if it does not end with a line feed
        """
        file_path = '/tmp/test_remove_last_line.txt'

        def compare_output(file_path, file_data, expected_output):
            """
            run the same test on each input output pair
            """
            with open(file_path, 'w') as f:
                f.write(file_data)

            utils.clean_up_last_line(file_path)

            with open(file_path, 'r') as f:
                file_data = f.read()
                self.assertTrue(file_data == expected_output, file_data)        

        ## test a multiline file
        file_data = """1362358424445914,2013-03-03 16:53:44,34.5,151.16345879,b
1362358458954466,2013-03-03 16:54:18,34.5,3.0,b
1362358630923094,2013-03-03 16:57:10,34.5,50.0,b
136235"""

        expected_output = """1362358424445914,2013-03-03 16:53:44,34.5,151.16345879,b
1362358458954466,2013-03-03 16:54:18,34.5,3.0,b
1362358630923094,2013-03-03 16:57:10,34.5,50.0,b
"""        
        compare_output(file_path, file_data, expected_output)

        ## test a file with no line break
        file_data = u"""1362358424445914,2013-03-03 16:53:44,34.5,151.16345879,b"""
        expected_output = "1362358424445914,2013-03-03 16:53:44,34.5,151.16345879,b"
        compare_output(file_path, file_data, expected_output)

        ## test a file a leading line break
        file_data = u"""\n1362358424445914,2013-03-03 16:53:44,34.5,151.16345879,b"""
        expected_output = "\n"
        compare_output(file_path, file_data, expected_output)

        ## test a file with one line break
        file_data = u"""1362358424445914,2013-03-03 16:53:44,34.5,151.16345879,b\n""" 
        expected_output = """1362358424445914,2013-03-03 16:53:44,34.5,151.16345879,b\n""" 
        compare_output(file_path, file_data, expected_output)

        os.remove(file_path)


if __name__ == '__main__':
    unittest.main()

Efficiently remove the last two lines of an extremely large text file

12 Answers12