How to remove duplicate lines inside a text file?

Question

A huge (up to 2 GiB) text file of mine contains about 100 exact duplicates of every line in it (useless in my case, as the file is a CSV-like data table).

What I need is to remove all the repetitions while (preferably, but this can be sacrificed for a significant performance boost) maintaining the original sequence order. In the result each line is to be unique. If there were 100 equal lines (usually the duplicates are spread across the file and won't be neighbours) there is to be only one of the kind left.

I have written a program in Scala (consider it Java if you don't know about Scala) to implement this. But maybe there are faster C-written native tools able to do this faster?

UPDATE: the awk '!seen[0ドル]++' filename solution seemed working just fine for me as long as the files were near 2 GiB or smaller but now as I am to clean-up a 8 GiB file it doesn't work any more. It seems taking infinity on a Mac with 4 GiB RAM and a 64-bit Windows 7 PC with 4 GiB RAM and 6 GiB swap just runs out of memory. And I don't feel enthusiastic about trying it on Linux with 4 GiB RAM given this experience.

• squareborg: this will destroy your ordering but,have you tried sort -u, I have no idea how or if it can run on such a massive file
• Kevin: C is often not significantly faster than Java, and if you're running it (in-order) now, there's a fair chance it'll finish before you get an answer here, implement it, and it finishes running; out of order, sort -u will probably be faster.

Answer 1

An awk solution seen on #bash (Freenode):

awk '!seen[0ドル]++' filename

If you want to edit the file in-place, you can use the following command (provided that you use a GNU awk version that implements this extension):

awk -i inplace '!seen[0ドル]++' filename

• mgjk: Just tried this on a 2G file and it took three minutes on my notebook. Not bad. I also tried uniq filename | awk '!seen[0ドル]++', but it wasn't any faster.
• enzotib: @HashWizard: this command does not sort, but eliminates every next occurrence of the same line
• supergra: Wondering how this command works? -- See here: unix.stackexchange.com/questions/159695/how-does-awk-a0-work
• setholopolus: @MaxWilliams yes, it works is they are randomly distributed.
• James O'Brien: preserve newlines or lines with spaces awk '/^\s*?$/||!seen[0ドル]++'

Answer 2

sort -u big-csv-file.csv > duplicates-removed.csv

Note that the output file will be sorted.

• Johann: Not as fast as the awk command in other answers, but conceptually simple!
• Vladislavs Dovgalecs: @Johann I am doing this pretty often on files with hundreds of thousands (even million) of short newline terminated strings. I get the results pretty quick for the experiments I am doing. It can be more important if used in scripts which are run again and again, savings in time can be considerable.
• Peter Cordes: Use sort -u to remove duplicates during the sort, rather than after. (And saves memory bandwidth) piping it to another program). This is only better than the awk version if you want your output sorted, too. (The OP on this question wants his original ordering preserved, so this is a good answer for a slightly different use-case.)
• Max Williams: Took about a minute, for me, for a 5.5 million line file (1.8 GB in total). Brilliant.

Answer 3

There's a simple (which is not to say obvious) method using standard utilities which doesn't require a large memory except to run sort, which in most implementations has specific optimizations for huge files (a good external sort algorithm). An advantage of this method is that it only loops over all the lines inside special-purpose utilities, never inside interpreted languages.

<input nl -b a -s : | # number the lines
sort -t : -k 2 -u | # sort and uniquify ignoring the line numbers
sort -t : -k 1n | # sort according to the line numbers
cut -d : -f 2- >output # remove the line numbers

If all lines begin with a non-whitespace character, you can dispense with some of the options:

<input nl | sort -k 2 -u | sort -k 1n | cut -f 2- >output

For a large amount of duplication, a method that only requires storing a single copy of each line in memory will perform better. With some interpretation overhead, there's a very concise awk script for that (already posted by enzotib):

<input awk '!seen[0ドル]++'

Less concisely: !seen[0ドル] {print} {seen[0ドル] += 1}, i.e. print the current line if it hasn't been seen yet, then increment the seen counter for this line (uninitialized variables or array elements have the numerical value 0).

For long lines, you can save memory by keeping only a non-spoofable checksum (e.g. a cryptographic digest) of each line. For example, using SHA-1, you only need 20 bytes plus a constant overhead per line. But computing digests is rather slow; this method will only win if you have a fast CPU (especially one with a hardware accelerator to compute the digests) and not a lot of memory relative to the size of the file and sufficiently long lines. No basic utility lets you compute a checksum for each line; you'd have to bear the interpretation overhead of Perl/Python/Ruby/... or write a dedicated compiled program.

<input perl -MDigest::MD5 -ne '$seen{Digest::MD5::md5($_)}++ or print' >output

• user779159: @Gilles Based on your explanation of awk '!seen[0ドル]++', does it mean that if awk sees 2 duplicate lines, it will keep the always first one and ignore all subsequent ones? (Or it will keep the last one?)
• Gilles 'SO- stop being evil': @user779159 It keeps the first one: each input line is either printed immediately (first occurrence) or not at all (repeat occurrence).
• HashWizard: But how does that compare to sort -u ...?
• Gilles 'SO- stop being evil': @HashWizard A plain sort -u changes the order. My answer shows solutions that preserve the order (the order of first occurrences, to be precise).
• HashWizard: @Gilles would you say that it is faster than sort -u for large files (10G) with 50% duplicates ?

Answer 4

Assuming you can afford to keep as much as the de-duplicated file in memory (if your data is indeed duplicated by a factor of 100, that should be about 20MiB + overhead), you can do this very easily with Perl.

$ perl -ne 'print unless $dup{$_}++;' input_file > output_file

This preserves the order too.

You could extract the number of occurrences of each line from the %dup hash if you so wished, as an added free bonus.

If you prefer awk, this should do it too (same logic as the perl version, same ordering, same data gathered in the dup variable):

$ awk '{if (++dup[0ドル] == 1) print 0ドル;}' input_file > output_file

• Nikhil Mulley: This is too good @Mat, I was about to slurp the file, lol ;-).
• Nikhil Mulley: Now waiting for @ManAtWork for his sed and awk magic weavery too :-)
• Nikhil Mulley: awesome again for the awk tip :-)
• dumbledad: Is it possible to change the perl script to only remove duplicate adjacent lines?
• Mat: @dumbledad: uniq does that all by itself

Answer 5

The Ultimate Line De-duper

gawk -i inplace 'FNR==1{delete a} !a[0ドル]++' SOME_FILE [OTHER_FILES...]

^{* The command requires GNU AWK version 4.1 from 2013, or newer.}

• ✅ Maintains Order
• ✅ Edits files directly
• ✅ Runs on multiple files

How It Works

The command uses an associative array to track unique lines and prints each line only once.
Here’s the algorithm in pseudocode:

if current_file_line_number is 1:
 clear array a
while read line into 0ドル:
 if a does not have key 0ドル:
 a[0ドル] = 0
 
 if a[0ドル] is 0:
 print 0ドル
 
 a[0ドル] = a[0ドル] + 1

Alternative versions

awk '!a[0ドル]++' < FILE_TO_DEDUP > DEDUPED_FILE
SOME_COMMAND | awk '!a[0ドル]++' | SOME_OTHER_COMMAND

---

• Leonid: Does this preserve the order? By the way, this did not work for me. My version is: GNU Awk 4.0.2
• rindeal: @Leonid yes, it does. It prints the first occurrence of any unique line. The inplace support was first introduced in version 4.1, which was released in 2013.
• MaXi32: This should be the answer. It's actually delete the duplicated string in the existing or current file where the top answer and most of the answers here only printout the uniq / duplicated strings and doing nothing and we have to create another output to store the result.
• alper: How does gawk differs from awk?
• rindeal: @alper gawk has way more features, such as the in-place editing support, for example

Answer 6

You can use uniq http://www.computerhope.com/unix/uuniq.htm

uniq reports or filters out repeated lines in a file.

• Stephen Rauch: When giving an answer it is preferable to give some explanation as to WHY your answer is the one. So, how does this answer differ from several of the previous answers?
• Vindolin: From the uniq man page:Note: 'uniq' does not detect repeated lines unless they are adjacent. So you have to first sort it and loose the order of the non duplicate lines.

Answer 7

SOLUTION WITHOUT MAINTAINING THE ORIGINAL SEQUENCE ORDER

I did it with the following code piece.

sort duplicates.txt | uniq > noDuplicates.txt

The sort command sorts the lines alphabetically, and the uniq command removes the duplicates.

NOTE: Why we sorted the lines first is that uniq does not detect duplicate lines unless they are adjacent.

• Stephen Kitt: The question asks for a method (preferably) which maintains the input order; could you edit your answer to address that? Note that there are existing answers using sort which maintain input order, and one answer using sort without maintaining input order but in a more efficient manner than piping to uniq.
• Caglayan Dokme: @StephenKitt Edited. I inspected other answers, but couldn't find anything only with basic commands. Thanks for your feedback.
• Stephen Kitt: I gave you a link to an answer with only basic commands, in fact only one command, sort -u (which is part of POSIX) ;-).
• Caglayan Dokme: @StephenKitt I saw that answer. Mine is also a way to handle the problem. What do you want me to do more? Should I delete the answer?
• Stephen Kitt: No, don’t delete your answer; I just wanted to make sure you were aware of the other answer, given that you said you "couldn't find anything only with basic commands".

Answer 8

Python One liners :

python -c "import sys; lines = sys.stdin.readlines(); print ''.join(sorted(set(lines)))" < InputFile

• iruvar: this causes the entire file to be slurped into memory and may not be a good fit for the OP's problem. Also not guaranteed to retain order
• Rahul Patil: Thanks for the suggestion, I've been just learning python.. just tried this for learning purpose.. :)
• iruvar: Here's a Python 2.7 version that is not a one-liner but (succinctly) returns unique lines preserving order without either loading the entire file into memory or creating a single gigantic string to feed to print
• Rahul Patil: Thanks @1_CR I have something learn today :) OrderedDict

Answer 9

Note that sort can write its output to any one of the files that it was given as input:

LC_ALL=C sort -u -o input input

That's fine as sort needs to have read all its input before it can start outputting anything (before it can tell which is the line that sorts first which could very well be the last line of the input).

sort will (intelligently) use temporary files so as to avoid loading the whole input in memory. You'll need enough space in $TMPDIR (or /tmp if that variable is not set). Some sort implementations can compress the temp files (like with --compress-program=lzop with GNU sort) which can help if you're short on disk space or have slow disks.

With LC_ALL=C sort order is by byte value which should speed things up and also guarantee a total and deterministic order (which you don't always get otherwise especially on GNU systems).

• iruvar: does sort -u maintain input order?

Answer 10

None of the answers here worked for me on my Mac so I wrote a simple python script that works for me. I am ignoring leading/trailing whitespace and also don't care about memory consumption.

import sys
inputfile = sys.argv[1]
outputfile = sys.argv[2]
with open(inputfile) as f:
 content = f.readlines()
content = [x.strip() for x in content]
my_list = list(set(content))
with open(outputfile, 'w') as output:
 for item in my_list:
 output.write("%s\n" % item)

Save the above to unique.py and run like this:

python unique.py inputfile.txt outputfile.txt

Answer 11

Using Raku (formerly known as Perl_6)

~$ raku -ne 'BEGIN my %dup; .put unless %dup{$_}++;' input_file > output_file

OR:

~$ raku -e '.put for lines.unique;' input_file > output_file

[ Note: compare first answer here with excellent Perl answer by @Mat ].

https://docs.raku.org
https://raku.org

Answer 12

With bash 4, a pure-bash solution that takes advantage of associative arrays can be used. Here is an example

unset llist; declare -A llist;
while read -r line; do
if [[ ${llist[$line]} ]]; then
 continue
else 
 printf '%s\n' "$line"
 llist[$line]="x"
fi
done < file.txt

• Peter Cordes: Don't use read loops to process big text files. bash has to read one-byte-at-a-time to avoid overshooting a newline. Bash is also not very fast at text processing in general compared to awk. If you do use this, read -ra will avoid eating backslashes in your input. Also, don't forget to unset llist after the loop, if you put this in a shell function or use it interactively.
• iruvar: @PeterCordes, or you could have just referenced this :-)