The sort command in linux does not work "correctly"

Question

I'm working on Linux, the sort command returns not as expected.

Input text:

$ cat input.txt
rep1_1.fq
rep1_2.fq
rep12_1.fq
rep12_2.fq

Command and output:

$ sort input.txt
rep1_1.fq
rep12_1.fq
rep12_2.fq
rep1_2.fq


$ sort --version
sort (GNU coreutils) 8.28
Copyright (C) 2017 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Written by Mike Haertel and Paul Eggert.

After sorting, I expected rep1_2.fq would be after rep1_1.fq, but the result is different.

Solved

according to @Federico klez Culloca's advice, use LC_ALL=C

$ LC_ALL=C sort input.txt
rep12_1.fq
rep12_2.fq
rep1_1.fq
rep1_2.fq

Edited

use LC_ALL=C also fix sorting files in a directory.

in case there are four files in current directory:

$ LC_ALL= ls
rep1_1.fq  rep12_1.fq  rep12_2.fq  rep1_2.fq

$ LC_ALL=C ls
rep12_1.fq  rep12_2.fq  rep1_1.fq  rep1_2.fq

Try this LC_ALL=C sort input.txt. See the manpage: "*** WARNING *** The locale specified by the environment affects sort order. Set LC_ALL=C to get the traditional sort order that uses native byte values." — Federico klez Culloca
– Federico klez Culloca, Commented Jun 10, 2019 at 8:32
Thanks so much, problem fixed. I find my default LC_ALL was empty, after appending export LC_ALL=C to ~/.bashrc file, sort command works. — wm3
– wm3, Commented Jun 10, 2019 at 9:02
I always chuckle a bit when I see a title like "The xyz command doesn't work correctly in Linux" (or in C, etc..) 99.99999% of the time, it isn't the command that is at fault. — David C. Rankin
– David C. Rankin, Commented Jun 11, 2019 at 1:53
Sure, I totally agree with you, it's not the command's fault, but the way to use it. While, this kind of title could tell what happened to users in direct way. — wm3
– wm3, Commented Jun 11, 2019 at 2:31

Kenrro · Accepted Answer · 2019-06-10 08:56:36Z

2

Try with version-sort. From the manual:

       -V, --version-sort
          natural sort of (version) numbers within text

This is the output using your example:

$ sort -V input.txt 
rep1_1.fq
rep1_2.fq
rep12_1.fq
rep12_2.fq

edited Jun 10, 2019 at 8:56

answered Jun 10, 2019 at 8:51

Kenrro

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1 Comment

wm3 Over a year ago

Thanks so much. It's an alternative way to fix my problem. I see Federico klez Culloca's method using "by native byte values" works better.

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