Extract only whole word using grep

Question

I've got a big text file. I need to extract all the lines which contains the exact word "DUSP1". Here an example of the lines:

9606    ENSP00000239223 DUSP1   BLAST
9606    ENSP00000239223 DUSP1-001 Ensembl

I want to retrieve the first line but not the second one.

I tried several commands as:

grep -E "^DUSP1"
grep '\<DUSP1\>'
grep '^DUSP1$'
grep -w DUSP1

But none of them seem to work. Which option should I use?

How exactly is the "exact word" defined? And your 3rd example would only find lines with only the word "DUSP1" ... So you want lines with "^DUSP1[[:space:]]+" ? — Dominik Sandjaja, Jul 12 '13 at 13:29
Could you provide sample file content. The 2nd, 3rd, 4th commands works for me. — falsetru, Jul 12 '13 at 13:29

score 32 · Answer 1 · answered May 05 '15 at 10:33

32

If you want to grep exactly the whole word, you can use word boundaries like this:

grep '\bDUSP1\b'

This matches for the exact word at the beginning and at the end.

answered May 05 '15 at 10:33

Phitherek_

6

This should be the accepted answer, there are not always spaces before and after (what about when it's the last word?). – user3671607 Feb 17 '16 at 15:29
1

this is great. It also matches `setting=DUSP1` and `my/folder/to/DUSP1`, but not `DUSP123` – vikingsteve Dec 07 '16 at 09:27
I had to use double quotes for the Windows version of GNU grep. Single quotes did not work. – Jesus H Apr 17 '17 at 23:42
1

Yep, this should be the answer with the big green checkmark. :D – Jesse Adelman May 02 '17 at 19:02
this still greps DUSP1-001 for me – Ömer An Dec 20 '19 at 07:18
no does not work - still greps words with DUSP1-xxx – MaurGi Jul 16 '20 at 21:45

Gilles Quénot · Accepted Answer · 2020-09-16T16:05:04.777

19

The problem you are facing is that a dash (-) is considered by grep as a word delimiter.

You should try this command :

grep '\sDUSP1\s' file

to ensure that there's spaces around your word.
Or use words boundaries :

grep '\bDUSP1\b' file

edited Sep 16 '20 at 16:05

answered Jul 12 '13 at 13:29

Gilles Quénot

score 2 · Answer 3 · edited Nov 03 '14 at 18:09

2

adding to what sputpick said, it could either be that or:

grep '\sDUSP1$' file

if the DUSP1 is the end of the line.

edited Nov 03 '14 at 18:09

slfan

answered Nov 03 '14 at 17:50

indradip

3 Answers3