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Old 05-17-2012, 08:24 AM   #1
nblarson
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Registered: May 2012
Posts: 2

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grep issue


So I banged my head against the wall for awhile trying to figure out this simple grep. Essentially, I have a field in a tab delimited file that can take on various forms:

A/T
TA/T
A/TGAC

I just want the lines where the field is [ACTG]/[ACTG], so

A/T - Yes
TA/T - No
A/TGAC - No

So I figured the following would be fine:

grep " [ACTG]\/[ACTG] " file.in > file.out

But I get nothing. Of course if I drop the spaces, I get everything. I've also tried:

grep \s[ACTG]\/[ACTG]\s
grep [:space:][ACTG]\/[ACTG][:space:]
grep \t[ACTG]\/[ACTG]\t

They all return nothing.

Is there something I'm forgetting?
 
Old 05-17-2012, 08:38 AM   #2
colucix
LQ Guru
 
Registered: Sep 2003
Location: Bologna
Distribution: CentOS 6.5 OpenSuSE 12.3
Posts: 10,509

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Yes. Word boundaries:
Code:
grep '\<[ACTG]\/[ACTG]\>' file
or using the proper grep option:
Code:
grep -w '[ACTG]\/[ACTG]' file
And welcome to LinuxQuestions!
 
Old 05-17-2012, 09:03 AM   #3
nblarson
LQ Newbie
 
Registered: May 2012
Posts: 2

Original Poster
Rep: Reputation: Disabled
Thanks, that did it!

Feel like I'm learning a new language and I've got all the big words down and none of the basics :P
 
  


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