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Deleting words between every appearance of two words

 
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# 1  
Old 09-24-2014
Deleting words between every appearance of two words
Hi there, newbie there. I've been browsing the forums hoping to find a solution that answers a problem similar to what I need, but haven't had much luck. Any help would be greatly appreciated. Thanks!

I need to delete a bunch of text between every appearance of two words in a really large file preferably using sed.

Eg:

Code:
>gi |544340954|emb|HG428755.1|:3360404-3364966 Fesd FMG
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
>gi |307625127|gb|CP002167.1|:319702-324264  Fesd GFT
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

and this goes on and on, and basically I want to delete everything from 'gi' and 'Fesd' without affecting anything else throughout the entire file to get something like this:

Code:
>FMG
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
>GFT
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Can anyone help me out with this? Thanks heaps!

Moderator's Comments:
Mod Comment edit by bakunin: these two pairs of shining new CODE-tags was devoted to your cause courtesy of the moderation team.
Last edited by bakunin; 09-24-2014 at 01:53 PM..
# 2  
Old 09-24-2014
Quote:
Originally Posted by lendl
Hi there, newbie there. I've been browsing the forums hoping to find a solution that answers a problem similar to what I need, but haven't had much luck. Any help would be greatly appreciated. Thanks!

I need to delete a bunch of text between every appearance of two words in a really large file preferably using sed.

Eg:

>gi |544340954|emb|HG428755.1|:3360404-3364966 Fesd FMG
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
>gi |307625127|gb|CP002167.1|:319702-324264 Fesd GFT
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

and this goes on and on, and basically I want to delete everything from 'gi' and 'Fesd' without affecting anything else throughout the entire file to get something like this:

>FMG
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
>GFT
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Can anyone help me out with this? Thanks heaps!
Hello lendl;

Welcome to forum, kindly use code tags while posting codes and commands in your post as per forum rules. Here is the solution for same.

Code:
awk '/gi.*Fesd/ {gsub(/[[:alpha:]]/,X,$1);print $1 $NF;next} 1' Input_file

Thanks,
R. Singh
Last edited by RavinderSingh13; 09-24-2014 at 03:11 AM..
This User Gave Thanks to RavinderSingh13 For This Post:
lendl
# 3  
Old 09-24-2014
As per your exact requirements, a space would remain between > and FMG or GFT.

The below sed command will produce the correct output:

Code:
sed 's/\(^.*\)gi.*Fesd\(.*$\)/\1\2/' file

To remove the space and get the output which you have shown you can amend the above command to the below:

Code:
sed 's/\(^.*\)gi.*Fesd[[:space:]]\(.*$\)/\1\2/' file

This User Gave Thanks to pilnet101 For This Post:
lendl
# 4  
Old 09-24-2014
Thank you very much for all your help! Much appreciated.

Also noted on the usage of code tags.
This User Gave Thanks to lendl For This Post:
RavinderSingh13
 
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