Need help in linux command

Priyabio · 12-21-2010, 07:13 AM

Hello,

I have a text file with some IDs something like this:

PF0001.14
PF0002.17
PF0003.2

I want to go through this IDs and for each one I want to search the corresponding line in which the line has the particular id which are stored in an another text file, which is:

A0T2N3#PF00001.14;51-316;#
A2ARI4#PF00001.14;555-801;#PF01462.11;29-56;#PF00560.26;59-80;130-152;154-176;226-247;344-364;390-412;#
A6QPC8#PF08743.3;81-378;#
A6NET4#PF00001.14;41-288;#
A6QPB3#PF01391.11;567-631;593-646;743-802;812-861;909-950;1417-1465;#
A6QPF4#PF04103.8;154-273;#
A6QPH8#PF03226.7;6-115;#
A6QLU6#PF00002.17;591-830;#PF01825.14;535-579;#
A6QPF8#PF07851.6;7-337;#
A6QPH1#PF09282.3;11-37;#
A6QP74#PF00002.17;139-381;#PF02793.15;63-131;#

below is the desired result:

A0T2N3#PF00001.14;51-316;#
A2ARI4#PF00001.14;555-801;#PF01462.11;29-56;#PF00560.26;59-80;130-152;154-176;226-247;344-364;390-412;#
A6NET4#PF00001.14;41-288;#

--------------------------------------------------

A6QLU6#PF00002.17;591-830;#PF01825.14;535-579;#
A6QP74#PF00002.17;139-381;#PF02793.15;63-131;#

---------------------------------------------------------

I would be really glad for any help.

Thanks
Riya

mesiol · 12-21-2010, 07:49 AM

Hi,

try

Code:

man grep

and use a bash

Code:

man bash

to learn about for construct.

catkin · 12-21-2010, 08:01 AM

Expanding a little on what mesiol wrote, you could write a bash script which loops (a while read loop is suitable) on each line of the first file and greps the second file for the contents of each line read. Many examples from LQ here.

colucix · 12-21-2010, 08:31 AM

You don't really need a loop by using grep's option -f.

GlennsPref · 12-21-2010, 06:27 PM

Nice search param. catkin

"while read" site:linuxquestions.org

I am still learning. I guess I'll never stop

cheers Glenn

catkin · 12-21-2010, 09:17 PM

And nice grep option, colucix

I guess I'll never stop learning either.

dharanivasan · 12-21-2010, 10:59 PM

grep [-f FILE] [FILE...]
Where -f will be pattern file.

Priyabio · 12-31-2010, 03:34 AM

THANK YOU FOR YOUR REPLY
HI DHARANIVASAN I TRIED WITH THE BELLOW GIVEN COMMAND BUT ITS NOT WORKING

grep -f patternfile file2 >output.txt

CAN YOU PLEASE HELP ME....

catkin · 12-31-2010, 04:48 AM

Quote:

Originally Posted by Priyabio

CAN YOU PLEASE HELP ME....

Probably not without more information.

What were the symptoms of "BUT ITS NOT WORKING"? Copying from the command prompt session and pasting into a post in this thread would be neat.

Priyabio · 01-01-2011, 07:38 AM

Hi

I am not getting the desired output by using the command grep -f patternfile file2 >output.txt
I got the same input file as the output...

The desired output is given below

A0T2N3#PF00001.14;51-316;#
A2ARI4#PF00001.14;555-801;#PF01462.11;29-56;#PF00560.26;59-80;130-152;154-176;226-247;344-364;390-412;#
A6NET4#PF00001.14;41-288;#

--------------------------------------------------

A6QLU6#PF00002.17;591-830;#PF01825.14;535-579;#
A6QP74#PF00002.17;139-381;#PF02793.15;63-131;#

---------------------------------------------------------