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[Solved] Find entries from one file in another

 
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Top Forums UNIX for Dummies Questions & Answers [Solved] Find entries from one file in another
# 1  
Old 04-21-2013
[Solved] Find entries from one file in another
Please help.
I want to read a file line by line (only 1 column) and print all corresponding rows from a second file (2 columns) . Only first column of second file has to be matched with only column of first file. Order of lines in output doesn't matter.


Simplified example

Code:
Input 1

A
B
Ca
D

Input 2

A Apple
B Bat
Ba Bad
Ax Axe
Ca Cat
C Cab
B Bag

Desired output

A Apple
B Bat
Ca Cat
B Bag

---------- Post updated at 04:42 PM ---------- Previous update was at 04:13 PM ----------

never mind..figured this out myself..thank you ...joy of being a biologist able to do this..

Moderator's Comments:
Mod Comment edit by bakunin: very good! Congrats. We would be overjoyed if you would have posted your solution because this would help all who have the same or a similar problem like you.
I changed the thread's title to [Solved].
Last edited by bakunin; 04-22-2013 at 01:11 PM..
# 2  
Old 04-21-2013
for i in `cat file1`
do
grep $i file2 >>output
done
This User Gave Thanks to zozoo For This Post:
newbie83
# 3  
Old 04-21-2013
I would highly recommend to avoid using this syntax: for i in `cat file1`

You can find the reason here
These 2 Users Gave Thanks to Yoda For This Post:
newbie83 zozoo
# 4  
Old 04-21-2013
Code:
cat file1|while read f;do
grep $f file2 >> output
done

This User Gave Thanks to zozoo For This Post:
newbie83
# 5  
Old 04-21-2013
That will search for matches in the whole line.
Code:
grep "^$f[[:blank:]]" "$file2"

is more promising.
Most efficient is awk... but this smells a bit like homework?
This User Gave Thanks to MadeInGermany For This Post:
newbie83
# 6  
Old 04-22-2013
Its not homework. I`m trying to extract look-up information for some genes, part of my research. Thank you all.
# 7  
Old 04-22-2013
If you have a look at the man page of "grep" you will notice the "-f" option. Quote from the man-page:

Code:
-f FILE, --file=FILE
	      Obtain  patterns	from  FILE, one per line.  The empty file con-
	      tains zero patterns, and therefore matches nothing.

Therefore, supposing your keys are in file "keys.txt" and you want to search for these keys in "search.txt":

Code:
grep -f keys.txt search.txt

does exactly what you want.

Reading man pages is a very commendable activity. I do it many times day when working with Unix.

I hope this helps.

bakunin
 
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