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I currently have two files that look something like this:

File 1:

2R 101 1:0:0:14:0:0 0:1:0:34:0:0 0:3:0:62:0:0 0:0:0:11:0:0 .02312
2R 201 0:2:0:24:0:0 0:0:0:44:0:0 0:0:0:15:0:0 0:0:0:22:0:0 .02312
2L 301 0:4:0:24:0:0 0:0:0:61:0:0 0:0:0:17:0:0 0:0:0:54:2:0 .02312
3R 551 0:2:0:64:0:1 0:1:0:67:0:0 0:0:0:22:0:0 0:0:0:31:1:0 .02312
3R 651 0:2:0:64:0:1 0:1:0:67:0:0 0:0:0:22:0:0 0:0:0:31:1:0 .02312
X 1312 0:0:3:24:0:0 0:5:0:65:0:0 0:0:0:55:0:0 0:0:0:14:0:0 .02312
X 5342 0:0:3:24:0:0 0:5:0:65:0:0 0:0:0:55:0:0 0:0:0:14:0:0 .02312

File 2:

2R 201
3R 551
X 5342

What I would like to do is extract all the rows from File 1 where the entries for the first two columns match rows in File 2. So, based on this example, I would want my output file to look like:

Output File:

2R 201 0:2:0:24:0:0 0:0:0:44:0:0 0:0:0:15:0:0 0:0:0:22:0:0 .02312
3R 551 0:2:0:64:0:1 0:1:0:67:0:0 0:0:0:22:0:0 0:0:0:31:1:0 .02312
X 5342 0:0:3:24:0:0 0:5:0:65:0:0 0:0:0:55:0:0 0:0:0:14:0:0 .02312
user3381331
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  • Also: http://unix.stackexchange.com/questions/125155/compare-two-files-for-matching-lines-and-store-positive-results **and** http://unix.stackexchange.com/questions/121222/identifying-genes-from-a-list-of-genes – jasonwryan Sep 24 '14 at 09:25

1 Answers1

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let's suppose file 2 is A and datafile (file 1) is b

 awk 'FILENAME == "A" { remember[$1 $2]=1 ;}
 FILENAME != "A" { if ( $1 $2 in remember ) print ; } ' A b

this would yield

2R 201 0:2:0:24:0:0 0:0:0:44:0:0 0:0:0:15:0:0 0:0:0:22:0:0 .02312
3R 551 0:2:0:64:0:1 0:1:0:67:0:0 0:0:0:22:0:0 0:0:0:31:1:0 .02312
X 5342 0:0:3:24:0:0 0:5:0:65:0:0 0:0:0:55:0:0 0:0:0:14:0:0 .02312
Archemar
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