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 04-09-2009, 06:06 AM #1 aditi_borkar LQ Newbie   Registered: Apr 2009 Posts: 2 Rep: Compare two fields on consecutive rows and print the two rows Hi, I have been trying really hard to get this done. I have an input (I have removed extra lines) that looks like the following: LC 1 C:G 24 -0.42 5.56 37.77 -0.19 0.54 3.48 LC 2 G:C 23 1.52 -5.21 35.68 0.65 0.54 3.43 LC 3 C:G 22 2.71 7.44 31.80 -0.01 0.95 3.44 LC 4 G:C 21 0.23 6.00 33.00 -0.23 0.10 3.40 LC 5 A:T 20 -1.35 2.32 37.16 -0.08 -0.16 3.13 LC 6 A:T 19 -1.04 2.17 34.61 -0.03 -0.61 3.32 LC 7 T:A 18 0.18 0.17 36.30 0.01 -0.28 3.26 LC 8 T:A 17 1.51 0.77 37.68 0.01 0.04 3.36 LC 9 C:G 16 -1.84 -0.91 30.29 0.30 1.16 3.45 LC 10 G:C 15 -1.56 -5.19 38.79 -0.93 0.85 3.52 LC 11 C:G 14 2.00 2.15 38.46 0.40 0.61 3.45 LC 12 G:C 13 From these 12 rows, I just want to extract the consecutive rows pairwise that will contain C:G in the first row and G:C in the second row. 4 such combinations can be seen in the lines that I have printed above (1 and 2, 3 and 4, 9 and 10 and 11 and 12). Thus, my output should look like: LC 1 C:G 24 -0.42 5.56 37.77 -0.19 0.54 3.48 LC 2 G:C 23 1.52 -5.21 35.68 0.65 0.54 3.43 LC 3 C:G 22 2.71 7.44 31.80 -0.01 0.95 3.44 LC 4 G:C 21 0.23 6.00 33.00 -0.23 0.10 3.40 LC 9 C:G 16 -1.84 -0.91 30.29 0.30 1.16 3.45 LC 10 G:C 15 -1.56 -5.19 38.79 -0.93 0.85 3.52 LC 11 C:G 14 2.00 2.15 38.46 0.40 0.61 3.45 LC 12 G:C 13 I have many such input files and it is difficult to manually extract the desired rows.
 04-09-2009, 06:27 AM #2 colucix Moderator   Registered: Sep 2003 Location: Bologna Distribution: CentOS 6.5 OpenSuSE 12.3 Posts: 10,509 Rep: You can try awk: Code: ```\$3 ~ "C:G" { first = \$0 getline if ( \$3 ~ "G:C" ) { print first print \$0 } }```
 04-09-2009, 06:37 AM #3 aditi_borkar LQ Newbie   Registered: Apr 2009 Posts: 2 Original Poster Rep: Thanx a lot!! I had been trying something similar, but it did not work. This script solves my purpose.
 04-09-2009, 06:49 AM #4 malekmustaq Senior Member   Registered: Dec 2008 Location: /root Distribution: Slackware & BSD Posts: 1,220 Rep: aditi_borkar: What is the type of input? If you mean a text file containing those lines you can easily extract the needed "G:C" or "C:G" lines therefrom and save it into a file. Use the terminal. \$ grep 'C:G' ./input.txt >./myGCfile \$ cat myGCfile there you got them into one file. Try expound more of your problem so that others in the forum will understand what you need and they might be able to help you the better than what I gave here. Hope this helps. Goodluck.