Comparing two files - The UNIX and Linux Forums

		The UNIX and Linux Forums > Top Forums > Shell Programming and Scripting
Comparing two files

google unix.com

Shell Programming and Scripting Post questions about KSH, CSH, SH, BASH, PERL, PHP, SED, AWK and OTHER shell scripts and shell scripting languages here.

More UNIX and Linux Forum Topics You Might Find Helpful
Thread	Thread Starter	Forum	Replies	Last Post
comparing of two files with output which is not in both files	suryanarayana	Shell Programming and Scripting	2	02-04-2009 08:41 AM
Need Help Comparing two Files	awknerd	Shell Programming and Scripting	4	09-03-2008 01:24 AM
Comparing two files	superstar003	Forum Support Area for Unregistered Users & Account Problems	1	05-08-2008 04:34 AM
Comparing 2 files	hdixon	UNIX for Dummies Questions & Answers	2	08-01-2007 01:24 PM
comparing shadow files with real files	terrym	UNIX for Advanced & Expert Users	4	02-09-2007 02:38 AM


	Powered by

LinkBack

Thread Tools

Search this Thread

Rate Thread

Display Modes

#1 (permalink)

09-28-2009

genehunter genehunter is offline

Registered User

Join Date: May 2009

Posts: 17

Comparing two files

Hello all, I am not a programmer, but I require a little help with a project I am doing. I did read several posts and looks like awk or python may help me, though I know very little about using them. Here is my question: I have first file with 6 column.

Code:

CHR             SNP   A1   A2          MAF  NCHROBS
    0   SNP_A-8414268    A    G       0.1522     5354
   1      rs12565286    C    G      0.04139     5340
   1       rs2980319    A    T       0.1503     5362
   1       rs2980300    T    C       0.1773     5346
   1       rs6603781    A    G       0.1149     5346

My second file is very similar to the first one, but it may or may not have the same Column 2(SNP). I suspect that the columns Col 3 and 4 (A1 & A2) may be different as well.

What I require is to get an output file with columns 1,2,3, 4, 5, 6 from the first file and the corresponding line that matches column 2 (SNP) of the FIRST file with the columns 2,3,4,5,6 (SNP, A1, A2, MAF, NCHROBS) from SECOND file at positions 7,8,9,10,11,2. The output file will hence have 11 columns; the first 6 from file 1.txt and the matching last five from file 2.txt

Code:

CHR             SNP   A1   A2          MAF  NCHROBS
       0   SNP_A-8414268    A    G       0.1522     5354
   1      rs12565286    C    G      0.04139     5340
   1       rs2980319    A    T       0.1503     5362    rs2980319    A    T       0.1503     4252
   1       rs2980300    T    C       0.1773     5346    rs2980300    T    C       0.1273     4546
   1       rs6603781    A    G       0.1149     5346    rs6603781    G    A       0.0249     4546

Thank you for reading

Bookmarks

« \n option in script | grep, awk, nawk combo »

Thread Tools	Search this Thread
Show Printable Version Email this Page	Search this Thread: Advanced Search
Display Modes	Rate This Thread
Switch to Linear Mode Switch to Hybrid Mode Threaded Mode	Rate This Thread:

Posting Rules
You may not post new threads You may not post replies You may not post attachments You may not edit your posts BB code is On Smilies are On [IMG] code is On HTML code is Off Trackbacks are On Pingbacks are On Refbacks are On Forum Rules

All times are GMT -4. The time now is 08:20 AM.