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Top Forums UNIX for Dummies Questions & Answers Merging two text files by a column Post 302548548 by evelibertine on Thursday 18th of August 2011 05:06:53 PM
Old 08-18-2011
Merging two text files by a column

So I have two text files. The first one looks like this:

refsnp_id chr_name chrom_start
1 rs1000000 12 126890980
2 rs10000010 4 21618674
3 rs10000012 4 1357325
4 rs10000013 4 37225069
5 rs1000002 3 183635768

And the second one looks like this:

AUC rs1000000 0.03 0.1240
AUC rs10000010 0.03 0.1462
AUC rs10000012 0.00 0.8628
AUC rs10000013 0.00 0.5459
AUC rs1000002 0.00 0.6439
AUC rs10000023 0.03 0.1337
AUC rs10000027 0.00 0.7142
AUC rs10000030 0.00 0.7634
AUC rs1000003 0.02 0.2226


The second columns of the two text files match but not completely. There are some missing lines in the first text file. I want to merge the two text files by their second columns and add the third and fourth column of the first file to the second file when the second columns of the two files are matching. How do I go about doing that? Thanks!
 

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COMM(1) 						    BSD General Commands Manual 						   COMM(1)

NAME
comm -- select or reject lines common to two files SYNOPSIS
comm [-123i] file1 file2 DESCRIPTION
The comm utility reads file1 and file2, which should be sorted lexically, and produces three text columns as output: lines only in file1; lines only in file2; and lines in both files. The filename ``-'' means the standard input. The following options are available: -1 Suppress printing of column 1. -2 Suppress printing of column 2. -3 Suppress printing of column 3. -i Case insensitive comparison of lines. Each column will have a number of tab characters prepended to it equal to the number of lower numbered columns that are being printed. For example, if column number two is being suppressed, lines printed in column number one will not have any tabs preceding them, and lines printed in column number three will have one. The comm utility assumes that the files are lexically sorted; all characters participate in line comparisons. ENVIRONMENT
The LANG, LC_ALL, LC_COLLATE, and LC_CTYPE environment variables affect the execution of comm as described in environ(7). EXIT STATUS
The comm utility exits 0 on success, and >0 if an error occurs. SEE ALSO
cmp(1), diff(1), sort(1), uniq(1) STANDARDS
The comm utility conforms to IEEE Std 1003.2-1992 (``POSIX.2''). The -i option is an extension to the POSIX standard. HISTORY
A comm command appeared in Version 4 AT&T UNIX. BUGS
Input lines are limited to LINE_MAX (2048) characters in length. BSD
January 26, 2005 BSD
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