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Top Forums UNIX for Dummies Questions & Answers if matching strings in file1 and file2, add column from file1 to file2 Post 302674389 by pathunkathunk on Thursday 19th of July 2012 01:47:12 PM
Old 07-19-2012
if matching strings in file1 and file2, add column from file1 to file2

I have very limited coding skills but I'm wondering if someone could help me with this. There are many threads about matching strings in two files, but I have no idea how to add a column from one file to another based on a matching string.

I'm looking to match column1 in file1 to the number following the string "Gene_" in file2. If there's a match, I want to add column 2 from file1 as the first column in file2.

file1
Code:
1    k48_101119
2    k48_103273
3    k48_103895
4    k48_108200
5    k48_11007
[...]

file2
(not all line numbers in file1 are represented in file2)
Code:
"Gene_2" 2.79393133358307e-119
"Gene_5" 3.58660951659928e-42
[...]

Desired output
Code:
k48_103273 "Gene_2" 2.79393133358307e-119
k48_110077 "Gene_5" 3.58660951659928e-42
[...]

Thanks in advance...
 

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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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