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Full Discussion: Awk: adding fields after matching $1
Top Forums Shell Programming and Scripting Awk: adding fields after matching $1 Post 302870417 by kben on Sunday 3rd of November 2013 01:36:19 PM
Old 11-03-2013
Awk: adding fields after matching $1
Dear AWK-experts!

I did get stuck in the task of combining files after matching fields, so I'm still awkward with learning AWK.

There are 2 files: one containing 3 columns with ID, coding status, and score for long noncoding RNAs:

file1 (1.txt) (>5000 lines)

Code:
TCONS_00017358;noncoding;0.968717
TCONS_00024657;noncoding;0.995485
TCONS_00005907;noncoding;0.808883 
TCONS_00013445;noncoding;0.998353 
TCONS_00001277;noncoding;0.934182 
TCONS_00047071;noncoding;0.919281 
TCONS_00040152;noncoding;0.988357

The second file contains the same ID ($1 == $1) and a corresponding Gene name in field $2:

file2 (2.txt)
Code:
TCONS_00024657;KCNC2 
TCONS_00005907;CDH11 
TCONS_00013445;TAF12 
TCONS_00047071;MYO19 
TCONS_00040152;KCNC2 
TCONS_00017358;PAIP1 
TCONS_00001277;CHAD4

I would like to add the Gene name ($2 from file2) as an additional column to file1 in a newly generated file3. Every Gene name is located somewhere in file2. Because of asymmetric distributed duplicates in file2 a simple sort after ID and cat doesn't work. At the moment I'm trying.

Code:
awk -F ";" > 3.txt 'NR == FNR {   
               _[$1] = $1; _[$2] = $2   
               next 
               } 
                  if (_[$1] == $1)  {   
                  print $0, _[$2]   
              }' 2.txt 1.txt

Any help would be awesome!!!
 

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LEARN ABOUT NETBSD

merge

MERGE(1)						      General Commands Manual							  MERGE(1)

NAME

       merge - three-way file merge

SYNOPSIS

       merge [ options ] file1 file2 file3

DESCRIPTION

       merge  incorporates all changes that lead from file2 to file3 into file1.  The result ordinarily goes into file1.  merge is useful for com-
       bining separate changes to an original.	Suppose file2 is the original, and both file1 and file3 are modifications of  file2.   Then  merge
       combines both changes.

       A  conflict  occurs  if	both  file1 and file3 have changes in a common segment of lines.  If a conflict is found, merge normally outputs a
       warning and brackets the conflict with and lines.  A typical conflict will look like this:

	       file A
	      lines in file A
	      =======
	      lines in file B
	       file B

       If there are conflicts, the user should edit the result and delete one of the alternatives.

OPTIONS

       -A     Output conflicts using the -A style of diff3(1), if supported by diff3.  This merges all changes leading from file2  to  file3  into
	      file1, and generates the most verbose output.

       -E, -e These  options  specify conflict styles that generate less information than -A.  See diff3(1) for details.  The default is -E.  With
	      -e, merge does not warn about conflicts.

       -L label
	      This option may be given up to three times, and specifies labels to be used in place of the corresponding  file  names  in  conflict
	      reports.	 That  is, merge -L x -L y -L z a b c generates output that looks like it came from files x, y and z instead of from files
	      a, b and c.

       -p     Send results to standard output instead of overwriting file1.

       -q     Quiet; do not warn about conflicts.

       -V     Print version number.

DIAGNOSTICS

       Exit status is 0 for no conflicts, 1 for some conflicts, 2 for trouble.

IDENTIFICATION

       Author: Walter F. Tichy.
       Manual Page Revision: ; Release Date: .
       Copyright (C) 1982, 1988, 1989 Walter F. Tichy.
       Copyright (C) 1990, 1991, 1992, 1993, 1994, 1995 Paul Eggert.

SEE ALSO

       diff3(1), diff(1), rcsmerge(1), co(1).

BUGS

       It normally does not make sense to merge binary files as if they were text, but merge tries to do it anyway.

									GNU								  MERGE(1)
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