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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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JOIN(1) 						      General Commands Manual							   JOIN(1)

NAME
join - relational database operator SYNOPSIS
join [-an] [-e s] [-o list] [-tc] file1 file2 DESCRIPTION
Join forms, on the standard output, a join of the two relations specified by the lines of file1 and file2. If file1 is `-', the standard input is used. File1 and file2 must be sorted in increasing ASCII collating sequence on the fields on which they are to be joined, normally the first in each line. There is one line in the output for each pair of lines in file1 and file2 that have identical join fields. The output line normally con- sists of the common field, then the rest of the line from file1, then the rest of the line from file2. Fields are normally separated by blank, tab or newline. In this case, multiple separators count as one, and leading separators are dis- carded. These options are recognized: -an In addition to the normal output, produce a line for each unpairable line in file n, where n is 1 or 2. -e s Replace empty output fields by string s. -o list Each output line comprises the fields specified in list, each element of which has the form n.m, where n is a file number and m is a field number. -tc Use character c as a separator (tab character). Every appearance of c in a line is significant. SEE ALSO
sort(1), comm(1), awk(1). BUGS
With default field separation, the collating sequence is that of sort -b; with -t, the sequence is that of a plain sort. The conventions of join, sort, comm, uniq, look and awk(1) are wildly incongruous. 7th Edition April 29, 1985 JOIN(1)
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