Ok, if you simply want to replace the values of 1 arbitrary column in 1 file with the values of 1 arbitrary column in another file, the modified version of what I previously posted will do it.

given the following original file:

1:2:3:4
5:6:7:8
9:10:11:12
13:14:15:16
17:18:19:20
[download]

and the following replacement file:

a:b:c:d:e
f:g:h:i:j
k:l:m:n:o
p:q:r:s:t
u:v:w:x:y
[download]

The following example will replace column 2 of the orginal file with column 3 of the replacement file

#!/usr/bin/perl
use File::Copy;
use strict;
my (@col, @vals, $val, $i);
open(COL, "<replace.txt");

while(<COL>) {
    chomp($_);
    (@vals) = split(":", $_);
    push @col, $vals[1]; #store values for column 2

}
close(COL);

open(OUT, ">out.txt");
open(COL, "<original.txt");
while(<COL>) {
    chomp($_);
    (@vals) = split(":", $_);
    $vals[2] = $col[$i++];    #replace values in column 3
    print OUT join(":", @vals) . "\n";
}
close(COL);
close(OUT);
copy("out.txt", "original.txt");
[download]

original file after running the program:

1:2:b:4
5:6:g:8
9:10:l:12
13:14:q:16
17:18:v:20
[download]

davidj