Very nicely indented and done. Just some minor points:
1. glob is not that portable (BSD,DOS,Windows,SYS V), it is a mess. I prefer readdir and grep over glob.
2. I prefer lining up the { and } brackets over the old style 'C' way.
3. The best thing I liked about your code was that it was nicely spaced out. Whitespace is one of the most important things to put into code! Yes, blank lines are important!
4. I may have some mistakes below, but I think it continues along your fine way. 
use strict;
use warnings;

my $dir = '.';

#  for my $file (glob("$dir/*.seq")) 
#  "glob" is not portable even amoungst *nix systems
#  and certainly not amoungst Windows systems.

opendir(DIR,$dir) 
       or die "unable to open directory $dir:$!";
       
foreach my $file ( grep{/\.seq$/ && -f $dir/$_}readdir DIR)   
{
    my $output_path = "$dir/$file.out";
    my $input_path  = "$dir/$file";
    
    open (my $in, '<',  $input_path) or 
        die "Unable to open $input_path: $!";

    open (my $out, '>', $output_path) or 
        die "Unable to open $output_path: $!";
        
    while (<$in>) 
    {
        s/\^\^/\n^^/g;
        print $out $_;  # oopps ; was missing...
    }

    close ($in);
    close ($out);
    
    unlink ($input_path) 
             or die "unable to unlink $input_path: $!";
    rename ($output_path, $input_path) or
        die "Unable to rename $output_path to $input_path:$!";
}

[download]
Update: the unlink before rename is not necessary.

In reply to Re^2: Writing to file... by Marshall
in thread Writing to file... by perl_n00b

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