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 $input_path:$!";
}