use strict;
use warnings;

my $dir = '.';

for my $file (glob("$dir/*.seq")) {
    my $output = "$file.out";
    
    open (my $in, '<', $file) or 
        die "Unable to open $file: $!";

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

    close ($in);
    close ($out);
    
    rename ($output, $file) or
        die "Unable to rename $output to $file:$!"
}