Thank you for all your guys' help so far! I just have 2 more questions about my code.
So far I have this... 
use strict;
use warnings;

my $dir = 'c:\seqs';

opendir(DIR,$dir) 
       or die "unable to open directory $dir:$!";
       
foreach my $file ( grep{/\.seq$/ && -f "$dir/$_"}readdir DIR)
   
{
    my $output_path = "$dir/$file.seq";
    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>) 
    {
        my $locus =~ /LOCUS\s*(\w+)/;
        s/\^\^/>$locus\n^^\n/g;
        print $out $_;

    }

    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]
If ^^ is not present I need to add it in with a new line character before the sequence.
Something like... 
while (<$in>) { 
if $in =~ /^^/ { s/\^\^/\n^^/g; 
print $out $_; 
else { s/[a]|[c]|[t]|[g]{6}/^^\n }

[download]

How would I correctly write the else?
I was thinking I could just find a series of bases and add the ^^ before it but I don't know how to get the same series of bases in the substitution.
Also I need to capture the locus name and place it before the ^^ like this but for the life of me I can not get it to capture.
    while (<$in>) 
    {
        my $locus =~ /LOCUS\s*(\w+)/;
        s/\^\^/>$locus\n^^\n/g;
        print $out $_;

    }

[download]

within the file the Locus name is formatted like this 
Created: Tuesday, July 12, 2005 4:17 PM
LOCUS       AJ877263                 663 bp    DNA     linear   INV 15
+-APR-2005

[download]

Thanks for any help in advance!

In reply to Writing to file part duex by perl_n00b

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