Many thanks!:D It works fine now. I realized I could speed up thing modifying some code and using a hash. Here's what I came up with. 
my %handle = ();
my $ref_db = FastaDb->new($fasta) or die("Unable to open Fasta file, $
+fasta\n");
while( my $seq = $ref_db->next_seq() ) {
    if($seq->header() =~ m/(K[0-9]{5})/){
        my $ko = $1;
        if(!exists $handle{$ko}){
            open my $fh, ">>".$outdir.$ko.".fasta";
            $handle{$ko} = $fh;
        }
  print {$handle{$ko}} $seq->header()."\n".$seq->seq()."\n";
    }

}

map { close $handle{$_} } keys %handle;

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In reply to Re^2: Write to multiple files by julio_514
in thread Write to multiple files by julio_514

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