sub save_output  {

    my ($self, $filename) = @_;
    if( ! defined $filename ) {
            $self->throw("Can't save blast output.  You must specify a filename to save to.");
    }
    #should be set when retrieving blast
       my $blastfile = $self->file;
       #open temp file and output file, have to filter out some HTML
    open(TMP, $blastfile) or $self->throw("cannot open $blastfile");
    open(SAVEOUT, ">$filename") or $self->throw("cannot open $filename");
    my $seentop=0;
    while(<TMP>) {
        next if (/<pre>/);    
        if( /^(?:[T]?BLAST[NPX])\s*.+$/i ||
               /^RPS-BLAST\s*.+$/i ) {
               $seentop=1;
           }
           next if !$seentop;
        if( $seentop ) {
            print SAVEOUT;
        }
    }
    close SAVEOUT;
    close TMP;
    return 1;

}