sub convert_raw_to_fasta {
    my $InFileName = shift;
    my $OutFileNameBase = shift or die "Missing argument(s)!";

    open $hu, '<', $InFileName or die $!;
    my $seq=<$hu>;
    close $hu or die $!;

    open $hu, '>', $OutFileNameBase . ".fa" or die $!;
    print $hu ">$maid\n$seq";
    close $hu or die $!;
}

##</code><code>##

sub blast_parse{
    my($maid,$maid_dir) = @_;
    my $url_hu = "http://hu_seq/";
    my $hu = get($url_hu.$maid);
    my $ltvec_small = $maid_dir.$maid."Ltvec_small.fa";

    convert_raw_to_fasta($hu, $maid);

    # syntax
    # bl2seq -p blastn -i nucleotide1 -j nucleotide2 -F F -D 1 
    my $command = "bl2seq -p blastn -i $ltvec_small -j $hu_fa -F F -D 1";
    print $command,"\n";
    open OUTPUT, '>',  "$maid_dir\\".$maid."_bl2seq.out" ;
    STDOUT->fdopen( \*OUTPUT, 'w');
    system($command); 
    bl2seq_parse();
}

sub blast_hd_parse{
    my($maid,$maid_dir) = @_;
    my $url_hd = "http://hd_seq/";
    my $hd = get($url_hd.$maid);
    my $ltvec_small = $maid_dir.$maid."Ltvec_small.fa";

    convert_raw_to_fasta($hu, $maid);
    
    my $command = "bl2seq -p blastn -i $ltvec_small -j $hd_fa -F F -D 1";
    print $command,"\n";
    open OUTPUT, '>',  "$maid_dir\\".$maid."_bl2seq.out" ;
    STDOUT->fdopen( \*OUTPUT, 'w');
    system($command); 
    bl2seq_parse();
}

##</code><code>##

sub process_and_parse {
    my $command = shift;
    my $output_file = shift or die "Missing argument(s)!";

    print $command,"\n";
    open OUTPUT, '>',  $output_file or die $!;
    STDOUT->fdopen( \*OUTPUT, 'w');
    system($command); 
    bl2seq_parse();
}

##</code><code>##

sub blast_parse{
    my($maid,$maid_dir) = @_;
    my $url_hu = "http://hu_seq/";
    my $hu = get($url_hu.$maid);
    my $ltvec_small = $maid_dir.$maid."Ltvec_small.fa";

    convert_raw_to_fasta($hu, $maid);

    process_and_parse(
        "bl2seq -p blastn -i $ltvec_small -j $hu_fa -F F -D 1",
        "$maid_dir/" . $maid . "_bl2seq.out"
    );
}

sub blast_hd_parse{
    my($maid,$maid_dir) = @_;
    my $url_hd = "http://hd_seq/";
    my $hd = get($url_hd.$maid);
    my $ltvec_small = $maid_dir.$maid."Ltvec_small.fa";

    convert_raw_to_fasta($hu, $maid);

    process_and_parse(
        "bl2seq -p blastn -i $ltvec_small -j $hd_fa -F F -D 1",
        "$maid_dir/" . $maid . "_bl2seq.out"
    );
}

##</code><code>##

# main task
initialize_frobnitz();
generate_zanzibar();
show_results();

sub initialize_frobnitz {
    my $frobber = allocate_frobnitz(1);
    send_to_frobber($frobber, 'INIT')
        or die "Can't initialize frobber!";
    send_to_frobber($frobber, 'configuration value 1') 
        or die "Can't configure frobber!";
}

sub send_to_frobber {
    my $serial_port = ... etc ...