1. Maintain a connection to a remote database
2. Call a remote BLAST server

To detect problems with the database, you can reconnect for every query so that when the database is down, you get an error message, or use a permanent connection and create a timeout handler using signals and the alarm system call.

You'll have to do something similar with the requests to the BLAST server. I don't know what a call to the BLAST server looks like, but I assume something like the database query can be done.

Using the temp file for intermediate results is a wise thing, because when a connection to one of the servers is down, you can detect it and wait for it to come back up (using sleep for example), possibly notify you, and go on its merry way. This way, you can do all error handling within the script and there's no need to monitor external processes.

Arjen

sub blast
{
    my $data = shift;
    my $temp = "$ENV{HOME}/temp/seq.tmp";
    my $fifo = "ssh myhost /path/to/blast";
    my @args = ('-p blastn', '-d nt', '-e 0.0000001', '-m 7');
    
    ### load input file with fasta-formatted queryid/sequence ###
    open  SEQ, ">$temp" or die "Could not open for write:$!";
    print SEQ  ">",$data->[0],"\n",$data->[1];    
    close SEQ;

    ### open a handle to BLAST output, retry if unsuccessfull ###
    {
        if (!open BLAST, "$fifo @args <$temp|")
        {
            #
            print LOG "BLAST connection refused, retrying...\n";
            #
            sleep(300);
            redo;
        }
    }

    ### process the report ###
    parse(*BLAST);
}
[download]