[Bioperl-l] Bio::DB:: fails

[michael]

	I'm having problems with both Bio::DB::GenBank and Bio::DB::EMBL
(see code below)  were using Bioperl 1.0.2.  I understand there were
some minor problems compiling (Module dependencys)

Bio::DB::GenBank fails to return a sequence handle 5-10% of the time

Bio::DB::EMBL is fairly reilable but every so often crashes with the
message:-

------------- EXCEPTION  -------------
MSG: EMBL stream with no ID. Not embl in my book
STACK Bio::SeqIO::embl::next_seq
/usr/local/perl/lib/site_perl/5.6.1/Bio/SeqIO/embl.pm:155
STACK Bio::DB::WebDBSeqI::get_Seq_by_acc
/usr/local/perl/lib/site_perl/5.6.1/Bio/DB/WebDBSeqI.pm:163
STACK main::test tst.pl:18
STACK toplevel tst.pl:11

--------------------------------------

	I get these problems running both Solaris (SunOS 5.8) and Linux
(mandrake 8.2).

	Suggestions?



~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Michael John Lush PhD		 	 Tel:44-20-7679-5027
Nomenclature Bioinformatics Support 	 Fax:44-20-7387-3496
HUGO Gene Nomenclature Committee Email:  nome@galton.ucl.ac.uk
The Galton Laboratory
University College London, UK
URL: http://www.gene.ucl.ac.uk/nomenclature/
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


#!/use/bin/perl -w
use strict;
use Bio::DB::GenBank;
use Bio::DB::EMBL;

my $genbank = new Bio::DB::GenBank;
my $embl = new Bio::DB::EMBL;

print "Genbank failed ". test($genbank) . "times\n";

print "EMBL failed ". test($embl) . "times\n";

sub test {
    my ($handle) = @_;
    my $seq;
    my $count = 0;
    for (my $x = 1; $x <= 100; $x++) {
        $seq = $handle->get_Seq_by_acc('AK002226');
        print "test $x\n";

        unless ($seq) {
            $count++;
        }
    }
    return ($count);
}