[Bioperl-l] embl.pm and virus names

[Neil Rawlings]

I am trying to use the Bio::SeqIO::EMBL to parse EMBL database entries,
but am having problems whenever I try to retrieve the organism name
whenever the EMBL entry is for a viral sequence.  I am using the embl.pm
module and a line such as:

My ($spec, $genus) = $entry->species->classification();

But for a virus (which doesn't have a species name - for example "apple
chlorotic leaf spot virus") I get "Apple chlorotic" as the organism
name.  I'm not just interested in viruses, so I'm happy when the name
comes back as "Drosophila melanogaster".  The problem is also apparent
for some bacteria, especially something like Synechocystis sp. PCC6803
in which PCC6803 is lost (probably assumed to be a subspecies name). 

If a solution exists to this problem, please let me know.

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Neil D. Rawlings
Sanger Institute
Wellcome Trust Genome Campus
Hinxton, Cambs CB10 1SA, UK

Tel: +1223 495330
Fax: +1223 494919
E-mail: <A HREF="mailto:ndr at sanger.ac.uk">ndr at sanger.ac.uk</A>
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Please visit the MEROPS database for peptidase classification.  The URL
is:
                         <a
href="merops.sanger.ac.uk">MEROPS.SANGER.AC.UK</a>