[Bioperl-l] retrieval of PRELIMINARY uniprot sequences using Bio::Registry fails

Sendu Bala bix at sendu.me.uk
Tue Sep 5 08:13:46 EDT 2006


Daniel Lang wrote:
[...]
> ------------- EXCEPTION  -------------
> MSG: The lineage 'Eukaryota, Metazoa, Chordata, Craniata, Vertebrata,
> Euteleostomi, Amphibia, Batrachia, Anura, Mesobatrachia, Pipoidea,
> Pipidae, Xenopodinae, Xenopus, Silurana, Xenopus, tropicalis' had two
> non-consecutive nodes with the same name. Can't cope!
[...]
> But I think this is connected to the new changes to taxonomy handling in
> Bio::Taxon...
> I'm unsure wether to submit this separately, but I could also provide an
> example of such a swissprot entry that causes this error.

Yes, it is to do with the taxonomy changes. If you can send me the 
problem entry that had a species of Xenopus tropicalis, I'll fix this 
particular problem.

I don't know about the original problem, but if Brian doesn't solve it 
please add a bug report to http://bugzilla.bioperl.org/index.cgi


Cheers,
Sendu.


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