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

Daniel Lang daniel.lang at biologie.uni-freiburg.de
Tue Sep 5 12:39:11 UTC 2006

Hi Sendu,

thanks for the fast response!
Here is the example...


Sendu Bala wrote:
> 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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