[ensembl-dev] Missing Tasmanian devil species aliases

Andreas Kusalananda Kähäri ak at ebi.ac.uk
Tue Oct 25 13:59:11 BST 2011

Good suggestion John.

I can't do anything about the missing aliases for the tasmanian devil,
but I've modified the get_adaptor() method to throw an exception if
the real name for a species alias can not be found. This will be in
release 65. I had a quick look, and the needed aliases are there in
the databases that later will become the release 65 databases.


On 25 October 2011 13:37, John Marshall <jm18 at sanger.ac.uk> wrote:
> Attempting to query Tasmanian devil data via the API (r64, of course) fails when asking for it by its latin name:
> my $slice_adaptor = $registry->get_adaptor('Sarcophilus harrisii', 'Core', 'Slice')
>   or die "can't get slice adaptor for Sarcophilus harrisii\n";
> Sarcophilus harrisii is not a valid species name for this instance
> Use of uninitialized value in hash element at /software/pubseq/PerlModules/Ensembl/www_64_1/ensembl/modules/Bio/EnsEMBL/Registry.pm line 958.
> Use of uninitialized value in hash element at /software/pubseq/PerlModules/Ensembl/www_64_1/ensembl/modules/Bio/EnsEMBL/Registry.pm line 969.
> can't get slice adaptor for Sarcophilus harrisii
> It works with "Devil", "Tasmanian devil", etc, but it would appear that the latin names that are present in other species' meta tables are missing from this one.
> (Also the excess "Use of uninitialized value" messages suggest that maybe get_adaptor() should fail immediately when its call to get_alias() fails.)
> Cheers,
>   John
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Andreas Kusalananda Kähäri, Ensembl Software Developer
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge CB10 1SD, United Kingdom

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