[ensembl-dev] Release 65 - 'not a valid species name' exception thrown by get_adaptor()

Giuseppe G G.Gallone at sms.ed.ac.uk
Tue Jan 31 15:54:15 GMT 2012


Hi again Uma,

I'm experiencing some more problems when using the API v.65 and 
ensemblgenomes species. I create a registry as above (ie multiple call) 
and use database "pan_homology". The following call

$registry->alias_exists('Plasmodium falciparum')

returns 1  - when it should return 0 - because this taxon name and its 
ID are not amongst the 605 pan_homologies species. So, trusting the 
alias_exists() output, I was  trying to get a genome adaptor as follows

my $gdb = $genomedb_adaptor->fetch_by_taxon_id('5833');

which fails with an exception.

Are there known problems when using alias_exists() with ensemblgenomes 
taxa?

Thanks in advance

Best
G

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.





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