[ensembl-dev] $NCBI_taxon_adaptor->fetch_node_by_name() broken in EnsemblGenomes 7

Giuseppe G. G.Gallone at sms.ed.ac.uk
Tue Dec 14 13:16:34 GMT 2010


Hi,

There is a problem with $NCBI_taxon_adaptor->fetch_node_by_name() in 
release 60.


STEPS TO REPRODUCE THE BUG
--------------------------

1) get a registry by doing
           $registry->load_registry_from_multiple_dbs(
           {    #VERTEBRATES
                   -host       => 'ensembldb.ensembl.org',
                   -user       => 'anonymous',
                   -verbose    => 1
               },
           {     #EnsemblGenomes
                      -host    => 'mysql.ebi.ac.uk',
                      -user    => 'anonymous',
                      -port    => 4157,
                      -verbose => 1
               }
           );

-this step is successful

2) get a taxon adaptor using pan_homology by doing

my $NCBI_taxon_adaptor = $registry->get_adaptor('pan_homology', 
'compara', "NCBITaxon");

-this step is successful

3) get a taxon id from the species name by using fetch_node_by_name()

my $source_taxon = 
$NCBI_taxon_adaptor->fetch_node_by_name($source_organism);

where for $source_organism I tried 'Plasmodium falciparum', 
'plasmodium_falciparum', 'drosophila_melanogaster', ecc ecc

-source_taxon is undefined
-----------------------------


ADDITIONAL INFORMATION
----------------------
-This worked  in release 59/6
-The method still works when the registry is connecting to vertebrate 
compara


Any help is particularly appreciated because a core feature of my 
scripts relies on this adaptor and its seamless functionality (as per 
API docs) across Multi, ensemblgenomes and pan compara.


Thanks a lot in advance.

Giuseppe


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