[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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