[ensembl-dev] [EnsemblGenomes] $NCBI_taxon_adaptor->fetch_node_by_name() not working for some divisions

Giuseppe Gallone G.Gallone at sms.ed.ac.uk
Sat Sep 25 13:47:25 BST 2010


I need to get NCBI taxon ids given the scientific name of the genome, 
for several genomes in EnsemblGenomes. So far I've been doing the following

my $NCBI_taxon_adaptor = $registry->get_adaptor($division,  'compara', 
my $source_taxon = 
my $source_NCBI_taxon_ID = $source_taxon->ncbi_taxid;

This works when the organism is one of those in the metazoa db, and 
$division is 'metazoa', but does not work in some other cases. Eg

my $NCBI_taxon_adaptor = $registry->get_adaptor('fungi',  'compara', 
my $source_taxon = $NCBI_taxon_adaptor->fetch_node_by_name('Aspergillus 
my $source_NCBI_taxon_ID = $source_taxon->ncbi_taxid;

will fail cause $source_taxon is undefined.

I haven't checked all the combinations division/scientific name, but 
from what I've seen the problem does not appear in metazoan genomes 
while it appears with many fungi, plants etc.

Any idea why this happens? Maybe some genome_name-taxon table is missing?

Thank you for your help


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