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

[Daniel Hughes]

Perhaps use pan compara and not division specific DBs:

mysql> use ensembl_compara_pan_homology_6_59
Database changed
mysql> select * from ncbi_taxa_name where name like 'Aspergillus nidulans'
\G
*************************** 1. row ***************************
  taxon_id: 162425
      name: Aspergillus nidulans
name_class: genbank anamorph
1 row in set (0.30 sec)

mysql> use ensembl_compara_fungi_6_59
Database changed
mysql> select * from ncbi_taxa_node;
Empty set (0.04 sec)

dan.

Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
-------------------------------------------------------------------------------------
dsth at cantab.net
dsth at cpan.org


2010/9/25 Daniel Hughes <dsth at ebi.ac.uk>

> Not very familiar with Compara, but perhaps:
>
> mysql> use aspergillus_nidulans_core_6_59_6e
> Database changed
> mysql> select meta_value from meta where meta_key = 'species.taxonomy_id'
> \G
> *************************** 1. row ***************************
> meta_value: 162425
> 1 row in set (0.09 sec)
>
> mysql> use ensembl_compara_metazoa_6_59
> Database changed
> mysql> select * from ncbi_taxa_name where name like 'Aspergillus nidulans'
> \G
> *************************** 1. row ***************************
>   taxon_id: 162425
>       name: Aspergillus nidulans
> name_class: genbank anamorph
> 1 row in set (0.10 sec)
>
> mysql> use ensembl_compara_fungi_6_59
> Database changed
> mysql> select * from ncbi_taxa_name where name like 'Aspergillus nidulans'
> \G
> Empty set (0.12 sec)
>
> Dan
>
> Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
>
> -------------------------------------------------------------------------------------
> dsth at cantab.net
> dsth at cpan.org
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20100925/1e9323a5/attachment.html>