[Bioperl-l] Local flat file implementation of Bio::DB::Taxonomy
jason.stajich at duke.edu
Tue Feb 21 14:51:39 UTC 2006
of course it should, and it does support this. Children query
definitely exists for the flatfile implementation I don't understand
why are you getting entrez errors when you are requesting the
I can't investigate but it definitely worked for me to get children
nodes. Did you actually try running the script that already should
work - scripts/taxa/local_taxonomdb_query ?
You definitely can't request children nodes via the entrez
implementation because NCBI doesn't (or didn't when this was written
I don't know about now) provide children id access so it is pretty
useful for that - although the eutils support may have expanded I'm
not sure. If someone has the itch, please scratch it and work on this.
I think you need to pass in $parent instead of $taxonid to
get_Children_Taxids -- although I guess I wrote the method to accept
On Feb 21, 2006, at 7:19 AM, Gabriel Valiente wrote:
> Thanks. There's still a problem with Bio::DB::Taxonomy:
> use strict;
> use Bio::DB::Taxonomy;
> my $nodesfile = "nodes.dmp";
> my $namesfile = "names.dmp";
> my $db = new Bio::DB::Taxonomy(-source => 'flatfile'
> -nodesfile => $nodesfile,
> -namesfile => $namesfile);
> my $taxonid = $db->get_taxonid('Homo sapiens');
> my $node = $db->get_Taxonomy_Node(-taxonid => $taxonid);
> So far so good. Now, access to the parent node via
> my $parent = $node->get_Parent_Node;
> is alright, but access to the children nodes via
> my @childrenids = $db->get_Children_Taxids($taxonid);
> ------------- EXCEPTION -------------
> MSG: Abstract method "Bio::DB::Taxonomy::get_Children_Taxids" is not
> implemented by package Bio::DB::Taxonomy::entrez.
> This is not your fault - author of Bio::DB::Taxonomy::entrez should be
> STACK Bio::Root::RootI::throw_not_implemented
> STACK Bio::DB::Taxonomy::get_Children_Taxids
> STACK toplevel fetch.pl:17
> Perhaps there could be a $node->get_Children_Nodes() method in
> Bio::DB::Taxonomy, instead ofg relying on Bio::DB::Taxonomy::entrez.
> You, know, efficient access to the children of a node is a quite
> important method for almost any interesting use of the NCBI Taxonomy.
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