[Bioperl-l] Local flat file implementation of Bio::DB::Taxonomy

Brian Osborne osborne1 at optonline.net
Tue Feb 21 09:46:56 EST 2006


Gabriel,

I don't think so, this works:

#!/usr/bin/perl -w



use strict;

use lib "/Users/bosborne/bioperl-live";


use Bio::DB::Taxonomy;


my $nodesfile = "nodes.dmp";

my $namefile = "names.dmp";

my $db = new Bio::DB::Taxonomy(-source => 'flatfile',

-nodesfile => $nodesfile,

-namesfile => $namefile);


my $taxonid = $db->get_taxonid('Homo sapiens');


my $node = $db->get_Taxonomy_Node(-taxonid => $taxonid); 


# Here, $taxonid is 9606. However,


my $parent = $node->get_Parent_Node;


# is alright, but access to the children nodes via


my @childrenids = $db->get_Children_Taxids($taxonid);


print "@childrenids";


What Bioperl version are you using?

Brian O.


On 2/21/06 7:19 AM, "Gabriel Valiente" <valiente at lsi.upc.edu> wrote:

> my $node = $db->get_Taxonomy_Node(-taxonid => $taxonid); 




More information about the Bioperl-l mailing list