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

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


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); 

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