[Bioperl-l] Problem with Bio::DB::Taxonomy

ANJAN PURKAYASTHA anjan.purkayastha at gmail.com
Mon Aug 15 10:32:39 EDT 2011

I wrote a short test script for the Bio::DB::Taxonomy module:
#!/usr/bin/perl -w
use strict;
use Bio::DB::Taxonomy;

my ($nodesfile, $namesfile)= ('nodes.dmp', 'names.dmp');

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

my $bacteria= $db->get_Taxonomy_Node(-taxonid => '2');

On running this script I expect the following output: 2 Bacteria.

Instead I get a warning:
UNIVERSAL->import is deprecated and will be removed in a future perl at
/usr/share/perl5/vendor_perl/Bio/Tree/TreeFunctionsI.pm line 94.

and the following ouput:
Bio::Taxon=HASH(0x158dbe0)->id    Bio::Taxon=HASH(0x158dbe0)->name

The script seems to be working but there seems to be a problem with
dereferencing a Bio::Taxon object.

Any leads on how to troubleshoot this will be much appreciated.

Anjan Purkayastha, PhD
Senior Computational Biologist
TessArae LLC
46090 Lake Center Plaza, Suite 304
Potomac Falls, VA 20165**
Office- 703.444.7188 ext. 116

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