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

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


Hello,
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= $db->get_Taxonomy_Node(-taxonid => '2');
print("$bacteria->id\t$bacteria->name\n");
================================================

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.
Thanks
Anjan



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Anjan Purkayastha, PhD
Senior Computational Biologist
TessArae LLC
46090 Lake Center Plaza, Suite 304
Potomac Falls, VA 20165**
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Mobile-703.740.6939
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