Hello all,
I posted this question in the bioperl forum- no replies after a day, so
let's see if anyone here can help.
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$bacteria->name\n");
================================================
For those of you who don't use BioPerl, the command
"$db->get_Taxonomy_Node(-
taxonid => '2')" returns a Bio::Taxon object.
After the execution of the print statement I expect to see the ouput " 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.
Can anyone suggest how I get to the attributes of the Bio::Taxon object?
TIA,
Anjan
--
===================================
Anjan Purkayastha, PhD
Senior Computational Biologist
TessArae LLC
46090 Lake Center Plaza, Suite 304
Potomac Falls, VA 20165**
Office- 703.444.7188 ext. 116
Mobile-703.740.6939
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