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 ===================================