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

Gabriel Valiente valiente at lsi.upc.edu
Mon Feb 20 13:51:35 EST 2006


The local flat file implementation of Bio::DB::Taxonomy seems to be fine:

use Bio::DB::Taxonomy;
my $nodesfile = "nodes.dmp";
my $namesfile = "names.dmp";
my $db = new Bio::DB::Taxonomy(-source => 'flatfile'
                               -nodesfile => $nodesfile,
                               -namesfile => $namefile);
my $taxonid = $db->get_taxonid('Homo sapiens');

Here, $taxonid is 9606. However,

my $species = $db->get_Taxonomy_Node(-taxonid => $taxonid);

raises:

-------------------- WARNING ---------------------
MSG: can't create a species object for Homo sapiens (human) because it isn't a species but is a '' instead
---------------------------------------------------

Thanks,

Gabriel



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