[Bioperl-l] Building a tree rooted at a node in the NCBI taxonomy (Bio::DB::Taxonomy)
Bremen Braun
bremen.braun at gmail.com
Thu Jul 11 22:42:42 UTC 2013
I've been attempting to build a taxonomy tree given an arbitrary nodeID but
I only ever get back zero or one descendant for any node. For this example
I'm trying to build a tree with the same structure as the taxonomic tree
shown here
http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=9604&lvl=10&lin=f&keep=1&srchmode=1&unlock
The problem is illustrated below:
use Bio::DB::Taxonomy;
my $hominidaeID = 9604;
my $db = Bio::DB::Taxonomy->new(-source => 'entrez');
my $node = $db->get_taxon(-taxonid => $hominidaeID); # successfully get
back a Bio::Taxon as expected
my @directDescendants = $db->each_Descendent($node); # PROBLEM: returns no
descendants but I expected "Homininae" and "Ponginae"
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