[Bioperl-l] Bio::Taxon get descendents

[Fields, Christopher J]

On Sep 10, 2013, at 7:53 PM, Jason Stajich <jason.stajich at gmail.com> wrote:

> A gotcha, not sure how I think we should fix this yet.
> 
> I discovered bug that the Bio::Taxon delegates to Bio::Tree for its each_Descendent calls but in the case of taxonomy these aren't loaded in to the tree - they require a DB object to request the children of a node from - so it doesn't work just querying the in-memory tree structure.
> 
> The following works because it queries the taxonomy db object for the children of a node (Bio::DB::Taxonomy::flatfile in this case is $taxdb; $taxon is a Bio::Taxon object )
> 
> for my $downstream ( $taxdb->each_Descendent($taxon) ) {
> 		print "downstream is $downstream\n";
> 		print "below ", join(" ", @{$downstream->name('scientific')}), "\n";
> 	    }
> 
> This won't because it is using the Bio::Taxon implementation of get_all_Descendents which relies on Bio::Tree::Node functions.
> for my $child ( $taxon->get_all_Descendents() ) {
> 		warn("child is $child\n");
> 		print $child->rank, " ", join(" ", @{$child->name('scientific')}), "\n";
> }
> 
> Also note that all DB implementations don't support the each_Descedent (e.g. NCBI Taxonomy via eutils or web query).
> 
> 
> --
> Jason Stajich

This seems like an API problem/inconsistency.  Do the changes that Greg Jordan introduced in the tree_api_refresh branch deal with this in any way?

chris