[Bioperl-l] Bio::Taxon get descendents

Jason Stajich jason.stajich at gmail.com
Wed Sep 11 00:53:28 UTC 2013

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

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