[Bioperl-l] Bio::DB::Taxonomy and each_Descendent

Eric Collins rec3141 at mcmaster.ca
Tue Apr 20 16:20:33 EDT 2010


I tried the Bio::DB::Taxonomy example on this wiki page using perl
5.8.5 with BioPerl 1.6.0

It ran for 100 cpu seconds and output:

33090 Viridiplantae kingdom

I was expecting it to also output the descendents. Some questions:

1) are calls to 'each_Descendent' or 'get_all_Descendents' actually
implemented? It looks to be in Taxon.pm but it is not documented and
when I ran Data::Dumper on $node the value '_desc' was empty.

2) is the flatfile reader always so slow? after replacing 'flatfile'
with a call to 'entrez' it took only 0.02 cpu seconds to come
up with the same result.


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