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

Chris Fields cjfields at illinois.edu
Tue Apr 20 16:48:24 EDT 2010


Sounds like this is going through an initial indexing step (for flatfiles).  I would expect the initial indexing of the tables to take time as you have to create the DB, but subsequent lookups post-indexing should be much faster if the index is already present.  Maybe Jason could answer in more detail?

chris

On Apr 20, 2010, at 3:20 PM, Eric Collins wrote:

> Hello,
> 
> I tried the Bio::DB::Taxonomy example on this wiki page using perl
> 5.8.5 with BioPerl 1.6.0
> http://www.bioperl.org/wiki/Module:Bio::DB::Taxonomy
> 
> 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.
> 
> thanks,
> Eric
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