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

Eric Collins rec3141 at mcmaster.ca
Fri Apr 16 21:49:08 UTC 2010


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? I ran Data::Dumper on $node and '_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.

thanks,
Eric



More information about the Bioperl-l mailing list