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

Eric Collins rec3141 at mcmaster.ca
Wed Apr 21 11:45:46 EDT 2010


Thanks, that was indeed the answer to #2. Any idea about each_Descendent?
Eric

On Tue, Apr 20, 2010 at 4:48 PM, Chris Fields <cjfields at illinois.edu> wrote:
> 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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>
>



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