Fields, Christopher J | 23 Jan 00:40 2013

Re: Bio::DB::Taxonomy example

Done.  Thanks for pointing that out!

chris

On Jan 23, 2013, at 5:45 AM, Shyam Saladi <saladi1 <at> illinois.edu>
 wrote:

> Hi,
> 
> There is an example on how to use Bio::DB::Taxonomy at
> http://www.bioperl.org/wiki/Module:Bio::DB::Taxonomy
> 
> I tried the script but could not get it to work properly. After looking
> through the documentation it seems that
> 
> my  <at> extant_children = grep { $_->rank eq 'species' }
> $node->get_all_Descendents;
> 
> should instead be
> 
> my  <at> extant_children = grep { $_->rank eq 'species' }
> $db->get_all_Descendents($node)
> 
> I found this solves the problem for me. If my fix is in fact correct, an
> admin may want to change the example script online.
> 
> Thanks,
> Shyam
> **
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Gmane