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

Jelle Scholtalbers j.scholtalbers at gmail.com
Mon Sep 20 04:04:34 EDT 2010


Hi,

I'm trying to get all descendents for a specific taxon using Entrez.
each_Descendent and get_all_Descendents don't seem to be implemented or
working.  I then tried by getting the tree for this taxon using
Bio::DB::Taxonomy's get_tree. However this only retrieves the
ancestors/parents.
What would be the best approach here?

Cheers,
Jelle

On Wed, Apr 21, 2010 at 5:45 PM, Eric Collins <rec3141 at mcmaster.ca> wrote:

> 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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