[Bioperl-l] Bio::Species / Bio::Taxonomy::Node

[Hilmar Lapp]

Very cool Jason!!

Now we can start hooking this into bioperl-db.

And what about porting the SeqIO parsers, the target being to be able 
to deprecate Bio::Species altogether? Alternatively, change the 
SeqI/RichSeqI implementations to silently convert a Bio::Species 
instance on set to a Bio::Taxonomy::Node instance?

	-hilmar

On Friday, January 30, 2004, at 02:07  PM, Jason Stajich wrote:

> I think I've finally committed code which will allow 
> Bio::Taxonomy::Node
> to act like Bio::Species while supporting the notion of being a node 
> in a
> taxonomy hierarchy.  Added tests in t/Species.t to this effect.
>
> For Bio::DB::Taxonomy::flatfile I've added indexing by parent Id so it 
> is
> quite fast to grab all the children for a given node.  So you can walk 
> up
> and down the classification system now.  Practically speaking
> this means to get all the taxon ids of species in the same genus with a
> few simple lines like below.
>
> Unfortunately the the NCBI taxonomy API as part of E-Utils doesn't 
> quite
> provide the information we need so the whole API can't be used without
> downloading the taxonomy db locally.
>
> nodefile and namesfile are the files from ncbi taxdump see
> Bio::DB::Taxonomy::flatfile for more info.
>
> #!/usr/bin/perl
> use strict;
> use warnings;
>
> use Bio::DB::Taxonomy;
> my $db = Bio::DB::Taxonomy->new
>     (-source => 'flatfile',
>      -nodesfile=> '/home/jason/taxonomy/nodes.dmp',
>      -namesfile=> '/home/jason/taxonomy/names.dmp');
>
> my $node = $db->get_Taxonomy_Node(-name => 'Caenorhabditis elegans');
>
> my $parent = $node->get_Parent_Node();
> for my $n ( $parent->get_Children_Nodes() ) {
>     print $n->binomial, "\t", $n->ncbi_taxid,"\n";
> }
>
> Someday I'll get around to making a HowTO unless someone else wants to 
> do
> it... =)
>
> -jason
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
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> Bioperl-l at portal.open-bio.org
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>
>
-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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