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

[Brian Osborne]

Jason,

So you'd automatically create the Node object without knowing if the
underlying names and nodes files are present? I agree with you, that could
be confusing.

Test for the existence of an env that specifies the directory that contains
these indexed files?

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Jason Stajich
Sent: Tuesday, February 03, 2004 4:28 PM
To: Hilmar Lapp
Cc: Bioperl
Subject: Re: [Bioperl-l] Bio::Species / Bio::Taxonomy::Node

We can start making things create Taxonomy::Node objects - I know there
code floating out there which does
if( $sp->isa('Bio::Species') ) { }

so presumably we could make Bio::Species interface s.t. taxonomy::Node
isa Bio::Species...?  I don't want to confuse people either.

There may still be a little more functionality that is needed in the
Taxonomy::Node objects and in the db - specifically how to deal with
some of the methods which are really specific to the species level of
the taxonomy (tips) such as classification/bionomial/ etc methods.

-jason

On Sat, 31 Jan 2004, Hilmar Lapp wrote:

> 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
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
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