[Bioperl-l] Bio::*Taxonomy* changes

[Chris Fields]

Look, you explaining this to me, as you see it, does not convince me  
that its the correct or right way to do it.  Okay?  Can we agree on  
that?  I do not think that Species and Taxonomy are the same thing.   
A species should not hold more than one node.  A species, by  
definition, is a rank in Taxonomy, and is a node, not a full  
Taxonomy, so Bio::Species should be a Node, not a Taxonomy.  I don't  
see how I can be any clearer...

The fact that it may work is beyond the point.  That's like putting  
duct tape on a leak to me.  Why not just simplify Bio::Species into a  
Node?  Or make it into a Node and get rid of it altogether.

You are going to do what you want to do, regardless of what I say.   
Seems to be par for the course here.  I'm REALLY tired of arguing the  
point.  Okay?  Just drop it.  I have other priorities in life besides  
goddamned bioperl right now...

Chris

On Jul 25, 2006, at 2:05 AM, Sendu Bala wrote:

> Chris Fields wrote:
>>
>> There is one thing I will make perfectly clear here: there should
>> never, ever be enforced lookups for SeqIO (even using caches), though
>> I have no problem having optional ones.  This is something I have
>> stated before and what you propose below steers dangerously in that
>> direction.  Where, for instance, do you store the lineage from a
>> GenBank file?  Do you want to do a series of Tax lookups to restore
>> that data?  I think that the number one complaint for sequence
>> parsing is speed, which would only get slower with lookups (even
>> cached).
>
> I already gave a code example of exactly how Bio::Taxonomy is perfect
> for storing the lineage data in a GenBank file with or without a
> database lookup. I think perhaps at the time you first read this you
> basically ignored it because you had trouble with the idea of adding
> nodes to a species. If you have been glossing over my argument, it may
> be instructive to go over what I've been saying with a clear eye.
> Anyway, here it is again, and remember in this example,  
> Bio::Species isa
> Bio::Taxonomy:
>
>
> ## the fully-manual way
> my $species = new Bio::Species;
> my $node = new Bio::Taxonomy::Node(-name => 'Saccharomyces  
> cerevisiae',
>                                     -rank => 'species', -object_id  
> => 1,
>                                     -parent_id => 2);
> my $n2 = new Bio::Taxonomy::Node(-name => 'Saccharomyces',
>                                   -object_id => 2, -parent_id => 3);
> # (no assumption that 'Saccharomyces' is the genus, so rank()  
> undefined)
> my $n3 = [etc]
> $species->add_node($node);
> $species->add_node($n2);
> [etc]
>
> ## Using a factory without db access
> # assume that Bio::Taxonomy::GenbankFactory implements
> # some modified Bio::Taxonomy::FactoryI
> my $factory = Bio::Taxonomy::GenbankFactory->new();
> my $species = $factory->generate(-classification => ['Saccharomyces
>               cerevisiae', 'Saccharomyces',  
> 'Saccharomycetaceae' ...]);
> # the generate() method above just does the fully-manual way for you
>
> ## Using a factory with db access
> # assume that Bio::Taxonomy::EntrezFactory implements some
> # modified Bio::Taxonomy::FactoryI and uses Bio::DB::Taxonomy::entrez
> # to get the nodes
> my $factory = Bio::Taxonomy::EntrezFactory->new();
> my $species = $factory->fetch(-scientifc_name => 'Saccharomyces
>                                                     cerevisiae');
>
>
> So now do you see how we're able to do the Genbank no-db way and the
> db-using way with the same object model? We're able to do it the same,
> sane way because a Node is just a node; you can make them yourself
> manually, or retrieve them from a database. Once you stick them in a
> Taxonomy you can then (potentially) ask all the questions of the data
> that you can with existing Bio::Species. No cruft is required anywhere
> at all. All the Taxonomy classes can be 'pure', while only  
> Bio::Species
> has to have backward-compatibility methods.
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign