[Bioperl-l] Re: Bio::Tools::Phylo::PAML::Codeml

[Aaron J Mackey]

On Tue, 18 Jun 2002, Jason Stajich wrote:

> <<Aaron showing that [he] does like some aspects of the OO in bioperl?>>

Well, if it's there it should be used, or abused.  I'm willing to play the
game, if it's already started ;)

> I'm a little confused because I use factory and parser interchangeably at
> times even though I shouldn't.

Well if you're confused, then I'm in trouble.

> Would we be able to build a single parser which can process output
> from all the different PAML programs?  Or should we be building a
> SeqIO/SearchIO style where each program has an associated parser but
> they end up being part of the same factory system (there I go again)
> called something like Bio::Tools::Phylo::PAML ?

I think it's like SearchIO::fasta.pm - you have to be able to handle a few
different flavors of output, with slightly different semantics, but
overall you're describing the same analytical process.  So I don't think
we need an IO system (since I don't see any O, just I in this case),
there's only one PAML; perhaps we should rename
Tools::Phylo::PAML::Codeml.pm to just Tools::Phylo::PAML.pm ???

> Are the result objects suitable usable by anything else that they
> should be moved out of the Tools directory and into a MolEvo/Phylo
> namespace (overkill I think)?

No, I'd think they'd be PAML::Result objects (themselves
Bio::AnalysisResultI objects).  It's not clear to me what a next_feature()
method would return (in runmode = -2 a pairwise kind of
Bio::SeqFeature::** could be made, I guess).

> Additionally would all the data from the output from the different
> programs fit nicely into a single type of Result object or will we need
> different objects for different output b/c there are different classes of
> data?

I think the classes of data I described previously remain the same between
baseml, codeml/codemlsites (additional codon-usage data) and yn00 (with
yn00 having only a subset of the data classes).  We're not talking about
evolver or mcmc or any other PAML program, at least not right now.

-Aaron