[BioRuby] CodeML wrapper for BioRuby

[Naohisa GOTO]

Thank you.

I think PAML programs other than codeml are also valuale
to write wrappers, especially for baseml and yn00.

In BioPerl, there are four PAML program wrappers.
(baseml, codeml, evolver, yn00)
http://code.open-bio.org/svnweb/index.cgi/bioperl/browse/bioperl-run/trunk/Bio/Tools/Run/Phylo/PAML

So, I decide to move the codeml classes under Bio::PAML.  

I renamed Bio::CodeML to Bio::PAML::Codeml. Files are moved
to bio/appl/paml/ and test/unit/bio/appl/paml/.

The reason why I changed CodeML to Codeml is that
it seems that authors of PAML do not use the word "codeML"
(the last two letters are uppercase). Indeed, I can't find
the word "codeML" (or "CodeML") in the PAML's documents.


Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org


On Sat, 16 Aug 2008 18:22:18 +0200
pjotr2008 at thebird.nl (Pjotr Prins) wrote:

> codeml is, by far, the most valuable tool.
> 
> Pj.
> 
> On Sat, Aug 16, 2008 at 05:45:21PM +0900, Naohisa GOTO wrote:
> > Hi Mike,
> > 
> > The CodeML wrappers is now included in bioruby git.
> > http://github.com/bioruby/bioruby/tree/master
> > 
> > As PAML has some executables other than codeml,
> > (baseml, basemlg, chi2, evolver, mcmctree, pamp, yn00)
> > I plan to move Bio::CodeML to Bio::PAML::CodeML, and
> > files are moved from bio/appl/codeml to bio/appl/paml/codeml.
> > 
> > Is it OK? (or, is codeml the only valuable component to write
> > wrapper/parser for bioruby?)
> > 
> > Do you (or someone) plan to write other PAML's wrappers/parsers?
> > 
> > Thanks,
> > 
> > Naohisa Goto
> > ngoto at bioruby.org / ng at bioruby.org
> > 
> > 
> > On Fri, 15 Aug 2008 20:15:09 +0900
> > Naohisa GOTO <ngoto at gen-info.osaka-u.ac.jp> wrote:
> > 
> > > Hi, 
> > > 
> > > It seems good. It will be included in BioRuby.
> > > 
> > > In my machine, a test was failed.
> > > Can you fix the problem?
> > (snip)
> > >
> > > On Wed, 13 Aug 2008 16:34:20 +0100
> > > "Michael Barton" <mail at michaelbarton.me.uk> wrote:
> > > 
> > > > Hi,
> > > > 
> > > > CodeML is a common tool for estimating evolutionary rate of protein encoding
> > > > sequences, and is part of the PAML package. I've created a codeml wrapper
> > > > and two parsers. Unit tests are also included. The code is in a Github fork
> > > > in BioRuby. The fork is located here
> > > > 
> > > > http://github.com/michaelbarton/bioruby/tree/master
> > > > 
> > > > I like to suggested that it for inclusion in the main BioRuby branch.
> > > > 
> > > > Thanks
> > > > 
> > > > Mike
> > > > _______________________________________________