[BioRuby] CodeML wrapper for BioRuby

[Naohisa GOTO]

Hi,

The changes are now included in bioruby git repository.
http://github.com/bioruby/bioruby/commits/master

Thanks for improvement.

In addition, changes for Blast classes made by me
(already appeared in github.com/ngoto/bioruby) are
also included now.

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

On Tue, 19 Aug 2008 14:52:43 +0100
"Michael Barton" <mail at michaelbarton.me.uk> wrote:

> Hi,
> 
> I've updated the Bio::PAML::Codeml::Rates class to pasrse columns with the
> '*', which indicate gaps in the alignment. For instance MM*M means that
> there is a gap in the alignment in the third sequence.
> 
> The changes are in my branch of bioruby.
> 
> Thanks
> 
> Mike
> 
> On Mon, Aug 18, 2008 at 7:18 AM, Naohisa GOTO
> <ngoto at gen-info.osaka-u.ac.jp>wrote:
> 
> > 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
> > > > > > _______________________________________________
> > _______________________________________________
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
> >
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