[BioRuby] BioRuby Digest, Vol 50, Issue 6

Tue Nov 17 05:40:31 UTC 2009

If Ruby itself is known to be slow compared to other interpreters, and
Diana;s code speeds up things, as a Bioruby user i would plead with the
developers to adopt her code in the next release with the speed
optimizations. The next release can only be better if the current code base
is overhauled and reviewed based on new developments like Diana's.

If Newick can be converted to a format which can then be converted to
PhyloXML, then conversion to newick is not a problem. Else I would question
the use of Newick format if it cannot be inter-converted to other file
formats.

On Mon, Nov 16, 2009 at 8:00 PM, <bioruby-request at lists.open-bio.org> wrote:

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> Today's Topics:
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>   1. Re: BioRuby Phyloxml update (Jan Aerts)
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>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 16 Nov 2009 10:11:24 +0000
> From: Jan Aerts <jan.aerts at gmail.com>
> Subject: Re: [BioRuby] BioRuby Phyloxml update
> To: Naohisa Goto <ngoto at gen-info.osaka-u.ac.jp>
> Cc: phyloxml at yahoogroups.com, Pjotr Prins <pjotr2009 at thebird.nl>,
>        bioruby at lists.open-bio.org, Diana Jaunzeikare <djaunzei at smith.edu>
> Message-ID:
>        <4c7507a70911160211v417fd748u4bf2dd5f2f14c4c9 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> All,
>
> I think we should make a good effort of merging Diana's code into the
> bioruby codebase. Even though I'm not completely familiar with
> bioruby's phylo implementation, an effort like hers should be welcomed
> with open arms.
>
> If her code speeds things up so immensely, why don't we start a new
> branch that will lead to bioruby 2.0? Let bioruby 2.0 break things.
> With a major new release things are allowed to be broken free from the
> legacy code.
>
> We definitely don't want Diana's efforts be in vain.
>
> jan.
>
> 2009/11/8 Naohisa Goto <ngoto at gen-info.osaka-u.ac.jp>:
> > Hi Diana,
> >
> > I'm sorry that the changes cannot be accepted, because the
> > modification of existing Bio::Tree methods breaks things.
> > Bio::Tree does not want to have children/parent information
> > in nodes. One of the reasons is that it is difficult to keep
> > consistency when copying a tree. Nodes can be shared with two
> > or more trees when copying a tree by using "dup" or "clone"
> > method.
> >
> > Normally, tests for existing classes shold not be modified
> > except when changing specification or the test's bug, because
> > they guarantee specification of the class. Adding new tests
> > are OK.
> >
> > If you really want nodes to have parent/children information
> > in each node, please do so in only PhyloXML classes (though
> > I'm negative). ?In this case, the problem is that reading phyloxml
> > data and write back again seems good, but it seems there are
> > currently no way to convert Bio::Tree to PhyloXML. Now, it seems
> > hard to convert Newick data to PhyloXML.
> >
> > Now, to prepare to include your PhyloXML code in BioRuby, I'm working
> > on my branch. Some API changes will be made.
> > http://github.com/ngoto/bioruby/tree/incoming
> >
> > Note that in your test code, argument order of assert_equal is wrong.
> > I've already fixed in my branch.
> >
> http://github.com/ngoto/bioruby/commit/a291af62ef262ee04f3a0e1b6415d4e256c56a94
> >
> >> * Updated ?Tree::add_edge, Tree::clear_edge, Tree::remove_edge,
> >> Tree::remove_edge_if, Tree:remove_nonsense_nodes in order to keep
> >> track of Node::parent and Node::children nodes correctly. ?Have I
> >> forgotten anything?
> >
> > Changing root with tree.root=().
> >
> > --
> > Naohisa Goto
> > ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
> >
> >
> >> Hi all,
> >>
> >> So finally I have updated Bio::Tree and Bio::Node classes to improve
> >> the phyloxml writer speed.
> >>
> >> * Added Bio::Node::parent and ?Bio::Node::children (array of nodes) in
> >> order to avoid calling Tree::parent(node) or Tree::children(node),
> >> because those methods call breath first search on the underlying
> >> graph, which makes PhyloXML writer and parser incredibly slow. In
> >> contrast, Bio::Node::parent and Bio::Node::children keeps references
> >> to the respective nodes.
> >> * Updated ?Tree::add_edge, Tree::clear_edge, Tree::remove_edge,
> >> Tree::remove_edge_if, Tree:remove_nonsense_nodes in order to keep
> >> track of Node::parent and Node::children nodes correctly. ?Have I
> >> forgotten anything?
> >> * Now for PhyloXML writer it takes less than 1 second instead of
> >> ~20minutes to write ncbi_taxonomy_mollusca.xml file 1.5MB
> >> * To write the tree of life taxonomy file (~46MB) it takes 10 seconds
> >> (On 2.4GHz, 2.9GB RAM, running Ubuntu)
> >>
> >> The code is in
> http://github.com/latvianlinuxgirl/bioruby/tree/tree_class
> >>
> >> I wrote unit tests for my changes and made sure my changes don't break
> >> anything else. However, does anybody has code laying around that uses
> >> Tree::parent and Tree::children methods so that I can test it more
> >> thoroughly?
> >>
> >> Cheers,
> >> Diana
> >> _______________________________________________
> >> BioRuby mailing list
> >> BioRuby at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioruby
> >
> > _______________________________________________
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> >
>
>
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> End of BioRuby Digest, Vol 50, Issue 6
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-- 
---------------
Sincerely
George

Skype: george_g2
Blog: http://biorelated.wordpress.com/