[BioRuby] [Wg-phyloinformatics] Update on phyloXML support for BioRubyproject

[Diana Jaunzeikare]

Both nexml and phyloxml are xml formats for holding information about
phylogenetic trees. Both seem to be fairly new. What's the difference? Isn't
there an ultimate goal to have one universal format for phylogenetic data
exchnage? If yes, which of these two formats would be better suitable for
it, or do they serve different purposes (as nexml is based on NEXUS format)?



My other question is about Perl phylogenetics related packages (warning: Iam
not familiar at all with BioPerl classes). Bio::TreeIO and Bio::Phylo::IO
for me seem to be doing the same task. What are the main differences between
them? If there are no fundamental differences, why there are two classes
which do the same thing.

Diana


On Wed, May 20, 2009 at 11:13 AM, Mark A. Jensen <maj at fortinbras.us> wrote:

> Should I plug my "web service blog":
>
> https://www.nescent.org/wg_evoinfo/User_talk:Mjensen#.22Streaming.22_NeXML.3F?
> Some possible useful ideas there. I've also written a flexible DOM
> implementation for Bio::Phylo, that could be
> generalized/cannibalized/stolen and
> used for iterating/streaming XML formats. It provides a standard interface
> for
> writing dom elements, but allows for easily swapping in different XML
> handling
> packages (in a BioPerly '-format => libxml' way). All in Perl I'm afraid
> (or
> proud?) to say, but it might provide ideas too. (I sent it to Rutger, but
> he
> hasn't passed judgment yet, so it's currently available 'by request to the
> author'.)
> cheers; excellent work Diana- MAJ
>
> ----- Original Message -----
> From: "Chris Fields" <cjfields at illinois.edu>
> To: "Hilmar Lapp" <hlapp at duke.edu>
> Cc: <bioruby at lists.open-bio.org>; "Phyloinformatics Group"
> <Wg-phyloinformatics at nescent.org>
> Sent: Wednesday, May 20, 2009 10:52 AM
> Subject: Re: [Wg-phyloinformatics] Update on phyloXML support for
> BioRubyproject
>
>
> >
> > On May 20, 2009, at 8:22 AM, Hilmar Lapp wrote:
> >
> >>
> >> On May 19, 2009, at 5:54 PM, Christian M Zmasek wrote:
> >>
> >>> I think it is perfectly acceptable to expect to have enough memory
> >>> to keep at least
> >>> one tree in memory
> >>
> >> Sounds like a good and perfectly reasonable starting point to me too.
> >> It's also the way other toolkits (such as BioPerl) work.
> >>
> >> Having said that, I don't find it inconceivable that we may be working
> >> with trees in the near future that don't fit into memory for a 1GB RAM
> >> machine if they are richly decorated (which is something that phyloXML
> >> wants to enable, isn't it?). Solving that to me though seems to be
> >> question of writing an appropriate Tree implementation that happens to
> >> store most of the data on disk rather than in memory, and not an issue
> >> for how to write a parser. Ideally though, the parser uses a factory
> >> for creating the (tree and/or node) objects, so that later it can be
> >> made to use an on-disk Tree implementation simply by passing it
> >> another factory. I.e., ideally the parser would not assume and hard-
> >> code the Tree implementation class.
> >>
> >> Just my $0.02.
> >>
> >> -hilmar
> >
> > This could be implemented in a lazy way or using lightweight objects.
> > The Tree object itself contains the XML parser or a reference thereof
> > (probably LibXML Reader-based) and creates the relevant nodes as
> > needed.  The only thing needed would be some light parsing to indicate
> > start-end file points.
> >
> > It's tricky with re: to a number of aspects, but it can be done.  For
> > instance, if one wanted to modify the created nodes (i.e. if the nodes
> > are mutable), or creating a generic Lazy set of classes capable of
> > dealing with multiple formats.
> >
> > Just in case anyone's wondering, I have been thinking along these
> > lines for a while re: BioPerl, Bio::Seq, and very large files... ;>
> >
> > chris
> > _______________________________________________
> > Wg-phyloinformatics mailing list
> > Wg-phyloinformatics at nescent.org
> > https://lists.nescent.org/mailman/listinfo/wg-phyloinformatics
> >
> >
>
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