[Bioperl-l] Phyloxml <alignment> - made-up 'align' xml-language 2

aaron.j.mackey at gsk.com aaron.j.mackey at gsk.com
Tue Jul 29 15:05:30 EDT 2008


Although it would be nicer to not ignore those blocks, but stuff them 
(verbatim) into a tag/annotation of the enclosing element.  This would 
provide round-tripping, and would also allow further processing of the 
tree objects to "unpack" those blocks foreign to phyloxml, but possibly 
quite relevant to the problem at hand.

-Aaron

bioperl-l-bounces at lists.open-bio.org wrote on 07/29/2008 02:09:46 PM:

> I forgot: What the parser should do if it encounters data from other
> namespaces (or simply unknown (new?) phyloxml elements) is to simply
> ignore them, without breaking.
> 
> 
> 
> 
> ----- Original Message ----
> From: Christian Zmasek <cmzmasek at yahoo.com>
> To: Jason Stajich <jason at bioperl.org>; "Han, Mira" <mirhan at indiana.edu>
> Cc: bioperl list <bioperl-l at lists.open-bio.org>
> Sent: Tuesday, July 29, 2008 11:07:24 AM
> Subject: Re: [Bioperl-l] Phyloxml <alignment> - made-up 'align' 
xml-language
> 
> Hi, Mira:
> 
> I am so sorry for being not more clear in my examples.
> The "<align:alignment></align:alignment>" data was intended as an 
> example of how xml data from other namespaces  (in this case 
> "align") could reside inside phyloxml documents.
> There is absolutely no need to parse and store these data from other
> namespaces/xml-languages by your parser/objects.
> 
> Christian
> 
> PS: To be clear "align", is the name of a _fictional_ xml language 
> which looks like it can store alignments.
> 
> 
> 
> 
> 
> ----- Original Message ----
> From: Jason Stajich <jason at bioperl.org>
> To: "Han, Mira" <mirhan at indiana.edu>
> Cc: bioperl list <bioperl-l at lists.open-bio.org>; Christian Zmasek 
> <cmzmasek at yahoo.com>
> Sent: Tuesday, July 29, 2008 9:45:06 AM
> Subject: Re: [Bioperl-l] Phyloxml <alignment>
> 
> Mira -
> 
> I've not thought too clearly about how this should go, certainly 
> Bio::AlignIO should be reused for the parsing aspect, although I'm 
> not clear what format the alignment is in?
> 
> At some point this is might need to be unified with the NEXUS-type 
> objects that the Bio::NEXUS group has worked on.  We may have to work 
> with them to define the proper object here that holds both tree and 
> alignment data and allows slicing out either from the object.
> 
> So a super-object is probably going to have to be created to marshall 
> out the trees and alignment data.  I didn't realize the spec was 
> going as far as to encapsulate all of the alignment data as well.  We 
> may need to think about whether we can support all of the aspects of 
> the spec at this time as well.
> 
> I hope other people have input here as well.
> 
> -jason
> 
> On Jul 29, 2008, at 9:20 AM, Han, Mira wrote:
> 
> >
> > Hi,
> > Sorry for bombarding the list
> > Thought this would be better on a separate thread.
> > Phyloxml documents have <phylogeny></phylogeny>s.
> > But also <align:alignment></align:alignment>s.
> > What would be the standard approach for parsing,
> > I guess TreeIO->next_tree
> > shouldn't take care of the alignments.
> > Would I need to make a AlignIO->next_aln for the phyloxml document 
> > as well?
> >
> > Mira
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
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