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

Christian Zmasek cmzmasek at yahoo.com
Tue Jul 29 14:09:46 EDT 2008


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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