[BioRuby] GSOC: Bioruby PhyloXML update 12

[Christian Zmasek]

Sounds very good!

________________________________________
From: Diana Jaunzeikare [rozziite at gmail.com]
Sent: Sunday, August 16, 2009 1:09 PM
To: Christian Zmasek
Cc: bioruby at lists.open-bio.org; Pjotr Prins; Naohisa GOTO; Phyloinformatics Group
Subject: Re: GSOC: Bioruby PhyloXML update 12

On Fri, Aug 14, 2009 at 2:52 PM, Christian M Zmasek <czmasek at burnham.org<mailto:czmasek at burnham.org>> wrote:
Hi, Diana:



   * How does integration to the master branch goes? Is all i have to
   do is pull_request on github?

I think so (never done this myself, though). Maybe the git experts can answer this?



   * I have implemented PhyloXML::Sequence#to_biosequence, however it
   returns incomplete data, since info for
   Bio::Sequence#classification, Bio::Sequence#species,
   Bio::Sequence#division would come from PhyloXML::Taxonomy class, but
   it is not accessible from Sequence class. Should there be
   PhyloXML::Node#to_biosequence method which would gather information
   from both PhyloXML::Sequence and PhyloXML::Taxonomy? or maybe
   Bio::Sequence should not hold taxonomic information?

Good point. Personally, I would leave your PhyloXML::Sequence#to_biosequence as it is (and add a warning about this  to the documentation) and, in addition, create PhyloXML::Node#to_biosequence -- although, I would not call it to_biosequence but maybe something like extract_biosequence.
Needless to say, that an almost infinite number of "solutions" to this exists, without a clear "winner" (in my opinion).

Christian


I added PhyloXML::Node#extract_biosequence method. It first calls sequence#to_biosequence and then adds additional information from taxonomy elements.

Diana