[BioRuby] GSOC: Bioruby PhyloXML update 12

[Diana Jaunzeikare]

On Fri, Aug 14, 2009 at 2:52 PM, Christian M Zmasek <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