[BioRuby] Bioruby PhyloXML update

[Diana Jaunzeikare]

Hi all!

Here is what was done during community bonding period:

   - subscribed to mailing lists
   - created a blog <http://latvianlinuxgirl.blogspot.com/>
   - got familiar with Git (this was particularly useful:
   http://www.gitcasts.com/posts/railsconf-git-talk )
   - created GitHub account and forked bioruby project.
   - made first commit by adding sample phyloxml data files from
   www.phyloxml.org
   - reviewed BioPerl phyloXML implementation (also
   http://www.bioperl.org/wiki/HOWTO:Trees )
   - got familiar with libxml-ruby. Wrote simple program using both
   LibXML::XML::Reader and LibXML::XML::SAXParser to parse a simple xml file.
   - reviewed Ruby classes - Bio:Tree, Bio::Pathways
   - After discussions in mailing lists it has been agreed to use
   LibXML-ruby library, the LibXML::XML::Reader class


This weeks plan:

   - Start writing parser using LibXML::XML::Reader. It should return a
   Bio::Tree object.
   - Implement function next_tree to parse and return the next phylogeny.
   - Design Tree::Node object for containing phyloxml elements.
   - Start mapping phyloxml elements to Bio::Tree::Node, start with
   taxonomy, branch_length, scientific_name
   - Write simple unit tests.


Diana

Project page:
https://www.nescent.org/wg_phyloinformatics/PhyloSoC:PhyloXML_support_in_BioRuby