[BioRuby] Bioruby PhyloXML update
Diana Jaunzeikare
rozziite at gmail.com
Tue May 26 12:17:24 UTC 2009
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
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