[BioRuby] BioRuby: newick parser

[Pjotr Prins]

Bio::Tree::distance(node1,node2)'s calculating the path distance is
pretty cool :)

http://bioruby.open-bio.org/rdoc/Bio/Pathway.html#method-i-breadth_first_search

  seq7.parent.should == root
  seq4 = tree.find("seq4")
  seq4.distance(seq7).should == 19.387756600000003 

Pj.

On Mon, Mar 12, 2012 at 06:05:26PM +0100, Pjotr Prins wrote:
> OK, this works:
> 
>   @aln.link_tree(@tree)  # @tree contains a parsed Newick tree
>   root = @aln.root # get the root of the tree
>   root.leaf?.should == false
>   children = root.children
>   children.map { |n| n.name }.sort.should == ["","seq7"]
>   seq7 = children.last
>   seq7.name.should == 'seq7'
>   seq7.leaf?.should == true
>   seq7.parent.should == root
> 
> the added functionality for BioRuby's Bio::Tree::Node can be seen here
> 
>   https://github.com/pjotrp/bioruby-alignment/blob/development/lib/bio-alignment/tree.rb
> 
> basically I inject the @tree info into every existing Node object.
> From then on, I can use it to make the interface nicer. A monkey
> patch, indeed.
> 
> Good enough for now.
> 
> Pj.
> 
> On Mon, Mar 12, 2012 at 05:24:38PM +0100, Pjotr Prins wrote:
> > On Mon, Mar 12, 2012 at 03:18:48PM +0900, Naohisa GOTO wrote:
> > > When writing HOWTO based on BioPerl HOWTO:Trees,
> > > (http://bioruby.open-bio.org/wiki/HOWTO:Trees but still incomplete)
> > > I'm thinking to add/modify some API about speficying nodes/edges.
> > 
> > After some trying I agree. The Bio::Tree::Node object should know
> > 'more' about its state. I would like to do something like:
> > 
> >   root.leaf?.should == false
> >   node = root.childeren.first
> >   node.leaf?.should == false
> >   node2 == node.childeren.first
> >   node.leaf?.should == true
> >   node2.edge(node).distance.should == 1.34
> > 
> > now I need to do something like 
> > 
> >   tree = @tree
> >   node = tree.get_node_by_name('node')
> >   tree.get_edge(node, tree.parent(node)).distance.should == 1.34
> > 
> > which uses the tree state to get a node edge, and does not feel that
> > intuitive.
> > 
> > I'll try to extend Bio::Tree for bio-alignment, see what works.
> > 
> > Pj.
> > 
>