[BioRuby] BioRuby: newick parser
Pjotr Prins
pjotr.public14 at thebird.nl
Mon Mar 12 16:24:38 UTC 2012
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.
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