[Biopython] saving tree data in phyloXML format
Michael Thon
mike.thon at gmail.com
Mon Oct 11 08:29:14 UTC 2010
I am now reading my trees and creating tree objects. For each clade in the tree I am adding a node_id attribute and one Property object. When I print the tree using:
print tree
I can see the new information that I've added to the tree. When I try to save the tree in phyloXML format, the node_id attribute and the Property object are not serialized. I'm saving the tree like this:
PhyloXMLIO.write(tree, 'mytree.xml')
Basically, what I'm trying to do is decorate the branches in the trees with some additional data (a node_id, branch labels, and a url) , and then render them in a web page, possibly using jsPhyloSVG (http://www.jsphylosvg.com). the examples on that website show <annotation> tags containing <desc> and <uri> tags. I don't see an 'annotation' property in Bio.Phylo.PhyloXML.Clade but I'm hoping that there is some other property that maps to <annotation> when I save the tree in phyloXML format.
TIA
Mike
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