[Biopython-dev] [Bug 3134] New: to_networkx returns weird stuff

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=3134

           Summary: to_networkx returns weird stuff
           Product: Biopython
           Version: 1.55b
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: john at nurfuerspam.de


Hi,

I tried to read 
http://www.phylosoft.org/archaeopteryx/examples/data/multiple_supports.xml 
and convert it using to_networkx(). Strangely, all nodes in the resulting graph
are named Clade, and when using networkx.write_dot() I get a file with a single
clade node, although the number of nodes in the graph object is correct. Also
using networkx.to_agraph() does not help.

tree = Phylo.read("multiple_support.xml", "phyloxml")
tree = Phylo.to_networkx(tree)
print set(tree.nodes())
print tree.number_of_nodes()
networkx.write_dot(tree, "test.dot")
tree = networkx.to_agraph(tree)
tree.draw("tree.pdf", prog = "dot")


For http://www.phylosoft.org/archaeopteryx/examples/data/bcl_2.xml I get a star
tree with a single Clade node in the center and leafs labeled by gene names.


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