[Biopython-dev] [Bug 2788] Bio.Nexus.Trees newick parser crash

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2788





------- Comment #1 from cymon.cox at gmail.com  2009-03-12 06:17 EST -------
(In reply to comment #0)
> The newick files I have been working with seem to open fine in several
> different programs/packages (Dendroscope, R's APE package, phylocom, python
> alfacinha module), but not the newick parser in Bio.Nexus.Trees.

[a big tree]

> tree_obj = Tree(tree_str)
> 
> print tree_obj
> ============
> 
> 
> This brings up the follow error for "tree_obj = Tree(tree_str)": 
> ========
> ValueError: invalid literal for float(): seedplant
> ========
> 
> It looks like it is looking for a floating point number where "seedplant" is.

Your tree is decorated with node labels, which the parser cannot handle.

This came up recently (within the last year?) but I can't find the bug/message.

Should probably catch this and return an informative error - or implement node
labels...

C.


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