[Biopython-dev] [Bug 2788] Bio.Nexus.Trees newick parser crash
bugzilla-daemon at portal.open-bio.org
bugzilla-daemon at portal.open-bio.org
Thu Mar 12 10:17:01 UTC 2009
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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