[Biopython-dev] [Bug 2788] Bio.Nexus.Trees newick parser does not support internal node labels

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

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


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
           Severity|normal                      |enhancement
         OS/Version|Mac OS                      |All
           Platform|Macintosh                   |All
            Summary|Bio.Nexus.Trees newick      |Bio.Nexus.Trees newick
                   |parser crash                |parser does not support
                   |                            |internal node labels




------- Comment #2 from biopython-bugzilla at maubp.freeserve.co.uk  2009-03-12 06:38 EST -------
I thought it looked familiar, but I must have only searched the currently open
bugs.  This looks *very* similar to Bug 2543 which dealt with internal node
names, which was fixed for Biopython 1.49 (and 1.49 beta).

Frank wrote:
> Nexus.Trees has been extended to deal with internal node names, or "special
> comments" in the format [& blablalba]. Such comments comments can appear
> directly after the taxon label, after the closing parentheses, or between
> branchlength / support values attached to a node or a taxon labels, ...

i.e. On Bug 2543, Frank didn't go as far as the enhancement to cope with
"naked" node labels, just those in the square brackets.

Consider this smaller example Cymon gave on Bug 2543:

>>> from Bio.Nexus.Trees import Tree
>>> tree_str2 = "(((t9:0.385832, (t8:0.445135,t4:0.41401)C:0.024032)B:0.041436, t6:0.392496)A:0.0291131, t2:0.497673, ((t0:0.301171, t7:0.482152)E:0.0268148, ((t5:0.0984167,t3:0.488578)G:0.0349662, t1:0.130208)F:0.0318288)D:0.0273876);"
>>> tree_obj = Tree(tree_str2)
Traceback (most recent call last):
...
ValueError: invalid literal for float(): A


I've retitled this and marked it as an enhancement.


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