[Biopython-dev] [Bug 2543] Bio.Nexus.Trees can't handle named ancestors

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2543


fkauff at biologie.uni-kl.de changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|ASSIGNED                    |RESOLVED
         Resolution|                            |FIXED




------- Comment #6 from fkauff at biologie.uni-kl.de  2008-10-07 04:03 EST -------
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, such as

(a,(b,(c,d)[&hi there]))
(a,(b[&hi there],c))
(a,(b:0.123[&hi there],c[&heyho]:0.3))
(a,(b,c)0.4[&comment]:0.95)

The comments are stored without change in the corresponding node object and can
be accessed like

>>> t=Trees.Tree('(a,(b:0.123[&hi there],c[&heyho]:0.3))')
>>> print t.node(3).data.comment
[&hi there]
>>> print t.node(4).data.comment
[&heyho]
>>>

The comments are not parsed in any way - internal labels vary greatly in
syntax, and are used to store all kinds of information. But at least they are
now read and stored, and users can deal with them the way they like.

Frank


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