[Biopython-dev] [Bug 2227] Writing Nexus files with Bio.SeqIO

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2227





------- Comment #9 from fkauff at biologie.uni-kl.de  2008-07-04 05:13 EST -------
(In reply to comment #5)
> Created an attachment (id=966)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=966&action=view) [details]
> Patch to Bio/AlignIO/NexusIO.py adding write support
> 
> This patch requires the Bio.Nexus handle fix (patch in attachment 965 [details], comment
> 4).
> 
> My method for constructing an empty DNA, RNA, or Protein Nexus object is
> perhaps inelegant.  This is required in order to setup the alphabet,
> ambiguous_values and unambiguous_letters properties which otherwise default to
> DNA.
> 
> Also note that the Nexus add_sequence() method does not seem to support
> duplicated taxa names.  Perhaps this method could update the
> unaltered_taxlabels property and use the _unique_label method to cope with
> duplicate names?
> 
Ok, I updated add_sequence and will commit the changes soon.

F


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