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

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





------- Comment #5 from biopython-bugzilla at maubp.freeserve.co.uk  2008-07-03 12:02 EST -------
Created an attachment (id=966)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=966&action=view)
Patch to Bio/AlignIO/NexusIO.py adding write support

This patch requires the Bio.Nexus handle fix (patch in attachment 965, 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?


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