[Biopython-dev] Recent Bio.Nexus updates

Peter biopython at maubp.freeserve.co.uk
Fri Jun 27 17:49:53 UTC 2008

Hi Frank,

I see you've got your CVS access working again - good :)

I wanted to ask you about two of your recent changes to Bio/Nexus/Nexus.py

First of all, you've added a new method export_phylip(), which seems
to be a simple function to record the Nexus object's alignment as a
PHYLIP format alignment.  One point of concern is code duplication
(Bio.AlignIO can write PHYLIP files).  Also, you don't seem to be
following the "spec" strictly, as the taxon names are not cropped to
ten characters, nor are any "illegal" characters dealt with.  More
generally, I wonder if this method is really needed - perhaps instead
a general method to return a Bio.Align.Generic.Alignment object would
be preferable.  This could then be used in conjunction with any of the
alignment formats supported in Bio.AlignIO.

Secondly, you seem to have reverted the alphabet change to
Bio/Nexus/Nexus.py made in revision 1.12 to fix Bug 2380.  Was this
deliberate or just accidental?



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