[Biopython-dev] Recent Bio.Nexus updates

Frank Kauff fkauff at biologie.uni-kl.de
Mon Jun 30 08:34:30 UTC 2008

Hi Peter and Michiel,

Peter wrote:
> 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.  
True - I ignored this delibaretely. I think except for old PHYLIP 
itself, all software I know handles longer taxon names by default. The 
format I used here is sometimes refered to as "relaxed phylip" but as it 
has become the standard for what people call phylip formt, so I just 
kept it this way.

> 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.
That is a possibility. I would then vouch for adding support for 
"relaxed phylip" to AlignIO.PhylipIO (which I could easily do with a 
little mofification of Nexus.export_phylip() myself)
> 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?
> http://bugzilla.open-bio.org/show_bug.cgi?id=2380
Sorry for that. I missed that bug. Thaks for re-fixing it.

> Thanks,
> Peter

J-Prof. Dr. Frank Kauff
Molecular Phylogenetics
FB Biologie, 13/276
TU Kaiserslautern
Postfach 3049
67653 Kaiserslautern

Tel. +49 (0)631 205-2562
Fax. +49 (0)631 205-2998
email: fkauff at biologie.uni-kl.de
skype: frank.kauff

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