[Biopython-dev] Code review request for phyloxml branch

[Jaime Huerta Cepas]

Hi,

( I'm the developer of ETE. )
I agree that PyQt4 is an important dependence. I chose it because
Qt4-QGraphicsScene environment offers many possibilities like openGL
rendering, unlimited image size, performance, and good bindings to python.
However, I am working on my code to allow the rendering algorithm to use any
other graphical library. So, you could render the same tree images using
different backends. If you think this is useful for you, please let me know
and we can think how to integrat it with biopython.
Regarding the GUI, it is not a standalone application but one more method
within the Tree objects. The GUI  can be started at any point of the
execution and the main program will continue after you close it. I did it
like this because I think is quite useful for working within interactive
python sessions.

I develop a lot of  code around tree handling, so if you think I can help,
please tell me.
jaime.



>  > *Graphics*
> > I finally fixed the networkx/graphviz/matplotlib drawing to leave
> unlabeled
> > nodes inconspicuous, so the resulting graphic is much cleaner, perhaps
> even
> > usable. Plus, the nodes are now a pretty shade of blue. Still, it would
> be
> > nice to have a Reportlab-based module in Bio.Graphics to print
> phylogenies
> > in the way biologists are used to seeing them. Does anyone know of
> existing
> > code that could be borrowed for this? I looked at ETE (announced on the
> main
> > biopython list last week) and liked the examples, but it uses PyQt4 and a
> > standalone GUI for display, which is a substantial departure from the
> > Biopython way of doing things.
>
> I still haven't tracked down my old report lab code, but it wasn't object
> orientated and would need a lot of work to bring up to standard...
>
>







> Peter
>
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>



-- 
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Jaime Huerta-Cepas, Ph.D.
CRG-Centre for Genomic Regulation
Doctor Aiguader, 88
PRBB Building
08003 Barcelona, Spain
http://www.crg.es/comparative_genomics
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