[bip] Mailing list for PyCogent?

[Peter]

On Thu, May 14, 2009 at 5:53 PM, Mark Fenner <mfenner at gmail.com> wrote:
>
> Hi folks,
>
> Just checking to see if you know of a mailing list for PyCogent or of
> a way to contact the developers.
>
> Should a pycogent developer see this, I have a few ideas/questions:
>
> (1) use epydoc to generate api/source code documentation, to ease
> "poking through" the source code.  very easy, _very_ useful

I'd second that - we use epydoc on Biopython, mostly with the
(default?) plaintext markup.  This is easy, it looks fine and is useful.

> (2) supposing I wanted to add an "app" class for some applications
> (some phylip programs and quicktree), where's the best place to start?
>  from other app files? Do any deal with the menu type system that
> phylip programs use?

I can't comment on pycogent, but regarding PHYLIP, if you want to
script it I would ignore the "official" package with its menu system,
and instead use the EMBOSS versions with have proper command
line switches (part of their EMBASSY suite):
http://emboss.sourceforge.net/apps/release/6.0/embassy/phylipnew/

> (3) quicktree does neighbor joining on a 4500 protein family in about
> 3 minutes .... the version in pycogent, by estimates, is going to take
> 48 hours to do the distance estimation before even getting to the
> neighbor joining portion.  Any thoughts?  Is quicktree taking short
> cuts?  There must be low hanging fruit optimizations in PyCogent's
> EstimateDistances.  I'll look myself, but I'm also looking for some
> discussion.

I can't comment on pycogent, but if you think quicktree is fast, provided
you have enough memory, quickjoin could be even faster.  See:
http://www.daimi.au.dk/~mailund/quick-join.html

Peter