[BioPython] Checked in Parsers for Phred and Ace files

[Brad Chapman]

Hi Frank;

> > The one caveat is that the Ace parser does not support RT, CT and WA 
> > tags.

> I couldn't stand a parser that's not completely doing its job,
> especially when it's written by myself :-). So I added supprt for these
> three tags. 

Great -- thanks. It's good to have you looking after, uh, yourself.
Someone's got to do it :-)

> It seems to work fine - however, before I submit it, I'd
> like to be sure that it complies to the specification of the ACE format.
> The consed documentation is not really exact about many things - so does
> anybody know where to find a more comprehensive descripion of the ace
> format? Is there any?

I don't know anything specific, but there is a section in the consed
docs (ACE FILE FORMAT): 

http://www.phrap.org/consed/distributions/README.13.0.txt

There is a brief description of those three tags there and what each
element of the tags stand for. Any more beyond that I personally
have no idea -- I guess if someone has experience working with and
adding these tags they might be able to chime in about how they are
used. 

But independent of that, parsing them into lists of lists or some
other "basic" data structure seems to be a decent enough way to
handle them.

Hope this helps -- thanks again for all the work!
Brad