[BioPython] Updates to CVS -- please do test

[Brad Chapman]

Hi Andy;
Thanks for checking out the changes in CVS.

> I tried running my fasta indexing script which normally works 
> and got the following error
[...]
> ImportError: No module named bsddb3
> 
> Do I need to install something? I did a check out of cvs and 
> installed it..

It's complaining about not having the bsddb3 module -- which are
bindings to BerkeleyDB.

After some reflection and digging around, I'm realizing that I made
a mistake in making the Berkeley indexing the default -- although
bsddb is included with Python, it seems like it will not be built on
a lot of platforms. Sounds like more trouble then it solves.

So, I've adjusted the scripts to use the Flat file indexing by
default, with an option for BerkeleyDB indexing if you want to do it
that way. Introducing new required dependencies is bad.

So, I've just fixed the index_file function in CVS -- please try out
the new version and let me know if it gives you any problems (it
also requires a fix to Bio/Mindy which is also checked in). Thanks
again for testing things out -- I'm very happy to have people
looking at this.

Brad