[Biopython-dev] Martel-0.35

[Brad Chapman]

Andrew:
> Okay, over the weekend I ended up not doing the work I was paid for
> and instead worked on Martel.  

Join the club :-). Seriously, thanks for this -- the new version looks 
great!

>   Migrated to Python 2.0 and its xml package.  No longer runs under
>   older (1.x) Pythons.

Thanks for catching all of the changes I missed for 2.0 support. 
This new version flushed out some errors I made in my Clustalw parser 
(changes are committed to CVS).

>   Experimental Iterator support ("make_iterator") as an alternate for
>   the pure SAX callback method.

I had a chance to play with this a little, and seem to be grokking
things a lot better. I modified my Martel based Fasta.py parser to
use an iterator, so it now acts a little more like the biopython 
Fasta parser and only reads one record if a file is passed to it.

Looks nice, although I definately need to play with it a lot more.

> For people like Brad who are learning how to use Martel, try
> "expression.make_parser(debug_level = 1)" or debug_level = 2.  That
> really helps pin down where an error is likely located.

This is a really nice feature. Thanks, this'll be a big help.

BTW, I took a minute to distutilize Martel (takes about as long as
copying everything to site-packages :-), which I guess we'll need
to do anyways to include it in the next release. I put everything into 
a Martel top level package, and install it like that. Anyways, do you
want this? 

Thanks again for the new release.

Brad