[BioPython] Parsing BLAST for ClustalW

[Bruce Southey]

Allan Kamau wrote:
> Hi Alex,
> I haven't yet used BioPython (therefore my suggestion may be quite 
> wrong).
> To generate CSV from XML may require use of general XML SAX parser 
> solution (unless BioPython has a package to output CSV from XML of 
> that particular structure).
> I prefer to use SAX (in many cases) as opposed to other more memory 
> resident XML parsing solutions (DOM etc) due to memory issues 
> especially if your XML is large.
> Have a look at 
> "http://www.devarticles.com/c/a/XML/Parsing-XML-with-SAX-and-Python/"
>
Note that the Elementtree XML parser is now standard in Python 2.5 see 
one of many examples: 
http://www.learningpython.com/2008/05/07/elegant-xml-parsing-using-the-elementtree-module/

As I understand things, elementtree does not fit into BioPython since it 
was not standard for earlier versions of Python supported by BioPython. 
This may change once BioPython supports Python 3K.

Bruce