[BioPython] Parsing BLAST for ClustalW

[Allan Kamau]

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/"

Allan.

Alex Garbino wrote:
> Hello,
>
> I'm a new python and biophython user.
> I'm trying to pull a BLAST result, parse it into a csv with the
> following fields:
> protein name, organism, common name, protein length, and FASTA sequence
> The goal is to then feed the fasta sequences into ClustalW (to do a
> phylogeny tree, look for conserved regions, etc).
>
> I've managed to do the blast search, and parse the results into xml
> from python. However, I'm not sure how to grab the above information
> and put it together, so that I can save a csv and push it into
> clustalw.
>
> Could someone help?
>
> Thanks!
> Alex
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