[BioPython] plain txt blast output - xml instead

[Michiel Jan Laurens de Hoon]

Peter wrote:
> According to the XML file, it is from BLASTP 2.2.14 [May-07-2006], maybe 
> they changed the XML format without telling anyone?
> 
It appears that the XML format did change.
With Blastp 2.2.14, multiple searches generate multiple 
<Iteration>...</Iteration> blocks, one for each search.
With an older Blastp, multiple searches effectively generate multiple 
XML files (each with one <Iteration>...</Iteration> block). These files 
are then concatenated into one output file. Biopython then parses this 
file by looking for the beginning of each XML file in this output file.

The new output is in a sense better because the output file is a valid 
XML file. It may be that Biopython's XML parser ignores the <Iteration> 
tags, since in the old format there was only one <Iteration> block 
anyway, and therefore fails with the new format.

--Michiel.

-- 
Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1130 St Nicholas Avenue
New York, NY 10032