[Biopython-dev] Blast

[Michiel De Hoon]

Hi everybody,

Recently there have been some problems with the Blast parser in Biopython, to
the degree that the example in 3.1.2 in the tutorial does not work as
advertised. The problem, of course, is that the NCBI file format as returned
by a www blast run keeps changing, so we are condemned to keep fixing our
parser to keep up with NCBI.
To my surprise, the parser in Blast.NCBIWWW tries to parse HTML output
instead of text output. My guess is that the HTML output changes more often
and is more difficult to parse than text output. So isn't it possible to make
NCBIWWW.qblast return text output instead of HTML and parse that instead?
So my question is, why was the choice made to parse HTML instead of text? Is
it simply because blast-on-the-web couldn't return text output in the past?

--Michiel.


Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1150 St Nicholas Avenue
New York, NY 10032