[Bioperl-l] No text blast output; strip_html output non-parseable.

[Vsevolod Ilyushchenko]

Hi,

Summary: I can't find a public method to save the output of Webblast in the
text format. If I save it in HTML and want to process it later, I can't. 
If I save it in text format using strip_html, I can't parse this text
later.

The reason I bring this up is that I am writing an app that will run blast
every week on certain sequences. If the latest run shows more hits than
last week (because of new data in the NCBI databases), the users are
notified. So I need to store blast results and later re-parse them for
comparison.

The problem is that bioperl does not seem to be honed for this. I can't
even save the results of Webblast in text format. I have found the
strip_html() function and used it to de-HTMLize the output of
Blast->to_html(). However, I can't parse this text using Blast.pm :( 

Alternatively, I can try to store blast output in the HTML format. However,
the public interface to Blast.pm does not parse it. I can probably dig
inside and force it to do this, but I will wind up calling the strip_html()
function anyway, which will fail.

What is the best approach here?
 
Thanks,
Simon
-- 
Simon (Vsevolod ILyushchenko)   simonf@cshl.edu   
http://www.simonf.com          simonf@simonf.com 

"A man who feels himself a citizen of the world whose 
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to any exclusive part of it; a man who loves his country 
because he loves mankind, and whose judgement is not 
warped by tribal loyalties." Erich Fromm