[Bioperl-l] Print alignments for several HSPs? (not for the whole report)

[Vsevolod (Simon) Ilyushchenko]

Hi,

I am running a script that does a keyword search on blast hits and then 
prints only the results whose descriptions match. Since I parse the 
blast output with Bio::Tools::Blast, I wind up with an array of 
Bio::Tools::Blast::Sbjct's and a 2-D array of Bio::Tools::Blast::HSPs, 
and I don't know how to produce a regular-looking blast report from 
them. In particular, I don't know how to pretty-print the alignments.
I suppose I could piece it together from the HSP parameters, but this 
must already have been written...

There is a to_html method in Bio::Tools::Blast, but it refers to the 
whole report, not to a collection of Sbjcts and HSPs.

Thanks in advance for any pointers.

Simon
-- 

Simon (Vsevolod ILyushchenko)   simonf@cshl.edu
				http://www.simonf.com

"Large software projects are like werewolves because
they transform unexpectedly from the familiar into horrors."
                     Fred Brooks