email@example.com (Steve A. Chervitz)
Wed, 22 Dec 1999 14:34:25 -0800 (PST)
Ewan Birney writes:
> On Tue, 21 Dec 1999, Ian Korf wrote:
> > I've been getting requests recently for old BLAST parsers.
> > Seems as though some people are looking for a lighweight
> > parser. At http://sapiens.wustl.edu/~ikorf/BPlite.pm you
> > can find my version of such a module. It parses both NCBI-
> > and WU-BLAST, and works well in pipes since it reads one
> > subject and one alignment at a time.
> I'd really like to see a lighter blast parser with less embedded
> functionality in bioperl, ideally with the main features of steve's
> blast parser. If I can persuade someone to look at this Ian, is it
> ok to bring it inside bioperl? (any chance of you wanting to do that? I
> guess not...)
I'd like to see a lightweight parser in there as well. Choice is
always a good thing. Jeff Chang's post about the Scanner-Consumer
SAX-like approach seems like a nice way to have multiple parsers with
different quality of service.
I'm thinking about how this would work within Aaron's Processor-Result
architecture. The Processor is a scanner but is also a Result
factory. This coupling would have to be broken up in order to
interpose alternative Consumers that construct different Result
objects. It could work well within the overall Request-Response design.
> Steve - we *do* need to think of upgrading the blast parser - only
> you know the code, and the largest set of bugs are found in it.
I hear ya, and still plan to fix it up. However, if Bioperl is to reap
the benefits of the open source model, we have to break out of the
"one person - one module" mentality. Reporting the bugs is great, but
if we could get others with access to cvs to pitch-in on the fixes, we
could really fly.
Bioperl has a bit of a developer bottleneck. As each of us has become
more involved in our own jobs and commitments, we've had less time to
devote to fixing bugs and implementing new tools, so development has
been slower that we would like. To remedy this, we could do a better
job of attracting new blood and making others comfortable with
modifying the code base.
So, as this is the season of giving, I'd like to convey the following
message (borrowing from a famous quote):
Ask not what Bioperl can do for you, ask what you can do for Bioperl!
Happy Holidays to all,
Steve A. Chervitz
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