[Bioperl-l] Re: BLAST parsers

[Brian Osborne]

Neil,

>>And despite
>>upgrading to the latest bioperl pretty much as it's released, I'm barely
>>aware of Bio::SearchIO, which I guess is the old documentation problem.

Please don't take this as a flame, it's not. SearchIO is specifically
mentioned in the bptutorial and the FAQ as the preferred approach. A large
part of the "documentation problem" is people not reading the docs. I'm much
the same way, I don't blame them. But if you've spent much time in this
newsgroup you've probably noted that some people commonly ask questions that
would be answered by reading the FAQ or bptutorial. Again, I've never
responded with a "RTFM" in my life, I'm a bit more polite, but some users
want to be spoon-fed when they'd get a lot more from the package after
browsing the basic documents for 30 minutes or so.

Now, what I'm about to do is to put a note about the FAQ into the README,
but it may not make a lot of difference to these lazy few.

Brian O.

-----Original Message-----
From: bioperl-l-admin@bioperl.org [mailto:bioperl-l-admin@bioperl.org]On
Behalf Of Neil Saunders
Sent: Tuesday, August 20, 2002 10:39 PM
To: bioperl-l@bioperl.org
Subject: [Bioperl-l] Re: BLAST parsers

Ewan wrote:
> But for the moment the 1.0 series is the stable series, and there one does
> have a choice of three BLAST parsers, with (in my view) BPlite currently
> the stablest and most robust.
> There is where we should point users with the caveat that we think
> Bio::SearchIO is the way of the future.

I think the BLAST parsing situation is getting a little confusing.  I
also prefer BPlite and have many scripts based around it.  There are
also 2 versions floating around IIRC; one spelt BPLite (large L), the
other BPlite (small l).  One of these supports the 'multi' method (parse
reports with multiple query sequences), the other doesn't.  I generally
find myself downloading BPlite.pm from Ian Korf's page each time I do a
bioperl upgrade and copying it to the correct path.  And despite
upgrading to the latest bioperl pretty much as it's released, I'm barely
aware of Bio::SearchIO, which I guess is the old documentation problem.

After all, our aim is that no-one should have to write a BLAST parser
again!  I think updating the documentation is an important step here, to
avoid newbie confusion.

Neil
--
School of Biotechnology and Biomolecular Sciences,
The University of New South Wales,
Sydney 2052,
Australia

ArchaeaWeb:     http://www.archaea.unsw.edu.au
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