Bioperl-guts: Response/Hit fields RE: DB work, request to Aaron M. RE: Bioperl- guts: REMINDER: ISMB sig n-ups (fwd)

Otillar, Robert {BIOI~Palo Alto} ROBERT.OTILLAR@Roche.COM
Tue, 24 Aug 1999 13:52:52 -0700


Thanks Aaron.
	A breakdown would be helpful if it is available.
	I think that would keep me from assuming unintended things from the
code-specifics.
Thanks,
	Bobby O

-----Original Message-----
From: Aaron J Mackey [mailto:ajm6q@virginia.edu]
Sent: Tuesday, August 24, 1999 10:51 AM
To: Otillar, Robert {BIOI~Palo Alto}
Cc: Ewan Birney; bioperl guts
Subject: Re: DB work, request to Aaron M. RE: Bioperl-guts: REMINDER:
ISMB sig n-ups (fwd)



The latest FASTA code is available on the bioperl-live cvs branch -
consider it pre-alpha, to be sure.  From the Bio/Search/Processor/Fasta.pm
module you can see all the fields I'm setting (get ready for a big
regexp-induced headache when you do).  Let me know if you have any
questions about what you're seeing.

BTW, when you say Smith-Waterman, do you mean ssearch?  If so, ssearch
parsing will be elementary after FASTA, since they use the same
output/formatting code base.

If necessary, I can post an entire breakdown of available fields from the
Response/Hit objects (but you said a perl data structure would be
sufficient).

Best,

-Aaron

On Tue, 24 Aug 1999, Otillar, Robert {BIOI~Palo Alto} wrote:

> 
> 	Perl DBI database with oracle, MS access, and CSV is underway for
> simple sequence-like and alignment-like data.
> 	A schema/plan for Aaron M's HTTP Request/Response model for analysis
> services would be helpful to me. 
> 		Even preliminary/pre-alpha perl data-structure for these on
> FASTA, BLAST, PSI-BLAST, and/or Smith-Waterman would be a nice. I would
like
> to remain consistent with how AM plans to represent these objects.
> 	I will put up a proposal/request-for-suggestions after I've worked
> with this a bit more, preferrably after some response from AM with info on
> his objects. 
> 
> Thanks,
> 	Bobby O
> 
> -----Original Message-----
> From: Ewan Birney [mailto:birney@sanger.ac.uk]
> Sent: Tuesday, August 24, 1999 7:47 AM
> To: bioperl guts
> Subject: Bioperl-guts: REMINDER: ISMB sign-ups (fwd)
> 
> 
> 
> Just to remind people who signed up as developers at ISMB... we will be
> expecting code (or at the very least, excuses) from you this fall, so I
> hope you are going to be working away at figuring out how you want to
> contribute.
> 
> Chris has put up a status page at 
> 
> http://bio.perl.org/Core/status.html
> 
> To remind you in this email, this is what you said you would do:
> 
> aaron - lead the 0.5.2 bug fix release
> 	get the new simsearch agent/processor/result system working for
> 	fasta
> stevec - do psi blast support in the current blast system
> wolfgang - do swissprot AnnSeqIO support and taxonomy
> ralf - publication object
> Adam moore + Keith Neil - figure out XML support
> Bobby O - figure out database persistence
> Kris Boulez - The bioperl cookbook
> george hartzell - lead the alignment discussion.
> 
> 
> I *am* looking forward to people just committing code and also making
> proposals on the list for the more complex stuff. Get stuck in.
> 
> (BTW - I am serious about flying over and standing over you in person to
> make you do stuff!).
> 
> 
> 
> Ewan Birney
> <birney@sanger.ac.uk>
> http://www.sanger.ac.uk/Users/birney/
> 
> 
> 
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-- 
 o ~   ~   ~   ~   ~   ~  o
/ Aaron J Mackey           \
\  Dr. Pearson Laboratory  / 
 \ University of Virginia  \     
 /  (804) 924-2821          \
 \  amackey@virginia.edu    /
  o ~   ~   ~   ~   ~   ~  o


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