[Bioperl-l] BPLite?

[Wiepert, Mathieu]

So, what you are saying is that it's not there, it would be good if it was
there, but certainly don't replace what is already there (never would have
done that anyway).  Should this be done in the same object then?  Sounds
like no one is supporting Blast or BPLite.  One thing about BPlite is that
it seems to parse GCG output as well as blastall output just fine.  Blast
was not doing it as well, though I thought it would since GCG is mentioned
in the docs (it may and I could have had a SUE).  

I think that if BPLite were passed an xml file it could recognize that.  As
a first pass it should not be tough to populate the same structures already
in BPLite.  That is not taking advantage of the full power of XML, but that
can be addressed later.   As an exercise for myself I am going to see about
taking in the xml and populating the BPLite objects, and see how that goes.
I am pretty new to all this, so it will take me awhile, but if anything
interesting comes of it I will submit it for review.

Mathieu Wiepert
Medical Information Resources
Mayo Foundation
(507) 266-2317
wiepert.mathieu@mayo.edu

 -----Original Message-----
From: 	Hilmar Lapp [mailto:lapp@gnf.org] 
Sent:	Wednesday, March 14, 2001 11:51 AM
To:	Wiepert, Mathieu
Cc:	'bioperl-l@bioperl.org'
Subject:	Re: [Bioperl-l] BPLite?

"Wiepert, Mathieu" wrote:
> 
> I have a few questions about BPLite, and the Blast parsing process.  Blast
> can output the ASN.1 or XML, as I understand it.   Do we have any parsers
> that use that as a starting point, to then fill objects like the current
> report, subject, and HSP objects, or the Blast object?
> 

We don't. I don't even know whether Ian's latest version of BPlite is
capable of that. Parsing XML instead of text was discussed for a
while, and I think the outcome basically was that it is very desirable
to have that, but at the same time people will want to continue using
text-format reports and be able to parse them, simply because they're
very well human readable and people tend to look at the reports from
time to time.

<attention: don't read further if you don't like solicitations>
Maybe I also take the opportunity to re-iterate that at present we
have no-one committed to keeping BPlite abreast with Ian's development
(Peter S volunteered to fix bugs as they appear), and we'd be glad if
someone is willing to step up ... 

	Hilmar
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp@gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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