[Bioperl-l] subclassing (?) BPLITE, etc.

[Jason Stajich]

The new SearchIO system is intended to be subclass-and-plug-in just like
SeqIO - so I would suggest it.  The basic structure is good but the
parsers will go under some more major revisions with Steve C's new code so
I would not reccomend it as starting point until the end of Jan unless
you're willing to get down and dirty and understand it pretty thoroughly.

Alternatively the BPlite structure is a fine one to adopt but you won't be
able to do a whole lot of code reuse for the parser - maybe the
Subject/HSP objects - not sure.

-jason

On Fri, 28 Dec 2001, Jonathan Epstein wrote:

> Hi,
>
> I need to parse a completely different type of blast output and fit it into one of the existing BioPerl blast frameworks (preferably either BLAST or bplite).  I'm having a lot of trouble figuring out where to create such a module (which will only be for my personal use, unfortunately), how to do the necessary subclassing, etc.
>
> When I use this object based upon a proprietary file format, I want almost all of my application code to just look as though I was using traditional BioPerl objects.
>
> Thanks in advance for any pointers,
>
> - Jonathan
>
>
>
>
> Jonathan Epstein                                Jonathan_Epstein@nih.gov
> Head, Unit on Biologic Computation              (301)402-4563
> Office of the Scientific Director               Bldg 31, Room 2A47
> Nat. Inst. of Child Health & Human Development  31 Center Drive
> National Institutes of Health                   Bethesda, MD 20892
>
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-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu