Bioperl: Re: FYI: Error:: Perl module

[Steve A. Chervitz]

Georg,

> >From the newest Module List:
> ----------------------------------------------------------------------
> Error          adpO  Error/exception handling in an OO-ish way    GBARR +

Thanks for the tip. I'll check it out.
 
> Also, I'm still waiting -re- Bio::UnivAln:: do you wanna bundle it,
> finally, at Stanford, as we said months ago ? 

Sure. Why don't you send along the latest version and I'll try and get 
SteveB and myself going on this.

> What's the best strategy for getting Bio::PreSeq and Bio::UnivAln
> finally out as betas, given rather tight time constraints at least 
> on my side ?

I think Chris is in the best position to getting PreSeq.pm wrapped up. I 
still feel we should bundle ReadSeq with it, so every installation is 
guaranteed full functionality. Before doing this, we should get Don 
Gilbert's approval so one of us (Chris?) should drop him a line.

 
> As the Blast example shows, WE'RE not getting done much :
> It's just talk we deliver... (include half a smiley here!!)

You could get us started by setting up the Blast Module Development page 
(or maybe just a new section on the Bioperl home page) in which we could 
put links to sites of the different existing implementations. I've 
recently started fleshing out the documentation for my Blast module, 
so you could add a link to this page:

http://genome-www.stanford.edu/~sac/perlOOP/bioperl/schema/blast.html

I don't yet have a distribution package ready to go, but there are links 
to source code.

I think Joe Ryan's recent suggestion about a Blast:: module 
name space makes alot of sense. My module would be more appropriately named 
Blast::Parse.pm since it has no methods for executing BLAST runs. My 
module also relies on two helper modules which could go in this name 
space.

Regards,
SteveC

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