Bioperl: send me pointers/links/code for your favorite Blast module !

[Georg Fuellen]

The one important RFI in this mail is:

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Please send me pointers/links/code of your favorite Blast module !
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I've started collecting these at
http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/
Currently I'm listing
                       Steve Chervitz' Bio::Tools::Blast.pm 
                       Chris Dagdigian's Blast.pm 
                       Steven Brenner's Blast code (part of Grit::AlnParse) 
                       Joe Ryan's Blast.pm 
But only Steve Chervitz' Blast.pm has a link.

SteveC wrote,
> Georg,
> > 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.

I'm currently testing -- will mail next week.

> > 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.

Ok! Should UnivAln.pm try to do the same ?

> > 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 

See above. I guess there will soon be a seperate page maintained by a volunteer
who is more concerned with Blast than I am. (any volunteer ? :-)

> 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.

What are other ppl's experiences with complicated namespaces ?
(In a followup-message, you suggested ``Bio::Tools::SeqAnal::Blast::Parse.pm''
which I think is unrealistically complicated... But maybe ppl actually use
such namespaces successfully, and others are not deterred ?)

> Regards,
> SteveC

best wishes,
Georg Fuellen,
Univ. Bielefeld, Research Group in Practical Comp. Science
http://www.techfak.uni-bielefeld.de/bcd/welcome.html


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