[Bioperl-l] Modules for Lucy and helixturnhelix

[Jason Stajich]

Andrew - great! 

Do send a link to the code and we'd be happy to review and incorperate
into the project.  You are welcome to a CVS login if you would like to be
able to commit the code yourself once it has been reviewed otherwise
someone else can definitely do it for you

Let me know what you want to do. 

I think that Peter's factory object is a good starting point for how to
run programs from within bioperl (same design used for StandAloneBlast and
TCoffee objects) but I hope that at BOSC the bioperl devs can design the
ApplicationFactory (or by a better name if someone wants to help)
Interface will be for this so we can attach to EMBOSS and other programs
in a unified way.

-Jason

On Tue, 10 Jul 2001, Andrew Walsh wrote:

> Hi Everyone,
> 
> I have written modules related to Lucy (a vector/quality trimming
> program from TIGR) and helixturnhelix (a DNA binding site detection
> program, part of the EMBOSS package).
> 
> For each program I've written a module that creates 'factory' objects
> for performing analysis (they are based on Peter Schattner's
> Bio::Tools::Run::Alignment::ClustalW).  These modules return
> references to objects created with another set of modules I wrote.  
> These returned objects have methods that will return parsed
> information from the Lucy or helixturnhelix output files.
> 
> I was wondering if this is the kind of thing anyone would be
> interested in, and if so, where should I send it (Script Central?).  
> I'm writing POD documention in the same format as for the Bioperl
> modules.  The code has been 'Bioperlized' in the sense that there is
> inheritance from Bio::Root::RootI and temp files are created with
> methods from Root::IO.  If there is interest, I can put the POD docs
> and code on our web server for someone to review.
> 
> Thanks,
> 
> Andrew 
> 
> -------------------------------------------
> Andrew Walsh
> Cereal Research Centre
> Agriculture and Agri-Food Canada
> 195 Dafoe Rd
> Winnipeg, MB, R3T 2M9
> Canada
> Phone: (204) 984-2179
> Fax: (204) 983-4604
> 
> 
> -------------------------------------------
> Andrew Walsh
> Cereal Research Centre
> Agriculture and Agri-Food Canada
> 195 Dafoe Rd
> Winnipeg, MB, R3T 2M9
> Canada
> Phone: (204) 984-2179
> Fax: (204) 983-4604
> 
> 
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Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/