[Bioperl-l] Consed.pm documentation complete, please comment

[Jason Stajich]

Chad -

I had a chance to read your document.  
Looks like a great solution to your needs.   I know a number of other
people would like to have similar functionality

If you were to make this a bioperl object I'd probably consider having
this in Bio::Tools::Assembly::Consed.   Perhaps some Phred/Phrap modules
might make there way in there as well although modules that RUN
these programs should probably end up in Bio::Tools::Run::Assembly.
Other people may have better ideas on namespaces as we trying to be good
about the organization and have a Good Naming Practice here.

Not having seen the actual code I can probably tell you that it won't be
much work to make it bioperl compliant - we have a couple of things we
like to see in our modules.

These are mostly laid out in this document:
http://www.bioperl.org/wiki/html/BioPerl/BioperlProgrammingConventions.html

Inheritance from RootI is a must - this also takes care of your
set_verbose method.  If you have I/O or tempfiles try and use the
Bio::Root::IO module.  I can point you to examples of its use in other
modules.

Also, named parameters in the constructor ie:
my $consed = new Bio::Tools::Assembly::Consed(-file => 'file.ace.1',
		  			      -verbose => 1);

are important so that constructors can be chained together to support
inheritance.

The POD documentation should look like the rest of the toolkit - we have
an emacs lisp snippet you can load in which will help you produce this
documentation w/o a lot of cut and paste.  in bioperl-live/bioperl.lisp if
you are an emacs fan.

I guess the next step is up to you, you should probably decide how you
want to release this as all the modules in bioperl are released under the
Perl Artistic License (which I have copied into the bioperl root dir).
You can still maintain copyright and/or publish with a reference to the
module that you wrote, however by submitting it to the repository you
are allowing people to make changes to it - you really had a copyright on
the version that was initially submitted but improvements are done by the
community.  At least this is my very small brain interpretation of what
happens when I put code in the CVS repository - legal experts who really
want to help us define if any of this is truly true with the Perl artistic
license feel free to set me straight, or better yet, write a document so
we can include it on the website....

You can also plop your code in an ftp dir and allow us to review it or
send it to a select few bioperl people who are willing to help you review
it before submission (I'm game).  We can set you up with an account and
see where it goes.  

Is this what you're thinking?  

-Jason

On Mon, 25 Jun 2001, Chad Matsalla wrote:

> 
> Hi all,
> 
> I have completed documenting my Consed.pm module. The documentation can be
> found here:
> 
> http://www.dieselwurks.com/bioinformatics/consedpm_documentation.pdf
> 
> The documentation include a rationale for design, general guiding
> principles, an explanation of the structure of the object, and
> explanations of each subroutine. A sample script is included.
> 
> I am asking for comments on the general documentation style and
> suggestions for what should and should not be included in pod
> documentation.
> 
> Any suggestions on how I can use bioperl objects within this module would
> also be gladly acccepted.
> 
> The code is ready to be released; I am just completing test scripts and
> verifying with my employer that it is ok to release it.
> 
> I hope it would be of use to somebody!
> 
> Chad Matsalla
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
> 

Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/