[Bioperl-l] Bio::Expression & Re: ReseqChip, module/package name

Chris Fields cjfields at uiuc.edu
Fri Aug 24 16:07:36 UTC 2007


First, apologies about not getting on this sooner.  It's shaping up  
to be a busy year!

The new package: How about Bio::Expression::Tools::MitoChip?  My  
reasoning: I don't think it's necessary to define a new  
Bio::Resequencing namespace for just one module; my inclination is  
towards using Bio::Expression namespace as Bio::Tools have been  
traditionally reserved for output parsers.  I am unsure what the  
Bio::Expression status is (very little is documented, no tests are  
written, nothing on the mail list archives); maybe Allen can answer  
that?  I don't see anything that precludes you from using that  
namespace as long as your tools are fairly well-defined (they are)  
and have tests (they do).

Also, your module deals with doing one specific thing (extraction and  
incorporation of information about redundant fragments) for the Affy  
MitoChip.  It might be worth genericizing the class a bit so that you  
can add new parser or analysis methods w/o having to define new  
classes to deal with the same Mitochip data.

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On Aug 24, 2007, at 5:05 AM, Marian Thieme wrote:

> Hi,
> 2 questions about the naming of the module I did submit
> (see http://bugzilla.open-bio.org/show_bug.cgi?id=2332)
> 1.) The package:
> because there exists already an expression package I suggest to  
> create a
> new package called resequencing
> 2.) I would suggest that the module is called RedundantFragments or
> AdditionalFragments
> so we would have something like:
> Bio::Resequencing::AdditionalFragments
> Any other ideas ?
> Marian
> By the way can anybody change my email adress to  
> marian.thieme at arcor.de
> in bugzilla as well as in the bioperl list, please ?!! didnt achieve
> that by my own...
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign

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