[Bioperl-l] Bio::Expression & Re: ReseqChip, module/package name
cjfields at uiuc.edu
Fri Aug 24 12:07:36 EDT 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:
> 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
> so we would have something like:
> Any other ideas ?
> 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...
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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Dept of Biochemistry
University of Illinois Urbana-Champaign
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