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

Marian Thieme marian.thieme at arcor.de
Fri Aug 24 17:01:07 UTC 2007

> 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).

The problem I see, with Bio::Expression, is that Resequencing chips are
not belongs to Expression chips.
(Expression chips are designed to hybridisize RNA strands and hence
measure RNA expression levels, on the other hand a resequencing chip is
based on DNA, also the design and the probe length is quite different).
So, from my point of view it make sence to differ between dna and rna
chips, at least.

> 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.

OK, need to think about that.

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