[Biopython-dev] PCR module

[Thomas Sicheritz-Ponten]

Yair Benita <Y.Benita at pharm.uu.nl> writes:

> on 24/5/02 12:23, Thomas Sicheritz-Ponten at thomas at cbs.dtu.dk wrote:
> 
> > Anyway, the purpose of sequtils was more like a temporary storage module for
> > commonly used sequence analyzing utilities/functions. I hoped that most of
> > the functions would eventually find their way into the modules they
> > actually should belong too ....
> > 
> > Whats the overall opinion of sequtils.py?
> > * Should we reorganize the code and move "movable" functions before
> > merging/adding PCR modules and documentation?
> > * Should we use it as it is (maybe after some cosmetic changes) and continue
> > adding sequence analyzing methods?
> > * Or, should we split it into core sequence utilities (like GC content and
> > sequence editing) and more user level defined sequence utilities (like 6
> > frame translations, gc skews, graphical GC content etc.) (inherited from
> > the core module)
> > 
> > Personally, I'd prefer the latter ... in this case we could have a PCR
> > module and avoiding duplicated code by putting common functions in the core
> > sequence utilities module (e.g. GC content, frames etc.)
> > 
> > Suggestions, ideas, critics???
> 
> I suggest 2 different modules: PCR module and Analysis module.
> The Analysis module will handle everything related to DNA and Protein
> sequence analysis.
> The PCR module will use some methods from the analysis module (such as GC
> content) and will have all methods relevant only to PCR (such as melting
> temperature).
> 

Sounds good, but that will leave us still with some functions (currently in
sequtils.py) which do not fit completely in either module ...
Hmmm, maybe they'll fit in an extra class inside the Analysis module.

Jeff a.o., any suggestions for naming and location for the possible PCR and Analysis
modules ?

cheers
-thomas

-- 
Sicheritz-Ponten Thomas, Ph.D, thomas at biopython.org      (
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