[Bioperl-l] Fwd: Code to contribute

Rutger Vos rvos at interchange.ubc.ca
Thu Aug 14 19:51:43 EDT 2008


Sounds exciting! I bet the general advice you'll get is to i) check
out the latest code from svn ii) see which bioperl objects/interfaces
(e.g. Bio::Seq) you'd use to integrate your algorithm into bioperl
iii) write a class that performs the algorithm as some sort of
analysis factory taking the sequence object (or ideally object
interface) as an input iv) run that class by the mailing list v) check
it into svn.

On Thu, Aug 14, 2008 at 4:37 PM, Michael Janis <mjanis at chem.ucla.edu> wrote:
> Hi,
>
>
>
> I've had some perl code lying around for what seems like forever and I'd
> like to contribute it to bioperl, if such facilities don't already exist in
> bioperl.  The code implements shuffling (DNA or RNA) keeping the
> dinucleotide composition (and codon usage) intact through a Eularian path
> approach as described in Altschul and Erickson (1985).  The code seeds the
> Eularian paths by keeping the first and last nucleotide invariant in the
> shuffle - which has minimal detrimental effects to the purpose of the
> algorithm, in my experience.
>
>
>
> A quick search on the bioperl website shows that there is a mutation.pls
> script, and facilities for using Sean Eddy's SQUID C library, which
> implements the same function (I wrote this particular function before I knew
> how to use C).  As such, it's probably not as elegant as Sean Eddy's
> implementation, but it works - and it's entirely in perl.
>
>
>
> The bioperl developer pages suggest a post to the mailing list as the best
> place to start contributing to bioperl.  Is this a useful function to add to
> the project?
>
>
>
> Best Regards,
>
>
>
> Michael
>
>
>
> -------------------------------
>
> Michael Janis
>
>  <mailto:mjanis at chem.ucla.edu> mjanis at chem.ucla.edu
>
> -------------------------------
>
>
>
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>



--
Dr. Rutger A. Vos
Department of zoology
University of British Columbia
http://www.nexml.org
http://rutgervos.blogspot.com



-- 
Dr. Rutger A. Vos
Department of zoology
University of British Columbia
http://www.nexml.org
http://rutgervos.blogspot.com


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