[Bioperl-l] Fwd: Code to contribute

Smithies, Russell Russell.Smithies at agresearch.co.nz
Thu Aug 14 21:17:23 EDT 2008


You forgot 2 points,

vi) write documentation/examples, and  vii) write tests

;-)



Russell

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-
> bio.org] On Behalf Of Rutger Vos
> Sent: Friday, 15 August 2008 11:52 a.m.
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Fwd: Code to contribute
> 
> 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
> >
> > -------------------------------
> >
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> 
> 
> 
> --
> 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
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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