[Bioperl-l] Fate of Bio::Tools::PCRSimulation

[Fields, Christopher J]

Seems like it was meant to be added at some point but was never committed.  Definitely not in the github history for 1.3.x, this commit corresponds to the v1.3.4 tag:

   https://github.com/bioperl/bioperl-live/tree/0a67fa444eb19a70876017607f70ab72be38755a

and it's not there.  

I agree with Roy, it would be nice to somehow make this a little more generic or pluggable on how it maps primers (maybe with a default pure perl method).  I also think this shouldn't be bound to bioperl-live considering our current plans, it would best happen in a separate repo.

chris

On Feb 29, 2012, at 9:06 AM, Roy Chaudhuri wrote:

> The code for Bio::Tools::PCRSimulation can be downloaded as part of this archive:
> http://www.salmonella.org/bioperl/primer3_v0.3.tgz
> 
> (There's supposedly a more recent version here:
> http://www.salmonella.org/bioperl/nucleotide_analyses.tgz
> but that file seems to be truncated).
> 
> I have no idea how much would be salvagable. It seems to just use index to map the primers to the sequence, I guess it would make more sense to at least give the option of something more sophisticated like Primer3, BLAST or even a short read mapper.
> 
> Cheers,
> Roy.
> 
> 
> On 27/02/2012 21:18, Fields, Christopher J wrote:
>> On Feb 26, 2012, at 12:44 AM, Florent Angly wrote:
>> 
>>> Hi all,
>>> 
>>> I am interested in the Bio::Tools::PCRSimulation module. Supposedly
>>> it was added to Bioperl 0.3 and is also mentionned in the
>>> Bio::PrimedSeq module. However, I cannot find in the current
>>> Bioperl codebase. Any idea where it went?
>> 
>> No idea; I can't find it anywhere in the code base either, and the
>> github repo contains history going back to the original CVS repo.
>> You can try contacting the author, possibly.
>> 
>>> The reason I am asking is because I have some code to do silico PCR
>>> using regular expressions. I wanted to modularize my code more and
>>> make it into a module for Bioperl. Of course, if there is something
>>> similar in Bioperl already, I need to have a look at it. If there
>>> is nothing similar, what namespace do you suggest to use?
>>> Bio::Tools::AmpliconExtractor? Bio::Tools::AmpliconSearch?
>>> Bio::Tools::InSilicoPCR?
>>> 
>>> Thanks,
>>> 
>>> Florent
>> 
>> 
>> Maybe the last (InSilicoPCR).
>> 
>> chris
>> 
>> 
>> _______________________________________________ Bioperl-l mailing
>> list Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>