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

Fields, Christopher J cjfields at illinois.edu
Wed Feb 29 10:23:54 EST 2012


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
>> 
>> 
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> 




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