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

Thu Mar 1 02:30:38 UTC 2012

There are a number of very good reasons to separate out common code and create new repos for new code.  The problem about adding new code into core is it ties your code development to bioperl-live's release cycle and versioning.  Also, what I (and others) would not like to see is any additional dependencies introduced, but a separate release allows you to (1) both add a dependency w/o affecting core, and (2) make it required, so no fiddling with checking for the module prior to running tests on it.  

As an example, I can easily see something like Bio::SearchIO::blastxml living on it's own since it has a set of outside dependencies.

BTW, separation of modules into separate distributions (even single modules) based on functionality above and beyond that defined in a core is very common in the perl world.  Beyond the obvious example of anything non-core in perl (all installable via CPAN), Moose, Dist::Zilla, Catalyst, Dancer, etc all have separately installable dists that layer additional functionality and have a separate maintenance path.  

chris

On Mar 1, 2012, at 6:12 PM, Florent Angly wrote:

> Thanks for everybody's feedback.
> 
> I am looking at existing modules to hold template sequence, amplicon sequence and primer information. There is the Bio::SeqFeature::Primer and Bio::Seq::PrimedSeq. At the moment the PrimedSeq object places Primer objects on the target sequence. I have been looking at refreshing these modules (they are quite old), add some sanity to them and make sure they are suitable for a generic implementation of PCR (or amplicon search, which I find a more suitable name since it is a far cry from simulating PCR cycles, etc).
> 
> I will make a remote branch today to make it easier for interested parties to experiment and contribute.
> 
> As you can see Chris, the amplicon search feature would use two existing bioperl-live modules and only add one, tentatively in the Bio::Tools::AmpliconSearch namespace. I am not convinced that this warrants a separate distro.
> 
> Florent
> 
> On 01/03/12 01:23, Fields, Christopher J wrote:
>> 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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> 