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

Wed Mar 14 18:25:55 EDT 2012

Thanks for the notification Chris!
I thought I had commited this file. I must have been daydreaming. It 
should be all good now.
Best,
Florent

On 14/03/12 03:46, Chris Fields wrote:
> Florent,
>
> Getting a test fail on the amplicon branch, seems to be missing a file.
>
> The only test consistently failing is t/Tools/AmpliconSearch.t (I'm 
> seeing NCBI-related test issues that are also occurring on master). 
> Using 'prove -lr t/Tools/AmpliconSearch.t':
>
> [cjfields at pyrimidine bioperl-live (amplicons=)]$ prove -lr 
> t/Tools/AmpliconSearch.t
> t/Tools/AmpliconSearch.t .. 1/174
> ------------- EXCEPTION -------------
> MSG: Could not open t/data/forward_primer.fa: No such file or directory
> STACK Bio::Root::IO::_initialize_io Bio/Root/IO.pm:351
> STACK Bio::SeqIO::_initialize Bio/SeqIO.pm:477
> STACK Bio::SeqIO::fasta::_initialize Bio/SeqIO/fasta.pm:93
> STACK Bio::SeqIO::new Bio/SeqIO.pm:358
> STACK Bio::SeqIO::new Bio/SeqIO.pm:399
> STACK Bio::Tools::AmpliconSearch::primer_file 
> Bio/Tools/AmpliconSearch.pm:292
> STACK Bio::Tools::AmpliconSearch::new Bio/Tools/AmpliconSearch.pm:151
> STACK toplevel t/Tools/AmpliconSearch.t:126
> -------------------------------------
>
> # Looks like you planned 174 tests but ran 53.
> # Looks like your test exited with 2 just after 53.
> t/Tools/AmpliconSearch.t .. Dubious, test returned 2 (wstat 512, 0x200)
> Failed 121/174 subtests
>
> Test Summary Report
> -------------------
> t/Tools/AmpliconSearch.t (Wstat: 512 Tests: 53 Failed: 0)
>   Non-zero exit status: 2
>   Parse errors: Bad plan.  You planned 174 tests but ran 53.
> Files=1, Tests=53,  0 wallclock secs ( 0.03 usr  0.01 sys +  0.18 cusr 
> 0.01 csys =  0.23 CPU)
> Result: FAIL
>
>
> chris
>
> On 03/06/2012 11:08 PM, Florent Angly wrote:
>>
>> Yes, thanks Chris. If you want to start splitting a Bio-Tools
>> distribution that would include Bio::Tools::AmpliconSearch, I am happy
>> to help.
>>
>> In general, I am not specifically attached to the namespace, so if you
>> guys prefer something different, just tell me.
>>
>> Note that AmpliconSearch uses a couple of new or re-worked objects,
>> namely Bio::SeqFeature::Primer, Bio::SeqFeature::Amplicon and
>> Bio::SeqFeature::SubSeq. Both Primer and Amplicons inherit from SubSeq,
>> which inherits from Bio::SeqFeature::Generic. The main goal of SubSeq is
>> to allow fetching a subsequence from the attached sequence or to
>> explicitly adding a sequence that represents the feature (the Generic
>> feature class does not support setting such a sequence, just getting the
>> subsequence). I think it would be good to add this functionality to the
>> Generic feature class, but I did not want to force things without asking
>> everybody first if this seems like a good idea.
>>
>> Florent
>>
>>
>> On 06/03/12 11:08, Fields, Christopher J wrote:
>>> I'll check it out. Want me to post test results here (I have access to
>>> a few systems to test on).
>>>
>>> chris
>>>
>>> On Mar 5, 2012, at 10:36 PM, Florent Angly wrote:
>>>
>>>> To all interested,
>>>> the AmpliconSearch module is in a decent state. If you want to test
>>>> it or improve it, head to
>>>> https://github.com/bioperl/bioperl-live/blob/amplicons/Bio/Tools/AmpliconSearch.pm 
>>>>
>>>>
>>>> Regards,
>>>> Florent
>>>>
>>>>
>>>> On 01/03/12 12:42, Fields, Christopher J wrote:
>>>>> Florent,
>>>>>
>>>>> Just want to add, my previous response isn't meant as an
>>>>> admonishment, hope it didn't come across that way, but sometimes
>>>>> email makes it hard to discern the difference. I simply meant to
>>>>> demonstrate my opinion that I find releasing one's code is much
>>>>> simpler (e.g. you can decide the rules and dictate when the code is
>>>>> ready for release), and if we can make getting good code into user's
>>>>> hands easier, more flexible, and more consistent I think that is
>>>>> always a better path.
>>>>>
>>>>> chris
>>>>>
>>>>> On Feb 29, 2012, at 8:30 PM, Fields, Christopher J wrote:
>>>>>
>>>>>> 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
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> _______________________________________________ Bioperl-l 
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>>
>