[Bioperl-l] SeqFeature/AnnotatableI and rel. 1.6

Chris Fields cjfields at uiuc.edu
Thu Aug 23 20:39:30 EDT 2007


Having an independent test would be great!  The reason I suggest  
there may be a speedup: one complaint popping up after 1.5 was the  
slowdown in sequence parsing, which could be related to the 'heavier'  
objectified tags.

chris

On Aug 23, 2007, at 4:59 PM, Scott Markel wrote:

> Chris,
>
> Pipeline Pilot's Sequence Analysis Collection wraps BioPerl.
> Once you think the branch changes have converged a bit we'd
> be happy to try running our regression suite and report what
> we find.
>
> Scott
>
> Scott Markel, Ph.D.
> Principal Bioinformatics Architect  email:  smarkel at accelrys.com
> Accelrys, Inc.                      mobile: +1 858 205 3653
> 10188 Telesis Court, Suite 100      voice:  +1 858 799 5603
> San Diego, CA 92121                 fax:    +1 858 799 5222
> USA                                 web:    http://www.accelrys.com
>
>
> bioperl-l-bounces at lists.open-bio.org wrote on 23.08.2007 14:33:25:
>
>> Scott,
>>
>> So far most of FeatureIO.t passes, with only a few exceptions dealing
>> with the from_feature method (I know what the problem is there).  A
>> large number of other tests crash horribly (not so surprising), so
>> I'll have to go through those.  Ergo any changes and testing will
>> definitely be conducted on a branch then merged back to main trunk
>> once everything is okay.  I'll probably start a branch in the next
>> few days or so.
>>
>> Here's what I have been working on so far, which I think is  
>> reasonable:
>>
>> 1) Move all *_tag_* related methods out of Bio::AnnotatableI and into
>> Bio::SeqFeature::Annotatable.
>>
>> 2) Reinstate the same tag methods in Bio::SeqFeatureI and remove
>> Bio::AnnotatableI from the inheritance tree.
>>
>> 3) Make Bio::SeqFeature::Annotatable Bio::AnnotatableI (which it
>> already was, strangely enough).  Now it simple implements the proper
>> methods from the interface classes SeqFeatureI and AnnotatableI.
>>
>> 4) Revert Bio::SeqFeature::Generic tags back to simple untyped
>> strings (reimplement the 1.4 rel methods).
>>
>> I'm interested in seeing whether this results in a significant
>> performance increase in SeqIO since the Annotation instantiation is
>> removed.
>>
>> ToDo: I plan on removing the operator overloading in Bio::Annotation,
>> which was a serious sticking point with most of the devs.  This won't
>> be done until after tests pass for everything else.
>>
>> What we will need at some point which I can't provide:
>> Bio::SeqFeature::Annotated has no docs (no synopsis, no
>> description).  The reason I bring this up is Sendu and I are
>> seriously considering running an automated code audits in order to
>> gauge which modules lack docs, test coverage, etc..  We're likely
>> splitting those without adequate test/doc coverage off into a
>> separate 'dev' release.
>>
>> chris
>>
>> On Aug 23, 2007, at 2:53 PM, Scott Cain wrote:
>>
>>> Hi Chris,
>>>
>>> GBrowse would be unaffected by this as it doesn't use
>>> Bio::SeqFeature::Annotated.  The GMOD GFF3 Chado loader on the other
>>> hand will almost certainly break horribly, as it depends on the  
>>> strong
>>> typing of Bio::FeatureIO/Bio::SeqFeature::Annotated.  If you  
>>> could try
>>> your ideas out in a branch that I could checkout and test on, that
>>> would
>>> be good.
>>>
>>> Thanks,
>>> Scott
>>>
>>>
>>> On Wed, 2007-08-22 at 23:53 -0500, Chris Fields wrote:
>>>> As many of the devs know, there are a number of Feature/Annotation
>>>> issues that need to be resolved prior to a 1.6 release:
>>>>
>>>> http://www.bioperl.org/wiki/Release_Schedule#SeqFeature.
>>>> 2FAnnotation_changes:_Keep_or_roll_back.3F
>>>>
>>>> There has been little work done over the last 2 1/2 years to  
>>>> undo or
>>>> rectify problems associated with those additions; I feel like those
>>>> of us still routinely contributing have been left holding the bag.
>>>> There has also been very little attempt to document any of this
>>>> adequately enough; as an example see POD for
>>>> Bio::SeqFeature::Annotated (what little there is).
>>>>
>>>> I would like to suggest the radical idea of rolling back
>>>> AnnotatableI/
>>>> SeqFeatureI changes to a much simpler rel. 1.4-like behavior (tags
>>>> are simple scalars) and possibly work in implementing Ewan's
>>>> SeqFeature::TypedSeqFeatureI for those who want strong data types
>>>> (i.e. Bio::FeatureIO/Bio::SeqFeature::Annotated).  The various
>>>> AnnotatableI changes, odd inheritance, and operator overloading  
>>>> have
>>>> really obfuscated the code to the point where no one wants to touch
>>>> it in case it breaks something important.  However, I believe it is
>>>> the one serious impediment to a new stable release.
>>>>
>>>> My thought is we simplify all the relevant interfaces, essentially
>>>> reverting back to rel 1.4.  For instance, we move the various
>>>> Bio::AnnotatableI tag methods back into Bio::SeqFeatureI.
>>>> Bio::SeqFeature::Annotated would implement Bio::AnnotatableI
>>>> directly, and (if needed) also implement
>>>> Bio::SeqFeature::TypedSeqFeatureI, so the impetus is on
>>>> Bio::SeqFeature::Annotated to overload the relevant SeqFeatureI
>>>> methods correctly, just as any other class would when  
>>>> implementing an
>>>> abstract interface.  I have played around with this a bit and  
>>>> managed
>>>> to get most tests working again for Bio::SeqFeature::Generic and
>>>> FeatureIO but a number of others break.
>>>>
>>>> If needed I can try this out on a branch (a bit ironic, since the
>>>> changes instigating this mess should have been tested on a  
>>>> branch!).
>>>> Maybe this will get the ball rolling towards a 1.6 release.  Any
>>>> thoughts?
>>>>
>>>> chris
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> -- 
>>> -------------------------------------------------------------------- 
>>> --
>
>>> --
>>> Scott Cain, Ph. D.
>>> cain at cshl.edu
>>> GMOD Coordinator (http://www.gmod.org/)
>>> 216-392-3087
>>> Cold Spring Harbor Laboratory
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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