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

Scott Markel smarkel at accelrys.com
Thu Aug 23 17:59:37 EDT 2007


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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