[Bioperl-l] Compliance of Bio::Seq add_SeqFeature() method

Dave Messina David.Messina at sbc.su.se
Tue Mar 6 05:17:22 EST 2012

Very nice! Thanks, Florent!


On Wed, Mar 7, 2012 at 06:00, Florent Angly <florent.angly at gmail.com> wrote:

> On 05/03/12 12:13, Fields, Christopher J wrote:
>> Actually, I misread Florent's original post, I was thinking that
>> FeatureHolderI was the outlier here, but it is Bio::Seq.  Yes, I think
>> Bio::Seq is abusing the FeatureHolderI interface, it should just be for a
>> single feature (it can safely ignore the 'EXPAND' option).  However, use of
>> 'EXPAND' assumes the FeatureHolderI is also a Bio::RangeI (must have a
>> start and end to expand), something that is not mentioned in the interface
>> as a requirement and is not guaranteed, for instance Bio::Seq is not
>> Bio::RangeI.
> Ok, I have:
> 1/ clarified in Bio::FeatureHolderI that there is no guarantee that
> 'EXPAND' will be honored
> 2/ made Bio::Seq comply to Bio::FeatureHolderI by accepting the 'EXPAND'
> keyword (but do nothing about it)
> 3/ deprecated the use of passing multiple features to add_SeqFeature() in
> Bio::Seq
> 4/ updated documentation and code that relied on passing multiple features
> That should take care of the issue at hand. See this commit:
> https://github.com/bioperl/**bioperl-live/commit/**
> a5bebe00c505fbf5279f5d717790ed**36eefcc2b8<https://github.com/bioperl/bioperl-live/commit/a5bebe00c505fbf5279f5d717790ed36eefcc2b8>
> Note that there are still some modules (e.g. Bio::DB::SeqFeature::Store,
> Bio::DB::SeqFeature::**NormalizedFeature, Bio::SeqFeature::Lite,
> Bio::DB::SeqFeature, Bio::Search::Tiling::**MapTileUtils) that have an
> add_SeqFeature() method that accepts an array of features but they are not
> Bio::FeatureHolderI, so that's ok. Maybe they should be Bio::FeatureHolderI
> but that's another story.
> However, I have found that Bio::SimpleAlign is a Bio::FeatureHolderI and
> is not compliant. I fixed it here: https://github.com/bioperl/**
> bioperl-live/commit/**29e0449d05f37c9c748aaaff8cfe59**6ca7c3d380<https://github.com/bioperl/bioperl-live/commit/29e0449d05f37c9c748aaaff8cfe596ca7c3d380>
> Florent
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