[Bioperl-l] Bio::FeatureIO::gff

Mark Johnson johnsonm at gmail.com
Thu Jun 19 16:47:57 EDT 2008


On Thu, Jun 19, 2008 at 3:19 PM, Chris Fields <cjfields at uiuc.edu> wrote:

> I think the general idea of Bio::FeatureIO will remain (read/write feature
> data) but it will definitely undergo significant reimplementation.  The
> typed SeqFeatureI class (Bio::SeqFeature::Annotated) would be deprecated in
> favor of something more lightweight.
>
> However, I don't see that happening until after 1.6 is released unless
> someone wants to take it on.
>
> chris

I suspect the 'something' you mention is going to require a fair bit
of discussion and design.  The best time for that would be after 1.6.
Otherwise, we're likely to end up with something just as problematic
as Bio::SeqFeature::Annotated.

However, people are using Bio::FeatureIO as it stands.  Unless the
plan is to remove it from source control (as opposed to just not
packaging it up as part of the 1.6 release), would there be any
objection to patching up the existing implementation?  If nothing
else, it will be the starting point for the reimplementation.  Might
as well correct obvious defects, so they *don't* get reimplemented.


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