[Bioperl-l] request for new feature types: Attn. esp. Hilmarand Ewan

[Jason Stajich]

In the general sense of building SeqFeature::Gene objects:

I was thinking we could also consider writing a factory object that would
take a Bio::SeqI and convert (or add) Bio::SeqFeature::Gene objects based
on the SeqFeatures contained within and some configuration of what type
of feature does what.  This would be highly customizable and I hope won't
spawn ontology discussions as there were on the DAS list.    

One could imagine a configuration file that overrides/sets the feature
type => SeqFeature object mapping.

Speaking of config files, I noticed that perl6 will probably have a
~/.perlrc file, perhaps we want to consider ~/.bioperlrc being a place
one could store variables rather than in the %ENV hash?  Or perhaps it can
be the place that %ENV vars are set?  Or create a %BIOENV var since
the file will be perl syntax?  All the code for sucking in the file could
live in Bio::Root::RootI I guess.  Pretty sure it would be a simple
eval().  Or is this adding unnecessary complexity?

-Jason

On Thu, 14 Jun 2001, Heikki Lehvaslaiho wrote:

> I agree.
> 
> I've already created a set of classes inheriting from
> Bio::SeqFeature::Generic. All the instatiable classes inherit from
> Bio::Variation::VariantI and have primary tag 'Variation'.
> 
> The same should be a practical approach to gene features. E.g.: The
> holder object can collect them into a single array (add_genefeature)
> and get methods pick the right ones (each_exon, each_intron,...). 
> 
> 
> 	-Heikki
>  
> Ewan Birney wrote:
> > 
> > I think that making inherieted SeqFeatures is *definitely* the way to
> > go. This is what we do (heavily) inside Ensembl.
> > 
> > Special methods like "translate" or "phase" are v. useful.
> > 
> > -----------------------------------------------------------------
> > Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> > <birney@ebi.ac.uk>.
> > -----------------------------------------------------------------
> > 
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> -- 
> ______ _/      _/_____________________________________________________
>       _/      _/                      http://www.ebi.ac.uk/mutations/
>      _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
>     _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
>    _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
>   _/  _/  _/  Cambs. CB10 1SD, United Kingdom
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Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/