[Bioperl-l] module for unflattening GenBank/EMBL/DDBJ records

[Chris Mungall]

I still have no idea what the name of this module should be

Hilmar likes it in Bio::SeqFeature

maybe
Bio::SeqFeature::Unflattener

isn't everything else in Bio::SeqFeature data classes? Surely data classes
and behaviour classes should be kept seperate? Also, I'm thinking this
module is an ideal candidate for BPAN, since it is not core. Whilst folk
could add stuff to Bio::SeqFeature in BPAN, should we not try and
separate?

Jason thinks Bio::Tools is too much of a mixed bag and we need an extra
level of namespacing. Aggregator has a different meaning and fluffer is
right out

what about
Bio::Tools::SeqFeature::Unflattener

Or maybe this should be a seperate namespace altogether - I like the idea
of a Bio::Util

Bio::Util::Unflattener
?

Also, whilst the module is fairly generic, I imagine 99% of the time it
will be used specifically for unflattening GenBank records, so maybe the
name should reflect that?

I'll check it in once there is a consensus

cheers
chris

On Wed, 18 Jun 2003, Jason Stajich wrote:

> I personally prefer a little grouping here as Bio::Tools is
> already way too much of a grabbag in its current disorganized
> state.
>
> Lincoln uses 'aggregator' as his descriptor for this type of thing - is it
> appropriate here?
>
>
> Although it definitely becomes a mouthful something like
> Bio::Tools::FeatureAggregator::Unflattener
>
> I guess that aggregator only implies one direction of collecting things...
> hmmm
>
>
> -j
>
> On Wed, 18 Jun 2003, Chris Mungall wrote:
>
> >
> >
> > On Wed, 18 Jun 2003, Ewan Birney wrote:
> >
> > >
> > >
> > > On Tue, 17 Jun 2003, Chris Mungall wrote:
> > >
> > > >
> > > > I have a module (and corresponding .t test) ready to commit to bioperl.
> > > > I'm including the pod docs below.
> > > >
> > > > It is called Bio::Tools::GenBankCollector - is this the correct namespace?
> > > > good name?
> > >
> > > Bio::Tools::GenBankFeatureCollector ???
> >
> > now's the time for a name change if required
> >
> > the idea is that it 'collects' features together, into groups then
> > hierarchies.
> >
> > perhaps 'GenBank' should be removed form the name; though i think the
> > primary use will be GenBank/EMBL/DDBJ sourced data
> >
> > Bio::Tools::Unflattener
> > Bio::Tools::HierarchyBuilder
> > Bio::Tools::NestedFeatureBuilder
> >
> > ?
> >
> > > >
> > > > Should I commit this? Main trunk or branch?
> > > >
> > >
> > > Main trunk.
> >
> > ok
> >
> > > > What is an acceptable size for a t/data file? Is ~400kb fine? Presumably I
> > > > should do a "cvs add -kb" (it is a genbank record).
> > > >
> > >
> > > Fine.
> >
> > ok
> >
> > _______________________________________________
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> >
>
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
>