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

[Jason Stajich]

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