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

[Chris Mungall]

I have committed this as

Bio::SeqFeature::Tools::Unflattener

there is one test
t/Unflattener.t

The namespace isn't final (is there a standard way to indicate this), I'm
not sure what it should be, let's see how the bio-cpan thing turns out.
this wouldn't be a core module.

On Mon, 23 Jun 2003, Chris Mungall wrote:

>
> 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
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at portal.open-bio.org
> > > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> > >
> >
> > --
> > Jason Stajich
> > Duke University
> > jason at cgt.mc.duke.edu
> >
>
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