[Bioperl-l] moltype/molecule ; circular sequences!

[Heikki Lehvaslaiho]

Heikki Lehvaslaiho wrote:
> 
> Having slept over the problem and talked with Ewan I propose to do the
> following:
> 
> - revert to previous genbank.pm behaviour on HEAD
> 
> - fix embl.pm to show moltype=dna on RNA entries on HEAD and BRANCH
> 
> - molecule() remains as it is; values are database dependent
> 
> - add new method into PrimarySeqI: is_circular (HEAD)
>   -- values (from ID/LOCUS line): undef/false, true
>   -- update genbank.pm and embl.pm to parse in circularity
>   -- update genbank.pm and embl.pm to write out circularity

All above done. 

If someone wants to think what changes should be done to take into account
that sequences can now be circular, that would be great. Think in terms of a
small cloning plasmid. Restiction sites and/or coding region extending from
the end of the sequence over the origin of the coordinate system.


> - change moltype() into alphabet(), keep moltype() as a depreciated method   (HEAD only) Opinions?

I'll leave this over the weekend rather than commit everything at one go.
(easier to revert CVS if we want to do that).

	-Heikki

> 
> We really should start putting into HEAD all API changes we can think of  so
> that we do not have to change things immediately after 1.0.
> 
> If you think you'll be hit badly by these changes, say so now.
> I will not commit anything until Friday (European time).
> 
>         -Heikki
> 
> Ewan Birney wrote:
> >
> > On Wed, 17 Oct 2001, Heikki Lehvaslaiho wrote:
> >
> > > Sounds like breaking a good old system.
> > >
> > > Why not :
> > > moltype() eq alphabet()
> > >
> > > molecule() could be a shortcut into source/sequenced_mol
> > >     and is it is not defined use the value from ID/Locus line
> > >
> > > I am being difficult?
> >
> > So moltype() ne molecule() - aren't we setting ourselves up for confusion
> > here?
> >
> > I appreciate the need for backward compatibility.
> >
> > What about
> >
> >   ->biological_molecule()
> 
>         ->source_molecule() RichSeqI
>            ->molecule() depreciated
> 
>         ->moltype() meaning alphabet
>         -- revert to old genbank behaviour
>         -- fix embl.pm
> 
> --
> ______ _/      _/_____________________________________________________
>       _/      _/                      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
>      _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
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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
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________