[Bioperl-l] Re: welcome back to your main trunk!

[Heikki Lehvaslaiho]

Ewan,

Sorry to spoil the fun, but I had to do the logical thing and change
the Bio::Tools::CodonTable::translate to throw when it does not get an
argument. If the attribute is an empty string, an empty string is
returned.
Changes are committed into bioperl-live.

You've got one more bug to track down...

	-Heikki


Heikki Lehvaslaiho wrote:
> 
> Ewan,
> 
> The warning from CodonTable.pm comes when translate function is called
> without a sequence argument. You should not be doing that.
> 
> I'll add code to check this. Would you like this to throw an error or
> return silently an empty string?
> 
>         -Heikki
> 
> Ewan Birney wrote:
> >
> > I'm pleased to say that tests now pass on the main trunk.
> >
> > Use of uninitialized value at
> > /home/birney/src/bioperl-live/Bio/Tools/CodonTable.pm line 407.
> > ok
> > All tests successful.
> > Files=30,  Tests=369, 75 wallclock secs (63.56 cusr +  4.31 csys = 67.87
> > CPU)
> >
> > This means people who were holding off committing to the main trunk, like
> > Frank, can now join the party
> >
> > I am pretty sure there will be some latent bugs to come out; I don't
> > suggest either the web or gene build crew to move to the main trunk
> > without either me or Arne within shouting distance.
> >
> > That said, I'm hopeful; many of the problems I fixed in the later tests
> > were solely to do with the id/stable_id change (detailed below) and
> > nearly everything else just was untouched.
> >
> > I'm planning on tuesday perhaps to spend time with Michele/Val on seeing
> > if we can move the pipeline to the main trunk when I am around. (I guess
> > this means you should make a 1.1 compatible branch of the analysis
> > pipeline). Would this be ok? I'll also look at getting a new schema web
> > site up for testing - we'll need some Eprof runs also at the object layer.
> >
> > In the given out business objects, the only *big* change is that rather
> > than
> >
> >   $exon->id,$gene->id etc
> >
> > you now have
> >
> >   $exon->stable_id (ENSE number) and $exon->dbID  (internal identifier)
> >
> > etc for all the other transcript, exon, gene, translation
> >
> >   $object->id still works; it gives a deprecation warning, indicates which
> > line you should change and then tries to guess what you want (probably
> > badly)
> >
> > The only real "it-will-break" change is making translation objects. Rather
> > than setting $transl->start_exon_id you set $transl->start_exon($exon).
> >
> > $transl->start_exon_id exists but throws an exception and says what you
> > should do.
> >
> > (ditto for end_exon_id etc).
> >
> > Internally you don't use Gene_Obj to get/write genes. Instead you use
> > GeneAdaptor. I'll leave Gene_Obj in with a big fat "remove this
> > now" warning. Or should I make it an exception? Probably. hmmmmm.
> >
> > The basic route is
> >
> >   $gad = $db->get_GeneAdaptor();
> >
> >   # read
> >
> >   $gene = $gad->fetch_by_dbID(12230);
> >
> >   $gene = $gad->fetch_by_stable_id("ENSG0000000000012");
> >
> >   # write
> >
> >   $dbid = $gad->store($gene);
> >
> >   ($gene->dbID also gets set in the store process)
> >
> > EMBLOAD system does work with this, but - Tim - no doubt there will be
> > some fiddles here with your stuff, in particular what we want to make the
> > "stable_id" to be in your system.
> >
> > The schema is much cleaner, but the big win is the code, which is 10 fold
> > cleaner. Respect to Arne and his new Adaptor scheme for really simplyfying
> > writing these persistence layers.
> >
> > ewan
> >
> > -----------------------------------------------------------------
> > Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> > <birney@ebi.ac.uk>.
> > -----------------------------------------------------------------
> 
> --
> ______ _/      _/_____________________________________________________
>       _/      _/                      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
> ___ _/_/_/_/_/________________________________________________________

-- 
______ _/      _/_____________________________________________________
      _/      _/                      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
___ _/_/_/_/_/________________________________________________________