[Bioperl-l] Re: Bioperl-l Digest, Vol 18, Issue 1

[Scott Cain]

Allen,

I apparently don't get mail addressed to scain at pub.open-bio.org, so I
didn't get this message until this morning when I read the bioperl
digest.

So, why can't I handle it this way?  It seems to work just fine for the
bulk loader.

Scott

On Fri, 2004-10-01 at 10:02, bioperl-l-request at portal.open-bio.org
wrote:
> Date: Wed, 29 Sep 2004 13:52:39 -0700 (PDT)
> From: Allen Day <allenday at ucla.edu>
> Subject: [Bioperl-l] Re: [Bioperl-guts-l] bioperl commit
> To: Scott Cain <scain at pub.open-bio.org>
> Cc: Bioperl <bioperl-l at bioperl.org>
> Message-ID: <Pine.LNX.4.58.0409291351410.27667 at sumo.ctrl.ucla.edu>
> Content-Type: TEXT/PLAIN; charset=US-ASCII
> 
> Scott,
> 
> You can't handle Ontology_term as a SimpleValue, that's why I didn't
> implement it that way.  You need to rather create a
> Bio::Annotation::OntologyTerm.
> 
> -Allen
> 
> On Sat, 25 Sep 2004, Scott Cain wrote:
> 
> > 
> > scain
> > Sat Sep 25 07:41:29 EDT 2004
> > Update of /home/repository/bioperl/bioperl-live/Bio/FeatureIO
> > In directory pub.open-bio.org:/tmp/cvs-serv2444/Bio/FeatureIO
> > 
> > Modified Files:
> > 	gff.pm 
> > Log Message:
> > two things:
> >   * adding SOFA as an available ontology to DocumentRegistry.pm
> >   * modifying FeatureIO::gff to use SOFA to validate, and to parse Ontology_term
> > 
> > bioperl-live/Bio/FeatureIO gff.pm,1.9,1.10
> > ===================================================================
> > RCS file: /home/repository/bioperl/bioperl-live/Bio/FeatureIO/gff.pm,v
> > retrieving revision 1.9
> > retrieving revision 1.10
> > diff -u -r1.9 -r1.10
> > --- /home/repository/bioperl/bioperl-live/Bio/FeatureIO/gff.pm	2004/09/21 23:15:22	1.9
> > +++ /home/repository/bioperl/bioperl-live/Bio/FeatureIO/gff.pm	2004/09/25 11:41:29	1.10
> > @@ -91,8 +91,9 @@
> >    }
> >    $self->_pushback($directive);
> >  
> > +  #need to validate against SOFA, no SO
> >    $self->so(
> > -            Bio::Ontology::OntologyStore->get_ontology('Sequence Ontology')
> > +            Bio::Ontology::OntologyStore->get_ontology('Sequence Ontology Feature Annotation')
> >             );
> >  }
> >  
> > @@ -315,9 +316,9 @@
> >    }
> >  
> >    #Handle Ontology_term attributes
> > -  if($attr{Ontology_term}){
> > -    $self->warn("Warning for line:\n$feature_string\nOntology_term attribute handling not yet implemented, skipping it");
> > -  }
> > +#  if($attr{Ontology_term}){
> > +#    $self->warn("Warning for line:\n$feature_string\nOntology_term attribute handling not yet implemented, skipping it");
> > +#  }
> >  
> >    #Handle Gap attributes
> >    if($attr{Gap}){
> > @@ -351,7 +352,7 @@
> >      $ac->add_Annotation('Name',$a);
> >    }
> >  
> > -  foreach my $other_canonical (qw(Alias Parent Note)){
> > +  foreach my $other_canonical (qw(Alias Parent Note Ontology_term)){
> >      if($attr{$other_canonical}){
> >        foreach my $value (@{ $attr{$other_canonical} }){
> >          my $a = Bio::Annotation::SimpleValue->new();
> > 
> > _______________________________________________
> > Bioperl-guts-l mailing list
> > Bioperl-guts-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-guts-l
> > 

-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.org
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory