[Bioperl-l] Bio::Tools::GFF

Scott Cain cain at cshl.edu
Fri Apr 28 09:14:35 EDT 2006


Hi Chris and Paul,

I committed the change--Paul is right, the list was really out of date.
Thanks for pointing it out.

Scott


On Fri, 2006-04-28 at 08:03 -0500, Chris Fields wrote:
> Lincoln's working on GFF3 integration into BioPerl at the moment  
> which will not use Bio::DB::GFF, so there's a bit of reluctance at  
> the moment to commit this unless Lincoln signals that it's fine.
> 
> http://article.gmane.org/gmane.comp.lang.perl.bio.general/10691/match=
> 
> http://www.bioperl.org/wiki/ListSummary:April_12-25%2C2006#Bioperl- 
> guts_.28for_the_die-hards.29
> 
> If you look in CVS in Bio::DB, several new modules have been added  
> (also in the ListSummary above).  You could try those out but I have  
> no idea what kind of working condition they are in and how stable the  
> API is at the moment.
> 
> You could email the GMOD lists as well (I get the GBrowse, which  
> Scott Cain and Lincoln regularly post to).  Info here:
> 
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> 
> Chris
> 
> On Apr 28, 2006, at 5:41 AM, Paul Mooney wrote:
> 
> > Hi,
> >
> > I've modified one line in my local copy of Bio::Tools::GFF so it takes
> > into account *all* of the special tags defined here;
> > http://song.sourceforge.net/gff3.shtml
> >
> > Current CVS version;
> > $tag= lcfirst($tag) unless ($tag =~/^ID|Name|Alias|Parent|Gap|Target 
> > $/);
> >
> > My version;
> > $tag= lcfirst($tag) unless ($tag
> > =~/
> > ^ID|Name|Alias|Parent|Gap|Target|Derives_from|Note|Dbxref| 
> > Ontology_term$
> > /);
> >
> > Could someone update cvs please?
> > Paul.
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory



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