[Bioperl-l] Re: GFF3

[Allen Day]

okay, let me know.  we should probably add some validation tests as well, 
right now i'm just making sure the lines can be processed but don't do any 
typechecking on the document.

Rob, would you mind writing some tests into FeatureIO.t for your 
validation code?

-allen


On Wed, 19 Jan 2005, Scott Cain wrote:

> I just did a cvs update and the last few tests are failing on MacOSX 10.3.
> I'll try to sort it out over the next couple of days.
> 
> Scott
> 
> ----------------------------------------------------------------------
> Scott Cain, Ph. D.				 	 cain at cshl.org
> GMOD Coordinator, http://www.gmod.org/			 (216)392-3087
> ----------------------------------------------------------------------
> 
> 
> On Tue, 18 Jan 2005, Allen Day wrote:
> 
> > > The first series of errors die because the feature ID=AB000114 in 
> > > t/data/knownGene.gff3 has several Dbxrefs separated with ';' instead of 
> > > ','
> > 
> > i'm not getting these errors, are you are in sync with cvs HEAD?
> > 
> > > The second failure is because  hybrid1.gff3 isn't in cvs
> > 
> > gff files are in cvs now.
> > 
> > > 
> > > Rob
> > > 
> > > 
> > > 
> > > % perl -I. -w t/FeatureIO.t
> > > 1..19
> > > ok 1
> > > ok 2
> > > ok 3
> > > ok 4
> > > ok 5
> > > ok 6
> > > Use of uninitialized value in substitution (s///) at 
> > > Bio/FeatureIO/gff.pm line 590, <GEN5> line 10.
> > > Use of uninitialized value in substitution (s///) at 
> > > Bio/FeatureIO/gff.pm line 591, <GEN5> line 10.
> > > Use of uninitialized value in split at Bio/FeatureIO/gff.pm line 593, 
> > > <GEN5> line 10.
> > > Use of uninitialized value in substitution (s///) at 
> > > Bio/FeatureIO/gff.pm line 590, <GEN5> line 10.
> > > Use of uninitialized value in substitution (s///) at 
> > > Bio/FeatureIO/gff.pm line 591, <GEN5> line 10.
> > > Use of uninitialized value in split at Bio/FeatureIO/gff.pm line 593, 
> > > <GEN5> line 10.
> > > Use of uninitialized value in substitution (s///) at 
> > > Bio/FeatureIO/gff.pm line 590, <GEN5> line 10.
> > > Use of uninitialized value in substitution (s///) at 
> > > Bio/FeatureIO/gff.pm line 591, <GEN5> line 10.
> > > Use of uninitialized value in split at Bio/FeatureIO/gff.pm line 593, 
> > > <GEN5> line 10.
> > > Use of uninitialized value in substitution (s///) at 
> > > Bio/FeatureIO/gff.pm line 590, <GEN5> line 10.
> > > Use of uninitialized value in substitution (s///) at 
> > > Bio/FeatureIO/gff.pm line 591, <GEN5> line 10.
> > > Use of uninitialized value in split at Bio/FeatureIO/gff.pm line 593, 
> > > <GEN5> line 10.
> > > Use of uninitialized value in substitution (s///) at 
> > > Bio/FeatureIO/gff.pm line 590, <GEN5> line 10.
> > > Use of uninitialized value in substitution (s///) at 
> > > Bio/FeatureIO/gff.pm line 591, <GEN5> line 10.
> > > Use of uninitialized value in split at Bio/FeatureIO/gff.pm line 593, 
> > > <GEN5> line 10.
> > > Use of uninitialized value in substitution (s///) at 
> > > Bio/FeatureIO/gff.pm line 590, <GEN5> line 10.
> > > Use of uninitialized value in substitution (s///) at 
> > > Bio/FeatureIO/gff.pm line 591, <GEN5> line 10.
> > > Use of uninitialized value in split at Bio/FeatureIO/gff.pm line 593, 
> > > <GEN5> line 10.
> > > ok 7
> > > ok 8
> > > 
> > > ------------- EXCEPTION  -------------
> > > MSG: Could not open t/data/hybrid1.gff3: No such file or directory
> > > STACK Bio::Root::IO::_initialize_io Bio/Root/IO.pm:314
> > > STACK Bio::FeatureIO::_initialize Bio/FeatureIO.pm:345
> > > STACK Bio::FeatureIO::gff::_initialize Bio/FeatureIO/gff.pm:92
> > > STACK Bio::FeatureIO::new Bio/FeatureIO.pm:268
> > > STACK Bio::FeatureIO::new Bio/FeatureIO.pm:288
> > > STACK toplevel t/FeatureIO.t:83
> > > 
> > > --------------------------------------
> > > 
> > 
>