[Bioperl-l] Re: GFF3

[Scott Cain]

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
> > 
> > --------------------------------------
> > 
>