[Bioperl-l] Re: GFF3

[Scott Cain]

Weird: when I run the FeatureIO test on the command line (via `perl
t/FeatureIO.t`), all tests pass.  When I run it as part of 'make test',
tests 20-22 fail.  Does anyone know why that sort of thing might happen?

thanks,
Scott

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


On Wed, 19 Jan 2005, Allen Day wrote:

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