[Bioperl-l] Re: GFF3

[Allen Day]

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