[Bioperl-l] Re: GFF3

[Rob Edwards]

Thanks for you help and comments. Here are a couple of points, and I'll 
work on filling in some of the other gaps.


>> SC> Excellent--Did you happen to relax the requirement that ID be 
>> unique
>> SC> for each line of the GFF?  Allen and I put that in due to a 
>> misreading
>> SC> of the spec.  The ID has to be unique for a *feature*, which can 
>> be
>> SC> spread across several lines.
>
> I'm not sure if this is taken care of in the code... actually, I'm a 
> bit
> foggy on exactly what the problem is.

It is not corrected yet. The problem is this section, around line 669. 
Its not true that each line can only have one ID, and this can be 
removed.

   if($attr{ID}){
     if(scalar( @{ $attr{ID} } ) > 1){
       $self->throw("Error in line:\n$feature_string\nA feature may have 
at most one ID value");
     }


>> For clarification and edification I have created a couple of tables
>> describing the module and the validation that is applied to GFF3 
>> files,
>> which you can see online: http://www.salmonella.org/bioperl/gff3.html
>>
>> SC> Very nice and well done--do you happen to have a pod-ified version
>> SC> of this page?  It would be nice to include in the pod for
>> SC> Bio::FeatureIO::gff.
>
> That's nice, I'd like to see it folded into the gff.pm perldoc as well.

I'll take care of PODify it over the next couple of days.


>> SC> I don't have the definative answer, but I would say it doesn't
>> SC> matter much, as long as it passes tests.  Bio::FeatureIO::gff is
>> SC> hardly a fully functional module as it is, so if we could
>> SC> squeeze a little more functionality into it before we
>> SC> release it, that would be fine with me.
>
> well it's in now.  and it passes tests.  there weren't any before, but 
> i
> wrote some.  look in t/FeatureIO.t

Thanks for those, however at the moment the tests failed. See below.

The first series of errors die because the feature ID=AB000114 in 
t/data/knownGene.gff3 has several Dbxrefs separated with ';' instead of 
','

The second failure is because  hybrid1.gff3 isn't in cvs

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

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