[Bioperl-l] writing gff - what's the minumum set of objects?

[Sean Davis]

Chad, is this what you are looking for?

http://www.sanger.ac.uk/Software/formats/GFF/

Sean

----- Original Message ----- 
From: "Matsalla, Chad" <MatsallaC at agr.gc.ca>
To: <bioperl-l at bioperl.org>
Sent: Wednesday, December 01, 2004 7:31 PM
Subject: [Bioperl-l] writing gff - what's the minumum set of objects?


> 
> Greetings all,
> 
> I'm trying to determine the **minimum**  required set of objects
> required to write a line of GFF. I'm doing this so that I can expand the
> types of annotations that can be geenrated from TIGR's Arabidopsis
> annotations.
> 
> Parsing the XML is not a problem. What _is_ a problem is writing the
> gff.
> 
> So far, I have found that this[1], which writes this[2], is the minimum
> required set of operations required to write, say, part of the reference
> sequence.
> 
> Am I missing something or is this **really** complicated? Is there a
> simpler way to do this?
> 
> As part of this effort, I've done a bit of work in gff.pm and
> Annotation.pm. I hope that this doesn't colide with similar work going
> on.
> 
> In addition can Hilmar or someone familiar tell me why the 'type'
> annotation must be a Bio::Annotation::OntologyTerm ? Why can't it be an
> arbitrary string?
> 
> An additional question is:
> in gff.pm, can I write an algorithm such that if a certain annotation
> occurs in an Annotated(say, GROUP) then it's used in the ninth field of
> the GFF rather than anything else.
> 
> The reason for that is that if people want to control what grouping is
> used they need control over that field of the gff.
> 
> Thanks for the input,
> 
> Chad Matsalla
> 
> 
> 
> [1]
> sub get_annotated_feature {
>     my ($name,$coordset,$type,$annotation_string) = @_;
>     my $feature = new Bio::SeqFeature::Annotated(
>          -seq_id     =>   $name,
>          -source   =>   "example",
>          -primary  =>   $name,
>          -type     =>   new Bio::Annotation::OntologyTerm(-name =>
> 'Chromosome'),
>          -start    =>   $coordset->getEND5()->getData(),
>          -end      =>   $coordset->getEND3()->getData(),
>          -strand   =>   '+'
>     );
>     $feature->add_Annotation('Name',new
> Bio::Annotation::SimpleValue($name));
>     return $feature;
> }
> 
> [2]
> F8G22   example Chromosome      1       42801   .       +       .
> Name=F8G22
> 
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