[Bioperl-l] Re: GFF3

[Allen Day]

Hi,

On Mon, 17 Jan 2005, Scott Cain wrote:

> Hi Rob,
> 
> Thanks for your work on this--I've put several comments in your
> original message below.
> 
> Scott
> 
> ---------Original Message--------
> Date: Sat, 15 Jan 2005 15:22:23 -0800
> From: Rob Edwards <rob at salmonella.org>
> Subject: [Bioperl-l] GFF3
> To: Bioperl list <bioperl-l at portal.open-bio.org>
> 
> Because I need it for some things that I am doing, I have worked quite 
> a bit on the GFF3 parser Bio::FeatureIO::gff. Several people have 
> written this module, I have just made some cosmetic changes:
> 
> I have improved the validation processes that are applied as a gff3 
> file is parsed, and the module should now validate essentially 
> everything in the file except alignments. Validation is optional and is 
> based on the specification described at : 
> http://song.sourceforge.net/gff3.shtml
> 
> 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.

> 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 also wrote a Bio::SeqIO::gff module. Since gff3 files can hold 
> sequences, it seems that you'd want to be able to call the next_seq 
> methods, and therefore SeqIO is more appropriate than FeatureIO for 
> those aspects. Currently the SeqIO module uses the FeatureIO module for 
> parsing the file, it just reorganizes things.
> 
> This provides two different interfaces for getting objects out of GFF3 
> files:
> 	Bio::FeatureIO::gff will return Bio::SeqFeature::Annotated objects 
> representing the annotations.
> 	Bio::SeqIO::gff will return Bio::Seq objects representing the 
> sequences with all the annotations attached.
> 
> The other difference between the two is that the former passes out the 
> objects as they are read, but the latter has to read the whole file to 
> get the annotations and the sequences.
> 
> SC> I thought about doing something similar with SeqIO, but I am worried 
> SC> about the case where somebody tries to use SeqIO on a well 
> SC> annotated human Chr1 GFF3 file (if one were ever to exist :-) ,
> SC> but I suppose the same machine killing thing could be done if
> SC> someone tried to use SeqIO on a genbank file of Chr1.

See my previous email, I don't think we need the SeqIO module.

> At the moment I focussed on reading GFF3 files.
> 
> I have not committed these to cvs yet, pending comments from others. I 
> have some specific questions:
> 	Should I wait until after 1.5 is out?
> 
> 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

> 	Is two separate modules really the right way to go about this?
> 
> SC> As long as it works for this case, I don't mind:  calling
> SC> 'next_feature' on a FeatureIO object until I run out of features
> SC> and then calling 'next_sequence' (and get a Bio::PrimarySeq) on
> SC> the same FeatureIO object until I run out of sequences.
> 
> 	What about other GFF modules (like Bio::Tools::GFF)?
> 
> SC> I am willing to let Bio::Tools::GFF die a terrible death.  While
> SC> it will have to be kept around for apps that depend on it, I don't
> SC> see adding any major functionality as time well spent.
> 
> 	Could someone give the modules a workout and let me know about bugs? I 
> am sure there are many.
> 
> SC> I will try to soon, but it won't be until next week at 
> SC> the earliest.
> 
> I have posted these modules online via anonymous ftp at 
> ftp://ftp.salmonella.org/rob/bioperl/GFF_modules.tgz
> Take a look and let me know what you do and don't like!
> 
> Rob
> 
> 
> ----------------------------------------------------------------------
> Scott Cain, Ph. D.				 	 cain at cshl.org
> GMOD Coordinator, http://www.gmod.org/			 (216)392-3087
> ----------------------------------------------------------------------
> 
> 
> 
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