[Bioperl-l] reading and writing GFF3

[Chris Fields]

Scott, 

Looks like Robert also submitted a bug report related to this as well.
Could you check into it (pretty-please)?  I'm still GFF3-illiterate.

http://bugzilla.open-bio.org/show_bug.cgi?id=2025

Chris

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Scott Cain
> Sent: Friday, June 16, 2006 9:18 AM
> To: Robert Buels
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] reading and writing GFF3
> 
> Hi Rob,
> 
> I sympathize with your pain--writing GFF3 isn't as easy as writing GFF2,
> but that is actually a good thing.  The tighter constraints results in a
> better, more consistent file format.
> 
> The reason only BSF::Annotated features are writable is that there needs
> to be tight control on the 'type' of the feature, to insure that the
> type is part of the Sequence Ontology.  It also makes it much easier to
> properly write out the attributes in the ninth column, particularly the
> ones that are 'reserved', like Parent, Dbxref, and Ontology_term.
> 
> BTG is still usable, but the GFF3 it puts out is actually more
> 'GFF3-like'; that is, it looks like GFF3, but because there are no
> constraints on the type and the terms that are used in the ninth column,
> you have to be very careful using it to produce GFF3, by making sure
> that your feature objects conform to the standard before BTG tries to
> write them out.  (Of course, one way to do that would be to convert your
> feature objects to BSF::Annotated objects, but then you could use
> BFIO::gff :-)
> 
> [Long pause while scott goes and monkeys with Bio::Tools::GFF]
> 
> OK, I just committed a fix Bio::Tools::GFF which produces valid GFF3 for
> your sample data.  Conveniently, since 'nucleotide_motif' is a SO term,
> this is completely valid.  (I even fixed the escaping the of the stray
> '=' in 'hind_R=2046'.)  The output I get is this:
> 
> ##gff-version 3
> C08HBa0001K22.1 RepeatMasker    nucleotide_motif        2095    2556
> 918     -       .       Target=Contig151 325 832
> C08HBa0001K22.1 RepeatMasker    nucleotide_motif        2590    2736
> 488     -       .       Target=Contig386 1 124
> C08HBa0001K22.1 RepeatMasker    nucleotide_motif        2787    3105
> 1718    +       .       Target=Contig358 1 311
> C08HBa0001K22.1 RepeatMasker    nucleotide_motif        3974    4036
> 312     -       .       Target=hind_R%3D2046 59 120
> 
> Scott
> 
> 
> 
> On Thu, 2006-06-15 at 18:37 -0700, Robert Buels wrote:
> > There is stuff in bioperl for reading and writing GFF3.  There's
> > Bio::Tools::GFF.  There's Bio::FeatureIO::gff.  Are there more?  Which
> > is the 'best' one to use?
> >
> > Neither of these is working very well for me.
> >
> > My proximate use case is reading in a RepeatMasker report with
> > Bio::Tools::RepeatMasker, which spits out FeaturePair objects, then
> > writing those out to a GFF3 file.
> >
> > Bio::Tools::GFF will take these things and write out something that
> > closely resembles GFF3, but with Target attributes that don't seem to
> > comply with Lincoln's GFF3 spec, since its coordinates are join()ed with
> > commas instead of spaces.  I'm attaching a little script that
> > illustrates this.
> >
> > Bio::FeatureIO::gff refuses to take these FeaturePairs or either of the
> > features contained in them, throwing 'only Bio::SeqFeature::Annotated
> > objects are writeable'.  This seems a bit silly, since one of the whole
> > points of Bioperl is using polymorphism to make it easy to connect
> > things together.  I've attached a little script to illustrate this one
> too.
> >
> > So my questions are:  what _should_ I be doing here?  Is Bio::Tools::GFF
> > deprecated?  Why does Bio::FeatureIO::gff only accept
> > Bio::SeqFeature::Annotated objects?
> >
> > Thanks in advance.
> >
> > Rob
> >
> > _______________________________________________
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> > Bioperl-l at lists.open-bio.org
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> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                         cain at cshl.edu
> GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
> Cold Spring Harbor Laboratory