[Bioperl-l] Write segments with Bio::Tools::GFF

[Daniel Standage]

I'm using a tool called AnnotationSketch (part of the GenomeTools package)
to create graphics from my GFF3 files. It complains when sequence-region
lines are not included, even when the reference is printed as a feature.
That's what got me interested in the problem in the first place.

Thanks for the info, I'll figure something out.

Daniel

On Wed, Nov 3, 2010 at 3:09 PM, Scott Cain <scott at scottcain.net> wrote:

> Hi Daniel,
>
> Why do you need the sequence-region line?  It is mostly just
> informational.  If you want to define the reference sequence for the
> features in the GFF file, I would suggest printing out a full GFF line
> for the reference sequence instead anyway.  That way, it can have all
> the information that a GFF line can encode, like a source and type, as
> well as information in the ninth column.
>
> That said, Bio::Tools::GFF probably does lack that method.  The code
> in it is probably a little outdated.
>
> Scott
>
>
> On Wed, Nov 3, 2010 at 2:42 PM, Daniel Standage
> <daniel.standage at gmail.com> wrote:
> > Hi
> >
> > I've got a simple script that is filtering some GFF3 data. The
> > Bio::Tools::GFF class has methods for reading and writing features and
> > reading regions (segments), but I cannot find a method for writing
> regions.
> > It's not hard to just print out the sequence-region line from the
> > LocatableSeq object, but then these lines are printed out before the
> > gff-version line (which is a no-no). Any suggestions about how to handle
> > this?
> >
> > Thanks.
> >
> > --
> > Daniel S. Standage
> > Graduate Research Assistant
> > Bioinformatics and Computational Biology Program
> > Iowa State University
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>



-- 
Daniel S. Standage
Graduate Research Assistant
Bioinformatics and Computational Biology Program
Iowa State University