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

Daniel Standage daniel.standage at gmail.com
Wed Nov 3 16:29:29 EDT 2010


Yeah, I guess it's not a show stopper, since it still generates the graphics
fine. The output that clutters the terminal is still annoying, but I can
live with that. Thanks!

Daniel

On Wed, Nov 3, 2010 at 3:19 PM, Scott Cain <scott at scottcain.net> wrote:

> Ah, I see.  Well, you should complain to the authors that
> sequence-region isn't a required directive (though if you made that
> complaint to me, I'd say "well, it is for this tool" :-)
>
> Of course, you could also use Bio::Graphics or GBrowse to do the
> drawing, then I could do more to help. :-)
>
> Scott
>
>
> On Wed, Nov 3, 2010 at 4:14 PM, Daniel Standage
> <daniel.standage at gmail.com> wrote:
> > 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 in it is probably a little outdated.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
> >
> >
>
>
>
> --
> ------------------------------------------------------------------------
> 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


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