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

Scott Cain scott at scottcain.net
Wed Nov 3 20:09:45 UTC 2010

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in it is probably a little outdated.


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
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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