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

Scott Cain scott at scottcain.net
Wed Nov 3 16:19:07 EDT 2010


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 in it is probably a little outdated.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



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