[Bioperl-l] [Gmod-gbrowse] Cannot dump GFF with relative coords using Bio::DB::SeqFeature backend

Lincoln Stein lstein at cshl.edu
Fri Mar 30 10:01:31 EDT 2007


Hi Dan,

This is an inadvertent omission. I will need to add the refseq() method bo
Bio::DB::SeqFeature::Segment. It simply stores the start and strand
information from the reference sequence and then uses that information to
offset the coordinates returned by start(), end() and strand().

Lincoln

On 3/30/07, Daniel Lang <daniel.lang at biologie.uni-freiburg.de> wrote:
>
> Hi,
>
> when trying to dump GFF (2, 2.5 or 3) with coordinates relative to
> dumped segment from "Bio::DB::SeqFeature-backended" gbrowse, I get the
> following error:
>
> Can't locate object method "refseq" via package
> "Bio::DB::SeqFeature::Segment" at
> /var/www/gbrowse/conf//gbrowse.conf/plugins/GFFDumper.pm line 128.,
>
> I'm using bioperl-live and gbrowse-stable (both cvs as of yesterday, but
> also looked in other branches for different versions of both modules).
>
> Looking into GFFDumper.pm and Segment.pm reveals, that Segment.pm indeed
> does not offer a method like Bio::DB::GFF::Segment::refseq, which seems
> to reset the seqments coords somehow. I didn't look deeper into what
> refseq really does...
>
> If I got it right...
> Currently the function would be handy for me - Can anyone think of a
> short-term work-around? I've seen there are functions in
> Bio::DB::SeqFeature::Segment to transform relative <-> absolute
> coordinates, but don't really know how to make them work in the context
> of GFFDumper.pm line 128.
>
> Thanks in advance!
>
> Daniel
>
> --
>
> Daniel Lang
> University of Freiburg, Plant Biotechnology
> Schaenzlestr. 1, D-79104 Freiburg
> fax: +49 761 203 6945
> phone: +49 761 203 6974
> homepage:  http://www.plant-biotech.net/
> e-mail: daniel.lang at biologie.uni-freiburg.de
>
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> #################################################
>
>
>
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Lincoln D. Stein
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