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

Daniel Lang daniel.lang at biologie.uni-freiburg.de
Fri Mar 30 05:20:53 EDT 2007


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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