Error with Gbrowse_syn tutorial: Can't locate object method "refseq" via package "Bio::DB::SeqFeature::Segment"

[Casey McGrath]

Hi,
I am attempting to follow the Gbrowse_syn tutorial to view the rice
and wild_rice data.  I am using the most current versions of Gbrowse
and Bioperl and I have followed the tutorial exactly (no changes to
conf files, etc.).  Gbrowse works fine to view the rice and wild_rice
genomes.  When using Gbrowse_syn
(http://localhost/cgi-bi/gbrowse_syn/oryza), I get this error message:

Software error:

Can't locate object method "refseq" via package
"Bio::DB::SeqFeature::Segment" at C:/Apache2.2/cgi-bin/gbrowse_syn
line 889.

When looking into Bio::DB::SeqFeature::Segment.pm, there does not in
fact appear to be a "refseq" method.  I'm not sure what refseq is
meant to do -- is it similar to abs2rel or rel2abs, which are in
Segment.pm?  I tried replacing the call to refseq on line 889 of
gbrowse_syn with a call to abs2rel, and this seems to work -- I am
able to view the rice and wild_rice synteny alignments.  However, I
then also replaced it with rel2abs, and this works too.  I can't
really see any difference in the alignment between the two calls, but
I'm sure it's there somewhere.  Any idea which call it should really
be -- abs2rel or rel2abs?

Thanks,
Casey

--
----------------------------
Casey McGrath
Graduate Student
Dept. of Biology, Indiana University
Lynch Lab
1001 E. 3rd St.
Bloomington, Indiana 47405
[phone]

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[Sheldon McKay-3]

Hi Casey,

I believe this is fixed in the latest version in CVS but what you can
do is just use $segment->ref, which is the alias of the refseq (or
vice versa) method in other database adapters but is missing in
Bio::DB::SeqFeature::Segment.  The purpose of this method call is just
to get the name of the sequence.

Sheldon


2009/9/11 Casey McGrath <clmcgrat@...>:

> Hi,
> I am attempting to follow the Gbrowse_syn tutorial to view the rice
> and wild_rice data.  I am using the most current versions of Gbrowse
> and Bioperl and I have followed the tutorial exactly (no changes to
> conf files, etc.).  Gbrowse works fine to view the rice and wild_rice
> genomes.  When using Gbrowse_syn
> (http://localhost/cgi-bi/gbrowse_syn/oryza), I get this error message:
>
> Software error:
>
> Can't locate object method "refseq" via package
> "Bio::DB::SeqFeature::Segment" at C:/Apache2.2/cgi-bin/gbrowse_syn
> line 889.
>
> When looking into Bio::DB::SeqFeature::Segment.pm, there does not in
> fact appear to be a "refseq" method.  I'm not sure what refseq is
> meant to do -- is it similar to abs2rel or rel2abs, which are in
> Segment.pm?  I tried replacing the call to refseq on line 889 of
> gbrowse_syn with a call to abs2rel, and this seems to work -- I am
> able to view the rice and wild_rice synteny alignments.  However, I
> then also replaced it with rel2abs, and this works too.  I can't
> really see any difference in the alignment between the two calls, but
> I'm sure it's there somewhere.  Any idea which call it should really
> be -- abs2rel or rel2abs?
>
> Thanks,
> Casey
>
> --
> ----------------------------
> Casey McGrath
> Graduate Student
> Dept. of Biology, Indiana University
> Lynch Lab
> 1001 E. 3rd St.
> Bloomington, Indiana 47405
> [phone]
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>

--
Sheldon McKay, PhD
Cold Spring Harbor Laboratory
Office/Mobile:  [phone]

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