Re: name searching in gbrowse_syn

HI Eva,

I am going to ask the list for help on this one.  The wormbase version
is using Bio::DB::GFF adapters for the species.

Sheldon


---------- Forwarded message ----------
From: Eva Huala <huala@...>
Date: Mon, May 11, 2009 at 2:30 PM
Subject: name searching in gbrowse_syn
To: Sheldon McKay <mckays@...>, Cynthia Lee <leech@...>


Hi Sheldon,

We've been working on getting name searching to work within
gbrowse_syn  but it keeps throwing an exception:

------------- EXCEPTION -------------
MSG: Can't locate object method "factory" via package "Bio::DB::SeqFeature"
STACK Bio::DB::SeqFeature::NormalizedFeature::AUTOLOAD
/usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/SeqFeature/NormalizedFeature.pm:390
STACK Bio::Graphics::Browser::Synteny::whole_segment
/usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/Synteny.pm:377
STACK main::navigation_table /var/www/gbrowse/cgi-bin/gbrowse_syn:992
STACK main::search_form /var/www/gbrowse/cgi-bin/gbrowse_syn:237
STACK toplevel /var/www/gbrowse/cgi-bin/gbrowse_syn:136
-------------------------------------

It looks like the wormbase dev gbrowse_syn was able to get it working.
Could it possibly be a GFF3 issue? Or is there something special with
the conf file that we need to do in able to do to enable it?

Eva



--
Sheldon McKay, PhD
Cold Spring Harbor Laboratory
Office/Mobile:  516-367-6998 / 631-651-9728

Sent from Toronto, Ontario, Canada

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