Re: name searching in gbrowse_syn

> Hi Sheldon,
>
> Today I updated the cvs and did a reinstall, however I'm still getting the
> error. It is still looking to call the factory method on Bio::DB::SeqFeature
> instead of Bio::DB::SeqFeature::Segment. :(
>
> Stacktrace:
>
> ------------- 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:378
> STACK main::navigation_table /var/www/gbrowse/cgi-bin/gbrowse_syn:996
> STACK main::search_form /var/www/gbrowse/cgi-bin/gbrowse_syn:236
>
> STACK toplevel /var/www/gbrowse/cgi-bin/gbrowse_syn:135
> -------------------------------------
>
> Cynthia
>
> On Wed, May 20, 2009 at 5:57 PM, Sheldon McKay <sheldon.mckay@...>
> wrote:
>>
>> Hi Cynthia,
>>
>> Thanks for the info.  I committed a solution to the sourceforge CVS
>> repository.
>> Next time you update, please let us know if this does what you need.
>>
>> Sheldon
>>
>>
>> On Wed, May 20, 2009 at 8:18 PM, Cynthia Lee <leech@...> wrote:
>> > Hi Scott and Sheldon,
>> >
>> > I've been poking around with the Bio::Graphics::Browser.pm code, and it
>> > seems like when you do a search for a chromosome region, it will do a
>> > $db->segment(@argv) and return to you a list of
>> > Bio::DB::SeqFeature::Segment
>> > value.
>> >
>> > However, if we do a search for a name, the code that is called is
>> > $db->get_features_by_name(@argv) which returns to you a list of
>> > Bio::DB::SeqFeature values. Therefore, later on when it tries to do a
>> > call
>> > on the factory() of the segment, it fails. If I add in some code that
>> > iterates through the list of SeqFeatures, and turns it into a list of
>> > its'
>> > segments, the synteny viewer name searching seems to work as expected.
>> >
>> > I hope this helps, and maybe we can get this fix up in the future.
>> >
>> > Thanks,
>> > Cynthia
>> >
>> > On Mon, May 11, 2009 at 11:42 AM, Scott Cain <scott@...>
>> > wrote:
>> >>
>> >> Hi Sheldon,
>> >>
>> >> I'm no expert on SeqFeature::Store but the "factory" in SFStore is the
>> >> Store object itself.  For example, calls to store in the
>> >> SFStore::Segment object returns the Store object.  Now, how this
>> >> information helps in the context of the synteny browser, I don't know.
>> >>  Perhaps the synteny browser software is making a call to factory in a
>> >> way that would work with Bio::DB::GFF but not with SFStore?
>> >>
>> >> Scott
>> >>
>> >>
>> >> On Mon, May 11, 2009 at 2:33 PM, Sheldon McKay
>> >> <sheldon.mckay@...>
>> >> wrote:
>> >> > 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
>> >> >
>> >> >
>> >> >
>> >> > ------------------------------------------------------------------------------
>> >> > The NEW KODAK i700 Series Scanners deliver under ANY circumstances!
>> >> > Your
>> >> > production scanning environment may not be a perfect world - but
>> >> > thanks
>> >> > to
>> >> > Kodak, there's a perfect scanner to get the job done! With the NEW
>> >> > KODAK
>> >> > i700
>> >> > Series Scanner you'll get full speed at 300 dpi even with all image
>> >> > processing features enabled. http://p.sf.net/sfu/kodak-com
>> >> > _______________________________________________
>> >> > Gmod-gbrowse mailing list
>> >> > Gmod-gbrowse@...
>> >> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >>
>> >> ------------------------------------------------------------------------
>> >> Scott Cain, Ph. D.                                   scott at scottcain
>> >> dot net
>> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >> Ontario Institute for Cancer Research
>> >
>> >
>>
>>
>>
>> --
>> Sheldon McKay, PhD
>> Cold Spring Harbor Laboratory
>> Office/Mobile:  516-367-6998 / 631-651-9728
>
>