Re: name searching in gbrowse_syn

> 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
>> >
>> >
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>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>
>