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Re: name searching in gbrowse_syn

by Cynthia Lee :: Rate this Message:

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

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