Re: name searching in gbrowse_syn
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Re: name searching in gbrowse_syn
by Scott Cain-4
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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 ------------------------------------------------------------------------------ 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 |
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Re: name searching in gbrowse_syn
by Cynthia Lee
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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, ------------------------------------------------------------------------------ Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers & brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, & iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian Group, R/GA, & Big Spaceship. http://www.creativitycat.com _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: name searching in gbrowse_syn
by Sheldon McKay-3
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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 ------------------------------------------------------------------------------ Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers & brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, & iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian Group, R/GA, & Big Spaceship. http://www.creativitycat.com _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: name searching in gbrowse_syn
by Cynthia Lee
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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 -------------Cynthia On Wed, May 20, 2009 at 5:57 PM, Sheldon McKay <sheldon.mckay@...> wrote: Hi Cynthia, ------------------------------------------------------------------------------ Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers & brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, & iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian Group, R/GA, & Big Spaceship. http://www.creativitycat.com _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: name searching in gbrowse_syn
by Sheldon McKay-3
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Hi Cynthia,
Sorry about that. You mentioned earlier that you had a patch that worked for you. Would you mind sharing it with me? Sheldon On Fri, May 22, 2009 at 8:13 PM, Cynthia Lee <leech@...> wrote: > 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 > > -- Sheldon McKay, PhD Cold Spring Harbor Laboratory Office/Mobile: 516-367-6998 / 631-651-9728 Sent from Milford, Connecticut, United States ------------------------------------------------------------------------------ Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers & brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, & iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian Group, R/GA, & Big Spaceship. http://www.creativitycat.com _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: name searching in gbrowse_syn
by Cynthia Lee
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Hi Sheldon,
Recently we updated the CVS and reinstalled GBrowse and now it seems like our VISTA plot is no longer working. The version we have of gbrowse is this one: # $Id: gbrowse.PLS,v 1.119.4.57.2.59.2.128 2009/05/11 13:41:38 scottcain Exp $ and the error we are now getting when we try to load the vista plot is this: (this is happening in the error_log. not on the actual gbrowse display page. on that page, no error is displayed, the track just simply does not show) >[Tue Jun 02 14:25:40 2009] [error] [client 10.10.50.22] Use of uninitialized value $nr_tracks_added in numeric eq (==) at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser.pm line 1397. >[Tue Jun 02 14:25:40 2009] [error] [client 10.10.50.22] Use of uninitialized value $nr_tracks_added in subtraction (-) at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser.pm line 1404. Is there something specific we need to do? I know when we were on this version the vista plot was still working : # $Id: gbrowse.PLS,v 1.119.4.57.2.59.2.121 2009/02/20 19:14:48 scottcain Exp $ Any help would be great. Thanks, Cynthia ------------------------------------------------------------------------------ OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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