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Re: [Gmod-ajax] 0 features found/no display of data
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From: Scott C. <sc...@sc...> - 2010-10-01 17:43:35
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Ah, OK, things changed; that's good. The fact that the biodb-to-json script reported that it found 1 feature (which is exactly as many as I would expect it to find), means that everything up to that point appears to be working as expected. What is happening beyond there I don't know and will punt to Mitch or Ian; my only guess is browser caching causing a problem. Scott On Fri, Oct 1, 2010 at 1:28 PM, anja <fri...@ho...> wrote: > Hi Scott, > > I used: > > anou@anou-laptop:/var/www$ bp_seqfeature_load.pl --d "dbi:Pg:dbname=test" > --a DBI::Pg --c taro.gff > loading taro.gff... > 98 features loaded in > 0.41s Building object > tree... 0.02s > load time: 0.46s > > anou@anou-laptop:/var/www$ bin/prepare-refseqs.pl --conf taro.json --refs > NC_010109.1 > anou@anou-laptop:/var/www$ bin/biodb-to-json.pl --conf taro.json > > working on refseq NC_010109.1 > working on track nested_tandem_repeat > got 1 features for nested_tandem_repeat > > looks alright, doesnt it? By not working I mean that I dont get to see > anything in my browser, only the data I was loading ages ago. Its like it > doesnt exist... > > Anja > > ------------------------------ > Date: Fri, 1 Oct 2010 10:00:11 -0700 > > From: [hidden email]<http://user/SendEmail.jtp?type=node&node=1615989&i=0> > To: [hidden email] <http://user/SendEmail.jtp?type=node&node=1615989&i=1> > Subject: Re: 0 features found/no display of data > > Hi Anja, > > This GFF looks OK (though I would suggest giving the top level feature > (whose ID is NTR-a) a Name, since JBrowse doesn't use ID values for naming > features, but that may not matter). > > So, when you say it isn't working, what does that mean? Is it doing > exactly the same thing? Did you reload the database you were using with the > corrected GFF file? > > Scott > > > On Fri, Oct 1, 2010 at 11:19 AM, Anja Friedrich <[hidden email]<http:///user/SendEmail.jtp?type=node&node=1615837&i=0> > > wrote: > > Hi Scott, > > Thank you > I chose the second way and attached the file again, because it is still not > working... Hope I got your substitution advice right? > > Anja > ------------------------------ > Date: Fri, 1 Oct 2010 11:02:04 -0400 > Subject: Re: [Gmod-ajax] 0 features found/no display of data > From: [hidden email]<http:///user/SendEmail.jtp?type=node&node=1615837&i=1> > To: [hidden email] <http:///user/SendEmail.jtp?type=node&node=1615837&i=2> > CC: [hidden email] <http:///user/SendEmail.jtp?type=node&node=1615837&i=3> > > > Hi Anja, > > The argument for the prepare-refseqs.pl<http://prepare-refseqs.pl?by-user=t&by-user=t>script is the name of the reference sequence you want prepared. In your > GFF, you sort of have two reference sequences: "NC_010109.1" and "1". The > problem is, NC_010109.1 doesn't have any features on it (it never appears in > the first column of the GFF) and 1 is never defined (it doesn't have a gff > line with "Name=1" or a sequence-region line). While this is valid GFF > (which is why it successfully loaded in to the SeqFeature::Store database), > it doesn't make logical sense. You can do 1 of two things: > > 1. Change the NC_010109.1 to 1 in the sequence-region line then you can > supply "1" as an argument for the prepare-refseqs script. > > 2. Substitute NC_010109.1 for 1 in all of the first columns in the whole > GFF file and supply "NC_010109.1" to the prepare-refseqs script. > > Scott > > > On Fri, Oct 1, 2010 at 9:29 AM, anja <[hidden email]<http:///user/SendEmail.jtp?type=node&node=1615837&i=4> > > wrote: > > Hi Scott, > > I attached it > > Anja > > ------------------------------ > Date: Fri, 1 Oct 2010 06:01:51 -0700 > From: [hidden email]<http://user/SendEmail.jtp?type=node&node=1614664&i=0> > To: [hidden email] <http://user/SendEmail.jtp?type=node&node=1614664&i=1> > Subject: Re: 0 features found/no display of data > > > Hi Anja, > > It is probably a problem with your GFF. Since there have been so many > revisions to it, can you remind us what it looks like? > > Scott > > > On Fri, Oct 1, 2010 at 5:10 AM, Anja Friedrich > <[hidden email] <http:///user/SendEmail.jtp?type=node&node=1614559&i=0>> > wrote: > > > Hi all, > > > > I finally managed to load the data and to run bin/prepare-refseqs.pl<http://prepare-refseqs.pl?by-user=t&by-user=t> > > > > anou@anou-laptop:/var/www$ bp_seqfeature_load.pl<http://bp_seqfeature_load.pl?by-user=t&by-user=t>--d "dbi:Pg:dbname=test" > > --a DBI::Pg --c taro.gff > > loading taro.gff... > > 98 features loaded in > > 0.20s Building object > > tree... 0.02s > > load time: 0.23s > > anou@anou-laptop:/var/www$ bin/prepare-refseqs.pl<http://prepare-refseqs.pl?by-user=t&by-user=t>--conf taro.json --refs > > NC_010109.1 > > anou@anou-laptop:/var/www$ bin/biodb-to-json.pl<http://biodb-to-json.pl?by-user=t&by-user=t>--conf taro.json > > > > working on refseq NC_010109.1 > > working on track nested_tandem_repeat > > got 0 features for nested_tandem_repeat > > > > But why 0 features? And when I try to see it in the browser I can only > see > > the old data I was loading before- like there is no entry of taro... > > > > Anja > > > > > ------------------------------------------------------------------------------ > > > Start uncovering the many advantages of virtual appliances > > and start using them to simplify application deployment and > > accelerate your shift to cloud computing. > > http://p.sf.net/sfu/novell-sfdev2dev > > _______________________________________________ > > Gmod-ajax mailing list > > [hidden email] <http:///user/SendEmail.jtp?type=node&node=1614559&i=1> > > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > > > > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain dot > net > GMOD Coordinator (http://gmod.org/) <http://gmod.org/%29%C2%A0> > 216-392-3087 > Ontario Institute for Cancer Research > > ------------------------------------------------------------------------------ > > Start uncovering the many advantages of virtual appliances > and start using them to simplify application deployment and > accelerate your shift to cloud computing. > http://p.sf.net/sfu/novell-sfdev2dev > _______________________________________________ > Gmod-ajax mailing list > [hidden email] <http:///user/SendEmail.jtp?type=node&node=1614559&i=2> > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > > > ------------------------------ > View message @ > http://gmod.827538.n3.nabble.com/Gmod-ajax-0-features-found-no-display-of-data-tp1613434p1614559.html<http://gmod.827538.n3.nabble.com/Gmod-ajax-0-features-found-no-display-of-data-tp1613434p1614559.html?by-user=t&by-user=t&by-user=t> > To start a new topic under GMOD, email [hidden email]<http://user/SendEmail.jtp?type=node&node=1614664&i=2> > To unsubscribe from GMOD, click here<http://gmod.827538.n3.nabble.com/template/TplServlet.jtp?tpl=unsubscribe_by_code&node=827538&code=ZnJpZWRyaWNoLmFuamFAaG90bWFpbC5kZXw4Mjc1Mzh8MzI2MTcxMzA3&by-user=t&by-user=t&by-user=t>. > > > > > *taro.gff* (11K) Download Attachment<http://attachment/1614664/0/taro.gff> > > ------------------------------ > View this message in context: RE: 0 features found/no display of data<http://gmod.827538.n3.nabble.com/Gmod-ajax-0-features-found-no-display-of-data-tp1613434p1614664.html?by-user=t&by-user=t> > Sent from the JBrowse mailing list archive<http://gmod.827538.n3.nabble.com/JBrowse-f815920.html?by-user=t&by-user=t>at Nabble.com. > > > ------------------------------------------------------------------------------ > Start uncovering the many advantages of virtual appliances > and start using them to simplify application deployment and > accelerate your shift to cloud computing. > http://p.sf.net/sfu/novell-sfdev2dev > _______________________________________________ > Gmod-ajax mailing list > [hidden email] <http:///user/SendEmail.jtp?type=node&node=1615837&i=5> > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain dot > net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > > > ------------------------------------------------------------------------------ > Start uncovering the many advantages of virtual appliances > and start using them to simplify application deployment and > accelerate your shift to cloud computing. > http://p.sf.net/sfu/novell-sfdev2dev > _______________________________________________ > Gmod-ajax mailing list > [hidden email] <http:///user/SendEmail.jtp?type=node&node=1615837&i=6> > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > > > > > -- > ------------------------------------------------------------------------ > > Scott Cain, Ph. D. scott at scottcain dot > net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > > ------------------------------------------------------------------------------ > > Start uncovering the many advantages of virtual appliances > and start using them to simplify application deployment and > accelerate your shift to cloud computing. > http://p.sf.net/sfu/novell-sfdev2dev > _______________________________________________ > Gmod-ajax mailing list > [hidden email] <http:///user/SendEmail.jtp?type=node&node=1615837&i=7> > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > > > ------------------------------ > View message @ > http://gmod.827538.n3.nabble.com/Gmod-ajax-0-features-found-no-display-of-data-tp1613434p1615837.html<http://gmod.827538.n3.nabble.com/Gmod-ajax-0-features-found-no-display-of-data-tp1613434p1615837.html?by-user=t> > To start a new topic under GMOD, email [hidden email]<http://user/SendEmail.jtp?type=node&node=1615989&i=2> > To unsubscribe from GMOD, click here<http://gmod.827538.n3.nabble.com/template/TplServlet.jtp?tpl=unsubscribe_by_code&node=827538&code=ZnJpZWRyaWNoLmFuamFAaG90bWFpbC5kZXw4Mjc1Mzh8MzI2MTcxMzA3&by-user=t>. > > > > ------------------------------ > View this message in context: RE: 0 features found/no display of data<http://gmod.827538.n3.nabble.com/Gmod-ajax-0-features-found-no-display-of-data-tp1613434p1615989.html> > Sent from the JBrowse mailing list archive<http://gmod.827538.n3.nabble.com/JBrowse-f815920.html>at Nabble.com. > > > ------------------------------------------------------------------------------ > Start uncovering the many advantages of virtual appliances > and start using them to simplify application deployment and > accelerate your shift to cloud computing. > http://p.sf.net/sfu/novell-sfdev2dev > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
