I am using bp_seqfeature_load.PLS to create and load the data into MySQL database. I have no clear knowledge whether score for each bin is stored properly.
Mustafa. --- Isabelle Blanc-Lenfle <[EMAIL PROTECTED]> wrote: > Syed Mustafa Hussain a écrit : > > Hi Scott, > > > > Sheldon's suggestion helped me fix the problem. I > was > > having primary reference type as chromosome in GFF > > data files which I changed to Sequence to match > with > > conf file, and it worked. > > > > I have one more question, I am drawing xyplot on > > overview. GFF file worked well earlier but when I > have > > loaded these in MySQL and used mysql adaptor it is > > just blank. > > Do you know where your score is stocked in MySQL. > have you tested that > each feature has really got a score. > I don't know how it is handled in a MySQL database, > I had some troubles > with scores in a chado database. Displaying scores > needs the data to be > loaded as analysis. > > Isabelle > > Sample data from GFF files looks like > > this: > > > > > > NC_004347 CDS bin 1270000 1280000 7 > > > + . > ID=NC_004347:CDS;Name=NC_004347:CDS > > NC_004347 CDS bin 320000 330000 9 > > > + . > ID=NC_004347:CDS;Name=NC_004347:CDS > > NC_004347 CDS bin 900000 910000 11 > > > + . > ID=NC_004347:CDS;Name=NC_004347:CDS > > NC_004347 CDS bin 2760000 2770000 10 > > > + . > ID=NC_004347:CDS;Name=NC_004347:CDS > > NC_004347 CDS bin 4430000 4440000 11 > > > + . > ID=NC_004347:CDS;Name=NC_004347:CDS > > NC_004347 CDS bin 710000 720000 9 > > > + . > ID=NC_004347:CDS;Name=NC_004347:CDS > > NC_004347 CDS bin 1180000 1190000 7 > > > + . > ID=NC_004347:CDS;Name=NC_004347:CDS > > NC_004347 CDS bin 2060000 2070000 11 > > > + . > ID=NC_004347:CDS;Name=NC_004347:CDS > > > > Any assistance in this regards is appreciated. > > > > Thanks, > > Mustafa Syed. > > > > --- Scott Cain <[EMAIL PROTECTED]> wrote: > > > >> Hi Mustafa, > >> > >> I am curious if Sheldon's suggestion fixed your > >> problem. It doesn't > >> feel to me like it should be necessary, assuming > you > >> have a reference > >> sequence line for your features in GFF, like > this: > >> > >> NC_009999 . region 1 1000000 . . . > >> ID=NC_009999 > >> > >> However, I'm currently trying to debug behavior > like > >> this right now, so > >> any information you could provide would be > >> appreciated. > >> > >> Thanks, > >> Scott > >> > >> On Mon, 2008-02-11 at 13:21 -0500, Sheldon McKay > >> wrote: > >>> Hi Mustafa, > >>> > >>> When I encounter this problem, I usually try > >> adding a sequence-region > >>> directive for each reference sequence (with the > >> absolute start and end > >>> coordinates), so that a full-length feature of > >> that name and length > >>> will be autogenerated when the GFF is processed > >> for database loading. > >>> ##sequence-region NC_009999 1 1000000 > >>> > >>> Sheldon > >>> > >>> On Feb 11, 2008 12:31 PM, Syed Mustafa Hussain > >> <[EMAIL PROTECTED]> wrote: > >>>> Hi, > >>>> > >>>> I recently switched from in-memory to MySQL and > >> have > >>>> used bp_seqfeature_load.PLS script to create > >> and load > >>>> MySQL tables. > >>>> > >>>> Gbrowse interface is giving me the following > >> error: > >>>> "The landmark named NC_004347:3359971..3369971 > >> is not > >>>> recognized. See the help pages for suggestions" > >>>> > >>>> What might be wrong with database causing this > >> error? > >>>> Where can I get schema diagram to understand > >>>> relational database created by above script. > >>>> > >>>> Mustafa. > >>>> > >>>> > >>>> > > > ____________________________________________________________________________________ > >>>> Never miss a thing. Make Yahoo your home page. > >>>> http://www.yahoo.com/r/hs > >>>> > >>>> > >>>> > > > ------------------------------------------------------------------------- > >>>> This SF.net email is sponsored by: Microsoft > >>>> Defy all challenges. Microsoft(R) Visual Studio > >> 2008. > > > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > >>>> _______________________________________________ > >>>> Gmod-gbrowse mailing list > >>>> [email protected] > >>>> > > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > >>> > >>> > >> -- > >> > > > ------------------------------------------------------------------------ > >> Scott Cain, Ph. D. > > >> [EMAIL PROTECTED] > >> GMOD Coordinator (http://www.gmod.org/) > > >> 216-392-3087 > >> Cold Spring Harbor Laboratory > >> > >> > > > > > > > > > ____________________________________________________________________________________ > > Never miss a thing. Make Yahoo your home page. > > http://www.yahoo.com/r/hs > > > > > ------------------------------------------------------------------------- > > This SF.net email is sponsored by: Microsoft > > Defy all challenges. Microsoft(R) Visual Studio > 2008. > > > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > > _______________________________________________ > > Gmod-gbrowse mailing list > > [email protected] > > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > > -- > Isabelle Blanc-Lenfle > INRA URGI > 523 place des terrasses de l'agora > 91000 Evry - France > > Tel : +33 1 60 87 37 59 > Fax : +33 1 60 87 37 00 > ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. 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