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 ------------------------------------------------------------------------- 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
