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Re: Re: [Gusdev-gusdev] GI Number
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From: Ed R. <ed_...@be...> - 2004-09-27 17:11:49
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I modified the views using Oracle Enterprise Manager. I did not make the modifications through a GUS Build. I have only done a straight GUS install, so I am not sure where to make the modifications in the project_home to make these changes correctly. Sorry, I'm still a newbie to GUS, and there isn't much documentation beyond he straight-forward installation docs. -Ed > > From: Jinal Jhaveri <jjh...@vb...> > Date: 2004/09/27 Mon PM 01:00:14 EDT > To: Ed Robinson <ed_...@be...> > CC: gus...@li... > Subject: Re: [Gusdev-gusdev] GI Number > > They are created automatically when you compile or build gus > > On Monday 27 September 2004 12:50 pm, you wrote: > > What about the PERL objects in Model/ ? Do we need to modify any of those > > so they will work with the modified views? > > > > -Ed > > > > > From: "Deborah F. Pinney" <pi...@pc...> > > > Date: 2004/09/27 Mon PM 12:28:38 EDT > > > To: Angel Pizarro <an...@pc...> > > > CC: Ed Robinson <ed_...@be...>, > > > Jinal Jhaveri <jjh...@vb...>, > > > gus...@li... > > > Subject: Re: [Gusdev-gusdev] GI Number > > > > > > Angel is correct. locus_tag is a relatively new (new to the GBParser) > > > qualifier for existing features, including gene which is already mapped > > > to dots.GeneFeature. Therefore, my advise was wrong, it should not be > > > added to the mapping list in the perl module. Adding this field to the > > > view should fix the problem for "gene" features. > > > > > > As genbank adds features and qualifiers and since the parser was tailored > > > for genbank records, we are going to encounter this problem again. A > > > compounding problem is that a qualifier is generally not exclusive to a > > > single feature. In this case, locus_id really should be added to many > > > views. > > > > > > -Debbie > > > > > > On Mon, 27 Sep 2004, Angel Pizarro wrote: > > > > Deborah F. Pinney wrote: > > > >> locus_tag is not in the list of features in the GBParser. It will have > > > >> to be added with a table(actually view) destination. Which view is > > > >> appropriate for this feature? What are the attributes (from the > > > >> Genbank feature table) for this feature? I'll gladly add this and you > > > >> can test it or you can add it and test and then commit to cvs. > > > > > > > > Let me clarify. "locus_tag" is not a GenBank feature, it is a feature > > > > attribute of the GenBank "gene" feature. The feature is belongs to is > > > > being mapped to DoTS::GeneFeature. Here is the example from the GB > > > > record for this feature attribute, available here : > > > > http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=462293 > > > >67 > > > > > > > > gene > > > > <http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=46229367&itemID=819 > > > >&view=gbwithparts> complement(<6844..>9270) > > > > /locus_tag="cgd7_10" > > > > > > > > > > > > Thomas' suggestion of adding the attribute "locus_tag" to the > > > > GeneFeature view and recompiling the objects will work in this case, > > > > but be a problem for anyone else trying to capture this feature > > > > attribute. > > > > > > > > The GBParser has several known problems, this being one of them. Maybe > > > > we should start up a wiki for it to aid in development and > > > > documentation. > > > > > > > > Angel > > > > > > > >> It should be added >line 808, following my %featureNameTableMapping = > > > >> ( > > > >> > > > >> If the attributes are correct in the mapped table (match the genbank > > > >> attributes), this should work. If this table is not in the > > > >> %classChildList, it should also be added to the appropriate line also. > > > >> > > > >> -Deborah > > > >> > > > >> On Mon, 27 Sep 2004, Ed Robinson wrote: > > > >>> So far, down here, I can tell that it is parsing the files for crypto > > > >>> correctly, but I is giving me the following error: > > > >>> > > > >>> > > > >>> ********GEtting loc below6844 > > > >>> > > > >>> Mon Sep 27 10:13:09 2004 INVALID QUALIFIER > > > >>> GUS::Model::DoTS::GeneFeature :: locus_tag :: > > > >>> cgd7_10 > > > >>> > > > >>> Mon Sep 27 10:13:09 2004 INVALID QUALIFIER > > > >>> GUS::Model::DoTS::Transcript :: locus_tag :: > > > >>> cgd7_10 > > > >>> > > > >>> Do you have any ideas why it is disliking my locus_tags? I am > > > >>> running this without the commit on, if it is looking for this again > > > >>> in the database. > > > >>> > > > >>> Thanks for all the help on this. I don't want to change anything > > > >>> that is working, just figure out how to use it. > > > >>> > > > >>> -Ed > > > >>> > > > >>> > > > >>> > > > >>> > > > >>> > > > >>> Ed Robinson > > > >>> 255 Deerfield Rd > > > >>> Bogart, GA 30622 > > > >>> (706)425-9181 > > > >>> http://www.electedrobinson.com > > > >>> > > > >>> --Learn more about the face of your neighbor, and less about your > > > >>> own. -Sargent Shriver > > > >> > > > >> ------------------------------------------------------- > > > >> This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170 > > > >> Project Admins to receive an Apple iPod Mini FREE for your judgement > > > >> on who ports your project to Linux PPC the best. Sponsored by IBM. > > > >> Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php > > > >> _______________________________________________ > > > >> Gusdev-gusdev mailing list > > > >> Gus...@li... > > > >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > Ed Robinson > > 255 Deerfield Rd > > Bogart, GA 30622 > > (706)425-9181 > > http://www.electedrobinson.com > > > > --Learn more about the face of your neighbor, and less about your own. > > -Sargent Shriver > > > ------------------------------------------------------- > This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170 > Project Admins to receive an Apple iPod Mini FREE for your judgement on > who ports your project to Linux PPC the best. Sponsored by IBM. > Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > Ed Robinson 255 Deerfield Rd Bogart, GA 30622 (706)425-9181 http://www.electedrobinson.com --Learn more about the face of your neighbor, and less about your own. -Sargent Shriver |
