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From: Ed R. <ed_...@be...> - 2004-09-27 14:47:40
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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 |
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From: Ed R. <ed_...@be...> - 2004-09-27 15:31:43
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Yeah, it's not in the mapping. I added it to the view GeneFeature on NaFeatureImp. I'll make a modification to the mapping in the plugin here. I'll keep notes on what I've done and once our stuff is in, I'll make the changes known and you can decide if you want to put it in the CVS. -Ed > > From: "Deborah F. Pinney" <pi...@pc...> > Date: 2004/09/27 Mon AM 11:08:12 EDT > To: Ed Robinson <ed_...@be...> > CC: Jinal Jhaveri <jjh...@vb...>, gus...@li... > Subject: Re: Re: [Gusdev-gusdev] GI Number > > 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. > > 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 |
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From: Ed R. <ed_...@be...> - 2004-09-27 16:51:10
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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=46229367 > > > > 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 |
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From: Jinal J. <jjh...@vb...> - 2004-09-27 17:00:27
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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 |
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From: Thomas O. <ot...@fi...> - 2004-09-27 17:21:31
Attachments:
generate.sh
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Hi, instead of doing touch $PROJECT_HOME/GUS/Model/schema/VERSION build GUS/Model install -append # in the $PROJECT_HOME directory... -- important is the touch you can also just use the programm generateGusObjects to just build the pm's (perl-modul) for this view I wrote a little bash file, attached, that already (chmod 755 generate.sh) ./generate.sh DoTS GeneFeatureJinal Cheers, Thomas Jhaveri wrote: >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 > > > |
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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 |
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From: Jinal J. <jjh...@vb...> - 2004-09-27 17:15:54
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Just rebuild gus by using following commands: touch $PROJECT_HOME/GUS/Model/schema/VERSION build GUS install -append or refer this document of wiki! http://www.gusdb.org/wiki/index.php/Installing%20GUS On Monday 27 September 2004 01:11 pm, Ed Robinson wrote: > 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=46 > > > > >2293 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 |
|
From: Thomas O. <ot...@fi...> - 2004-09-27 14:58:52
|
Hi, that means, that in the views Genefeature and Transcript, the column locus_tag does not exist. My workaround: I added them to the views (in the oracle), and recompiled them the perl modules for the tables touch $PROJECT_HOME/GUS/Model/schema/VERSION build GUS/Model install -append # takes time, but easier, would be sufficient just the recompile the two changed views Cheers, Thomas >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 > > > |
|
From: Deborah F. P. <pi...@pc...> - 2004-09-27 15:08:18
|
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.
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
>
>
>
|
|
From: Angel P. <an...@pc...> - 2004-09-27 15:50:53
|
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=46229367 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 |
|
From: Deborah F. P. <pi...@pc...> - 2004-09-27 16:28:52
|
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=46229367
>
> 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
>
>
|
|
From: Thomas O. <ot...@fi...> - 2004-09-27 17:30:38
Attachments:
stuff_missing
|
Hi, because we are alreaday talking about the GBParser. I wrote a genbank file with all possible features...(hope it is so)... the result of missing stuff is attached... I do not know if it makes sense to include all, or maybe try to do it automatically... Cheers, Thomas |
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