Re: [Gusdev-gusdev] GenBank, Gene Ontology questions

[Deborah F. P. <pi...@pc...>]

Sorry, there's no log option.


On Mon, 12 May 2003, Deborah F. Pinney wrote:

> Hi Chetna,
> 
> Is your GBParser.pm updated from CVS? There were several changes made to 
> the plugin for GUS3.0. I used the plugin in it's current form and it 
> performed well. 
> 
> Here is a sample command line I used when testing the plugin:
> 
> ga GUS::Common::Plugin::GBParser --gbRel 132 --file 
> /ptolemy/share/data/thirdparty/genbank/133/gbrod4.seq.gz --debug --log 
> gbrod5.seq.log --db_rel_id 6547 > & gbrod5.err &
> 
> 
> Your command is missing the --db_rel_id option which is the 
> external_database_release_id of GenBank release 133 from the 
> ExternalDatabaseRelease table. I just made this a required option so you 
> can update from CVS to get that change. 
> 
> Can you e-mail the actual errors you get? It should not be necessary for 
> the dbref table to be filled to run GBParser.
> 
>                                                   Debbie 
> 
> 
> 
> 
> 
> 
> 
> On Mon, 12 May 2003, Chetna D. Warade wrote:
> 
> > Hi all,
> > 
> > It would be great if I can get insight into following:
> > 
> > 1) GenBank
> > 
> > I am trying to load data from GenBank with the  command
> > 
> > ga GUS::Common::Plugin::GBParser --gbRel=133 
> > --file=/home/gusdev/GenBank/TcNCBIgenomic.gb
> > 
> > I am getting SQL Error: foreign  key violation for tables SRes.DbRef and 
> > DoTS.ExternalNASequence.
> > 
> > I wanted to know more about how to solve the dependencies in these 
> > tables.
> > 
> > In order to solve this dependency I might need the 
> > InsertDbRefAndDbRefNASequence.pm and thats not functional as of yet. I 
> > was wondering if its up and running.
> > 
> > 2) GeneOntology
> > 
> > We have successfully  installed Taxonomy in the gus 3.0 database at this 
> > end. I need to know what version and files do I need to put all the 3 
> > ontologies in the database.  Also what are the dependencies in loading 
> > Gene Ontology in terms of data.
> > 
> > 3) Following is the list of tables we have filled in to work with gus:
> > Core.Algorithm
> > Core.AlgorithmInvocation
> > Core.Userinfo
> > Core.Projectinfo
> > Core.Groupinfo
> > Core.Machine
> > SRes.Taxon
> > SRes.Taxonname
> > SRes.GeneticCode
> > 
> > I would be very happy to call you guys over phone (if possible) at a 
> > good time if you think that the answers are really long and complex to 
> > talk over email.
> > 
> > Hope to hear from you all,
> > Thanks,
> > Chetna
> > 
> > 
> > 
> > 
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> 
> 
> 
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