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

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

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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