Re: [Fwd: [Gusdev-gusdev] dbest.pm plugin]

[Sucheta T. <su...@vb...>]

Hi Debbie,

Thanks.

In my case I need to upload a big file with sequences in genbank format to
EST related tables in GUS. If I were to use dbEST how do I pass on the
input file name.
Is it not the --update_file option?

Sucheta

>
> Hi Sucheta,
>
> I use the dbEST plugin frequently. We have made a few changes in the
> plugin lately so you may want to update it from cvs. The changes all
> relate to the option --taxon_id being changed to taxon_id_list which now
> takes a string (a comma delimited list of taxons) rather than an int (a
> single taxon_id).
>
> We maintain a mirrored dbEST database and this plugin was created to load
> data into GUS from our copy of the dbEST db. I didn't write the plugin and
> have never used the --update_file option, but I think it would be a list
> of id_est's that identify ests in the dbEST mirror that need to be updated
> but not a list of records that can be loaded directly into GUS.
>
> One other point, I don't think you should use = between an option and a
> value. I believe that may be why it is hanging.
>
>                                                      Debbie
>
>
>
>
>
>
> On Thu, 22 Apr 2004, Steve Fischer wrote:
>
>>
>>
>> -------- Original Message --------
>> Subject: 	[Gusdev-gusdev] dbest.pm plugin
>> Date: 	Wed, 21 Apr 2004 18:48:32 -0400 (EDT)
>> From: 	Sucheta Tripathy <su...@vb...>
>> To: 	gus...@li...
>>
>>
>>
>> Hi,
>>
>> has anyone used dbest plugin. I have been trying to upload data with
>> sequence files in genbank format using the following parameter, but it
>> keeps hanging.
>>
>> ga GUS::Common::Plugin::dbEST  --debug --fullupdate
>> --log=/home/apps/oracle/data
>> _load_dbest.log  --restart_number=1 --sqlVerbose --taxon_id=143371
>> --update_fil
>> e=/usr/local/src/gus-related/dbest/tmp >&
>> /home/apps/oracle/gusdev/dbest_err1
>>
>> Any suggestion what file type I should be using etc..
>>
>> Thanks
>>
>> Sucheta
>>
>>
>
>
>
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-- 
Sucheta Tripathy
Virginia Bioinformatics Institute Phase-I
Washington street.
Virginia Tech.
Blacksburg,VA 24061-0447
phone:(540)231-8138
Fax:  (540) 231-2606