Re: [Gusdev-gusdev] GBParser

[MICHAEL L. <lu...@cs...>]

Actually I answered the second question.  But I was willing to give a try
at the third.  But upon looking at my GBParser module, there IS NO
arguement for algoinvo.  I have CVS version 1.17.  Jinal, what are you
running?  Unfortunately, I can't remember if we modified these here or
not, but I don't think that we did.  Here is our module, attached.


Michael Luchtan
http://www.cs.uga.edu/~luchtan


On Thu, 20 May 2004, Steve Fischer wrote:

> jinal-
>
> see below
>
> jinal jhaveri wrote:
>
> >Hi,
> >
> >I have some questions regarding the GBParser module
> >
> >1) First required field  is --gbRel. As I understand this is genbank's db realease id. Now where do I get this number from? ( genbanks website????) Does anybody has idea about what is the release right now on web?
> >
> >
> yes, this is from the readme file .   it is stored in GUS in the
> created_rel_ver and updated_rel_ver attributes of the DoTS::NAEntry table:
> http://www.gusdb.org/cgi-bin/schemaBrowser?db=CBILBLD&table=DoTS::NAEntry&path=DoTS::NAEntry
>
> >2) --db_rel_id : As the documentation describes, this is external database id. Do I create this id on my own? Do I need to keep this entry in any other table? Does this id has one to one correspondence with the project I am working on (and the one I described in my .gus.properties file?)
> >
> gus is strict about its data.   we track pretty much everything.  so,
> for example, in order to put data in from an external database, or, to
> mention source ids of an external database, the external database must
> be known by gus.   the two tables that hold this are:
> SRes.ExternalDatabase and SRes.ExternalDatabaseRelease.  The former
> describes the DB, the latter the particular release of the DB, and it
> points back to the former.   The GBParser is asking you for a primary
> key in the ExternalDatabaseRelease table so that all the data you load
> will be associated with it.
>
> in the case of GenBank, we at cbil only store one version of it, which
> we update periodically.  so, for it, we set the 'version' attribute to
> "continuous."   for other DBs, we store multiple copies.  in that case
> we use a real version number, and create a new ExternalDatabaseRelease
> row each time we load a new one in.
>
> one of the known weaknesses of the current GUS install process is that
> we don't provide a bunch of standard databases as part of the data that
> we load to get you off the ground.   but, paul mooney has been handing
> out an xml file which you can load with the UpdateGusFromXML plugin.
> his mail is pj...@sa...
>
> that file only works for databases that you will only maintain one
> release of.   if you want to load multiple versions of a db (eg, pfam),
> you will need to add new rows.
>
> >3) --algoinvo=s: What is this? (I looked at the docs but they talk about some invocation id. Is this to change the algorithm to be invoked?)
> >
> >
> >
> i see that michael answered this
>
> >Any help will be really appreciated
> >
> >
> >thanks
> >--Jinal
> >
> >
> >
> >
> >
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