[Gmod-help] gff database

[Barrasa, Inmaculada]

Great Thanks a lot, that' what I was looking for.

One more question, in the sub schema for mysql.pm at the end of the create table code there is code like: "type=MyISAM". What is that for?

For example:
		fgroup =>{ 
table=> q{
create table fgroup (
    gid	    int not null  auto_increment,
    gclass  varchar(100),
    gname   varchar(100),
    primary key(gid),
    unique(gclass,gname)
) type=MyISAM
}
},

What is the code type=MyISAM for?

I am creating a database which will include the GFF tables so I can relate my data to the WormBase annotations and may be at some point have Gbrowser running locally too.
I will only use the create code, not the type=MyISAM.


Thanks again

Inma


-----Original Message-----
From: Scott Cain [mailto:cain.cshl at gmail.com]
Sent: Fri 8/8/2008 12:39 PM
To: Barrasa, Inmaculada
Cc: help at gmod.org
Subject: Re: [Gmod-help] gff database
 
Hello Inma,

I don't think the Bio::DB::GFF schema has changed much since 2002, so
the current incarnation should be just fine.  The schema itself is
contained within the database adaptors for Bio::DB::GFF.  For example,
if you wanted the MySQL schema, you would have to look at the schema
method of the Bio::DB::GFF::Adaptors::dbi::mysql.  That module is
contained in the BioPerl distribution, and the current version of that
file can be browsed here:

http://code.open-bio.org/svnweb/index.cgi/bioperl/view/bioperl-live/trunk/Bio/DB/GFF/Adaptor/dbi/mysql.pm

Look for the line that starts "sub schema."

Scott




On Fri, Aug 8, 2008 at 11:39 AM, Barrasa, Inmaculada
<Inmaculada.Barrasa at umassmed.edu> wrote:
>
> Hi,
>
> Could you please tell me where I can find the sql statements to create the
> gff tables?
> I would like just to have the basic tables defined in 2002.
>
> The Generic Genome Browser: A Building Block
> for a Model Organism System Database
> Lincoln D. Stein,1,5 Christopher Mungall,2 ShengQiang Shu,2 Michael Caudy,3
> Marco Mangone,1 Allen Day,1 Elizabeth Nickerson,1 Jason E. Stajich,4
> Todd W. Harris,1 Adrian Arva,1 and Suzanna Lewis2
>
>
>
> Thanks a lot your your help
>
>
> Inma Barrasa
>
>
> Walhout laboratory



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D. cain.cshl at gmail.com
GMOD Coordinator (http://www.gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory


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