[Gmod-help] RE: [Gmod-gbrowse] Custom GBrowse adaptor

[Rytsareva, Inna (I)]

Hello, 

Of course, it is easier and faster to write a program to convert the
contents of the DB to GFF3, but here is a problem - "redundancy" as well
as we will have 2 similar datasets. And I'm not sure that it's possible
to write a new adaptor by myself for 1 month. 

Well, I'm thinking about to create GFF3 file on-fly as a temporary file.
An idea is to write a perl script what parses the DB and creates GFF3
according with a search query. But it's still an idea and I'm not sure
that it works.

How do you think, is this implementation possible? 
 
Inna Rytsareva
Discovery Information Management
Dow AgroSciences
Indianapolis, IN 
317-337-4716

-----Original Message-----
From: Dave Clements, GMOD Help Desk [mailto:gmodhelp at googlemail.com] 
Sent: Wednesday, July 15, 2009 4:19 PM
To: Rytsareva, Inna (I)
Cc: Gbrowse Mailing List
Subject: Re: [Gmod-gbrowse] Custom GBrowse adaptor

Hi Inna,

Writing a GBrowse adaptor is a large undertaking.  It is almost always
easier to write a program to convert the contents of your DB to GFF3,
then it is to write your own adaptor.

Now, before reading any more, imagine that I typed that paragraph
several hundred times.  Really, writing a database adaptor is not for
the faint of heart.


However, if you absolutely have to have an adaptor, I would start by
looking at existing adaptors.  Several are in the gbrowse-adaptors CVS
project:

  http://gmod.cvs.sourceforge.net/viewvc/gmod/gbrowse-adaptors/

The Chado and BioSql adaptors are probably good places to start.  I
don't know of any doc on how to write a GBrowse adaptor.

Thanks,

Dave C

On Wed, Jul 15, 2009 at 9:17 AM, Rytsareva, Inna (I)<IRytsareva at dow.com>
wrote:
> Hello,
> As I understood, to get GBrowse to use my custom database (MySQL, not
GFF,
> not Chado), I would need to write my own GBrowse adaptor.
>
> How can I get started?
> Thanks,
> Inna Rytsareva
>
>
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