[BioPython] sql create tables script in tutorial

[Peter]

On Wed, Aug 27, 2008 at 9:48 PM, Pavel SRB <srbanator at heckler-koch.cz> wrote:
> hi all, as i am reading through "Basic BioSQL with Biopython"
> http://biopython.org/DIST/docs/biosql/python_biosql_basic.html

Those are old and haven't been updated.  See below...

> after executing
>
>>>> db = server.new_database("cold")
>
> i have got an "XXX.biodatabase' doesn't exist" error.

You must have skipped over section "3.1 Prerequisites" which does say
it assumes you have installed a database, a python binding to this
database, and loaded the BioSQL schema into the database.

> At "BioSQL" http://www.biopython.org/wiki/BioSQL
> i have found out sql create table batch script
>
> mysql -u root bioseqdb < biosqldb-mysql.sql
>
> Maybe it should also be in the first tutorial, maybe not. Just mentioning
> it.

I'm glad http://www.biopython.org/wiki/BioSQL is proving useful at least.

Due to an accident of history, the source for python_biosql_basic.html
and python_biosql_basic.pdf currently lives in BioSQL's SVN repository
rather than in Biopython's (which has led to them being more
complicated to update).  Do you think it is worth trying to fully
update those documents, or just add a link at the top of those
documents directing people to http://biopython.org/wiki/BioSQL
instead?

Peter