[BioSQL-l] Problem with example in python_biosql_basic.txt

[Yves Bastide]

Robert Roth wrote:
> Hi,
> 
> I am completly new to Biopython and BioSQL so my problems might arise from something trivial that I have missed. After installing MySQL, Biopython, MySQLdb and BioSQL I loaded the scheme for BioSQL into the database and everything is in place. The machine is running WinXP and python 2.3.
> 
> But when I try to follow the simple example in the documentation for using Biopython with BioSQL that is described in 
> biosql/biosql-schema/doc/python_biosql_basic.txt it chokes (see below).
> 
> -----
> 
>>>>import MySQLdb
>>>>from BioSQL import BioSeqDatabase
>>>>server = BioSeqDatabase.open_database(driver = "MySQLdb", user = "test", passwd = "biopython", host = "localhost", db = "bioseqdb")
>>>>db = server.new_database("cold")
>>>>from Bio import GenBank
>>>>parser = GenBank.FeatureParser()
>>>>iterator = GenBank.Iterator(open("cor6_6.gb"), parser)
>>>>db.load(iterator)
> 
> 

[snip]

> 
> When looking at Loader.py there is a call to MySQL (snippet above). 
> But when I look at the ERD for BioSQL I cant find either binomial or variant in the taxon table. Am I completely of here (as I said I'm a complete newbie) or is this the reason its choking?
> Any help on what is going wrong would be greatly appreciated.
> 
> Thanks in advance,

Biopython is still using an old version of the schema.  This should 
change in the not-too-far future...

> Robert

yves