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

[Brad Chapman]

Hilmar and Robert;

> Jeff/Brad or anybody else who can comment: is there anything more 
> precise that we can tell people inquiring about biopython supporting 
> the singapore version of biosql?

Yves Bastide kindly sent updates to the Biopython BioSQL code to the
dev list last week:

http://www.biopython.org/pipermail/biopython-dev/2003-September/001485.html

This should bring it up to date with the current SQL. I haven't had
a chance to integrate this yet but was hoping to Thursday night.
Hopefully it will then make it into the new release that Jeff has
planned for real-soon-now.

If things need to be up and running sooner then that the SQL that
the Biopython code works with can be found in the Tests/BioSQL
directory.

Sorry to have been slack on this. I have been feelin' really bad
about not having time to get it in, if that is any consolation for
anyone :-). But Thursday, Thursday...

Brad

> On Friday, September 12, 2003, at 09:05  AM, Yves Bastide wrote:
> 
> >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
> >
> >_______________________________________________
> >BioSQL-l mailing list
> >BioSQL-l at open-bio.org
> >http://open-bio.org/mailman/listinfo/biosql-l
> >
> -- 
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
> 
> 
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