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

[Hilmar Lapp]

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?

	-hilmar

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
>
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-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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