[Biopython-dev] [BioPython] BioSQL documentation for Biopython

[Sebastian Bassi]

On Sat, Feb 23, 2008 at 3:58 PM, Hilmar Lapp <hlapp at gmx.net> wrote:
>  You mean from SVN, probably? I don't know but it seems to me that
>  problem is in some (Bio)Python code?

Yes, the problem was that I was using 1.44 biopython without the new
BioSQL code from Peter.
Biopython repository is still in CVS, not SVN (at least biopython is
not listed here: http://code.open-bio.org/svnweb/index.cgi/)
Now with the new code, I could reproduce the tutorial, up to here:

>>> from BioSQL import BioSeqDatabase
>>> server=BioSeqDatabase.open_database(driver = "MySQLdb", user =
"X",passwd="X", 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)
6

But when I look into the mysql, there is no new record!. The "6" is
supposed to be the number of records loaded into the database. But my
database is empty (it has the schema, but w/o data).

>  That would be a question for the Biopython folks (I actually don't
>  use Biopython).

I am copying this into biopython and biopython-dev mailing list.


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