[BioPython] BioSQL documentation for Biopython

[Sebastian Bassi]

On Sat, Feb 23, 2008 at 1:28 AM, Hilmar Lapp <hlapp at gmx.net> wrote:
>  Yes, sorry that was my mistake. The URL was to the anonymous access
>  mirror, which gets updated only every hour or so.

Thats OK. Here is my next report:

There is a part here: "For this example, we are going to assume we
have a GenBank file on our computer called cor6_6.gb that we are going
to work with."
I think the tutorial should state that the cor6_6.gb is included with
Biopython (under Test/Genbank). Also a link to the file won't hurt.

When I tried to follow the step by step guide, I found this error (I
am using Biopython 1.44):

>>> from BioSQL import BioSeqDatabase
>>> server=BioSeqDatabase.open_database(driver = "MySQLdb", user = "",
passwd="", 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)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "BioSQL/BioSeqDatabase.py", line 414, in load
    db_loader.load_seqrecord(cur_record)
  File "BioSQL/Loader.py", line 30, in load_seqrecord
    bioentry_id = self._load_bioentry_table(record)
  File "BioSQL/Loader.py", line 250, in _load_bioentry_table
    version))
  File "BioSQL/BioSeqDatabase.py", line 277, in execute
    self.cursor.execute(sql, args or ())
  File "/var/lib/python-support/python2.5/MySQLdb/cursors.py", line
151, in execute
    query = query % db.literal(args)
TypeError: not all arguments converted during string formatting

Should I donwload the BioSQL from CVS?



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