[Biopython-dev] [Bug 1816] New: Error when importing GenBank file into BioSQL database

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Mon Jun 13 16:24:19 EDT 2005


           Summary: Error when importing GenBank file into BioSQL database
           Product: Biopython
           Version: Not Applicable
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: BioSQL
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: scresawn at ufl.edu

When importing a GenBank file with accession number AY243312 into a BioSQL
database, I get an error.  (See below.)  Importing the file was done according
to the documentation at http://biopython.org/docs/biosql/python_biosql_basic.html
I'm using python-2.3.4 and biopython-1.40b.  The biosql-schema was checked out
today (6/13/05) from cvs.
The error follows:

>>> db.load(iterator)
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "BioSQL/BioSeqDatabase.py", line 414, in load
  File "BioSQL/Loader.py", line 43, in load_seqrecord
    self._load_reference(reference, rank, bioentry_id)
  File "BioSQL/Loader.py", line 324, in _load_reference
  File "BioSQL/BioSeqDatabase.py", line 287, in execute_and_fetch_col0
    self.cursor.execute(sql, args or ())
  File "/usr/lib/python2.3/site-packages/MySQLdb/cursors.py", line 95, in execute
    return self._execute(query, args)
  File "/usr/lib/python2.3/site-packages/MySQLdb/cursors.py", line 114, in _execute
    self.errorhandler(self, exc, value)
  File "/usr/lib/python2.3/site-packages/MySQLdb/connections.py", line 33, in
    raise errorclass, errorvalue
_mysql_exceptions.ProgrammingError: (1064, "You have an error in your SQL syntax
near 'USING (dbxref_id) WHERE dbname = 'PUBMED' AND accession = '7060133'' at
line 1")

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