[Biopython-dev] [Bug 2390] New: Error importing Swiss Prot in BioSQL

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2390

           Summary: Error importing Swiss Prot in BioSQL
           Product: Biopython
           Version: Not Applicable
          Platform: Macintosh
        OS/Version: MacOS X
            Status: NEW
          Severity: normal
          Priority: P2
         Component: BioSQL
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: Biosql at hotmail.com


Hello, 

I already submitted this problem in the mailing list, where I can't import the
SwissProt flat file in BioSQL, even with the new version (1.44) of Biopython.  

Here's the script I'm using :

from BioSQL import BioSeqDatabase
from Bio.SwissProt import SProt

server = BioSeqDatabase.open_database(driver = 'MySQLdb', user = '', passwd =
'', host = 'localhost', db = 'bioseqdb')
s_parser = SProt.SequenceParser()
s_iterator = SProt.Iterator(open('path to/uniprot_sprot.dat', 'r'), s_parser)
db = server.new_database('Swiss')
db.load(s_iterator)

And here's the error: 

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


Thanks for the help !

Jonathan


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