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

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

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





------- Comment #3 from Biosql at hotmail.com  2007-10-30 14:02 EST -------
(In reply to comment #2)
> I'm trying to narrow down the problem:
> * Have you tried different input SwissProt files?
> * Have you tried a GenBank file (using the GenBank parser)?
> * Did you check the username/password as suggested on the mailing list (empty
> strings look wrong to me)?
> 
> Peter
> 

I'm sorry Peter, the reply you sent me on the mailing list was cut in half and
I didn't see the rest of your message until I've read it directly on the
mailing list.

I tried to parse the cor6_6.gb with the Genbank parser and I'm getting the same
result, sorry I didn't tried this before. I also tried what you suggest with
the SeqIO module with the cor6_6.gb and also a SwissProt file and I'm still
getting the same TypeError, which is : 

Traceback (most recent call last):
  File "DB_Gen.py", line 25, in <module>
    db.load(iterator)
  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 "build/bdist.macosx-10.4-ppc/egg/MySQLdb/cursors.py", line 151, in
execute
TypeError: not all arguments converted during string formatting

It seems to me that the problem could be with the MySQLdb module, but I don't
understant since I'm using the latest release 1.2.2c1, but I've also tried it
with the stable 1.2.2 release. 

Am I right ?


-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.