[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 #4 from biopython-bugzilla at maubp.freeserve.co.uk  2007-10-30 15:06 EST -------
Thanks for that.  It looks like we can *probably* rule out a problem in the
sequence parsing.

Unfortunately I personally haven't used BioSQL myself (yet), and don't have a
system setup here I can try this on.

It appears (just from reading the stack error) that there is some mis-match
between the SQL query (which I assume contains python % placeholders) and the
list of arguments (to go in these placeholders).

If you fancy trying to investigate this further yourself, I would start by
adding a break point on BioSQL/BioSeqDatabase.py line 277 to check out what
contents of the sql and args variables are.  Or, just add some print statements
just before line 277: self.cursor.execute(sql, args or ())

I hope someone else on the mailing list will have some suggestions...


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