[BioPython] BioSQL problems on load

[Daniel Tomso]

Thanks--
I'll get the last bug logged ASAP.

Regarding the main problem--I'm pretty sure I'm up-to-date via CVS--I
have persistent configuration problems on this Ubuntu box.  I suspect
right now that something is digging down some alternate hierarchy and
coming up with this error, even though the correct versions are lurking
somewhere else.

I'll dig it up eventually.  Thanks again.
DT


-----Original Message-----
From: p.j.a.cock at googlemail.com [mailto:p.j.a.cock at googlemail.com] On
Behalf Of Peter
Sent: Friday, December 21, 2007 12:56 PM
To: Daniel Tomso
Cc: biopython at biopython.org
Subject: Re: [BioPython] BioSQL problems on load

> This is possibly a simple configuration problem, but I'm having some
> problems loading files into BioSQL.
>
> ...
>
>   warnings.warn("Bio.crc is deprecated; use crc32 and crc64 in
> Bio.SeqUtils.CheckSum instead", DeprecationWarning)

We should fix that - I hadn't seen that warning being triggered on my
machine.
>   File
>
"/home/dtomso/repository/biopython/build/lib.linux-i686-2.5/BioSQL/BioSe
> qDatabase.py", line 277, in execute
>
>     self.cursor.execute(sql, args or ())
>
>   File "/usr/lib/python2.5/site-packages/MySQLdb/cursors.py", line
149,
> in execute
>
>     query = query % db.literal(args)
>
> TypeError: not all arguments converted during string formatting
>
> This happens with standard genbank and fasta files pulled off of NCBI.
> Any suggestions?

That looks like Bug 2390,
http://bugzilla.open-bio.org/show_bug.cgi?id=2390

You didn't say what version of Biopython you are using, but that has
been fixed in CVS.  Could you update to CVS, or wait for the next
release (hopefully in January?).

> There's another issue regarding standard parsing of accession numbers
to
> get version IDs (the code doesn't like non-NCBI fasta headers, e.g.
> those produced by phrap), but that is pretty minor and doesn't seem to
> be related to this.

Perhaps the parser or BioSQL can be a bit more robust here.  Could you
file a bug on this issue, and then attach an example input file with
some code showing the problem?

Thanks

Peter