[BioPython] saving pickled objects in MySQL database

[Daniel Tomso]

Hi--

There's probably a better way to do this - - -

But - - - 

You could use StringIO (or cStringIO) to create a file handle in memory,
write to it w/ Pickle (or cPickle), read the contents from it with
readlines(), then drop the result into a memo field in MySQL using
MySQLdb.

Seems like it would work . . .

I've also done similar semi-workaround solutions using a ramdisk, which
is straightforward and relatively fast.

Dan T.




Daniel J. Tomso

Senior Scientist, Bioinformatics
Athenix Corporation

2202 Ellis Road

Suite B

Durham, NC 27703

 

919.281.0920

dtomso at athenixcorp.com

www.athenixcorp.com

 

 

 

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-----Original Message-----
From: biopython-bounces at portal.open-bio.org
[mailto:biopython-bounces at portal.open-bio.org] On Behalf Of Ann Loraine
Sent: Wednesday, November 23, 2005 10:49 PM
To: biopython at biopython.org
Cc: Ann Loraine
Subject: [BioPython] saving pickled objects in MySQL database

Hi,

This may be a bit off topic - my apologies if so.

Can anybody point me to some good references or recipes on the best
way to save pickled Python objects in a MySQL database?

I'm using MySQLdb to talk to the database.

Ideally, I'd like to find a way to stream object data directly into
the database without an intermediate step of writing data to a file on
disk.

Thanks in advance for your help!

-Ann

--
Ann Loraine
Assistant Professor
Section on Statistical Genetics
University of Alabama at Birmingham
http://www.ssg.uab.edu
http://www.transvar.org

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