[BioPython] mysql trouble

[aurelie.bornot at free.fr]

Hi,

I had a similar problem and I tried Rafael 's script on windows :
it didn't work either.... for me....  :'(
But I tried to add :
db.commit()
after
cursor.execute("""---""")
and it worked !!!

hope this help !
cheers,
Aurelie



Rafael C. Jimenez rafael at nbn.ac.za wrote :

>Try to create a cursor of  "conn" and then use the method execute to
>process the query.

>See one example from the MySQLdb help:

>#!/usr/bin/python
># import MySQL module
>import MySQLdb
># connect
>db = MySQLdb.connect(host="localhost", user="joe",
>passwd="secret",
>db="db56a")
># create a cursor
>cursor = db.cursor()
># execute SQL statement
>cursor.execute("""INSERT INTO animals (name, species) VALUES
>("Harry",
>"Hamster")""")

>Good luck with your project!
>Cheers,
>Rafael.

On 31/03/2005, at 12:30, pap501 at york.ac.uk wrote:

> Hi
>
> I am a masters student at the University of York working on a project
> to create a database of DNA sequences.
>
> I am trying to grab information from text files using a python script
> to insert data into a MySQL table. The problem is that although I can
> query MySQL through Python I cannot write into MySQL through Python. I
> am using the Windows platform with Python version 2.4 with Biopython
> installed and MySQL Server 4.1.
>
> I have attached my python script to this email.
> The script takes each text file in turn (although only one is listed
> in the script at the mo) and inserts the library code, Genbank code
> (primary key), TiGR code (if there is one, null otherwise) and the DNA
> sequence (string of characters). Each file is a library of ~2000 DNA
> sequences. The python script runs but does not write the information
> into my MySQL table. When I query the table in MySQL it says that the
> table is empty.
>
> Can anyone advise me what to do? Is it soemthing to do with the setup
> of MySQL and/or Python or a problem with the Python script?
>
> Any advice would be greatly appreciated.
>
> Many thanks
>
> Phil<library.py>_______________________________________________
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