[BioPython] mysql trouble

[pap501 at york.ac.uk]

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
-------------- next part --------------
import cStringIO
import os
import MySQLdb
conn= MySQLdb.connect (host="localhost",
                       user ="root",
                      passwd ="p1geon1",
                       db="phil")
allfilenames=('F50',)

for a in allfilenames:
    print a
    input8=open ('SsGI_library_#'+a+'.txt','r')
    outfile=open('outtest.txt', 'w')

    i8=input8.read()
 #   print i8
    listofentries=i8.split('>')
    

    for li in listofentries:
        print li
        numbers=li.split('\n')[0]
        print numbers
        seq=li.split('\n')[1]
       # print numbers
        bothnumbers=numbers.split('\t')
        print bothnumbers
        gb=bothnumbers[0]

        if len(bothnumbers)==2:
             tnum= bothnumbers [1]

        else:
            tnum='NULL'

        qry="insert into sequences2 values('%s','%s','%s','%s');"% (a, gb, tnum, seq)
        print qry
        conn.query(qry)