Retrieve blob field from mySQL database with MATLAB
- by yuk
I'm accessing public mySQL database using JDBC and mySQL java connector. exonCount is int(10), exonStarts and exonEnds are longblob fields.
javaaddpath('mysql-connector-java-5.1.12-bin.jar')
host = 'genome-mysql.cse.ucsc.edu';
user = 'genome';
password = '';
dbName = 'hg18';
jdbcString = sprintf('jdbc:mysql://%s/%s', host, dbName);
jdbcDriver = 'com.mysql.jdbc.Driver';
dbConn = database(dbName, user , password, jdbcDriver, jdbcString);
gene.Symb = 'CDKN2B';
% Check to make sure that we successfully connected
if isconnection(dbConn)
qry = sprintf('SELECT exonCount, exonStarts, exonEnds FROM refFlat WHERE geneName=''%s''',gene.Symb);
result = get(fetch(exec(dbConn, qry)), 'Data');
fprintf('Connection failed: %s\n', dbConn.Message);
end
Here is the result:
result =
[2] [18x1 int8] [18x1 int8]
[2] [18x1 int8] [18x1 int8]
result{1,2}'
ans =
50 49 57 57 50 57 48 49 44 50 49 57 57 56 54 55 51 44
This is wrong. The length of 2nd and 3rd columnsshould match the number in the 1st column.
The 1st blob, for example, should be [21992901; 21998673]. How I can convert it?
Update:
Just after submitting this question I thought it might be hex representation of a string.
And it was confirmed:
>> char(result{1,2}')
ans =
21992901,21998673,
So now I need to convert all blobs hex data into numeric vectors. Still thinking to do it in a vectorized way, since number of rows can be large.
