Database for fungal protein domain information

--

##Database creation

create_db.sql generates the MySQL database schema. It contains a tailored version of Pfam 27.0 database and protein information from UniProtKB. A user capable to create databases is needed*. Open a mysql console with administrative privileges and type:

> mysql -Dpfam27 -u your_user -p < create_db.sql

*By default, mysql-server has a 'root' superuser. Use it unless you have a customized administartor user

You will need to grant CRUD privileges on fungidom database to your mysql user. Open a mysql console with administrative privileges and type:

mysql> GRANT ALL on pfam27.* TO 'your_user'.

The credential used to access the MySQL database have to be placed under a [pfam] tag in your mysql configuration file (typically ~/.my.cnf file). It should look something like this:

##########################################################
#   Configuration for Python scripts to work with Pfam   #
##########################################################
[pfam]
host=127.0.0.1
port=3307
database=pfam27
default-character-set=utf8
password=***your_password

###Python dependencies:

• MySQLdb --If you have a Debian distribution try this: sudo apt-get install python-mysqldb