PyCTD 0.5.7

Installation

PyCTD can be installed with pip.

pip install pyctd

If you fail because you have no rights to install use superuser (sudo on Linux before the commend) or …

pip install --user pyctd

If you want to make sure you are installing this under python3 use …

python3 -m pip install pyctd

SQLite

If you don’t know what all that means skip the section MySQL/MariaDB setup.

Don’t worry! You can always later change the configuration. For more information about changing database system later go to the subtitle Changing database configuration Changing database configuration in the documentation on readthedocs.

MySQL/MariaDB setup

Log in MySQL as root user and create a new database, create a user, assign the rights and flush privileges.

CREATE DATABASE pyctd CHARACTER SET utf8 COLLATE utf8_general_ci;
GRANT ALL PRIVILEGES ON pyctd.* TO 'pyctd_user'@'%' IDENTIFIED BY 'pyctd_passwd';
FLUSH PRIVILEGES;

Start a python shell and set the MySQL configuration. If you have not changed anything in the SQL statements …

import pyctd
pyctd.set_mysql_connection()

If you have used you own settings, please adapt the following command to you requirements.

import pyctd
pyctd.set_mysql_connection()
pyctd.set_mysql_connection(host='localhost', user='pyctd_user', passwd='pyctd_passwd', db='pyctd')

Updating

The updating process will download the files provided by the CTD team on the download page

import pyctd
pyctd.update()

Test a query function

>>> query = pyctd.query()
>>> results =query.get_chem_gene_interaction_actions(gene_name='APP', interaction_action='meman%', limit=1)
>>> first_result = r
>>> r.chemical
Memantine
>>> r.pubmed_ids
[21290839]
>>> r.chemical.drugbank_ids
[DB014043]