PyHGNC 0.2.4

Installation

PyHGNC can be installed with pip.

pip install pyhgnc

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

pip install --user pyhgnc

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

python3 -m pip install pyhgnc

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 pyhgnc CHARACTER SET utf8 COLLATE utf8_general_ci;
GRANT ALL PRIVILEGES ON pyhgnc.* TO 'pyhgnc_user'@'%' IDENTIFIED BY 'pyhgnc_passwd';
FLUSH PRIVILEGES;

There are two options to set the MySQL/MariaDB.

1. The simplest is to start the command line tool

pyhgnc mysql

You will be guided with input prompts. Accept the default value in squared brackets with RETURN. You will see something like this

server name/ IP address database is hosted [localhost]:
MySQL/MariaDB user [pyhgnc_user]:
MySQL/MariaDB password [pyhgnc_passwd]:
database name [pyhgnc]:
character set [utf8]:

Connection will be tested and in case of success return Connection was successful. Otherwise you will see following hint

Test was NOT successful

Please use one of the following connection schemas
MySQL/MariaDB (strongly recommended):
        mysql+pymysql://user:passwd@localhost/database?charset=utf8

PostgreSQL:
        postgresql://user:passwd@localhost/database

MsSQL (pyodbc needed):
        mssql+pyodbc://user:passwd@database

SQLite (always works):

- Linux:
        sqlite:////absolute/path/to/database.db

- Windows:
        sqlite:///C:\absolute\path\to\database.db

Oracle:
        oracle://user:passwd@localhost:1521/database

2. The second option is to start a python shell and set the MySQL configuration. If you have not changed anything in the SQL statements above …

import pyhgnc
pyhgnc.set_mysql_connection()

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

import pyhgnc
pyhgnc.set_mysql_connection(host='localhost', user='pyhgnc_user', passwd='pyhgnc_passwd', db='pyhgnc')

Updating

The updating process will download the complete HGNC json file and the HCOP file.

import pyhgnc
pyhgnc.manager.database.update()

This will use either the default connection settings of PyHGNC or the settings defined by the user. It is also possible to run the update process from shell.

pyhgnc update

Quick start with query functions

Initialize the query object

query = pyhgnc.query()

Get all HGNC entries:

all_entries = query.hgnc()