7. Benchmarks

All benchmarks created on a standard notebook:

• OS: Linux Ubuntu 16.04.2 LTS (xenial)
• Python: 3.5.2
• Hardware: x86_64, Intel(R) Core(TM) i7-6560U CPU @ 2.20GHz, 4 CPUs, Mem 16Gb
• MariaDB: Server version: 10.0.29-MariaDB-0ubuntu0.16.04.1 Ubuntu 16.04

7.1. MySQL/MariaDB

Database created with following command in MySQL/MariaDB as root:

CREATE DATABASE pyhgnc CHARACTER SET utf8 COLLATE utf8_general_ci;

User created with following command in MySQL/MariaDB:

GRANT ALL PRIVILEGES ON pyhgnc.* TO 'pyhgnc_user'@'%' IDENTIFIED BY 'pyhgnc_passwd';
FLUSH PRIVILEGES;

7.2. Update

To import HGNC data executed following commands in python console:

import pyhgnc
pyhgnc.set_mysql_connection()
pyhgnc.update()

The other possibility is to use the command line interface

pyhgnc mysql # accept all default values
pyhgnc update

• CPU times:

  • real 3m52.311s
  • user 3m4.964s
  • sys 0m6.340s

7.3. Low memory option

If you have low memory available please use the –low_memory option in command line

pyhgnc mysql # accept all default values
pyhgnc update --low_memory
# or short
pyhgnc update -l

• CPU times:

  • real 6m40.913s
  • user 5m22.724s
  • sys 0m9.016s