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