Usage
This page shows how to quickly access the refinegems toolbox. For more detailed examples see About different applications.
Access points
via command line/terminal
The main functionalities of refineGEMs can be accessed directly from the command line after a successfull installation.
For more information, call the following in your command line or terminal:
refinegems --help
or refer to the following section: Command Line access points.
access from inside Python
Alternatively, refineGEMs can be directly imported into Python or a python script for full access of all modules, classes and more.
import refinegems as rg
Or, e.g.:
from refinegems.analysis.growth import growth_analysis
The media database
The media database can be accessed via a mutitude of different routes.
Hint
For more information about the database and its contents, refer to Media & Subsets.
Direct access via SQL
One way to inspect the database is to download it from the GitHub page and open it with an IDE with an SQL-extension (e.g. VSCode) or with a graphical SQL interface like SQLite.
Access via the command line
The refineGEMs command line tool provides limited access to some of the basic functionalities concering
the media database, including downloading a config file and retrieving a list of all available media:
refinegems media --help
For more information, see section refinegems media.
Access via Python
To access the media from inside a Python script, the medium
provides classes and functions.
For example, to extract the medium LB run:
from refinegems.classes import Medium
lb = medium.load_medium_from_db('LB')
Access the database via a config.yaml
If the idea is to load a list of media - from the database or externel, with or without modifications -
it might be useful to use the media configuration file. There, different media names with options for
modifications can be listed and subsequently loaded using medium or used as input for other
entry points that requires a list of media or the config itself.