rhapsody.utils package¶
This subpackage contains modules for the initial package configuration and for accessing installation settings and other parameters.
- rhapsody.utils.initialSetup(working_dir=None, refresh=False, download_EVmutation=True)[source]¶
Function to be run right after installation for setting up the environment and main parameters and for training the default classifiers. By default, a working directory will be created in the user home directory (
~/rhapsody/
). Previous configuration data will be recovered. Additional data from EVmutation website will be automatically downloaded (~1.4GB).- Parameters
working_dir (str) – path to a local folder
refresh (bool) – if True, previous trained classifiers will be deleted, if found
download_EVmutation (bool) – if True, precomputed EVmutation scores will be downloaded (recommended)
- rhapsody.utils.getDefaultClassifiers()[source]¶
Returns a dictionary with the paths to the three default classifiers (
'full'
,'reduced'
and'EVmut'
)
- rhapsody.utils.importDefaultClassifier(version)[source]¶
Imports the specified classifier and its summary
- Parameters
version (str) – either ‘full’, ‘reduced’ or ‘EVmut’
- rhapsody.utils.getSettings(print=True)[source]¶
Returns and prints essential information about the current Rhapsody configuration, such as the location of working directory and default classifiers
Submodules¶
rhapsody.utils.misc module¶
This module defines default configuration parameters and a function for the initial setup and training of Rhapsody.
- rhapsody.utils.misc.initialSetup(working_dir=None, refresh=False, download_EVmutation=True)[source]¶
Function to be run right after installation for setting up the environment and main parameters and for training the default classifiers. By default, a working directory will be created in the user home directory (
~/rhapsody/
). Previous configuration data will be recovered. Additional data from EVmutation website will be automatically downloaded (~1.4GB).- Parameters
working_dir (str) – path to a local folder
refresh (bool) – if True, previous trained classifiers will be deleted, if found
download_EVmutation (bool) – if True, precomputed EVmutation scores will be downloaded (recommended)
- rhapsody.utils.misc.getDefaultClassifiers()[source]¶
Returns a dictionary with the paths to the three default classifiers (
'full'
,'reduced'
and'EVmut'
)
rhapsody.utils.settings module¶
This module defines default configuration parameters and a function for the initial setup and training of Rhapsody.
- rhapsody.utils.settings.initialSetup(working_dir=None, refresh=False, download_EVmutation=True)[source]¶
Function to be run right after installation for setting up the environment and main parameters and for training the default classifiers. By default, a working directory will be created in the user home directory (
~/rhapsody/
). Previous configuration data will be recovered. Additional data from EVmutation website will be automatically downloaded (~1.4GB).- Parameters
working_dir (str) – path to a local folder
refresh (bool) – if True, previous trained classifiers will be deleted, if found
download_EVmutation (bool) – if True, precomputed EVmutation scores will be downloaded (recommended)
- rhapsody.utils.settings.getDefaultClassifiers()[source]¶
Returns a dictionary with the paths to the three default classifiers (
'full'
,'reduced'
and'EVmut'
)