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)

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.getDefaultTrainingDataset()

rhapsody.utils.getDefaultClassifiers()

Returns a dictionary with the paths to the three default classifiers ('full', 'reduced' and 'EVmut')

rhapsody.utils.importDefaultClassifier(version)

Imports the specified classifier and its summary

Parameters

version (str) – either ‘full’, ‘reduced’ or ‘EVmut’

rhapsody.utils.delSettings()

rhapsody.utils.getSettings(print=True)

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)

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.getDefaultTrainingDataset()

rhapsody.utils.misc.getDefaultClassifiers()

Returns a dictionary with the paths to the three default classifiers ('full', 'reduced' and 'EVmut')

rhapsody.utils.misc.importDefaultClassifier(version)

Imports the specified classifier and its summary

Parameters

version (str) – either ‘full’, ‘reduced’ or ‘EVmut’

rhapsody.utils.misc.delSettings()

rhapsody.utils.misc.getSettings(print=True)

Returns and prints essential information about the current Rhapsody configuration, such as the location of working directory and default classifiers

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)

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.getDefaultTrainingDataset()

rhapsody.utils.settings.getDefaultClassifiers()

Returns a dictionary with the paths to the three default classifiers ('full', 'reduced' and 'EVmut')

rhapsody.utils.settings.importDefaultClassifier(version)

Imports the specified classifier and its summary

Parameters

version (str) – either ‘full’, ‘reduced’ or ‘EVmut’

rhapsody.utils.settings.delSettings()

rhapsody.utils.settings.getSettings(print=True)

Returns and prints essential information about the current Rhapsody configuration, such as the location of working directory and default classifiers