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- get_config_boolean(config, section, option, default_value)
- tries to retrieve a boolean value from config or returns the default
- get_config_int(config, section, option, default_value=None)
- tries to retrieve an int value from config or returns the default
- get_config_str(config, section, option, default_value=None)
- tries to retrieve a str value from config or returns the default
- read_ratios(params, args)
- reading ratios matrix
- set_config(config)
- Returns a dictionary containing the configuration contained in
the config parser object. Note that there are only 3 fixed sections:
General, Membership and Scoring
- set_config_general(config, params)
- Process General section
- set_config_membership(config, params)
- membership default parameters
- set_config_motifs(config, params)
- process the Motifs section
- set_config_scoring_functions(config, params)
- processing scoring function specific stuff
- setup(arg_ext=None)
- main configuration function - does everything. It reads and configures
everything that can be derived from the configuration files and input
parameters and returns the configuration in a dictionary as well as
the normalized ratios matrix.
The arg_ext parameter can be used to add additional argements to the
argparser that can be processed outside of the core application.
- setup_default(args, config_parser)
- default configuration method
- setup_resume(args, config_parser)
- setup from out directory
- write_general_settings(outfile, config_params)
- Writes the General section of the final.ini file
- write_membership_settings(outfile, config_params)
- Writes the Membership section of the final.ini file
- write_section(outfile, section, settings)
- Writes a scoring function specific section to the final.ini file
- write_setup(config_params)
- Write all active configuration settings to <outputdir>/final.ini
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