randomize_pam - CLI interface

Randomize a binary presence-absence matrix (PAM) while maintaining marginal totals.

randomize_pam [-h] [--config_file CONFIG_FILE] [--log_filename LOG_FILENAME] [--log_console]
              [-r REPORT_FILENAME] [--randomization_method {grady}]
              [--output_pam_count OUTPUT_PAM_COUNT]
              [--output_pam_basefilename OUTPUT_PAM_BASEFILENAME [OUTPUT_PAM_BASEFILENAME ...]]
              [--output_pam_filename OUTPUT_PAM_FILENAME [OUTPUT_PAM_FILENAME ...]]
              input_pam_filename

randomize_pam positional arguments

randomize_pam optional arguments

  • -h, --help - show this help message and exit

  • --config_file CONFIG_FILE - Path to configuration file. (default: None)

  • --log_filename LOG_FILENAME, -l LOG_FILENAME - A file location to write logging data. (default: None)

  • --log_console - If provided, write logging statements to console.

  • -r REPORT_FILENAME, --report_filename REPORT_FILENAME - File location to write the summary report. (default: None)

  • --randomization_method RANDOMIZATION_METHOD, -m RANDOMIZATION_METHOD - The method to use to randomize the matrix. (default: grady)

  • --output_pam_count OUTPUT_PAM_COUNT - Number of randomized PAMs to create. (default: None)

  • --output_pam_basefilename OUTPUT_PAM_BASEFILENAME - The path and base filename (without extension) for randomized PAMs. (default: None)

  • --output_pam_filename OUTPUT_PAM_FILENAME - The file location to write the randomized PAM(s). (default: None)