calculate_pam_stats - CLI interface

Compute statistics for a PAM and optionally a tree.

calculate_pam_stats [-h] [--config_file CONFIG_FILE] [--log_filename LOG_FILENAME]
                    [--log_console] [-r REPORT_FILENAME] [--tree_filename TREE_FILENAME]
                    [--tree_matrix TREE_MATRIX TREE_MATRIX TREE_MATRIX]
                    [--covariance_matrix COVARIANCE_MATRIX]
                    [--diversity_matrix DIVERSITY_MATRIX]
                    [--site_stats_matrix SITE_STATS_MATRIX]
                    [--species_stats_matrix SPECIES_STATS_MATRIX]
                    pam_filename

calculate_pam_stats positional arguments

• pam_filename - Path to PAM file. (default: None)

calculate_pam_stats 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 log to console.

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

• --tree_filename TREE_FILENAME - Path to matching tree. (default: None)

• --tree_matrix TREE_MATRIX - Path to tree matrix. (default: None)

• --covariance_matrix COVARIANCE_MATRIX - Path to write covariance matrix if desired. (default: None)

• --diversity_matrix DIVERSITY_MATRIX - Path to write diversity matrix if desired. (default: None)

• --site_stats_matrix SITE_STATS_MATRIX - Path to write site statistics matrix if desired. (default: None)

• --species_stats_matrix SPECIES_STATS_MATRIX - Path to write species statistics matrix if desired. (default: None)