aphylogeo.params

class aphylogeo.params.Params[source]

Bases: object

Class that contains the parameters of the program. Loads the parameters from a yaml file or from a dictionary.

PARAMETER_KEYS = {'alignment_method': '2', 'bootstrap_amount': 100, 'bootstrap_threshold': 0, 'data_names': ['ALLSKY_SFC_SW_DWN_newick', 'T2M_newick', 'QV2M_newick', 'PRECTOTCORR_newick', 'WS10M_newick'], 'dist_threshold': 60, 'distance_method': '0', 'file_name': './datasets/example/geo.csv', 'fit_method': '1', 'makeDebugFiles': False, 'method_similarity': '1', 'names': ['id', 'ALLSKY_SFC_SW_DWN', 'T2M', 'PRECTOTCORR', 'QV2M', 'WS10M'], 'rate_similarity': 90, 'reference_gene_dir': './datasets/example', 'reference_gene_file': 'sequences.fasta', 'specimen': 'id', 'step_size': 100, 'tree_type': '2', 'window_size': 20}

classmethod update_from_dict(params_content)[source]

Method that updates the parameters from a dictionary.

Parameters:: params_content (dict) – the dictionary with the parameters

classmethod validate_and_set_params(params_dict)[source]

Method that validates and sets the parameters.