choppa.IO.input.FitnessFactory
- class choppa.IO.input.FitnessFactory(input_fitness_csv: Path, resindex_colname: str | None = 'residue_index', wildtype_colname: str | None = 'wildtype', mutant_colname: str | None = 'mutant', fitness_colname: str | None = 'fitness', confidence_colname: str | None = None)[source]
Base class for handling Fitness data within choppa.
- __init__(input_fitness_csv: Path, resindex_colname: str | None = 'residue_index', wildtype_colname: str | None = 'wildtype', mutant_colname: str | None = 'mutant', fitness_colname: str | None = 'fitness', confidence_colname: str | None = None)[source]
Methods
__init__(input_fitness_csv[, ...])check_validity(fitness_df)Does some quick checks to make sure the imported CSV file is valid.
Converts a pandas fitness dataframe (read by FitnessFactory.read_fitness_csv) into a fitness basedict which is essentially just an OrderedDict.
Reads in a fitness CSV file and checks that all requested columns are present, complete and numeric.
- check_validity(fitness_df)[source]
Does some quick checks to make sure the imported CSV file is valid.
- get_fitness_basedict()[source]
Converts a pandas fitness dataframe (read by FitnessFactory.read_fitness_csv) into a fitness basedict which is essentially just an OrderedDict.
We want the dict to have the form: { residue_index: {
fitness_csv_index, # this is the original index in the fitness CSV for provenance wildtype: {AA, fitness, confidence}, mutants: [{AA, fitness, confidence}, {AA, fitness, confidence}, etc]
}
}