augur.filter.io
- augur.filter.io.cleanup_outputs(args)
Remove output files. Useful when terminating midway through a loop of metadata chunks.
- augur.filter.io.filter_kwargs_to_str(kwargs)
Convert a dictionary of kwargs to a JSON string for downstream reporting.
This structured string can be converted back into a Python data structure later for more sophisticated reporting by specific kwargs.
This function excludes data types from arguments like pandas DataFrames and also converts floating point numbers to a fixed precision for better readability and reproducibility.
- Parameters:
kwargs (dict) – Dictionary of kwargs passed to a given filter function.
- Returns:
String representation of the kwargs for reporting.
- Return type:
Examples
>>> from augur.dates import numeric_date >>> from augur.filter.include_exclude_rules import filter_by_sequence_length, filter_by_date >>> sequence_index = pd.DataFrame([{"strain": "strain1", "ACGT": 28000}, {"strain": "strain2", "ACGT": 26000}, {"strain": "strain3", "ACGT": 5000}]).set_index("strain") >>> exclude_by = [(filter_by_sequence_length, {"sequence_index": sequence_index, "min_length": 27000})] >>> filter_kwargs_to_str(exclude_by[0][1]) '[["min_length", 27000]]' >>> exclude_by = [(filter_by_date, {"max_date": numeric_date("2020-04-01"), "min_date": numeric_date("2020-03-01")})] >>> filter_kwargs_to_str(exclude_by[0][1]) '[["max_date", 2020.25], ["min_date", 2020.17]]'
- augur.filter.io.read_priority_scores(fname)