def main(args): result = TypingResult(fromfile=args.result) config = None if args.config: config = pd.read_csv(args.config, sep=None, engine="python") result.filter(static=args.static, dynamic=args.dynamic, config=config) result.dump(args.out)
def test_filter_config_file(): config = pd.read_csv(data_file("filters.csv"), sep=None, engine="python") result = TypingResult(fromfile=data_file("prof/deep-raw.json")) result.filter(static=5, dynamic=0.02, config=config) assert len(result.haplotypes("mh01XYZ-1")) == 8 assert len(result.haplotypes("mh02XYZ-2")) == 2 assert len(result.haplotypes("mh02XYZ-3")) == 2
def test_filter_dupl_marker(): config = pd.read_csv(data_file("filters-redundant.csv"), sep=None, engine="python") result = TypingResult(fromfile=data_file("prof/deep-raw.json")) message = "filter config file contains duplicate entries for some markers" with pytest.raises(ValueError, match=message): result.filter(static=5, dynamic=0.02, config=config)
def test_filter_missing_column(): config = pd.read_csv(data_file("filters-missing.csv"), sep=None, engine="python") result = TypingResult(fromfile=data_file("prof/deep-raw.json")) with pytest.raises( ValueError, match=r"filter config file missing column\(s\): Static"): result.filter(static=5, dynamic=0.02, config=config)