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)
