def test_resolution_warning(self):
"""Warn when overlapping isotopologues."""
data = pd.read_csv(Path("tests/test_dataset.csv"), index_col=0)
data.drop(columns=["dummy column int", "dummy column str"],
inplace=True)
data.rename(columns={"4C13 6H02 3N15": "1H02"}, inplace=True)
molecule_name = "Test1"
with self.assertWarns(UserWarning):
ic.calc_isotopologue_correction(
data,
molecule_name,
resolution_correction=True,
molecules_file=self.molecules_file,
isotopes_file=self.isotopes_file,
)
def test_result(self):
"""Result with default values."""
data = pd.read_csv(Path("tests/test_dataset.csv"), index_col=0)
data.drop(columns=["dummy column int", "dummy column str"],
inplace=True)
molecule_name = "NAD"
res = ic.calc_isotopologue_correction(
data,
molecule_name,
)
data_corrected = pd.read_csv(Path("tests/test_dataset_corrected.csv"),
index_col=0)
pd.testing.assert_frame_equal(data_corrected, res)
def test_resolution_ultra_high_result(self):
"""Result with ultra high resolution."""
data = pd.read_csv(Path("tests/test_dataset.csv"), index_col=0)
data.drop(columns=["dummy column int", "dummy column str"],
inplace=True)
data.rename(columns={"4C13 6H02 3N15": "2H02"}, inplace=True)
molecule_name = "Test1"
res_w_cor = ic.calc_isotopologue_correction(
data,
molecule_name,
resolution_correction=True,
resolution=1e8,
molecules_file=self.molecules_file,
isotopes_file=self.isotopes_file,
)
res_wo_cor = ic.calc_isotopologue_correction(
data,
molecule_name,
resolution_correction=False,
molecules_file=self.molecules_file,
isotopes_file=self.isotopes_file,
)
pd.testing.assert_frame_equal(res_wo_cor, res_w_cor, rtol=1e-4)
def test_result_files(self):
"""Result with given molecule and isotopes file paths."""
data = pd.read_csv(Path("tests/test_dataset.csv"), index_col=0)
data.drop(columns=["dummy column int", "dummy column str"],
inplace=True)
molecule_name = "Test1"
res = ic.calc_isotopologue_correction(
data,
molecule_name,
molecules_file=self.molecules_file,
isotopes_file=self.isotopes_file,
)
data_corrected = pd.read_csv(Path("tests/test_dataset_corrected.csv"),
index_col=0)
pd.testing.assert_frame_equal(data_corrected, res)
def test_result_exclude_col(self):
"""Result with exclude_col parameter."""
data = pd.read_csv(Path("tests/test_dataset.csv"), index_col=0)
exclude_col = ["dummy column int", "dummy column str"]
molecule_name = "Test1"
res = ic.calc_isotopologue_correction(
data,
molecule_name,
exclude_col=exclude_col,
molecules_file=self.molecules_file,
isotopes_file=self.isotopes_file,
)
assert res.shape == data.shape
res.drop(columns=["dummy column int", "dummy column str"],
inplace=True)
data_corrected = pd.read_csv(Path("tests/test_dataset_corrected.csv"),
index_col=0)
pd.testing.assert_frame_equal(data_corrected, res)
def test_result_subset(self):
"""Result with explicit subset."""
data = pd.read_csv(Path("tests/test_dataset.csv"), index_col=0)
subset = ["No label", "1C13", "4C13 6H02 3N15"]
molecule_name = "Test1"
res = ic.calc_isotopologue_correction(
data,
molecule_name,
subset=subset,
molecules_file=self.molecules_file,
isotopes_file=self.isotopes_file,
)
assert res.shape == data.shape
res.drop(columns=["dummy column int", "dummy column str"],
inplace=True)
data_corrected = pd.read_csv(Path("tests/test_dataset_corrected.csv"),
index_col=0)
pd.testing.assert_frame_equal(data_corrected, res)