def test_with_missing(mock_conf, tmp_path):
"""Test that missing columns causes errors"""
conf = mock_conf
cols = conf._optional_columns.copy()
for col in ["filename", "calcmass", "rt", "charge"]:
new_cols = cols.copy()
new_cols[col] = None
conf._optional_columns = new_cols
with pytest.raises(ValueError):
mokapot.to_flashlfq(conf, tmp_path / "test.txt")
def test_fasta_proteins(mock_conf, mock_proteins, tmp_path):
"""Test that using mokapot protein groups works"""
conf = mock_conf
conf._proteins = mock_proteins
conf._has_proteins = True
df = pd.read_table(mokapot.to_flashlfq(conf, tmp_path / "test.txt"))
expected = pd.Series(["X|Y|Z", "A|B|C; X|Y|Z"], name="Protein Accession")
pd.testing.assert_series_equal(df["Protein Accession"], expected)
conf._proteins.shared_peptides = {}
df = pd.read_table(mokapot.to_flashlfq(conf, tmp_path / "test.txt"))
expected = pd.Series(["X|Y|Z"], name="Protein Accession")
pd.testing.assert_series_equal(df["Protein Accession"], expected)
def test_sanity(psms, tmp_path):
"""Run simple sanity checks"""
conf = psms.assign_confidence()
test1 = conf.to_flashlfq(tmp_path / "test1.txt")
test2 = mokapot.to_flashlfq(conf, tmp_path / "test2.txt")
test3 = mokapot.to_flashlfq([conf, conf], tmp_path / "test3.txt")
with pytest.raises(ValueError):
mokapot.to_flashlfq("blah", tmp_path / "test4.txt")
df1 = pd.read_table(test1)
df3 = pd.read_table(test3)
assert 2 * len(df1) == len(df3)
assert len(df1.columns) == 7
def test_no_proteins(mock_conf, tmp_path):
"""Test when no proteins are available"""
conf = mock_conf
conf._protein_column = None
df = pd.read_table(mokapot.to_flashlfq(conf, tmp_path / "test.txt"))
expected = pd.Series([np.nan, np.nan], name="Protein Accession")
pd.testing.assert_series_equal(df["Protein Accession"], expected)
def test_basic(mock_conf, tmp_path):
"""Test that the basic output works"""
conf = mock_conf
df = pd.read_table(mokapot.to_flashlfq(conf, tmp_path / "test.txt"))
expected = pd.DataFrame(
{
"File Name": ["c.mzML"] * 2,
"Base Sequence": ["ABCDXYZ", "ABCDEFG"],
"Full Sequence": ["B.ABCD[+2.817]XYZ.A", "ABCDE(shcah8)FG"],
"Peptide Monoisotopic Mass": [1, 2],
"Scan Retention Time": [1.0, 2.0],
"Precursor Charge": [2, 3],
"Protein Accession": ["A|B|C; B|C|A", "A|B|C"],
}
)
pd.testing.assert_frame_equal(df, expected)