def test_pin_parsing(std_pin):
"""Test pin parsing"""
df = mokapot.read_pin(std_pin, to_df=True)
assert df["LaBel"].dtype == "bool"
assert len(df) == 2
assert len(df[df["LaBel"]]) == 1
assert len(df[df["LaBel"]]) == 1
dat = mokapot.read_pin(std_pin)
pd.testing.assert_frame_equal(df.loc[:, ("sCore", )], dat.features)
def test_compare_to_percolator():
"""Test that mokapot get almost the same answer as Percolator"""
dat = mokapot.read_pin(os.path.join("data", "phospho_rep1.pin"))
dat.add_proteins(os.path.join("data", "human_sp_td.fasta"))
res, _ = mokapot.brew(dat)
perc_path = os.path.join("data", "percolator.{l}.txt")
perc_res = {
l: mokapot.read_percolator(perc_path.format(l=l))
for l in ["psms", "peptides", "proteins"]
}
for level in ["psms", "peptides", "proteins"]:
logging.info("Testing level: %s", level)
if level != "proteins":
perc = perc_res[level].rename(columns={
"PSMId": "SpecId",
"peptide": "Peptide"
})
else:
perc = perc_res[level]
res.proteins["ProteinId"] = res.proteins[
"mokapot protein group"].str.split(", ", expand=True)[0]
merged = pd.merge(res.confidence_estimates[level], perc)
assert merged["mokapot q-value"].corr(merged["q-value"]) > 0.99
assert (merged["mokapot PEP"].corr(merged["posterior_error_prob"]) >
0.99)
def test_compare_to_percolator():
"""Test that mokapot get almost the same answer as Percolator"""
dat = mokapot.read_pin(os.path.join("data", "phospho_rep1.pin"))
res, _ = mokapot.brew(dat)
perc_path = os.path.join("data", "percolator.{l}.txt")
perc_res = {
l: mokapot.parsers.read_percolator(perc_path.format(l=l))
for l in ["psms", "peptides"]
}
for level in ["psms", "peptides"]:
logging.info("Testing level: %s", level)
perc = perc_res[level].rename(
columns={"PSMId": "SpecId", "peptide": "Peptide"}
)
merged = pd.merge(res._confidence_estimates[level], perc)
assert merged["mokapot q-value"].corr(merged["q-value"]) > 0.99
assert (
merged["mokapot PEP"].corr(merged["posterior_error_prob"]) > 0.99
)
def test_assign_confidence():
"""Test that assign_confidence() methods run"""
dset = mokapot.read_pin(EX_FILE)
dset.assign_confidence()
def test_pin_wo_dir():
"""Test a PIN file without a DefaultDirection line"""
dat = mokapot.read_pin("data/scope2_FP97AA.pin")