def test_mgf_empty(empty_mgf, ignore_unknown):
"""An empty mgf file should not throw an error but yield an empty list
"""
data = list(read_mgf(str(empty_mgf), ignore_unknown=ignore_unknown))
assert isinstance(data, list)
assert len(data) == 0
def test_mgf_pepmass_comma(invalid_mgf, ignore_unknown):
"""Comma can be used as decimal separator for `pepmass`"""
mzs, _, p = invalid_mgf
gen = read_mgf(str(p), ignore_unknown=ignore_unknown)
for i, (params, _) in enumerate(gen):
assert params['pepmass'] == mzs[i]
def test_mgf_data(valid_mgf, ignore_unknown):
"""`read` should return the same data arrays than the ones written in mgf.
"""
_, spectra, p = valid_mgf
gen = read_mgf(str(p), ignore_unknown=ignore_unknown)
for i, (_, data) in enumerate(gen):
assert pytest.approx(data) == spectra[i]
def test_mgf_pepmass(valid_mgf, ignore_unknown):
"""`read` should return the same *m/z* values than the ones written in mgf.
"""
mzs, _, p = valid_mgf
gen = read_mgf(str(p), ignore_unknown=ignore_unknown)
for i, (params, _) in enumerate(gen):
assert params['pepmass'] == mzs[i]
def test_mgf_invalid(invalid_mgf, ignore_unknown):
"""Invalid pepmass declaration should be ignored.
"""
_, _, p = invalid_mgf
gen = read_mgf(str(p), ignore_unknown=ignore_unknown)
for i, (params, data) in enumerate(gen):
if i == 2:
assert 'pepmass' not in params
def test_mgf_data_comma(invalid_mgf, ignore_unknown):
"""Comma use as a separator in data arrays will lead to truncated floats.
"""
_, spectra, p = invalid_mgf
gen = read_mgf(str(p), ignore_unknown=ignore_unknown)
for i, (_, data) in enumerate(gen):
if i == 2:
assert data[:, MZ] == pytest.approx(spectra[i][:, MZ], abs=1)
assert np.count_nonzero(data[:, INTENSITY]) == 0
def test_mgf_noions(noions_mgf, ignore_unknown):
"""A mgf file with only one entry where there is no ions should not throw an
error.
"""
data = list(read_mgf(str(noions_mgf), ignore_unknown=ignore_unknown))
assert isinstance(data, list)
assert len(data) == 1
assert data[0][1].size == 0
assert data[0][1].shape == (0, 2)
def test_mgf_ignore_unknown(valid_mgf, ignore_unknown):
"""`ignore_unknown` parameter should never ignore pepmass.
"""
_, _, p = valid_mgf
gen = read_mgf(str(p), ignore_unknown=ignore_unknown)
for i, (params, _) in enumerate(gen):
assert 'pepmass' in params
if ignore_unknown:
assert 'formula' not in params
else:
assert 'formula' in params
def test_mgf_python_cython(valid_mgf):
"""Cythonized `read_mgf` and it's fallback Python version should give the
same results.
"""
_, _, p = valid_mgf
# Python version does not use `ignore_unknown` parameter
gen_p = read_mgf.__wrapped__(str(p), ignore_unknown=False)
gen_c = read_mgf(str(p), ignore_unknown=False)
for (params_p, data_p), (params_c, data_c) in zip(gen_p, gen_c):
assert params_p == params_c
assert pytest.approx(data_p) == data_c
def test_mgf_non_existing(filename, ignore_unknown):
"""A filename that does not exists should throw a FileNotFoundError
"""
with pytest.raises(FileNotFoundError):
data = list(read_mgf(filename, ignore_unknown=ignore_unknown))