def test_mgf_empty(empty_mgf, ignore_unknown, read_mgf_f):
"""An empty mgf file should not throw an error but yield an empty list
"""
data = list(read_mgf_f(str(empty_mgf), ignore_unknown=ignore_unknown))
assert isinstance(data, list)
assert len(data) == 0
def test_mgf_pepmass_comma(invalid_mgf, ignore_unknown, read_mgf_f):
"""Comma can be used as decimal separator for `pepmass`"""
mzs, _, p = invalid_mgf
gen = read_mgf_f(str(p), ignore_unknown=ignore_unknown)
for i, (params, _) in enumerate(gen):
assert pytest.approx(params['pepmass']) == mzs[i]
def test_mgf_data(valid_mgf, ignore_unknown, read_mgf_f):
"""`read` should return the same data arrays than the ones written in mgf.
"""
_, spectra, p = valid_mgf
gen = read_mgf_f(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_mgf_f):
"""`read` should return the same *m/z* values than the ones written in mgf.
"""
mzs, _, p = valid_mgf
gen = read_mgf_f(str(p), ignore_unknown=ignore_unknown)
for i, (params, _) in enumerate(gen):
assert pytest.approx(params['pepmass']) == mzs[i]
def test_mgf_invalid(invalid_mgf, ignore_unknown, read_mgf_f):
"""Invalid pepmass declaration should be ignored.
"""
_, _, p = invalid_mgf
gen = read_mgf_f(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, read_mgf_f):
"""Comma use as a separator in data arrays will lead to truncated floats.
"""
_, spectra, p = invalid_mgf
gen = read_mgf_f(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, read_mgf_f):
"""A mgf file with only one entry where there is no ions should not throw an
error.
"""
data = list(read_mgf_f(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_mz_zero(invalid_mgf, read_mgf_f):
"""A peak with an mz equal to zero should be ignored."""
mzs, spectra, p = invalid_mgf
data = list(read_mgf_f(str(p), ignore_unknown=True))
assert len(data) == len(mzs)
for i, (params, d) in enumerate(data):
if i == 2:
assert len(d) == len(spectra[i]) - 1
assert pytest.approx(d) == spectra[i][1:]
else:
assert len(d) == len(spectra[i])
assert pytest.approx(d) == spectra[i]
def test_mgf_non_existing(filename, ignore_unknown, read_mgf_f):
"""A filename that does not exists should throw a FileNotFoundError
"""
with pytest.raises(FileNotFoundError):
data = list(read_mgf_f(filename, ignore_unknown=ignore_unknown))