def test_msp_empty(empty_msp, ignore_unknown, read_msp_f):
"""An empty msp file should not throw an error but yield an empty list
"""
data = list(read_msp_f(str(empty_msp), ignore_unknown=ignore_unknown))
assert isinstance(data, list)
assert len(data) == 0
def test_msp_pepmass(valid_msp, ignore_unknown, read_msp_f):
"""`read` should return the same *m/z* values than the ones written in msp.
"""
mzs, _, p = valid_msp
gen = read_msp_f(str(p), ignore_unknown=ignore_unknown)
for i, (params, _) in enumerate(gen):
assert pytest.approx(params['precursormz']) == mzs[i]
def test_msp_data(valid_msp, ignore_unknown, read_msp_f):
"""`read` should return the same data arrays than the ones written in msp.
"""
_, spectra, p = valid_msp
gen = read_msp_f(str(p), ignore_unknown=ignore_unknown)
for i, (_, data) in enumerate(gen):
assert pytest.approx(data) == spectra[i]
def test_msp_invalid(invalid_msp, ignore_unknown, read_msp_f):
"""Invalid precursormz declaration should be ignored.
"""
_, _, p = invalid_msp
gen = read_msp_f(str(p), ignore_unknown=ignore_unknown)
for i, (params, data) in enumerate(gen):
if i == 2:
assert 'precursormz' not in params
def test_msp_wrongfloat(invalid_msp, read_msp_f):
"""Characters after a float value should be ignored and not raise any error.
"""
mzs, _, p = invalid_msp
data = list(read_msp_f(str(p), ignore_unknown=True))
assert len(data) == len(mzs)
for i, (params, d) in enumerate(data):
assert pytest.approx(params['precursormz']) == mzs[i]
def test_msp_noions(noions_msp, ignore_unknown, read_msp_f):
"""A msp file with only one entry where there is no ions should not throw an
error.
"""
data = list(read_msp_f(str(noions_msp), 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_msp_nonumpeaks(invalid_msp, ignore_unknown, read_msp_f):
"""Entries where num peaks field is missing should be ignored.
"""
mzs, _, p = invalid_msp
data = list(read_msp_f(str(p), ignore_unknown=ignore_unknown))
assert len(data) == len(mzs) - 1
for i, (params, d) in enumerate(data):
if i < 2:
assert pytest.approx(params['precursormz']) == mzs[i]
else:
assert pytest.approx(params['precursormz']) == mzs[i+1]
def test_msp_twonames(invalid_msp, read_msp_f):
"""If two names sections, the spectrum will be ignored
"""
mzs, _, p = invalid_msp
data = list(read_msp_f(str(p), ignore_unknown=True))
assert len(data) == len(mzs) - 1
for i, (params, d) in enumerate(data):
if i < 2:
assert pytest.approx(params['precursormz']) == mzs[i]
else:
assert pytest.approx(params['precursormz']) == mzs[i+1]
def test_msp_mz_zero(invalid_msp, read_msp_f):
"""A peak with an mz equal to zero should be ignored."""
mzs, spectra, p = invalid_msp
data = list(read_msp_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_msp_numpeakszero(invalid_msp, ignore_unknown, read_msp_f):
"""Entries where num peaks field is zero should be not have peaks
"""
mzs, spectra, p = invalid_msp
data = list(read_msp_f(str(p), ignore_unknown=ignore_unknown))
assert len(data) == len(mzs)
for i, (params, d) in enumerate(data):
assert pytest.approx(params['precursormz']) == mzs[i]
if i == 2:
assert len(d) == 0
else:
assert len(d) == len(spectra[i])
def test_msp_non_existing(filename, ignore_unknown, read_msp_f):
"""A filename that does not exists should throw a FileNotFoundError
"""
with pytest.raises(FileNotFoundError):
data = list(read_msp_f(filename, ignore_unknown=ignore_unknown))