def test_init_annotation_order():
num_peaks = 150
mz = np.random.uniform(100, 1400, num_peaks)
intensity = np.random.lognormal(0, 1, num_peaks)
annotation = [
spectrum.PeptideFragmentAnnotation(1, this_mz, 'y', i)
for i, this_mz in enumerate(mz)
]
spec = spectrum.MsmsSpectrum('test_spectrum', 500, 2, mz, intensity,
annotation)
for this_mz, this_annotation in zip(spec.mz, spec.annotation):
assert this_mz == pytest.approx(this_annotation.calc_mz)
def test_filter_intensity_keep_all():
num_peaks = 150
mz = np.random.uniform(100, 1400, num_peaks)
intensity = np.random.lognormal(0, 1, num_peaks)
annotation = [
spectrum.PeptideFragmentAnnotation(1, this_mz, 'y', i)
for i, this_mz in enumerate(mz)
]
spec = spectrum.MsmsSpectrum('test_spectrum', 500, 2, mz, intensity,
annotation)
spec.filter_intensity()
assert len(spec.mz) == num_peaks
assert len(spec.intensity) == num_peaks
assert len(spec.annotation) == num_peaks
def test_annotation_none():
num_peaks = 150
mz = np.random.uniform(100, 1400, num_peaks)
intensity = np.random.lognormal(0, 1, num_peaks)
spec = spectrum.MsmsSpectrum('test_spectrum', 500, 2, mz, intensity)
assert spec.annotation is None
annotation = [
spectrum.PeptideFragmentAnnotation(1, this_mz, 'y', i)
for i, this_mz in enumerate(mz)
]
spec.annotation = annotation
assert type(spec.annotation) == np.ndarray
spec.annotation = None
assert spec.annotation is None
def test_set_mz_range_none():
num_peaks = 150
mz = np.random.uniform(100, 1400, num_peaks)
intensity = np.random.lognormal(0, 1, num_peaks)
annotation = [
spectrum.PeptideFragmentAnnotation('y', i, 1, this_mz)
for i, this_mz in enumerate(mz)
]
spec = spectrum.MsmsSpectrum('test_spectrum', 500, 2, mz, intensity,
annotation)
spec.set_mz_range(None, None)
assert len(spec.mz) == num_peaks
assert len(spec.intensity) == num_peaks
assert len(spec.annotation) == num_peaks
def test_annotation_array():
num_peaks = 150
mz = np.random.uniform(100, 1400, num_peaks)
intensity = np.random.lognormal(0, 1, num_peaks)
annotation = [
spectrum.PeptideFragmentAnnotation(1, this_mz, 'y', i)
for i, this_mz in enumerate(mz)
]
spec = spectrum.MsmsSpectrum('test_spectrum', 500, 2, mz, intensity,
annotation)
assert type(spec.annotation) == np.ndarray
spec.annotation = annotation
assert type(spec.annotation) == np.ndarray
with pytest.raises(ValueError):
spec.annotation = 14
def test_filter_intensity_max_num_peaks():
num_peaks = 150
mz = np.random.uniform(100, 1400, num_peaks)
intensity = np.random.lognormal(0, 1, num_peaks)
max_intensity = intensity.max()
annotation = [
spectrum.PeptideFragmentAnnotation(1, this_mz, 'y', i)
for i, this_mz in enumerate(mz)
]
spec = spectrum.MsmsSpectrum('test_spectrum', 500, 2, mz, intensity,
annotation)
max_num_peaks = 50
spec.filter_intensity(max_num_peaks=max_num_peaks)
assert len(spec.mz) == max_num_peaks
assert len(spec.intensity) == max_num_peaks
assert len(spec.annotation) == max_num_peaks
assert spec.intensity.max() == pytest.approx(max_intensity)
def test_set_mz_range_truncate_right():
num_peaks = 150
mz = np.random.uniform(100, 1400, num_peaks)
intensity = np.random.lognormal(0, 1, num_peaks)
annotation = [
spectrum.PeptideFragmentAnnotation(1, this_mz, 'y', i)
for i, this_mz in enumerate(mz)
]
spec = spectrum.MsmsSpectrum('test_spectrum', 500, 2, mz, intensity,
annotation)
min_mz, max_mz = 0, 1200
assert spec.mz.max() > max_mz
spec.set_mz_range(min_mz, max_mz)
assert len(spec.mz) < num_peaks
assert len(spec.intensity) < num_peaks
assert len(spec.annotation) < num_peaks
assert spec.mz.max() <= max_mz
def test_round_merge_len():
num_peaks = 10
mz = np.arange(1, num_peaks + 1) + np.random.uniform(-0.2, 0.2, num_peaks)
mz[4] = mz[3] + 0.0002
mz[5] = mz[3] + 0.0005
mz[7] = mz[8] - 0.00037
intensity = np.random.exponential(1, num_peaks)
annotation = [
spectrum.PeptideFragmentAnnotation(1, this_mz, 'y', i)
for i, this_mz in enumerate(mz)
]
spec = spectrum.MsmsSpectrum('test_spectrum', 500, 2, mz, intensity,
annotation)
spec.round(1)
assert len(spec.mz) == len(mz) - 3
assert len(spec.mz) == len(spec.intensity)
assert len(spec.mz) == len(spec.annotation)
def test_round_no_merge():
num_peaks = 150
mz = np.arange(1, num_peaks + 1) + np.random.uniform(-0.49, 0.5, num_peaks)
intensity = np.random.exponential(1, num_peaks)
annotation = [
spectrum.PeptideFragmentAnnotation(1, this_mz, 'y', i)
for i, this_mz in enumerate(mz)
]
spec = spectrum.MsmsSpectrum('test_spectrum', 500, 2, mz.copy(),
intensity.copy(), annotation.copy())
decimals = 0
spec.round(decimals)
assert len(spec.mz) == num_peaks
assert len(spec.intensity) == num_peaks
assert len(spec.annotation) == num_peaks
np.testing.assert_allclose(spec.mz, np.around(mz, decimals))
np.testing.assert_allclose(spec.intensity, intensity)
def test_remove_precursor_peak_none():
num_peaks = 150
mz = np.random.uniform(100, 1400, num_peaks)
fragment_tol_mass = np.random.uniform(0, 0.5)
fragment_tol_mode = 'Da'
precursor_mz = mz[np.random.randint(0, num_peaks)] + fragment_tol_mass * 2
intensity = np.random.lognormal(0, 1, num_peaks)
annotation = [
spectrum.PeptideFragmentAnnotation(1, this_mz, 'y', i)
for i, this_mz in enumerate(mz)
]
spec = spectrum.MsmsSpectrum('test_spectrum', precursor_mz, 2, mz,
intensity, annotation)
spec.remove_precursor_peak(fragment_tol_mass, fragment_tol_mode)
assert len(spec.mz) == num_peaks
assert len(spec.intensity) == num_peaks
assert len(spec.annotation) == num_peaks
assert np.abs(precursor_mz - spec.mz).all() > fragment_tol_mass
def test_filter_intensity_remove_low_intensity():
num_peaks = 150
mz = np.random.uniform(100, 1400, num_peaks)
intensity = np.random.lognormal(0, 1, num_peaks)
max_intensity = intensity.max()
annotation = [
spectrum.PeptideFragmentAnnotation(1, this_mz, 'y', i)
for i, this_mz in enumerate(mz)
]
spec = spectrum.MsmsSpectrum('test_spectrum', 500, 2, mz, intensity,
annotation)
min_intensity = 0.05
assert spec.intensity.min() < min_intensity * spec.intensity.max()
spec.filter_intensity(min_intensity=min_intensity)
assert len(spec.mz) < num_peaks
assert len(spec.intensity) < num_peaks
assert len(spec.annotation) < num_peaks
assert spec.intensity.max() == pytest.approx(max_intensity)
assert spec.intensity.min() >= min_intensity * max_intensity
def test_remove_precursor_peak_isotope():
num_peaks = 150
mz = np.random.uniform(100, 1400, num_peaks)
fragment_tol_mass = np.random.uniform(0, 0.5)
fragment_tol_mode = 'Da'
precursor_mz = mz[np.random.randint(0, num_peaks)] + fragment_tol_mass / 2
precursor_charge = 3
mz[-1] = precursor_mz + 1 / precursor_charge
mz[-2] = precursor_mz + 2 / precursor_charge
intensity = np.random.lognormal(0, 1, num_peaks)
annotation = [
spectrum.PeptideFragmentAnnotation(1, this_mz, 'y', i)
for i, this_mz in enumerate(mz)
]
spec = spectrum.MsmsSpectrum('test_spectrum', precursor_mz,
precursor_charge, mz, intensity, annotation)
spec.remove_precursor_peak(fragment_tol_mass, fragment_tol_mode, 2)
assert np.abs(precursor_mz - spec.mz).all() > fragment_tol_mass
assert len(spec.mz) <= num_peaks - 3
assert len(spec.intensity) <= num_peaks - 3
assert len(spec.annotation) <= num_peaks - 3
def test_annotate_peptide_fragments_most_intense():
fragment_tol_mass = 0.02
fragment_tol_mode = 'Da'
peptide = 'YLYEIAR'
fragment_mz = np.asarray([
fragment.calc_mz
for fragment in spectrum._get_theoretical_peptide_fragments(peptide)
])
mz = np.asarray([fragment_mz[0] - 0.01, fragment_mz[0] + 0.01])
intensity = np.asarray([10, 20])
charge = 2
spec = spectrum.MsmsSpectrum('test_spectrum',
mass.calculate_mass(sequence=peptide,
charge=charge),
charge,
mz,
intensity,
peptide=peptide)
spec.annotate_peptide_fragments(fragment_tol_mass,
fragment_tol_mode,
peak_assignment='most_intense')
assert spec.annotation[0] is None
assert spec.annotation[1] == spectrum.PeptideFragmentAnnotation(
1, fragment_mz[0], 'b', 1)
def test_round_merge_annotation():
num_peaks = 10
mz = np.arange(1, num_peaks + 1) + np.random.uniform(-0.2, 0.2, num_peaks)
mz[4] = mz[3] + 0.0002
mz[5] = mz[3] + 0.0005
mz[7] = mz[8] - 0.00037
intensity = np.arange(1, 11)
annotation = [
None, None, None,
spectrum.PeptideFragmentAnnotation(1, mz[3], 'b', 4), None,
spectrum.PeptideFragmentAnnotation(1, mz[5], 'b', 6),
spectrum.PeptideFragmentAnnotation(1, mz[6], 'b', 7), None, None,
spectrum.PeptideFragmentAnnotation(1, mz[9], 'b', 10)
]
spec = spectrum.MsmsSpectrum('test_spectrum', 500, 2, mz.copy(), intensity,
annotation.copy())
spec.round(1, 'max')
np.testing.assert_array_equal(spec.annotation, [
None, None, None,
spectrum.PeptideFragmentAnnotation(1, mz[5], 'b', 6),
spectrum.PeptideFragmentAnnotation(1, mz[6], 'b', 7), None,
spectrum.PeptideFragmentAnnotation(1, mz[9], 'b', 10)
])
def _get_sus_annotation(mz, annotation):
"""Get spectrum_utils.PeptideFragmentAnnotation objects."""
return [
sus.PeptideFragmentAnnotation(1, mz, annotation[0], annotation[1:])
for mz, annotation in zip(mz, annotation)
]