def test_is_not_empty_if_annotated(self):
m1 = Molecule(name='test', sum_formula="C1H2O3")
m1.save()
s1 = Standard(molecule=m1)
s1.save()
d1 = Dataset()
d1.save()
fs1 = FragmentationSpectrum(ms1_intensity=42, dataset=d1, standard=s1)
fs1.save()
molecule_table, molecules_with_spectra = self.get_table_and_count()
self.assertEqual(len(molecule_table.rows), 1)
self.assertEqual(molecules_with_spectra, 1)
def test_make_FragmentationSpectrum_with_centroids(self):
d1 = Dataset(name='Dataset1')
d1.save()
f1 = FragmentationSpectrum(precursor_mz='123.456',
spec_num=0, dataset=d1)
mzs = [10., 20, 50]
ints = [1., 1., 1.]
f1.set_centroid_mzs(mzs)
f1.set_centroid_ints(ints)
f1.save()
np.testing.assert_array_almost_equal(mzs, f1.centroid_mzs)
np.testing.assert_array_almost_equal(ints, f1.centroid_ints)
def handle_uploaded_files(metadata, mzml_filepath, d):
logger = logging.getLogger(__file__ + str(d.id))
logger.addHandler(DatabaseLogHandler(d, level=logging.ERROR))
msrun = pymzml.run.Reader(mzml_filepath)
ppm = float(metadata['mass_accuracy_ppm'])
mz_tol_quad = float(metadata['quad_window_mz'])
scan_time = []
standards = Standard.objects.all().filter(pk__in=metadata['standards'])
adducts = Adduct.objects.all().filter(pk__in=metadata['adducts'])
mz_upper = {}
mz_lower = {}
mz = {}
logger.debug(standards.count())
for standard in standards:
mz_upper[standard] = {}
mz_lower[standard] = {}
mz[standard] = {}
for adduct in adducts:
mz[standard][adduct] = standard.molecule.get_mz(adduct)
logger.debug(standard)
logger.debug(mz[standard][adduct])
delta_mz = mz[standard][adduct] * ppm * 1e-6
mz_upper[standard][adduct] = mz[standard][adduct] + delta_mz
mz_lower[standard][adduct] = mz[standard][adduct] - delta_mz
logger.debug('adding dataset')
try:
lc_info = metadata['lc_info']
ms_info = metadata['ms_info']
except LookupError:
logger.debug('no instrument information supplied; using empty string instead')
lc_info = ms_info = ''
lc_info_stripped = set()
ms_info_stripped = set()
for lc in lc_info.split(', '):
if lc:
lc_stripped = lc.replace(',', '').strip()
lc_info_stripped.add(lc_stripped)
for ms in ms_info.split(', '):
if ms:
ms_stripped = ms.replace(',', '').strip()
ms_info_stripped.add(ms_stripped)
for lc in lc_info_stripped:
lc_obj = LcInfo.objects.get_or_create(content=lc)[0]
if lc_obj not in d.lc_info.all():
d.lc_info.add(lc_obj)
for ms in ms_info_stripped:
ms_obj = MsInfo.objects.get_or_create(content=ms)[0]
if ms_obj not in d.ms_info.all():
d.ms_info.add(ms_obj)
d.mass_accuracy_ppm = ppm
d.save()
for standard in standards:
d.standards_present.add(standard)
for adduct in adducts:
d.adducts_present.add(adduct)
d.save()
logger.debug('adding msms')
xics = {}
spec_n = 0
for spectrum in msrun:
spec_n += 1
if spectrum['ms level'] == 1:
scan_time.append(spectrum['scan start time'])
# Iterate adducts/standards and get values as required
for standard in standards:
if standard not in xics:
xics[standard] = {}
for adduct in adducts:
if adduct not in xics[standard]:
xics[standard][adduct] = []
if spectrum['ms level'] == 1:
x = 0
for m, i in spectrum.centroidedPeaks:
if all([m >= mz_lower[standard][adduct], m <= mz_upper[standard][adduct]]):
x += i
xics[standard][adduct].append(x)
if spectrum['ms level'] == 2:
add_msms = False
pre_mz = float(spectrum['precursors'][0]['mz'])
mz_tol_this_adduct = mz[standard][adduct] * ppm * 1e-6
if any((abs(pre_mz - mz[standard][adduct]) <= mz_tol_this_adduct,
abs(pre_mz - mz[standard][adduct]) <= mz_tol_quad)): # frag spectrum probably the target
add_msms = True
if add_msms:
ms1_intensity = xics[standard][adduct][-1]
mzs = spectrum.mz
ints = spectrum.i
quad_ints = [ii for m, ii in zip(mzs, ints) if
all((m >= pre_mz - mz_tol_quad, m <= pre_mz + mz_tol_quad))]
ppm_ints = [ii for m, ii in zip(mzs, ints) if
all((m >= pre_mz - mz_tol_this_adduct, m <= pre_mz + mz_tol_this_adduct))]
quad_ints_sum = sum(quad_ints)
ppm_ints_sum = sum(ppm_ints)
ce_type = ''
ce_energy = ''
ce_gas = ''
for element in spectrum.xmlTree:
if element.get('accession') == "MS:1000133":
ce_type = element.items()
elif element.get('accession') == "MS:1000045":
ce_energy = dict(element.items())
ce_str = "{} {} {}".format(ce_energy['name'], ce_energy['value'], ce_energy['unitName'])
if ppm_ints_sum == 0:
pre_fraction = 0
else:
pre_fraction = sum(ppm_ints) / sum(quad_ints)
f = FragmentationSpectrum(precursor_mz=pre_mz,
rt=spectrum['scan start time'], dataset=d, spec_num=spec_n,
precursor_quad_fraction=pre_fraction, ms1_intensity=ms1_intensity,
collision_energy=ce_str)
f.set_centroid_mzs(spectrum.mz)
f.set_centroid_ints(spectrum.i)
f.collision = ce_str
f.save()
logger.debug("adding xics")
for standard in standards:
for adduct in adducts:
# if np.sum(xics[standard][adduct]) > 0:
x = Xic(mz=standard.molecule.get_mz(adduct), dataset=d)
x.set_xic(xics[standard][adduct])
x.set_rt(scan_time)
x.standard = standard
x.adduct = adduct
x.save()
d.processing_finished = True
d.save()
logger.debug('done')
logger.debug("added = True")
return True
