def test_sec_profile_2(self):
""" """
peakspath = settings.get('peaks_gltpd1_invivo')
secpath = settings.get('sec_gltpd1_invivo')
reader = sample.SampleReader(
input_type='peaks',
fname=peakspath,
)
samples = reader.get_sampleset(
sample_id_proc=sampleattrs.plate_sample_id_processor(), )
secprofile = sampleattrs.SECProfile(
sec_path=secpath,
samples=samples,
start_volume=1.2,
offsets=(0.015, 0.045),
start_col=9,
start_row='A',
length=samples.numof_samples,
)
assert secprofile.numof_samples == samples.numof_samples
assert np.all(secprofile.attrs.sample_index_to_id ==
samples.attrs.sample_index_to_id)
assert id(samples) in secprofile._sample_data
assert id(secprofile) in samples._sample_data
assert secprofile.profile015.max() - 20.92373913043478 < 0.0001
assert secprofile.profile045.argmax() == 2
assert secprofile.profile015.argmax() == 3
assert secprofile.profiles == {'profile045', 'profile015'}
def test_sec_profile_1(self):
""" """
peakspath = settings.get('peaks_gltpd1_invitro')
secpath = settings.get('sec_gltpd1_invitro')
reader = sample.SampleReader(
input_type='peaks',
fname=peakspath,
)
samples = reader.get_sampleset(
sample_id_proc=sampleattrs.plate_sample_id_processor(), )
secprofile = sampleattrs.SECProfile(
sec_path=secpath,
samples=samples,
)
assert secprofile.numof_samples == samples.numof_samples
assert np.all(secprofile.attrs.sample_index_to_id ==
samples.attrs.sample_index_to_id)
assert id(samples) in secprofile._sample_data
assert id(secprofile) in samples._sample_data
assert secprofile.profile.max() - 143.40397368421048 < 0.0001
def read_peaks(self):
reader = sample.SampleReader(
input_type='peaks',
fname=self.peaks_fname,
)
self.samples = reader.get_sampleset(
sampleset_args={
'sample_id_proc': sampleattrs.plate_sample_id_processor(),
})
self.sample_selected = self.samples.mzs_by_sample[:,
self.samples.attrs.
sample_id_to_index[
self.sample_id]]
idx = self.sample_selected.argsort()
self.samples.sort_all(by=idx)
self.sample_selected = self.samples.mzs_by_sample[:,
self.samples.attrs.
sample_id_to_index[
self.sample_id]]
def preprocess_peaks(self):
self._log(
'Starting LC MS/MS data preprocessing using PEAKS output files.')
preproc_peaks = sample.SampleReader(
fname=self.input_path,
input_type=self.input_type,
ionmode=self.ionmode,
)
self._log('Preprocessing of PEAKS output finished.')
self.samples = preproc_peaks.get_sampleset()
def test_sampleset_from_peaks(self):
""" """
peaksfile = settings.get('peaks_example')
reader = sample.SampleReader(input_type='peaks', fname=peaksfile)
samples = reader.get_sampleset(
sampleset_args={
'sample_id_proc': sampleattrs.plate_sample_id_processor(),
})
assert abs(samples.mzs_by_sample[7, 3] - 375.0018) < 0.0001
assert samples.attrs.sample_index_to_id[-1] == ('A', 12)
assert samples.attrs.attrs[0].attrs['label']['sample_id'] == ('A', 6)
def test_protein_containing_samples(self):
""" """
peakspath = settings.get('peaks_gltpd1_invivo')
secpath = settings.get('sec_gltpd1_invivo')
reader = sample.SampleReader(
input_type='peaks',
fname=peakspath,
)
samples = reader.get_sampleset(
sample_id_proc=sampleattrs.plate_sample_id_processor(), )
secprofile = sampleattrs.SECProfile(
sec_path=secpath,
samples=samples,
start_volume=1.2,
offsets=(0.015, 0.045),
start_col=9,
start_row='A',
length=samples.numof_samples,
)
pcs = secprofile.protein_containing_samples()
assert np.all(
pcs.selection == np.array([False, False, True, True, False]))
pcs = secprofile.protein_containing_samples(manual=['A10', 'A11'])
assert np.all(
pcs.selection == np.array([False, True, True, False, False]))
pcs = secprofile.protein_containing_samples(exclude=['A12'])
assert np.all(
pcs.selection == np.array([False, False, True, False, False]))
from lipyd import settings
from lipyd import sample
from lipyd import sampleattrs
peaksfile = settings.get('peaks_example')
peaksfile = 'stard10_pos.csv'
reader = sample.SampleReader(
input_type = 'peaks',
fname = peaksfile
)
samples = reader.get_sampleset(
sampleset_args = {
'sample_id_proc': sampleattrs.plate_sample_id_processor(),
}
)
idx = samples.mzs_by_sample[
:,samples.attrs.sample_id_to_index[('A', 10)]
].argsort()
samples.sort_all(by = idx)
# m/z's for one sample:
samples.mzs_by_sample[:,samples.attrs.sample_id_to_index[('A', 10)]]
# intensities for one sample:
samples.intensities[:,samples.attrs.sample_id_to_index[('A', 10)]]
# RTs for one sample:
samples.rts[:,samples.attrs.sample_id_to_index[('A', 10)]]