def load(self):
win = LoadWindow()
res = win.exec_()
if res == QtWidgets.QDialog.Accepted:
tablefname = str(win.wTableFile.text())
mapfname = str(win.wMapFile.text())
if mapfname == '':
mapfname = None
gnpsfname = str(win.wGNPSFile.text())
if gnpsfname == '':
gnpsfname = None
expname = str(win.wNewName.text())
exptype = str(win.wType.currentText())
if exptype == 'Amplicon':
try:
expdat = ca.read_amplicon(tablefname,
mapfname,
normalize=10000,
filter_reads=1000)
except:
logger.warn(
'Load for amplicon biom table %s map %s failed' %
(tablefname, mapfname))
return
elif exptype == 'Metabolomics (rows are samples)':
try:
expdat = ca.read_open_ms(tablefname,
mapfname,
gnps_file=gnpsfname,
normalize=None,
rows_are_samples=True)
except:
logger.warn('Load for openms table %s map %s failed' %
(tablefname, mapfname))
return
elif exptype == 'Metabolomics (rows are features)':
try:
expdat = ca.read_open_ms(tablefname,
mapfname,
gnps_file=gnpsfname,
normalize=None,
rows_are_samples=False)
except:
logger.warn('Load for openms table %s map %s failed' %
(tablefname, mapfname))
return
elif exptype == 'Amplicon':
try:
expdat = ca.read(tablefname, mapfname)
except:
logger.warn('Load for biom table %s map %s failed' %
(tablefname, mapfname))
return
expdat._studyname = expname
self.addexp(expdat)
def test_read_open_ms(self):
exp = ca.read_open_ms(self.openms_csv, normalize=None)
# test we get the MZ and RT correct
self.assertIn('MZ', exp.feature_metadata)
self.assertIn('RT', exp.feature_metadata)
self.assertAlmostEqual(exp.feature_metadata['MZ'].iloc[1], 118.0869)
self.assertAlmostEqual(exp.feature_metadata['RT'].iloc[1], 23.9214)
# test normalizing
exp = ca.read_open_ms(self.openms_csv, normalize=10000)
assert_array_almost_equal(exp.data.sum(axis=1),
np.ones(exp.shape[0]) * 10000)
# test load sparse
exp = ca.read_open_ms(self.openms_csv, sparse=True, normalize=None)
self.assertEqual(exp.sparse, True)
def test_read_open_ms_samples_rows(self):
exp = ca.read_open_ms(self.openms_samples_rows_csv,
normalize=None,
rows_are_samples=True)
# test we get the MZ and RT correct
self.assertIn('MZ', exp.feature_metadata)
self.assertIn('RT', exp.feature_metadata)
self.assertAlmostEqual(exp.feature_metadata['MZ'].iloc[1], 118.0869)
self.assertAlmostEqual(exp.feature_metadata['RT'].iloc[1], 23.9214)
def setUp(self):
super().setUp()
self.ms1 = ca.read_open_ms(self.openms_csv,
None,
gnps_file=self.ms1_gnps,
normalize=None)