def test_fragmentation_trees_exception(self):
ions = self.ions.view(MGFDirFmt)
with self.assertRaises(ValueError):
compute_fragmentation_trees(sirius_path=self.goodsirpath,
features=ions,
ppm_max=15,
profile='orbitrap',
ionization_mode='n3gativ3')
def test_fragmentation_trees(self):
ions = self.ions.view(MGFDirFmt)
result = compute_fragmentation_trees(sirius_path=self.goodsirpath,
features=ions,
ppm_max=15, profile='orbitrap')
contents = os.listdir(result.get_path())
self.assertTrue(('version.txt' in contents))
def test_fragmentation_trees(self):
ions = self.ions.view(MGFDirFmt)
result = compute_fragmentation_trees(sirius_path=self.goodsirpath,
features=ions,
ppm_max=15,
profile='orbitrap',
ions_considered=['[M+H]+'])
contents = os.listdir(result.get_path())
self.assertTrue(('formula_identifications.tsv' in contents))
contents = os.listdir(result.path)
self.assertTrue(('stderr.txt' in contents))
self.assertTrue(('stdout.txt' in contents))
def test_fragmentation_trees_negative_ionization(self):
ions = self.ions.view(MGFDirFmt)
result = compute_fragmentation_trees(sirius_path=self.goodsirpath,
features=ions,
ppm_max=15,
profile='orbitrap',
ions_considered=['[M-H]-'])
_path = os.path.join(result.get_path(), 'formula_identifications.tsv')
identifications = pd.read_csv(_path, sep='\t')
self.assertTrue(len(identifications) < 2)
contents = os.listdir(result.path)
self.assertTrue(('stderr.txt' in contents))
self.assertTrue(('stdout.txt' in contents))