def test_global_eff(self):
# Load regular data
expected_medium = {
'EX_MNXM83': 2000.0,
'EX_pi_e': 2000.0,
'EX_fe3_e': 1000.0
}
specie_missing_id = 'MNXM83'
medium = load_medium_file(os_path.join(self.medium_path, 'medium.fmt.c.csv'))
medium = crossref_medium_id(
df=medium,
model=self.rpsbml,
compartment_id='MNXC2'
)
exchange = self.rpsbml.build_exchange_reaction('c')
df = merge_medium_exchange(
medium = medium,
exchange_reaction = exchange
)
rpsbml = add_missing_specie(
self.rpsbml,
df,
'c'
)
cobra_model = None
with NamedTemporaryFile(dir=self.temp_d, delete=False) as tempf:
rpsbml.write_to_file(tempf.name)
cobra_model=cobra_io.read_sbml_model(tempf.name, use_fbc_package=True)
cobra_model.medium = df_to_medium(df)
self.assertEqual(
cobra_model.medium,
expected_medium
)
tempf.close()
remove(tempf.name)
def test_add_missing_specie(self):
# Load regular data
specie_missing_id = 'MNXM83'
medium = load_medium_file(os_path.join(self.medium_path, 'medium.fmt.c.csv'))
medium = crossref_medium_id(
df=medium,
model=self.rpsbml,
compartment_id='MNXC2'
)
exchange = self.rpsbml.build_exchange_reaction('c')
df = merge_medium_exchange(
medium = medium,
exchange_reaction = exchange
)
rpsbml = add_missing_specie(
self.rpsbml,
df,
'c'
)
# Return type
self.assertIsInstance(rpsbml, rpSBML)
# Values
species = rpsbml.getModel().getListOfSpecies()
self.assertEqual(
len([x for x in species if x.getId() == specie_missing_id]),
1
)
specie = rpsbml.getModel().getSpecies(specie_missing_id)
self.assertTrue(specie.getBoundaryCondition())
def test_df_to_medium(self):
# Load.
medium_a = load_medium_file(os_path.join(self.medium_path, 'medium.fmt.a.csv'))
dfa = crossref_medium_id(
df=medium_a,
model=self.rpsbml,
compartment_id='MNXC2'
)
exchange = self.rpsbml.build_exchange_reaction('c')
dfa = merge_medium_exchange(
medium = dfa,
exchange_reaction = exchange
)
# Return Type.
dfad = dfa.drop(columns=['reaction_name'])
medium = df_to_medium(dfad)
self.assertIsInstance(medium, Dict)
dfad = dfa.drop(columns=['reaction_name'])
medium = df_to_medium(dfad)
self.assertIsInstance(medium, Dict)
medium = df_to_medium(dfa)
self.assertIsInstance(medium, Dict)
# Values.
self.assertEqual(
sum([x.startswith('EX') for x in medium.keys()]),
dfa.shape[0]
)
def test_merge_medium_exchange(self):
# Load
medium = load_medium_file(os_path.join(self.medium_path, 'medium.fmt.a.csv'))
medium = crossref_medium_id(
df=medium,
model=self.rpsbml,
compartment_id='MNXC2'
)
exchange = self.rpsbml.build_exchange_reaction('c')
df = merge_medium_exchange(
medium = medium,
exchange_reaction = exchange
)
# Return type.
self.assertIsInstance(
df,
pd.DataFrame
)
# Values.
self.assertEqual(
df.shape,
(331, len(exchange.columns)+len(df.columns)-2)
)
self.assertEqual(
df[self.__MEDIUM_HEADER_COMPOUND_ID].isna().sum(),
331-2
)
self.assertTrue(pd.api.types.is_float_dtype(df[self.__MEDIUM_HEADER_BOUND]))
def test_crossref_medium_id(self):
# Load.
medium = load_medium_file(os_path.join(self.medium_path, 'medium.annotation.b.csv'))
# Return type.
df = crossref_medium_id(
df=None,
model=self.rpsbml,
compartment_id='MNXC2'
)
self.assertEqual(df, None)
df = crossref_medium_id(
df=medium,
model=self.rpsbml,
compartment_id='MNXC2'
)
self.assertTrue(isinstance(df, pd.DataFrame))
# Values.
self.assertEqual(
['M_pi_e', 'M_fe3_e', 'M_pi_e', 'M_pi_e'],
df['model_id'].tolist()[:4]
)
self.assertEqual(
df['model_id'].isna().sum(),
2
)
df = crossref_medium_id(
df=medium,
model=self.rpsbml,
compartment_id='MNXC'
)
self.assertEqual(
df['model_id'].isna().sum(),
6
)
def test_load_medium_file(self):
df = load_medium_file(os_path.join(self.medium_path, 'medium.io.a.tsv'))
# Return type
self.assertTrue(isinstance(df, pd.DataFrame))
# Basic io profile
self.assertTrue(is_df_medium_defined(df))
df = load_medium_file(os_path.join(self.medium_path, 'medium.io.d.csv'))
self.assertFalse(is_df_medium_defined(df))
df = load_medium_file(os_path.join(self.medium_path, 'medium.io.a.xlsx'))
self.assertFalse(is_df_medium_defined(df))
df = load_medium_file(os_path.join(self.medium_path, 'medium.io.a.csv'))
self.assertTrue(is_df_medium_defined(df))
# Type expected
self.assertTrue(pd.api.types.is_float_dtype(df[self.__MEDIUM_HEADER_BOUND]))
self.assertEqual(
sum(
df['rp_compound'].apply(lambda x: isinstance(x, rpCompound) or pd.isna(x))
),
len(df['rp_compound'])
)
# Challenge on column labels
df_columns = df.columns.tolist()
df_columns.remove('rp_compound')
self.assertEqual(
sorted(df_columns),
sorted(self.__MEDIUM_HEADER)
)
tmp_file = tempfile.NamedTemporaryFile(
suffix='.csv',
dir=self.temp_d,
delete=False
)
for ix in range(len(self.__MEDIUM_HEADER)):
tmp_header = deepcopy(self.__MEDIUM_HEADER)
tmp_header = tmp_header.pop(ix)
df_tmp = df[tmp_header]
df_tmp.to_csv(
tmp_file.name,
index=False
)
df_tmp = load_medium_file(tmp_file.name)
self.assertFalse(is_df_medium_defined(df_tmp))
tmp_file.close()
remove(tmp_file.name)
def test_merge_medium(self):
medium_a = load_medium_file(os_path.join(self.medium_path, 'medium.fmt.a.csv'))
medium_b = load_medium_file(os_path.join(self.medium_path, 'medium.fmt.b.csv'))
dfa = crossref_medium_id(
df=medium_a,
model=self.rpsbml,
compartment_id='MNXC2'
)
dfb = crossref_medium_id(
df=medium_b,
model=self.rpsbml,
compartment_id='MNXC2'
)
df = merge_medium(first=None, second=dfa)
self.assertIsInstance(df, pd.DataFrame)
df = merge_medium(first=dfa, second=None)
self.assertIsInstance(df, pd.DataFrame)
df = merge_medium(first=dfa, second=pd.DataFrame())
self.assertEqual(
df.shape,
dfa.shape
)
df = merge_medium(first=pd.DataFrame(), second=dfa)
self.assertEqual(
df.shape,
dfa.shape
)
# Values
df = merge_medium(dfa, dfb)
self.assertIsInstance(df, pd.DataFrame) # Return type
self.assertEqual(
df.shape[0],
3
)
self.assertNotIn('MNXM9', df[self.__MEDIUM_HEADER_COMPOUND_ID])
df = merge_medium(dfb, dfa)
self.assertEqual(
df.shape[0],
3
)
self.assertNotIn('14791', df[self.__MEDIUM_HEADER_COMPOUND_ID])