def testProcessUnequalSOMReaction(self):
if IGNORE_TEST:
return
games_pp2 = GAMES_PP(self.simple2)
self.assertTrue(len(games_pp2.edges) == 0)
reaction = games_pp2.simple.getReaction(CH2FH4toHCHO)
som_reaction = games_pp2.convertReactionToSOMReaction(reaction)
games_pp2.processUnequalSOMReaction(som_reaction)
self.assertTrue(len(games_pp2.edges) == 2)
reactant1 = games_pp2.simple.getMolecule(FH4)
reactant2 = games_pp2.simple.getMolecule(HCHO)
product1 = games_pp2.simple.getMolecule(CH2FH4)
games_pp2.processUniMultiReaction(reaction)
som_product1 = games_pp2.getNode(product1)
som_reactant1 = games_pp2.getNode(reactant1)
som_reactant2 = games_pp2.getNode(reactant2)
self.assertTrue(games_pp2.has_edge(som_reactant1, som_product1))
self.assertTrue(games_pp2.has_edge(som_reactant2, som_product1))
class TestGAMES_PP(unittest.TestCase):
def setUp(self):
# BIOMD0000000383
self.simple1 = SimpleSBML()
self.simple1.initialize(cn.TEST_FILE_GAMES_PP1)
self.games_pp = GAMES_PP(self.simple1)
# BIOMD0000000018
self.simple2 = SimpleSBML()
self.simple2.initialize(cn.TEST_FILE_GAMES_PP2)
def testConstructor(self):
if IGNORE_TEST:
return
self.assertEqual(len(self.games_pp.reactions), NUM_REACTIONS)
for r in self.games_pp.reactions:
print(r.category)
self.assertFalse(r.category == cn.REACTION_BOUNDARY)
self.assertEqual(len(self.games_pp.molecules), NUM_MOLECULES)
for m in self.games_pp.molecules:
self.assertTrue(isinstance(m, Molecule))
self.assertEqual(len(self.games_pp.soms), NUM_MOLECULES)
self.assertTrue(isinstance(self.games_pp.soms[0], SOM))
init_identifier = ""
for som in self.games_pp.soms:
init_identifier = init_identifier + som.identifier
if som != self.games_pp.soms[-1]:
init_identifier = init_identifier + ";"
self.assertEqual(self.games_pp.identifier, init_identifier)
def testConvertReactionToSOMReaction(self):
if IGNORE_TEST:
return
reaction1 = self.games_pp.simple.getReaction(PGA_CONS)
reaction2 = self.games_pp.simple.getReaction(PGA_PROD_VC)
som_reaction1 = self.games_pp.convertReactionToSOMReaction(reaction1)
som_reaction2 = self.games_pp.convertReactionToSOMReaction(reaction2)
self.assertTrue(isinstance(som_reaction1, SOMReaction))
self.assertTrue(isinstance(som_reaction2, SOMReaction))
ms_rubp = som_reaction1.products[0]
self.assertTrue(isinstance(ms_rubp, SOMStoichiometry))
self.assertEqual(
list(ms_rubp.som.molecules)[0],
self.games_pp.simple.getMolecule(RUBP))
ms_nadph = None
for ms in som_reaction2.reactants:
if ms.som.identifier == SOM_NADPH:
ms_nadph = ms
break
self.assertTrue(ms_nadph.som.identifier == SOM_NADPH)
self.assertEqual(ms_nadph.stoichiometry, NADPH_STOICHIOMETRY)
def testGetStoichiometryMatrix(self):
if IGNORE_TEST:
return
# For regular stoichiometry matrix
mat = self.games_pp.getStoichiometryMatrix(self.games_pp.reactions,
self.games_pp.molecules,
som=False)
self.assertTrue(isinstance(mat, pd.DataFrame))
self.assertEqual(mat.shape, (NUM_MOLECULES, NUM_REACTIONS))
self.assertEqual(mat[PGA_CONS][PGA], PGA_CONS_WITH_PGA)
self.assertEqual(mat[PGA_PROD_VC][RUBP], PGA_PROD_VC_WITH_RUBP)
# For SOM stoichiometry matrix
som_reactions = []
for r in self.games_pp.reactions:
som_reactions.append(self.games_pp.convertReactionToSOMReaction(r))
som_mat = self.games_pp.getStoichiometryMatrix(som_reactions,
self.games_pp.nodes,
som=True)
self.assertTrue(isinstance(som_mat, pd.DataFrame))
self.assertEqual(som_mat[PGA_CONS][SOM_PGA], PGA_CONS_WITH_PGA)
self.assertEqual(som_mat[PGA_PROD_VC][SOM_RUBP], PGA_PROD_VC_WITH_RUBP)
def testDecomposeMatrix(self):
if IGNORE_TEST:
return
# should be all None before decomposition
self.assertTrue(self.games_pp.perm_inverse is None)
self.assertTrue(self.games_pp.permuted_matrix is None)
self.assertTrue(self.games_pp.lower_inverse is None)
self.assertTrue(self.games_pp.echelon_df is None)
som_reactions = []
for r in self.games_pp.reactions:
som_reactions.append(self.games_pp.convertReactionToSOMReaction(r))
som_mat = self.games_pp.getStoichiometryMatrix(som_reactions,
self.games_pp.nodes,
som=True)
echelon = self.games_pp.decomposeMatrix(som_mat).T
self.assertFalse(self.games_pp.perm_inverse is None)
self.assertFalse(self.games_pp.permuted_matrix is None)
self.assertFalse(self.games_pp.lower_inverse is None)
self.assertFalse(self.games_pp.echelon_df is None)
self.assertTrue(isinstance(self.games_pp.perm_inverse, np.ndarray))
self.assertTrue(isinstance(self.games_pp.permuted_matrix,
pd.DataFrame))
self.assertTrue(isinstance(self.games_pp.lower_inverse, pd.DataFrame))
self.assertTrue(isinstance(self.games_pp.echelon_df, pd.DataFrame))
# Checking lower echelon - lower left element should be 0.0 (zero)
self.assertTrue(echelon.iloc[echelon.shape[0] - 1][0] == ZERO_F)
# On the ohter hand, upper left should be nonzero
self.assertFalse(echelon.iloc[0][0] == ZERO_F)
def testGetRREFMatrix(self):
if IGNORE_TEST:
return
self.assertTrue(self.games_pp.rref_operation is None)
self.assertTrue(self.games_pp.rref_df is None)
som_reactions = []
for r in self.games_pp.reactions:
som_reactions.append(self.games_pp.convertReactionToSOMReaction(r))
som_mat = self.games_pp.getStoichiometryMatrix(som_reactions,
self.games_pp.nodes,
som=True)
echelon = self.games_pp.decomposeMatrix(som_mat).T
rref = self.games_pp.getRREFMatrix(echelon)
self.assertTrue(isinstance(self.games_pp.rref_operation, pd.DataFrame))
self.assertTrue(isinstance(self.games_pp.rref_df, pd.DataFrame))
# Choose the last row of rref.T
last_row = rref.T.iloc[-1:]
# Get the first nonzero index
nonzero_species = (last_row != 0).idxmax(axis=1)[0]
# The SUM of nonzero species column must be the same as the single value
self.assertEqual(last_row[nonzero_species][0],
sum(rref.T[nonzero_species]))
def testConverMatrixToSOMReactions(self):
if IGNORE_TEST:
return
som_reactions1 = []
for r in self.games_pp.reactions:
som_reactions1.append(
self.games_pp.convertReactionToSOMReaction(r))
som_mat = self.games_pp.getStoichiometryMatrix(som_reactions1,
self.games_pp.nodes,
som=True)
som_reactions2 = self.games_pp.convertMatrixToSOMReactions(som_mat)
sr1 = None
sr2 = None
for sr in som_reactions1:
if sr.label == PGA_PROD_VC:
sr1 = sr
break
for sr in som_reactions2:
if sr.label == PGA_PROD_VC:
sr2 = sr
break
sr1_reactants = {ms.som for ms in sr1.reactants}
sr2_reactants = {ms.som for ms in sr2.reactants}
sr1_products = {ms.som for ms in sr1.products}
sr2_products = {ms.som for ms in sr2.products}
sr1_reactsom = sum([ms.stoichiometry for ms in sr1.reactants])
sr2_reactsom = sum([ms.stoichiometry for ms in sr2.reactants])
sr1_prodsom = sum([ms.stoichiometry for ms in sr1.products])
sr2_prodsom = sum([ms.stoichiometry for ms in sr2.products])
self.assertEqual(sr1_reactants, sr2_reactants)
self.assertEqual(sr1_products, sr2_products)
self.assertEqual(sr1_reactsom, sr2_reactsom)
self.assertEqual(sr1_prodsom, sr2_prodsom)
def testGetNode(self):
if IGNORE_TEST:
return
co2 = self.games_pp.simple.getMolecule(CO2)
co2_node = self.games_pp.getNode(co2)
self.assertEqual(type(co2_node), SOM)
self.assertEqual(co2_node.molecules, {co2})
def testMergeNodes(self):
if IGNORE_TEST:
return
reaction = self.games_pp.simple.getReaction(PGA_CONS)
pga = self.games_pp.simple.getMolecule(PGA)
rubp = self.games_pp.simple.getMolecule(RUBP)
som_pga = self.games_pp.getNode(pga)
som_rubp = self.games_pp.getNode(rubp)
som_pga_rubp = self.games_pp.mergeNodes(som_pga, som_rubp, reaction)
self.assertTrue(isinstance(som_pga_rubp, SOM))
self.assertTrue(pga in som_pga_rubp.molecules)
self.assertTrue(rubp in som_pga_rubp.molecules)
self.assertTrue(reaction in som_pga_rubp.reactions)
def testAddReaction(self):
if IGNORE_TEST:
return
self.assertEqual(len(self.games_pp.reactions_lu), 0)
reaction = self.games_pp.simple.getReaction(PGA_CONS)
self.games_pp.addReaction(reaction)
self.assertTrue(reaction in self.games_pp.reactions_lu)
self.games_pp.addReaction(reaction)
self.assertTrue(len(self.games_pp.reactions_lu), 1)
def testProcessUniUniReaction(self):
if IGNORE_TEST:
return
reaction = self.games_pp.simple.getReaction(PGA_CONS)
som = self.games_pp.processUniUniReaction(reaction)
self.assertTrue(isinstance(som, SOM))
self.assertTrue(som in self.games_pp.nodes)
pga = self.games_pp.simple.getMolecule(PGA)
rubp = self.games_pp.simple.getMolecule(RUBP)
self.assertTrue(pga in som.molecules)
self.assertTrue(rubp in som.molecules)
def testAddArc(self):
if IGNORE_TEST:
return
reaction = self.games_pp.simple.getReaction(PGA_PROD_VC)
co2 = self.games_pp.simple.getMolecule(CO2)
pga = self.games_pp.simple.getMolecule(PGA)
som_co2 = self.games_pp.getNode(co2)
som_pga = self.games_pp.getNode(pga)
self.games_pp.addArc(som_co2, som_pga, reaction)
self.assertTrue(self.games_pp.has_edge(som_co2, som_pga))
self.assertEqual(
self.games_pp.get_edge_data(som_co2, som_pga)[REACTION],
[PGA_PROD_VC])
def testProcessUniMultiReaction(self):
if IGNORE_TEST:
return
games_pp2 = GAMES_PP(self.simple2)
self.assertTrue(isinstance(games_pp2, GAMES_PP))
reaction = games_pp2.simple.getReaction(CH2FH4toHCHO)
reactant1 = games_pp2.simple.getMolecule(CH2FH4)
product1 = games_pp2.simple.getMolecule(FH4)
product2 = games_pp2.simple.getMolecule(HCHO)
games_pp2.processUniMultiReaction(reaction)
som_reactant1 = games_pp2.getNode(reactant1)
som_product1 = games_pp2.getNode(product1)
som_product2 = games_pp2.getNode(product2)
self.assertTrue(games_pp2.has_edge(som_product1, som_reactant1))
self.assertTrue(games_pp2.has_edge(som_product2, som_reactant1))
def testProcessMultiUniReaction(self):
if IGNORE_TEST:
return
games_pp2 = GAMES_PP(self.simple2)
self.assertTrue(isinstance(games_pp2, GAMES_PP))
reaction = games_pp2.simple.getReaction(HCHOtoCH2FH4)
reactant1 = games_pp2.simple.getMolecule(FH4)
reactant2 = games_pp2.simple.getMolecule(HCHO)
product1 = games_pp2.simple.getMolecule(CH2FH4)
games_pp2.processMultiUniReaction(reaction)
som_product1 = games_pp2.getNode(product1)
som_reactant1 = games_pp2.getNode(reactant1)
som_reactant2 = games_pp2.getNode(reactant2)
self.assertTrue(games_pp2.has_edge(som_reactant1, som_product1))
self.assertTrue(games_pp2.has_edge(som_reactant2, som_product1))
def testProcessEqualSOMReaction(self):
if IGNORE_TEST:
return
print("type three", self.games_pp.type_three_errors)
self.assertEqual(len(self.games_pp.type_three_errors), ZERO)
# Add an arc
reaction = self.games_pp.simple.getReaction(PGA_PROD_VC)
co2 = self.games_pp.simple.getMolecule(CO2)
pga = self.games_pp.simple.getMolecule(PGA)
som_co2 = self.games_pp.getNode(co2)
som_pga = self.games_pp.getNode(pga)
self.games_pp.addArc(som_co2, som_pga, reaction)
# Process a dummy reaction
soms_co2 = SOMStoichiometry(som_co2, 1.0)
soms_pga = SOMStoichiometry(som_pga, 1.0)
som_reaction = SOMReaction([soms_co2], [soms_pga], "dummy")
self.games_pp.processEqualSOMReaction(som_reaction)
self.assertTrue(len(self.games_pp.type_three_errors) > ZERO)
def testProcessUnequalSOMReaction(self):
if IGNORE_TEST:
return
games_pp2 = GAMES_PP(self.simple2)
self.assertTrue(len(games_pp2.edges) == 0)
reaction = games_pp2.simple.getReaction(CH2FH4toHCHO)
som_reaction = games_pp2.convertReactionToSOMReaction(reaction)
games_pp2.processUnequalSOMReaction(som_reaction)
self.assertTrue(len(games_pp2.edges) == 2)
reactant1 = games_pp2.simple.getMolecule(FH4)
reactant2 = games_pp2.simple.getMolecule(HCHO)
product1 = games_pp2.simple.getMolecule(CH2FH4)
games_pp2.processUniMultiReaction(reaction)
som_product1 = games_pp2.getNode(product1)
som_reactant1 = games_pp2.getNode(reactant1)
som_reactant2 = games_pp2.getNode(reactant2)
self.assertTrue(games_pp2.has_edge(som_reactant1, som_product1))
self.assertTrue(games_pp2.has_edge(som_reactant2, som_product1))
def testAddTypeOneError(self):
if IGNORE_TEST:
return
games_pp2 = GAMES_PP(self.simple2)
self.assertTrue(len(games_pp2.type_one_errors) == ZERO)
reaction = games_pp2.simple.getReaction(CH2FH4toHCHO)
reactant1 = games_pp2.simple.getMolecule(FH4)
product1 = games_pp2.simple.getMolecule(CH2FH4)
games_pp2.addTypeOneError(reactant1, product1, reaction)
self.assertTrue(len(games_pp2.type_one_errors) == ONE)
error = games_pp2.type_one_errors[ZERO]
self.assertEqual(error.node1, reactant1.name)
self.assertEqual(error.node2, product1.name)
self.assertEqual(error.reactions, [reaction.label])
def testChekcTypeOneError(self):
if IGNORE_TEST:
return
games_pp1 = GAMES_PP(self.simple1)
reaction = games_pp1.simple.getReaction(PGA_CONS)
pga = games_pp1.simple.getMolecule(PGA)
rubp = games_pp1.simple.getMolecule(RUBP)
som_pga = games_pp1.getNode(pga)
som_rubp = games_pp1.getNode(rubp)
som_pga_rubp = games_pp1.mergeNodes(som_pga, som_rubp, reaction)
self.assertTrue(len(games_pp1.type_one_errors) == ZERO)
is_error = games_pp1.checkTypeOneError((pga, rubp), reaction)
self.assertTrue(is_error)
error = games_pp1.type_one_errors[ZERO]
self.assertEqual(error.node1, pga.name)
self.assertEqual(error.node2, rubp.name)
self.assertEqual(error.reactions, [reaction.label])
def testCheckTypeTwoError(self):
if IGNORE_TEST:
return
# Create a dummy cycle by adding two conflicting arcs
games_pp2 = GAMES_PP(self.simple2)
self.assertTrue(isinstance(games_pp2, GAMES_PP))
unimulti_reaction = games_pp2.simple.getReaction(CH2FH4toHCHO)
multiuni_reaction = games_pp2.simple.getReaction(HCHOtoCH2FH4)
fh4 = games_pp2.simple.getMolecule(FH4)
# hcho = games_pp2.simple.getMolecule(HCHO)
ch2fh4 = games_pp2.simple.getMolecule(CH2FH4)
som_fh4 = games_pp2.getNode(fh4)
som_ch2fh4 = games_pp2.getNode(ch2fh4)
# do we need the next two methods if we're giving a cycle?
games_pp2.addArc(som_fh4, som_ch2fh4, unimulti_reaction)
games_pp2.addArc(som_ch2fh4, som_fh4, multiuni_reaction)
self.assertTrue(len(games_pp2.type_two_errors) == ZERO)
games_pp2.checkTypeTwoError()
self.assertTrue(len(games_pp2.type_two_errors) == ONE)
error = games_pp2.type_two_errors[ZERO]
self.assertTrue(games_pp2.has_edge(error[ZERO], error[ONE]))
self.assertTrue(games_pp2.has_edge(error[ONE], error[ZERO]))
error_reactions = set(
games_pp2.get_edge_data(error[ZERO], error[ONE])[REACTION])
error_reactions = error_reactions.union(
set(games_pp2.get_edge_data(error[ONE], error[ZERO])[REACTION]))
self.assertTrue(CH2FH4toHCHO in error_reactions)
self.assertTrue(HCHOtoCH2FH4 in error_reactions)
def testProcessErrorReaction(self):
if IGNORE_TEST:
return
games_pp1 = GAMES_PP(self.simple1)
self.assertTrue(len(games_pp1.echelon_errors) == ZERO)
reaction = self.games_pp.simple.getReaction(PGA_PROD_VO)
games_pp1.processErrorReaction(reaction)
self.assertTrue(len(games_pp1.echelon_errors) == ONE)
self.assertTrue(reaction in games_pp1.echelon_errors)
def testAnalyze(self):
if IGNORE_TEST:
return
games_pp1 = GAMES_PP(self.simple1)
games_pp2 = GAMES_PP(self.simple2)
self.assertTrue(games_pp1.analyze(rref=False))
self.assertTrue(games_pp2.analyze())
self.assertTrue(len(games_pp1.echelon_errors) > ZERO)
self.assertTrue(len(games_pp1.type_one_errors) == ZERO)
self.assertTrue(len(games_pp1.type_two_errors) == ZERO)
self.assertTrue(len(games_pp2.type_one_errors) > ZERO)