def is_reverse(self, the_inverse):
"""Returns true if the given reaction is the reverse of
the current reaction
"""
if (utils.equal_lists(self.reactants, the_inverse.products) and
utils.equal_lists(self.products, the_inverse.reactants)):
return True
else:
return False
def reaction_knockout_table(filename, ignore_sources, ignore_sinks):
"""Given an sbml file, perform composite reduction analysis and
print the results. This basically means perform invariant analysis
once for each reaction in the model. For a reaction's analysis we
ignore that reaction and calculate the set of invariants and the
set of species not covered by any invariant. The idea is to compare
this with the set of invariants for all reactions thus giving us
some idea which reactions may be violating an expected invariant
"""
kig_dictionary = reaction_knockout_kigs(filename,
ignore_sources,
ignore_sinks)
def get_length_uncovered(my_pair):
"""Return the number of uncovered species"""
return len(my_pair[1])
def get_uncovered(kig):
"""Return the uncovered species from a kig"""
inv_inferer = InvariantInferer(kig)
return inv_inferer.get_uncovered()
orig_uncovered = get_uncovered_model_file(filename,
ignore_sources,
ignore_sinks)
uncovered_map = [ (rname, get_uncovered(kig) )
for (rname, kig) in kig_dictionary.items() ]
sorted_uncovereds = sorted(uncovered_map, key=get_length_uncovered)
print ("----- no reactions ignored -----")
print (", ".join(orig_uncovered))
for (reaction_name, uncovered) in sorted_uncovereds:
print ("----- " + reaction_name + " -------")
if utils.equal_lists(orig_uncovered, uncovered):
print ("no change")
else:
print (", ".join(uncovered))
