# Read wildtype solution from file
wtSolution = MetabolicFlux()
try:
wtSolution.readFromFile(options.wtSolution)
except IOError, strerror:
print("An error occurred while trying to read file %s:" %
os.path.basename(options.wtSolution))
print strerror
_mpi_exit(comm, 1)
except SyntaxError, strerror:
print("An error occurred parsing file %s:" %
os.path.basename(options.wtSolution))
print strerror
_mpi_exit(comm, 1)
if not wtSolution.hasSameReactions(model):
print(
"Error in file %s: FBA solution and model must have the "
"same reactions." % os.path.basename(options.wtSolution))
_mpi_exit(comm, 1)
# Build coefficient vector of linear objective function
objective = array(
ParamParser.convertObjFuncToLinVec(objStr, model.reactionDict))
wt_obj_value = dot(objective,
wtSolution.getVecOrderedByModel(model))
# 7.b If FBA solution is not given, perform FBA
else:
# Compute wildtype solution via FBA
wtFlux = MetabolicFlux()
try:
wtFlux.readFromFile(options.wtSolution)
except IOError, strerror:
print("An error occurred while trying to read file %s:" %
os.path.basename(options.wtSolution))
print strerror
exit()
except SyntaxError, strerror:
print("An error occurred parsing file %s:" %
os.path.basename(options.wtSolution))
print strerror
exit()
if not wtFlux.hasSameReactions(model):
print "Error: Solution and model must have the same reactions."
exit()
# 5. (Optionally) Read FVA solution for reducing the solution space
# - skip if full matrix is to be used
if options.redFvaFile and not options.useFullMatrix:
try:
fbaSolution, redMinmax = \
FvAnalyzer.parseSolutionFile(options.redFvaFile)
except IOError, strerror:
print("An error occurred while trying to read file %s:" %
os.path.basename(options.redFvaFile))
print strerror
exit()