blastResultFile = worker.runBlast(fastaFile) # Calculate roleset probabilities. rolestringTuples = worker.rolesetProbabilitiesMarble(blastResultFile) # Calculate per-gene role probabilities. roleProbs = worker.rolesetProbabilitiesToRoleProbabilities(rolestringTuples) # Calculate whole cell role probabilities. totalRoleProbs = worker.totalRoleProbabilities(roleProbs) # Calculate complex probabilities. complexProbs = worker.complexProbabilities(totalRoleProbs, complexesToRequiredRoles = complexesToRoles) # Calculate reaction probabilities. reactionProbs = worker.reactionProbabilities(complexProbs, rxnsToComplexes = reactionsToComplexes) # Cleanup work directory. worker.cleanup() except Exception as e: worker.cleanup() sys.stderr.write('Failed to run probabilistic annotation algorithm: %s\n' %(e.message)) tb = traceback.format_exc() sys.stderr.write(tb) exit(1) # Create the rxnprobs object in the workspace. data = dict() data['reaction_probabilities'] = reactionProbs putObject(wsClient, args.rxnprobsref, 'rxnprobs', data)
blastResultFile = worker.runBlast(fastaFile) # Calculate roleset probabilities. rolestringTuples = worker.rolesetProbabilitiesMarble(blastResultFile) # Calculate per-gene role probabilities. roleProbs = worker.rolesetProbabilitiesToRoleProbabilities(rolestringTuples) # Calculate whole cell role probabilities. totalRoleProbs = worker.totalRoleProbabilities(roleProbs) # Calculate complex probabilities. complexProbs = worker.complexProbabilities(totalRoleProbs) # Calculate reaction probabilities. reactionProbs = worker.reactionProbabilities(complexProbs) # Cleanup work directory. worker.cleanup() except Exception as e: worker.cleanup() sys.stderr.write('Failed to run probabilistic annotation algorithm: %s\n' %(e.message)) tb = traceback.format_exc() sys.stderr.write(tb) exit(1) # Create the rxnprobs object in the workspace. try: data = dict() data['reaction_probabilities'] = reactionProbs
# Calculate roleset probabilities. rolestringTuples = worker.rolesetProbabilitiesMarble(blastResultFile) # Calculate per-gene role probabilities. roleProbs = worker.rolesetProbabilitiesToRoleProbabilities( rolestringTuples) # Calculate whole cell role probabilities. totalRoleProbs = worker.totalRoleProbabilities(roleProbs) # Calculate complex probabilities. complexProbs = worker.complexProbabilities( totalRoleProbs, complexesToRequiredRoles=complexesToRoles) # Calculate reaction probabilities. reactionProbs = worker.reactionProbabilities( complexProbs, rxnsToComplexes=reactionsToComplexes) # Cleanup work directory. worker.cleanup() except Exception as e: worker.cleanup() sys.stderr.write( 'Failed to run probabilistic annotation algorithm: %s\n' % (e.message)) tb = traceback.format_exc() sys.stderr.write(tb) exit(1) # Create the rxnprobs object in the workspace. data = dict()