fastaFile = worker.genomeToFasta(genome['features'])
# Run blast using the fasta file.
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.
fastaFile = worker.genomeToFasta(genome['features'])
# Run blast using the fasta file.
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.
# Run blast using the fasta file.
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)
