def readAnnotatedTargets(self,targetFile,model,annotationName,regex,bNames = False,orderGenes = False):
parser = FlatFileParser()
modelFactory = ModelFactory()
modelFactory.orderGenes = orderGenes
report = parser.parseToReport(targetFile, "Row Names", header=["Control","Flux","Reaction Control","Flux Changes"])
controlValues = report.getColumn("Control")
if bNames:
controlValues = self._deannotateGenes(controlValues, model, annotationName, regex)
if self.orderGenes:
controlValues = modelFactory.refactorStringMap(controlValues, sep="_")
controlScore = report.getColumn("Flux")
if bNames:
controlScore = self._deannotateGenes(controlScore, model, annotationName, regex)
return(controlValues,controlScore)
def main_function():
parser = OptionParser()
parser.add_option("-v", "--verbose", action="store_true", dest="verbose", default=False, help="set verbose mode")
parser.add_option("-c","--config", dest="config", default="redirector.config", help="master configuration file", metavar="FILE")
parser.add_option("--model_config", dest="modelConfig", default="model.config", help="configuration file", metavar="FILE")
parser.add_option("-n","--configNames", type = "string", dest = "configNames", default = "Default", help = "comma separated list of configuration settings to include", metavar="FILE")
parser.add_option("-m","--modelname", type = "string", dest="modelName", default="", help="name of model from configuration file", metavar="String")
parser.add_option("-b","--bioObjective", type = "string", dest="bioObj", default = 'Biomass', help="name of biological objective reaction", metavar="String")
parser.add_option("-s","--synthObjective", type = "string", dest="synthObj", default='', help="name of synthetic objective reaction", metavar="String")
parser.add_option("--sn", "--searchNeighborhood", dest = "searchNeighborhood", default = 1, type = int, help = "size of search neighborhood", metavar = "int")
parser.add_option("--iter", "--searchIterations", dest = "iterations", default = 1, type = int, help = "maximum number of iterations, if blank no max", metavar = "int")
parser.add_option("--report", action = "store_true", dest = "isReport", default = False, help = "Write report", metavar = "boolean")
parser.add_option("--pl","--preload", dest = "preload", default = 0, type = int, help = "indicate size of pre-made library to load for faster start", metavar="int")
parser.add_option("--ps", "--preStart", dest = "preStart", default = 0, type = int, help = "start from previous iteration state", metavar = "int")
parser.add_option("--gm", "--GeneMap", action="store_true", dest = "useGeneMap", default = False, help = "Use Gene Map")
parser.add_option("--control", dest="control", default = "flat", help = "control library type, flat,binary,sense", metavar="String")
parser.add_option("--simocontrol", dest="simoControl", default = 1.0, help = "number of simultaneously active controls", metavar="int")
parser.add_option("--section", dest="subSections", default = '', help = "Comma separated list of sections of the model files to use", metavar="String")
parser.add_option("-o", dest="resultDirectory", default = './Result', help = "Directory to store analysis results", metavar="String")
# Parse options
(options,args) = parser.parse_args()
config = ReflectionConfig()
config.readfp(open("Redirector.config"))
'''
0. configure analysis
'''
configNames = options.configNames.split(",")
configNames.insert(0,"Redirector Model")
for name in configNames:
config.merge(name,"Redirector",append=True)
#----------------------------------------
# reflect options from configuration
#----------------------------------------
config.reflect("Redirector",options)
config.load("Redirector", options.__dict__,override=False)
#-----------------------------------------
# Check and Build Storage Directories
#-----------------------------------------
dataDirectory = config.getValue("Redirector","dataDirectory",classType=''.__class__)
libraryDirectory = config.getValue("Redirector","libraryDirectory",classType=''.__class__)
resultsDirectory = config.getValue("Redirector","resultDirectory",classType=''.__class__)
analysisDirectory = config.getValue("Redirector","analysisDirectory",classType=''.__class__)
if not os.path.exists(dataDirectory):
raise IOError("unable to find required data directory" % dataDirectory)
if not os.path.exists(resultsDirectory):
os.makedirs(resultsDirectory)
if not os.path.exists(libraryDirectory):
os.makedirs(libraryDirectory)
if not os.path.exists(analysisDirectory):
os.makedirs(analysisDirectory)
#----------------------------
# Parse Inputs
#----------------------------
verbose = config.get("Redirector","verbose")
modelName = config.get("Redirector","modelName")
objectiveName = config.get("Redirector","bioObj")
syntheticObjectiveName = config.get("Redirector","synthObj")
searchSize = config.get("Redirector","searchNeighborhood")
searchIter = config.get("Redirector","iterations")
objectiveMinPercent = float(config.get("Redirector","bioTarget"))
usePrimeBounds = config.get("Redirector","primeBounds") == "True"
#----------------------------------------------------
# Initialize and set values for tools and factories
#----------------------------------------------------
naturalObjective = {objectiveName:-1.0}
syntheticObjective = {syntheticObjectiveName:-1.0}
protectedTargets = set(naturalObjective.keys()).union(syntheticObjective.keys())
if verbose: print "Redirector Version 1.0"
if verbose: print "Model names: [%s]" % (modelName)
if verbose: print "Synthetic objective: [%s]" % (syntheticObjectiveName)
if verbose: print "Parsing data files for [%s]" % (modelName)
if verbose: print "Search Size [%s] Iterations [%s]" % (searchSize,searchIter)
'''
I. Parse data files and configuration settings
'''
if verbose: print "----------------Loading Metabolic Models---------------"
modelNames = modelName.split(",")
modelFactory = ModelFactory()
config.reflect("Redirector",modelFactory)
modelFactory.protectedTargets = protectedTargets
(fluxModel,modelMatrix) = modelFactory.loadModel(modelNames)
if verbose: print "Removing objectives from target set"
targets = modelMatrix.targets
targets = set(targets).difference(protectedTargets)
if verbose: print "Targets List Size [%s]" % len(targets)
simControl = options.simoControl
if verbose: print "Simultaneous Control %s" % simControl
#-------------------------------------------------------------------
# Pre-discovery of flux bound current not used due to instability
#-------------------------------------------------------------------
primeFluxBoundaries = {}
boundarySearchSize = 1
boundaryTargets = targets
boundaryReportFileName = "rd_flux_boundary_M_%s_t_%s_p_%s_s_%s_analysis.csv" % (modelName,len(targets),objectiveMinPercent,boundarySearchSize)
fluxBoundariesFile = "ControlLibraries/FluxBounds_M_%s_O_%s_T_%s_S_%s" % (modelName,objectiveName,objectiveMinPercent,syntheticObjectiveName)
naturalFluxBounds = None
if usePrimeBounds:
print "finding natural flux bounds [%s]" % (usePrimeBounds)
#return False
naturalFluxBounds = LinearModelVariableBoundarys(modelMatrix, objectiveName=objectiveName, targets=boundaryTargets, pickleFileName = fluxBoundariesFile, minObjectivePercent=objectiveMinPercent,searchSize=boundarySearchSize)
print "finding production flux bounds"
#syntheticFluxBounds = LinearModelVariableBoundarys(modelMatrix, objectiveName=syntheticObjectiveName, targets=boundaryTargets, pickleFileName = fluxBoundariesFile, minObjectivePercent=objectiveMinPercent,searchSize=boundarySearchSize)
if verbose: print "Prime flux boundaries found."
boundaryReport = Report()
boundaryReport.addColumnHash(objectiveName, naturalFluxBounds)
#boundaryReport.addColumnHash(syntheticObjectiveName, syntheticFluxBounds)
writer = ReportWriter()
writer.setFile(boundaryReportFileName)
writer.write(boundaryReport)
writer.closeFile()
'''
II. Generate Control Library(ies)
'''
if verbose: print "===============Setting up control libraries================="
processLibrary = OptimizationControlFactory()
config.reflect("Redirector",processLibrary)
processLibrary.geneMap = modelMatrix.controlMap
processLibrary.fluxBounds = primeFluxBoundaries
processLibrary.naturalObjectiveName = objectiveName
processLibrary.syntheticObjectiveName = syntheticObjectiveName
controlLibraries = []
controlMap = {}
controlTags = options.control.split(",")
if "sense" in controlTags:
print "====>Using sensitivity control library"
(icontrolLibraries, controlMap) = processLibrary.generateControl(modelMatrix,targets,targetsOnly = False)
icontrolLibraries = processLibrary._filterControl(icontrolLibraries, targets)
controlLibraries.extend(icontrolLibraries)
if "flat" in controlTags:
print "====>Using flat control library"
(icontrolLibraries) = processLibrary.seedTestLibrary(targets, randomize=False)
controlLibraries.extend(icontrolLibraries)
if "random" in controlTags:
print "====>Using random control library"
(icontrolLibraries) = processLibrary.seedTestLibrary(targets, randomize=True, factor = 2.0)
controlLibraries.extend(icontrolLibraries)
if "binary" in controlTags:
print "====>Using binary control library"
binaryRange =[-3,-2,-1,0]
icontrolLibraries = processLibrary.generateBinaryControl(targets,binaryRange)
controlLibraries.extend(icontrolLibraries)
controlReportName = "ControlLibraries/ControlReport_%s_%s_%s_%s.csv" % (options.configNames,objectiveName,syntheticObjectiveName,len(targets))
processLibrary.controlReport(modelMatrix, controlLibraries, controlMap, targets, controlReportName)
print "============Control Constructed============="
#--------------------------------------------------
#configure Redirector model construction object
#--------------------------------------------------
if verbose: print "==Formulating Framework=="
con = ConstructRegulationOptimization()
config.reflect("Redirector",con)
con.controlMax = options.searchNeighborhood
con.newObjective = syntheticObjectiveName
#----------------------------------------
# Initialize redirector analysis object
#----------------------------------------
if verbose: print "==Running Optimization=="
redirector = OptimizationControlRedirector()
config.reflect("Redirector",redirector)
redirector.modelFactory = modelFactory
redirector.con = con
redirector.controlFactory = processLibrary
redirector.controlLibraries = controlLibraries
redirector.primeBounds = naturalFluxBounds
#redirector.targets = targets
redirector.rGeneMap = modelMatrix.controlMap
#redirector.modelName = modelName
redirector.naturalObjectiveName = objectiveName
redirector.syntheticObjectiveName = syntheticObjectiveName
#--------------------------------------------------------
# Debugging option which tests addition / removal of
# reactions from the objective
#--------------------------------------------------------
if "toggle0" in options.control.split(","):
if verbose: print "-----------control test toggle 0-------------------"
redirector.testDesignOptimization(modelMatrix)
if "toggle" in options.control.split(","):
if verbose: print "-----------control test toggle all-------------------"
redirector.testDesignOptimization(modelMatrix,fullTest=True)
(ltReport,oPredVal,sPredVal,finalCheckValue,fObjective) = redirector.optimizeControl(modelMatrix)
finalPredictionValue = ltReport["flux"]
if verbose: print "Final Production: %s" % (finalPredictionValue[syntheticObjectiveName])
#-----------------------------
# Write Report
#----------------------------
if options.isReport:
try:
print "Writing Full Model Report in %s" % (options.resultDirectory)
redirector.writeReport(ltReport,fluxModel,oPredVal,sPredVal,searchSize,searchIter,fObjective,resultsDirectory)
except Exception, e:
print "Unable to write report: %s" % (e)
try:
targetReportName = "Target_Report_M_%s_N_%s_S_%s_K_%s_I_%s.txt" % (modelName,objectiveName,syntheticObjectiveName,options.searchNeighborhood,options.iterations)
print "Writing Optimization target Report %s" % (targetReportName)
iteration = options.preStart + options.iterations
redirector.writeAnnotatedTargets(fObjective, modelMatrix, annotationName = "bnumber", regex="[a-zA-Z0-9\(\)]+", iteration = iteration, oPrediction = oPredVal, nPrediction = finalPredictionValue)
except:
print "failed to write %s" % (targetReportName)
def main_function():
parser = OptionParser()
parser.add_option("-v", "--verbose", action="store_true", dest="verbose", default=False, help="set verbose mode")
parser.add_option(
"--config",
type="string",
metavar="FILE",
dest="config",
default="redirector.config",
help="Master configuration file that provides most setting for the Flux Balanace Analysis. Extra variable settings will be ingnored. Hence the same config can be used for multiple analysis functions",
)
parser.add_option(
"-c",
"--modelConfig",
type="string",
metavar="FILE",
dest="configFileName",
default="model_config.txt",
help="Configuration file which sets model files",
)
parser.add_option(
"-n",
"--configNames",
type="string",
metavar="String",
dest="configNames",
default="Default",
help="A comma separated list of the names of configurations to use, as set out in the configuration file",
)
parser.add_option(
"-m",
"--modelname",
type="string",
metavar="String",
dest="modelName",
default="",
help="Name of model(s) from the modelconfiguration file",
)
parser.add_option(
"-b",
"--bioObjective",
type="string",
dest="bioObj",
default="Biomass",
help="Name / ID of biological objective reaction",
metavar="String",
)
parser.add_option(
"-o",
"--outputfile",
dest="outputFileName",
default=None,
help="Name of report file to be generated",
metavar="FILE",
)
parser.add_option(
"-r",
"--result_directory",
type="string",
metavar="directory",
dest="resultDirectory",
default="../../results/",
help="Directory where results are stored",
)
parser.add_option(
"--targets",
type="string",
metavar="String",
dest="targets",
default="",
help="List of valid reaction target, if left blank will be automatically filled in from metabolic network file",
)
parser.add_option(
"--report",
action="store_true",
dest="isReport",
default=False,
help="When this tag is used a report will be generated when the analysis is finished",
metavar="boolean",
)
parser.add_option("--debug", action="store_true", dest="debug", default=False, help="turn on debug mode")
parser.add_option("--gm", "--GeneMap", action="store_true", dest="useGeneMap", default=False, help="Use Gene Map")
parser.add_option(
"--section",
type="string",
metavar="String",
dest="subSections",
default="",
help="Comma separated list of sections of the model files to use",
)
# -------------------------------
# Parse options
# -------------------------------
(options, args) = parser.parse_args()
config = ReflectionConfig()
config.readfp(open("Redirector.config"))
# ---------------------------
# configure preset analysis
# ---------------------------
configNames = options.configNames.split(",")
configNames.insert(0, "Redirector Model")
for name in configNames:
config.merge(name, "Redirector", append=True)
# ----------------------------------------
# reflect options from configuration
# ----------------------------------------
config.reflect("Redirector", options)
config.load("Redirector", options.__dict__, override=False)
# -----------------------------------------
# Check and Build Storage Directories
# -----------------------------------------
dataDirectory = config.getValue("Redirector", "dataDirectory", classType="".__class__)
resultsDirectory = config.getValue("Redirector", "resultDirectory", classType="".__class__)
analysisDirectory = config.getValue("Redirector", "analysisDirectory", classType="".__class__)
if not os.path.exists(dataDirectory):
raise IOError("unable to find required data directory" % dataDirectory)
if not os.path.exists(resultsDirectory):
os.makedirs(resultsDirectory)
if not os.path.exists(analysisDirectory):
os.makedirs(analysisDirectory)
# ----------------------------
# Parse Inputs
# ----------------------------
verbose = options.verbose
modelName = options.modelName
objectiveName = options.bioObj
outputFileName = options.outputFileName
"""
#----------------------------------------------------
# Initialize and set values for tools and factories
#----------------------------------------------------
"""
naturalObjective = {objectiveName: -1.0}
if verbose:
print "Flux Balanace Analysis Version 1.6"
if verbose:
print "Model names: [%s]" % (modelName)
if verbose:
print "Parsing data files for [%s]" % (modelName)
"""
I. Parse data files and configuration settings
"""
if verbose:
print "----------------Loading Metabolic Models---------------"
modelNames = modelName.split(",")
modelFactory = ModelFactory()
config.reflect("Redirector", modelFactory)
(fluxModel, modelMatrix, reducer, geneReduction) = modelFactory.loadModel(modelNames)
model = modelMatrix
if verbose:
print "removing objectives from target set"
targets = modelMatrix.targets
if verbose:
print "Targets List Size [%s]" % len(targets)
lps = LPSolver()
predictions = lps.run(model, naturalObjective)
objectiveValue = predictions[objectiveName]
lps.clear()
if verbose:
print "Optimized Objective [%s] Value [%s]" % (objectiveName, objectiveValue)
report = fluxModel.getReport()
report.addColumnHash("Flux", predictions)
if outputFileName == None or outputFileName == "":
outputFileName = resultsDirectory + "FBA_%s_%s.txt" % (modelName, strftime("%Y%m%dT%H%M%S"))
writer = ReportWriter()
writer.setFile(outputFileName)
writer.write(report)
writer.closeFile()
if verbose:
print "Report Written [%s]" % (outputFileName)
if verbose: print "Parsing data files for [%s]" % (modelName)
'''
* 0. Process target files into overview table
'''
targetFileObjectives = options.targetFileObjectives
if targetFileObjectives != '':
findBestTargetSets(targetFileObjectives, k, n)
'''
I. Parse data files and configuration settings
'''
modelNames = modelName.split(",")
modelFactory = ModelFactory()
config.reflect("Redirector",modelFactory)
modelFactory.protectedTargets = protectedTargets
if verbose: print "----------------Loading Metabolic Models---------------"
(fluxModel,modelMatrix,reducer,geneReduction) = modelFactory.loadModel(modelNames)
targets = modelMatrix.targets
persistTag= "%s_%s_%s_%s_k%s_n%s_s%s" % (resultTag,options.modelName,naturalObjectiveName,syntheticObjectiveName,k,n,str(searchDepth))
persistFileName = "ControlSearches/Persist_Cdependency_%s.bac" % persistTag
'''
II. Dependency analysis
if option search depth != 0:
